From d7455437cc5fbcb90e2e0f5361ccaded868295b5 Mon Sep 17 00:00:00 2001 From: Irfan Date: Tue, 8 Nov 2022 15:51:12 +0000 Subject: [PATCH 1/6] Start adding perses edges --- data/cdk2/00_data/edges.yml | 100 ----------------------- data/cdk2/03_edges/01_perses_openfe.yaml | 76 +++++++++++++++++ preparation/mappers/perses-mapper.py | 47 +++++++++++ 3 files changed, 123 insertions(+), 100 deletions(-) delete mode 100644 data/cdk2/00_data/edges.yml create mode 100644 data/cdk2/03_edges/01_perses_openfe.yaml create mode 100644 preparation/mappers/perses-mapper.py diff --git a/data/cdk2/00_data/edges.yml b/data/cdk2/00_data/edges.yml deleted file mode 100644 index 70536d2d5..000000000 --- a/data/cdk2/00_data/edges.yml +++ /dev/null @@ -1,100 +0,0 @@ -edge_17_1h1q: - ligand_a: lig_17 - ligand_b: lig_1h1q - name: edge_17_1h1q -edge_17_21: - ligand_a: lig_17 - ligand_b: lig_21 - name: edge_17_21 -edge_17_22: - ligand_a: lig_17 - ligand_b: lig_22 - name: edge_17_22 -edge_1h1r_1oi9: - ligand_a: lig_1h1r - ligand_b: lig_1oi9 - name: edge_1h1r_1oi9 -edge_1h1r_21: - ligand_a: lig_1h1r - ligand_b: lig_21 - name: edge_1h1r_21 -edge_1h1s_1oiy: - ligand_a: lig_1h1s - ligand_b: lig_1oiy - name: edge_1h1s_1oiy -edge_1h1s_26: - ligand_a: lig_1h1s - ligand_b: lig_26 - name: edge_1h1s_26 -edge_1oi9_20: - ligand_a: lig_1oi9 - ligand_b: lig_20 - name: edge_1oi9_20 -edge_1oiu_1h1q: - ligand_a: lig_1oiu - ligand_b: lig_1h1q - name: edge_1oiu_1h1q -edge_1oiu_26: - ligand_a: lig_1oiu - ligand_b: lig_26 - name: edge_1oiu_26 -edge_1oiy_1h1q: - ligand_a: lig_1oiy - ligand_b: lig_1h1q - name: edge_1oiy_1h1q -edge_1oiy_1oi9: - ligand_a: lig_1oiy - ligand_b: lig_1oi9 - name: edge_1oiy_1oi9 -edge_1oiy_29: - ligand_a: lig_1oiy - ligand_b: lig_29 - name: edge_1oiy_29 -edge_1oiy_31: - ligand_a: lig_1oiy - ligand_b: lig_31 - name: edge_1oiy_31 -edge_1oiy_32: - ligand_a: lig_1oiy - ligand_b: lig_32 - name: edge_1oiy_32 -edge_20_1h1q: - ligand_a: lig_20 - ligand_b: lig_1h1q - name: edge_20_1h1q -edge_22_1h1r: - ligand_a: lig_22 - ligand_b: lig_1h1r - name: edge_22_1h1r -edge_26_1h1q: - ligand_a: lig_26 - ligand_b: lig_1h1q - name: edge_26_1h1q -edge_26_1oi9: - ligand_a: lig_26 - ligand_b: lig_1oi9 - name: edge_26_1oi9 -edge_28_26: - ligand_a: lig_28 - ligand_b: lig_26 - name: edge_28_26 -edge_28_31: - ligand_a: lig_28 - ligand_b: lig_31 - name: edge_28_31 -edge_29_26: - ligand_a: lig_29 - ligand_b: lig_26 - name: edge_29_26 -edge_30_26: - ligand_a: lig_30 - ligand_b: lig_26 - name: edge_30_26 -edge_30_31: - ligand_a: lig_30 - ligand_b: lig_31 - name: edge_30_31 -edge_31_32: - ligand_a: lig_31 - ligand_b: lig_32 - name: edge_31_32 diff --git a/data/cdk2/03_edges/01_perses_openfe.yaml b/data/cdk2/03_edges/01_perses_openfe.yaml new file mode 100644 index 000000000..45004a6e9 --- /dev/null +++ b/data/cdk2/03_edges/01_perses_openfe.yaml @@ -0,0 +1,76 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_1oiu_lig_1h1q: + ligand_a: lig_1oiu + ligand_b: lig_1h1q + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 13) (13, 12) (14, 14) (15, 16) (16, 15) (17, 17) (18, + 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 25) (25, 24) (26, 26) + (27, 27) (28, 28) (29, 29) (30, 30) (31, 39) (32, 40) (33, 37) (40, 35) (41, + 36) (42, 33) (43, 34) (44, 31) (45, 32) (46, 41) (47, 42) (48, 43) (49, 44) + score: '0.961' + edge_lig_26_lig_1oiu: + ligand_a: lig_26 + ligand_b: lig_1oiu + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 13) (13, 12) (14, 14) (15, 16) (16, 15) (17, 17) (18, + 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 25) (25, 24) (26, 26) + (27, 27) (28, 28) (29, 29) (30, 30) (31, 44) (32, 45) (33, 42) (34, 43) (35, + 40) (41, 33) (43, 31) (44, 32) (45, 46) (46, 47) (47, 48) (48, 49) + score: '0.901' + edge_lig_22_lig_26: + ligand_a: lig_22 + ligand_b: lig_26 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 13) (13, 12) (14, 14) (15, 16) (16, 15) (17, 17) (18, + 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 25) (25, 24) (26, 26) + (27, 27) (28, 28) (29, 29) (30, 30) (31, 43) (32, 44) (33, 41) (34, 42) (35, + 35) (37, 33) (43, 31) (44, 32) (45, 45) (46, 46) (47, 47) (48, 48) + score: '0.912' + edge_lig_17_lig_26: + ligand_a: lig_17 + ligand_b: lig_26 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 13) (13, 12) (14, 14) (15, 16) (16, 15) (17, 17) (18, + 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 25) (25, 24) (26, 26) + (27, 27) (28, 28) (29, 29) (30, 30) (31, 43) (32, 44) (33, 41) (34, 42) (35, + 35) (37, 33) (39, 31) (40, 32) (41, 45) (42, 46) (43, 47) (44, 48) + score: '0.961' + edge_lig_21_lig_26: + ligand_a: lig_21 + ligand_b: lig_26 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 13) (13, 12) (14, 14) (15, 16) (16, 15) (17, 17) (18, + 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 25) (25, 24) (26, 26) + (27, 27) (28, 28) (29, 29) (30, 30) (31, 43) (32, 44) (33, 41) (34, 42) (35, + 35) (37, 33) (43, 31) (44, 32) (45, 45) (46, 46) (47, 47) (48, 48) + score: '0.912' + edge_lig_1h1r_lig_1oiu: + ligand_a: lig_1h1r + ligand_b: lig_1oiu + atom mapping: (1, 33) (2, 31) (3, 30) (4, 44) (5, 42) (6, 40) (7, 41) (9, 45) + (10, 28) (11, 29) (12, 27) (13, 46) (14, 47) (15, 3) (16, 4) (17, 26) (18, 5) + (19, 6) (20, 7) (21, 8) (22, 9) (23, 23) (24, 20) (25, 17) (26, 14) (27, 11) + (28, 13) (29, 12) (30, 16) (31, 15) (32, 18) (33, 19) (34, 21) (35, 22) (36, + 24) (37, 25) (38, 10) (39, 2) (40, 1) (41, 48) (42, 49) (43, 0) (44, 32) + score: '0.948' + edge_lig_20_lig_26: + ligand_a: lig_20 + ligand_b: lig_26 + atom mapping: (5, 33) (6, 35) (8, 41) (9, 42) (10, 43) (11, 44) (12, 30) (13, + 28) (14, 29) (15, 27) (16, 26) (17, 4) (18, 5) (19, 6) (20, 8) (21, 7) (22, + 9) (23, 10) (24, 23) (25, 24) (26, 25) (27, 20) (28, 21) (29, 22) (30, 17) (31, + 19) (32, 18) (33, 14) (34, 16) (35, 15) (36, 11) (37, 12) (38, 13) (39, 3) (40, + 2) (41, 1) (42, 0) (43, 47) (44, 48) (45, 46) (46, 45) (47, 31) (48, 32) + score: '0.912' + edge_lig_1oi9_lig_1oiu: + ligand_a: lig_1oi9 + ligand_b: lig_1oiu + atom mapping: (2, 40) (3, 33) (5, 31) (6, 32) (7, 30) (8, 28) (9, 29) (10, 27) + (11, 26) (12, 4) (13, 5) (14, 6) (15, 7) (16, 8) (17, 9) (18, 10) (19, 11) (20, + 12) (21, 13) (22, 14) (23, 16) (24, 15) (25, 17) (26, 18) (27, 19) (28, 20) + (29, 22) (30, 21) (31, 23) (32, 24) (33, 25) (34, 3) (35, 2) (36, 1) (37, 0) + (38, 48) (39, 49) (40, 47) (41, 46) (42, 44) (43, 45) (44, 42) (45, 43) + score: '0.936' diff --git a/preparation/mappers/perses-mapper.py b/preparation/mappers/perses-mapper.py new file mode 100644 index 000000000..845845765 --- /dev/null +++ b/preparation/mappers/perses-mapper.py @@ -0,0 +1,47 @@ +import yaml +import numpy as np +from rdkit import Chem +from openfe.setup import SmallMoleculeComponent +from openfe.setup.ligand_network_planning import minimal_spanning_graph +from openfe.setup.atom_mapping.perses_mapper import PersesAtomMapper +from openfe.setup.atom_mapping.perses_scorers import default_perses_scorer +from openmm import unit + +# load ligands +ligands_supp = Chem.SDMolSupplier('../02_ligands/ligands.sdf', removeHs=False) +ligand_mols = [SmallMoleculeComponent(m) for m in ligands_supp] + +# create minimum spanning graph +mapper = PersesAtomMapper(allow_ring_breaking=False, preserve_chirality=True, + use_positions=True, coordinate_tolerance=0.2*unit.angstrom) + +network = minimal_spanning_graph(ligand_mols, [mapper,], default_perses_scorer) + +# Get edges +edges = [edge for edge in network.edges] + +# Analyze distance overlap for manual validation +for i, edge in enumerate(edges): + if np.any(edge.get_distances() > 1): + name = f"{edge.componentA.name}_{edge.componentB.name}" + print(f"{name} exceeds 1 A pairwise distance") + +output = {} +output['mapper'] = "Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, coordinate_tolerance=0.2), default non geometric scorer" +output['planner'] = "openfe v0.4 minimal_spanning_graph" + +edges_dict = {} + +for edge in network.edges: + edge_name = f'edge_{edge.componentA.name}_{edge.componentB.name}' + mapping = list(edge.componentA_to_componentB.items()) + edges_dict[edge_name] = { + 'ligand_a': edge.componentA.name, + 'ligand_b': edge.componentB.name, + 'atom mapping': ' '.join(str(i) for i in mapping), + 'score': f"{edge.annotations['score']:.3f}",} + +output['edges'] = edges_dict + +with open('01_perses_openfe.yaml', 'w') as yaml_file: + yaml.dump(output, yaml_file, default_flow_style=False, sort_keys=False) From d45f7621580c8c53d243c303e1350347c8fb9045 Mon Sep 17 00:00:00 2001 From: Irfan Date: Tue, 8 Nov 2022 16:10:37 +0000 Subject: [PATCH 2/6] Add edges, eg5 left --- data/cdk8/00_data/edges.yml | 216 ---------- data/cdk8/03_edges/01_perses_openfe.yaml | 210 ++++++++++ data/cdk8/03_edges/nohup.out | 26 ++ data/cmet/00_data/edges.yml | 100 ----- data/cmet/03_edges/01_perses_openfe.yaml | 28 ++ data/cmet/03_edges/nohup.out | 12 + data/eg5/00_data/edges.yml | 260 ------------ data/eg5/03_edges/nohup.out | 9 + data/hif2a/00_data/edges.yml | 368 ----------------- data/hif2a/03_edges/01_perses_openfe.yaml | 210 ++++++++++ data/hif2a/03_edges/nohup.out | 36 ++ data/mcl1/00_data/edges.yml | 284 ------------- data/mcl1/03_edges/01_perses_openfe.yaml | 180 +++++++++ data/mcl1/03_edges/nohup.out | 31 ++ data/p38/00_data/edges.yml | 224 ---------- data/p38/03_edges/01_perses_openfe.yaml | 225 +++++++++++ data/p38/03_edges/nohup.out | 39 ++ data/pde2/00_data/edges.yml | 136 ------- data/pde2/03_edges/01_perses_openfe.yaml | 202 ++++++++++ data/pde2/03_edges/nohup.out | 29 ++ data/pfkfb3/00_data/edges.yml | 264 ------------ data/pfkfb3/03_edges/01_perses_openfe.yaml | 279 +++++++++++++ data/pfkfb3/03_edges/nohup.out | 45 +++ data/ptp1b/00_data/edges.yml | 196 --------- data/ptp1b/03_edges/01_perses_openfe.yaml | 172 ++++++++ data/ptp1b/03_edges/nohup.out | 24 ++ data/shp2/00_data/edges.yml | 224 ---------- data/shp2/03_edges/01_perses_openfe.yaml | 153 +++++++ data/shp2/03_edges/nohup.out | 29 ++ data/syk/00_data/edges.yml | 404 ------------------- data/syk/03_edges/01_perses_openfe.yaml | 312 ++++++++++++++ data/syk/03_edges/nohup.out | 25 ++ data/thrombin/00_data/edges.yml | 64 --- data/thrombin/03_edges/01_perses_openfe.yaml | 94 +++++ data/thrombin/03_edges/nohup.out | 18 + data/tnks2/00_data/edges.yml | 240 ----------- data/tnks2/03_edges/01_perses_openfe.yaml | 180 +++++++++ data/tnks2/03_edges/nohup.out | 22 + data/tyk2/00_data/edges.yml | 96 ----- data/tyk2/03_edges/01_perses_openfe.yaml | 108 +++++ data/tyk2/03_edges/nohup.out | 21 + 41 files changed, 2719 insertions(+), 3076 deletions(-) delete mode 100644 data/cdk8/00_data/edges.yml create mode 100644 data/cdk8/03_edges/01_perses_openfe.yaml create mode 100644 data/cdk8/03_edges/nohup.out delete mode 100644 data/cmet/00_data/edges.yml create mode 100644 data/cmet/03_edges/01_perses_openfe.yaml create mode 100644 data/cmet/03_edges/nohup.out delete mode 100644 data/eg5/00_data/edges.yml create mode 100644 data/eg5/03_edges/nohup.out delete mode 100644 data/hif2a/00_data/edges.yml create mode 100644 data/hif2a/03_edges/01_perses_openfe.yaml create mode 100644 data/hif2a/03_edges/nohup.out delete mode 100644 data/mcl1/00_data/edges.yml create mode 100644 data/mcl1/03_edges/01_perses_openfe.yaml create mode 100644 data/mcl1/03_edges/nohup.out delete mode 100644 data/p38/00_data/edges.yml create mode 100644 data/p38/03_edges/01_perses_openfe.yaml create mode 100644 data/p38/03_edges/nohup.out delete mode 100644 data/pde2/00_data/edges.yml create mode 100644 data/pde2/03_edges/01_perses_openfe.yaml create mode 100644 data/pde2/03_edges/nohup.out delete mode 100644 data/pfkfb3/00_data/edges.yml create mode 100644 data/pfkfb3/03_edges/01_perses_openfe.yaml create mode 100644 data/pfkfb3/03_edges/nohup.out delete mode 100644 data/ptp1b/00_data/edges.yml create mode 100644 data/ptp1b/03_edges/01_perses_openfe.yaml create mode 100644 data/ptp1b/03_edges/nohup.out delete mode 100644 data/shp2/00_data/edges.yml create mode 100644 data/shp2/03_edges/01_perses_openfe.yaml create mode 100644 data/shp2/03_edges/nohup.out delete mode 100644 data/syk/00_data/edges.yml create mode 100644 data/syk/03_edges/01_perses_openfe.yaml create mode 100644 data/syk/03_edges/nohup.out delete mode 100644 data/thrombin/00_data/edges.yml create mode 100644 data/thrombin/03_edges/01_perses_openfe.yaml create mode 100644 data/thrombin/03_edges/nohup.out delete mode 100644 data/tnks2/00_data/edges.yml create mode 100644 data/tnks2/03_edges/01_perses_openfe.yaml create mode 100644 data/tnks2/03_edges/nohup.out delete mode 100644 data/tyk2/00_data/edges.yml create mode 100644 data/tyk2/03_edges/01_perses_openfe.yaml create mode 100644 data/tyk2/03_edges/nohup.out diff --git a/data/cdk8/00_data/edges.yml b/data/cdk8/00_data/edges.yml deleted file mode 100644 index 8314f22f4..000000000 --- a/data/cdk8/00_data/edges.yml +++ /dev/null @@ -1,216 +0,0 @@ -edge_13_14: - ligand_a: lig_13 - ligand_b: lig_14 - name: edge_13_14 -edge_16_14: - ligand_a: lig_16 - ligand_b: lig_14 - name: edge_16_14 -edge_16_15: - ligand_a: lig_16 - ligand_b: lig_15 - name: edge_16_15 -edge_16_19: - ligand_a: lig_16 - ligand_b: lig_19 - name: edge_16_19 -edge_16_20: - ligand_a: lig_16 - ligand_b: lig_20 - name: edge_16_20 -edge_17_16: - ligand_a: lig_17 - ligand_b: lig_16 - name: edge_17_16 -edge_17_25: - ligand_a: lig_17 - ligand_b: lig_25 - name: edge_17_25 -edge_17_45: - ligand_a: lig_17 - ligand_b: lig_45 - name: edge_17_45 -edge_18_13: - ligand_a: lig_18 - ligand_b: lig_13 - name: edge_18_13 -edge_18_15: - ligand_a: lig_18 - ligand_b: lig_15 - name: edge_18_15 -edge_18_45: - ligand_a: lig_18 - ligand_b: lig_45 - name: edge_18_45 -edge_19_25: - ligand_a: lig_19 - ligand_b: lig_25 - name: edge_19_25 -edge_19_32: - ligand_a: lig_19 - ligand_b: lig_32 - name: edge_19_32 -edge_20_35: - ligand_a: lig_20 - ligand_b: lig_35 - name: edge_20_35 -edge_21_20: - ligand_a: lig_21 - ligand_b: lig_20 - name: edge_21_20 -edge_21_26: - ligand_a: lig_21 - ligand_b: lig_26 - name: edge_21_26 -edge_21_29: - ligand_a: lig_21 - ligand_b: lig_29 - name: edge_21_29 -edge_21_41: - ligand_a: lig_21 - ligand_b: lig_41 - name: edge_21_41 -edge_22_21: - ligand_a: lig_22 - ligand_b: lig_21 - name: edge_22_21 -edge_22_26: - ligand_a: lig_22 - ligand_b: lig_26 - name: edge_22_26 -edge_22_32: - ligand_a: lig_22 - ligand_b: lig_32 - name: edge_22_32 -edge_23_14: - ligand_a: lig_23 - ligand_b: lig_14 - name: edge_23_14 -edge_23_34: - ligand_a: lig_23 - ligand_b: lig_34 - name: edge_23_34 -edge_24_33: - ligand_a: lig_24 - ligand_b: lig_33 - name: edge_24_33 -edge_24_42: - ligand_a: lig_24 - ligand_b: lig_42 - name: edge_24_42 -edge_27_36: - ligand_a: lig_27 - ligand_b: lig_36 - name: edge_27_36 -edge_28_25: - ligand_a: lig_28 - ligand_b: lig_25 - name: edge_28_25 -edge_28_30: - ligand_a: lig_28 - ligand_b: lig_30 - name: edge_28_30 -edge_28_39: - ligand_a: lig_28 - ligand_b: lig_39 - name: edge_28_39 -edge_29_33: - ligand_a: lig_29 - ligand_b: lig_33 - name: edge_29_33 -edge_30_33: - ligand_a: lig_30 - ligand_b: lig_33 - name: edge_30_33 -edge_30_37: - ligand_a: lig_30 - ligand_b: lig_37 - name: edge_30_37 -edge_31_25: - ligand_a: lig_31 - ligand_b: lig_25 - name: edge_31_25 -edge_31_37: - ligand_a: lig_31 - ligand_b: lig_37 - name: edge_31_37 -edge_32_23: - ligand_a: lig_32 - ligand_b: lig_23 - name: edge_32_23 -edge_33_32: - ligand_a: lig_33 - ligand_b: lig_32 - name: edge_33_32 -edge_33_34: - ligand_a: lig_33 - ligand_b: lig_34 - name: edge_33_34 -edge_34_36: - ligand_a: lig_34 - ligand_b: lig_36 - name: edge_34_36 -edge_35_18: - ligand_a: lig_35 - ligand_b: lig_18 - name: edge_35_18 -edge_35_27: - ligand_a: lig_35 - ligand_b: lig_27 - name: edge_35_27 -edge_35_36: - ligand_a: lig_35 - ligand_b: lig_36 - name: edge_35_36 -edge_35_37: - ligand_a: lig_35 - ligand_b: lig_37 - name: edge_35_37 -edge_38_29: - ligand_a: lig_38 - ligand_b: lig_29 - name: edge_38_29 -edge_39_32: - ligand_a: lig_39 - ligand_b: lig_32 - name: edge_39_32 -edge_40_19: - ligand_a: lig_40 - ligand_b: lig_19 - name: edge_40_19 -edge_40_33: - ligand_a: lig_40 - ligand_b: lig_33 - name: edge_40_33 -edge_41_39: - ligand_a: lig_41 - ligand_b: lig_39 - name: edge_41_39 -edge_41_40: - ligand_a: lig_41 - ligand_b: lig_40 - name: edge_41_40 -edge_42_13: - ligand_a: lig_42 - ligand_b: lig_13 - name: edge_42_13 -edge_43_38: - ligand_a: lig_43 - ligand_b: lig_38 - name: edge_43_38 -edge_43_42: - ligand_a: lig_43 - ligand_b: lig_42 - name: edge_43_42 -edge_43_45: - ligand_a: lig_43 - ligand_b: lig_45 - name: edge_43_45 -edge_44_32: - ligand_a: lig_44 - ligand_b: lig_32 - name: edge_44_32 -edge_44_36: - ligand_a: lig_44 - ligand_b: lig_36 - name: edge_44_36 diff --git a/data/cdk8/03_edges/01_perses_openfe.yaml b/data/cdk8/03_edges/01_perses_openfe.yaml new file mode 100644 index 000000000..4b788d5f9 --- /dev/null +++ b/data/cdk8/03_edges/01_perses_openfe.yaml @@ -0,0 +1,210 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_28_lig_45: + ligand_a: lig_28 + ligand_b: lig_45 + atom mapping: (17, 13) (18, 15) (19, 14) (20, 16) (21, 17) (22, 18) (23, 19) (24, + 20) (25, 21) (26, 22) (27, 23) (28, 24) (43, 41) (44, 42) (45, 43) (46, 44) + score: '0.354' + edge_lig_30_lig_45: + ligand_a: lig_30 + ligand_b: lig_45 + atom mapping: (8, 25) (9, 26) (10, 24) (11, 22) (12, 23) (13, 21) (14, 20) (15, + 43) (16, 44) (17, 41) (18, 42) (19, 18) (20, 19) (21, 17) (22, 16) (23, 13) + (24, 15) (25, 14) + score: '0.388' + edge_lig_42_lig_23: + ligand_a: lig_42 + ligand_b: lig_23 + atom mapping: (10, 28) (11, 26) (12, 27) (13, 25) (14, 24) (15, 43) (16, 44) (17, + 41) (18, 42) (19, 22) (20, 23) (21, 21) (22, 20) (23, 17) (24, 19) (25, 18) + score: '0.333' + edge_lig_43_lig_24: + ligand_a: lig_43 + ligand_b: lig_24 + atom mapping: (13, 17) (14, 19) (15, 18) (16, 20) (17, 21) (18, 22) (19, 23) (20, + 24) (21, 25) (22, 26) (23, 27) (24, 28) (25, 29) (40, 37) (41, 38) (42, 39) + (43, 40) + score: '0.395' + edge_lig_18_lig_23: + ligand_a: lig_18 + ligand_b: lig_23 + atom mapping: (13, 17) (14, 18) (15, 19) (16, 20) (17, 21) (18, 22) (19, 23) (20, + 24) (21, 25) (22, 26) (23, 27) (24, 28) (33, 41) (34, 42) (35, 43) (36, 44) + score: '0.366' + edge_lig_43_lig_15: + ligand_a: lig_43 + ligand_b: lig_15 + atom mapping: (13, 5) (14, 6) (15, 7) (16, 8) (17, 9) (18, 10) (19, 11) (20, 12) + (21, 13) (22, 14) (23, 15) (24, 16) (25, 17) (26, 18) (40, 25) (41, 26) (42, + 27) (43, 28) + score: '0.425' + edge_lig_43_lig_19: + ligand_a: lig_43 + ligand_b: lig_19 + atom mapping: (13, 17) (14, 19) (15, 18) (16, 20) (17, 21) (18, 22) (19, 23) (20, + 24) (21, 25) (22, 26) (23, 27) (24, 28) (25, 29) (26, 30) (40, 37) (41, 38) + (42, 39) (43, 40) + score: '0.414' + edge_lig_42_lig_20: + ligand_a: lig_42 + ligand_b: lig_20 + atom mapping: (8, 37) (9, 38) (10, 36) (11, 34) (12, 35) (13, 33) (14, 32) (15, + 47) (16, 48) (17, 45) (18, 46) (19, 30) (20, 31) (21, 29) (22, 28) (23, 25) + (24, 27) (25, 26) + score: '0.391' + edge_lig_42_lig_36: + ligand_a: lig_42 + ligand_b: lig_36 + atom mapping: (8, 29) (9, 30) (10, 28) (11, 26) (12, 27) (13, 25) (14, 24) (15, + 47) (16, 48) (17, 45) (18, 46) (19, 22) (20, 23) (21, 21) (22, 20) (23, 17) + (24, 19) (25, 18) + score: '0.389' + edge_lig_44_lig_23: + ligand_a: lig_44 + ligand_b: lig_23 + atom mapping: (10, 28) (11, 26) (12, 27) (13, 25) (14, 24) (15, 43) (16, 44) (17, + 41) (18, 42) (19, 22) (20, 23) (21, 21) (22, 20) (23, 17) (24, 19) (25, 18) + score: '0.345' + edge_lig_43_lig_23: + ligand_a: lig_43 + ligand_b: lig_23 + atom mapping: (13, 17) (14, 19) (15, 18) (16, 20) (17, 21) (18, 22) (19, 23) (20, + 24) (21, 25) (22, 26) (23, 27) (24, 28) (40, 41) (41, 42) (42, 43) (43, 44) + score: '0.337' + edge_lig_29_lig_45: + ligand_a: lig_29 + ligand_b: lig_45 + atom mapping: (17, 13) (18, 14) (19, 15) (20, 16) (21, 17) (22, 18) (23, 19) (24, + 20) (25, 21) (26, 22) (27, 23) (28, 24) (29, 25) (30, 26) (42, 41) (43, 42) + (44, 43) (45, 44) + score: '0.394' + edge_lig_17_lig_23: + ligand_a: lig_17 + ligand_b: lig_23 + atom mapping: (15, 17) (16, 19) (17, 18) (18, 20) (19, 21) (20, 22) (21, 23) (22, + 24) (23, 25) (24, 26) (25, 27) (26, 28) (35, 41) (36, 42) (37, 43) (38, 44) + score: '0.366' + edge_lig_43_lig_32: + ligand_a: lig_43 + ligand_b: lig_32 + atom mapping: (13, 17) (14, 19) (15, 18) (16, 20) (17, 21) (18, 22) (19, 23) (20, + 24) (21, 25) (22, 26) (23, 27) (24, 28) (25, 29) (26, 30) (40, 34) (41, 35) + (42, 36) (43, 37) + score: '0.430' + edge_lig_13_lig_45: + ligand_a: lig_13 + ligand_b: lig_45 + atom mapping: (2, 41) (3, 24) (4, 25) (5, 26) (20, 22) (21, 23) (22, 21) (23, + 16) (24, 13) (25, 15) (26, 14) (41, 17) (42, 18) (43, 19) (44, 20) (45, 43) + (46, 44) + score: '0.395' + edge_lig_42_lig_35: + ligand_a: lig_42 + ligand_b: lig_35 + atom mapping: (8, 8) (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, + 15) (16, 16) (17, 17) (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) + (24, 25) (25, 24) + score: '0.392' + edge_lig_38_lig_45: + ligand_a: lig_38 + ligand_b: lig_45 + atom mapping: (17, 13) (18, 14) (19, 15) (20, 16) (21, 17) (22, 18) (23, 19) (24, + 20) (25, 21) (26, 22) (27, 23) (28, 24) (29, 25) (30, 26) (44, 41) (45, 42) + (46, 43) (47, 44) + score: '0.385' + edge_lig_14_lig_23: + ligand_a: lig_14 + ligand_b: lig_23 + atom mapping: (0, 42) (1, 41) (2, 43) (3, 44) (4, 24) (5, 25) (6, 20) (7, 17) + (9, 19) (20, 21) (21, 22) (22, 23) (23, 26) (24, 27) (25, 28) + score: '0.387' + edge_lig_22_lig_43: + ligand_a: lig_22 + ligand_b: lig_43 + atom mapping: (17, 13) (18, 14) (19, 15) (20, 16) (21, 17) (22, 18) (23, 19) (24, + 20) (25, 21) (26, 22) (27, 23) (28, 24) (40, 40) (41, 41) (42, 42) (43, 43) + score: '0.358' + edge_lig_39_lig_45: + ligand_a: lig_39 + ligand_b: lig_45 + atom mapping: (17, 13) (18, 15) (19, 14) (20, 16) (21, 17) (22, 18) (23, 19) (24, + 20) (25, 21) (26, 22) (27, 23) (28, 24) (29, 25) (30, 26) (45, 41) (46, 42) + (47, 43) (48, 44) + score: '0.386' + edge_lig_26_lig_45: + ligand_a: lig_26 + ligand_b: lig_45 + atom mapping: (17, 13) (18, 15) (19, 14) (20, 16) (21, 17) (22, 18) (23, 19) (24, + 20) (25, 21) (26, 22) (27, 23) (28, 24) (41, 41) (42, 42) (43, 43) (44, 44) + score: '0.356' + edge_lig_42_lig_27: + ligand_a: lig_42 + ligand_b: lig_27 + atom mapping: (8, 29) (10, 28) (11, 26) (12, 27) (13, 25) (14, 24) (15, 47) (16, + 48) (17, 45) (18, 46) (19, 22) (20, 23) (21, 21) (22, 20) (23, 17) (24, 19) + (25, 18) + score: '0.375' + edge_lig_45_lig_23: + ligand_a: lig_45 + ligand_b: lig_23 + atom mapping: (13, 17) (14, 18) (15, 19) (16, 20) (17, 21) (18, 22) (19, 23) (20, + 24) (21, 25) (22, 26) (23, 27) (24, 28) (41, 41) (42, 42) (43, 43) (44, 44) + score: '0.333' + edge_lig_43_lig_25: + ligand_a: lig_43 + ligand_b: lig_25 + atom mapping: (13, 17) (14, 19) (15, 18) (16, 20) (17, 21) (18, 22) (19, 23) (20, + 24) (21, 25) (22, 26) (23, 27) (24, 28) (25, 29) (40, 38) (41, 39) (42, 40) + (43, 41) + score: '0.390' + edge_lig_43_lig_16: + ligand_a: lig_43 + ligand_b: lig_16 + atom mapping: (13, 5) (14, 6) (15, 7) (16, 8) (17, 9) (18, 10) (19, 11) (20, 12) + (21, 13) (22, 14) (23, 15) (24, 16) (25, 17) (26, 18) (40, 25) (41, 26) (42, + 27) (43, 28) + score: '0.454' + edge_lig_33_lig_45: + ligand_a: lig_33 + ligand_b: lig_45 + atom mapping: (17, 13) (18, 15) (19, 14) (20, 16) (21, 17) (22, 18) (23, 19) (24, + 20) (25, 21) (26, 22) (27, 23) (28, 24) (29, 25) (30, 26) (41, 41) (42, 42) + (43, 43) (44, 44) + score: '0.396' + edge_lig_41_lig_45: + ligand_a: lig_41 + ligand_b: lig_45 + atom mapping: (17, 13) (18, 14) (19, 15) (20, 16) (21, 17) (22, 18) (23, 19) (24, + 20) (25, 21) (26, 22) (27, 23) (28, 24) (29, 25) (30, 26) (47, 41) (48, 42) + (49, 43) (50, 44) + score: '0.386' + edge_lig_21_lig_43: + ligand_a: lig_21 + ligand_b: lig_43 + atom mapping: (17, 13) (18, 14) (19, 15) (20, 16) (21, 17) (22, 18) (23, 19) (24, + 20) (25, 21) (26, 22) (27, 23) (28, 24) (40, 40) (41, 41) (42, 42) (43, 43) + score: '0.358' + edge_lig_40_lig_45: + ligand_a: lig_40 + ligand_b: lig_45 + atom mapping: (17, 13) (18, 14) (19, 15) (20, 16) (21, 17) (22, 18) (23, 19) (24, + 20) (25, 21) (26, 22) (27, 23) (28, 24) (29, 25) (30, 26) (46, 41) (47, 42) + (48, 43) (49, 44) + score: '0.386' + edge_lig_42_lig_34: + ligand_a: lig_42 + ligand_b: lig_34 + atom mapping: (8, 29) (9, 30) (10, 28) (11, 26) (12, 27) (13, 25) (14, 24) (15, + 43) (16, 44) (17, 41) (18, 42) (19, 22) (20, 23) (21, 21) (22, 20) (23, 17) + (24, 19) (25, 18) + score: '0.389' + edge_lig_37_lig_45: + ligand_a: lig_37 + ligand_b: lig_45 + atom mapping: (17, 13) (18, 15) (19, 14) (20, 16) (21, 17) (22, 18) (23, 19) (24, + 20) (25, 21) (26, 22) (27, 23) (28, 24) (29, 25) (30, 26) (44, 41) (45, 42) + (46, 43) (47, 44) + score: '0.390' diff --git a/data/cdk8/03_edges/nohup.out b/data/cdk8/03_edges/nohup.out new file mode 100644 index 000000000..fdb137b26 --- /dev/null +++ b/data/cdk8/03_edges/nohup.out @@ -0,0 +1,26 @@ +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. +lig_30_lig_45 exceeds 1 A pairwise distance +lig_43_lig_24 exceeds 1 A pairwise distance +lig_18_lig_23 exceeds 1 A pairwise distance +lig_43_lig_19 exceeds 1 A pairwise distance +lig_42_lig_36 exceeds 1 A pairwise distance +lig_29_lig_45 exceeds 1 A pairwise distance +lig_43_lig_32 exceeds 1 A pairwise distance +lig_13_lig_45 exceeds 1 A pairwise distance +lig_42_lig_35 exceeds 1 A pairwise distance +lig_22_lig_43 exceeds 1 A pairwise distance +lig_39_lig_45 exceeds 1 A pairwise distance +lig_42_lig_27 exceeds 1 A pairwise distance +lig_45_lig_23 exceeds 1 A pairwise distance +lig_33_lig_45 exceeds 1 A pairwise distance +lig_21_lig_43 exceeds 1 A pairwise distance +lig_42_lig_34 exceeds 1 A pairwise distance +lig_37_lig_45 exceeds 1 A pairwise distance diff --git a/data/cmet/00_data/edges.yml b/data/cmet/00_data/edges.yml deleted file mode 100644 index b73933e05..000000000 --- a/data/cmet/00_data/edges.yml +++ /dev/null @@ -1,100 +0,0 @@ -edge_CHEMBL3402744_300_4_CHEMBL3402745_200_5: - ligand_a: lig_CHEMBL3402744_300_4 - ligand_b: lig_CHEMBL3402745_200_5 - name: edge_CHEMBL3402744_300_4_CHEMBL3402745_200_5 -edge_CHEMBL3402747_3400_7_CHEMBL3402745_200_5: - ligand_a: lig_CHEMBL3402747_3400_7 - ligand_b: lig_CHEMBL3402745_200_5 - name: edge_CHEMBL3402747_3400_7_CHEMBL3402745_200_5 -edge_CHEMBL3402747_3400_7_CHEMBL3402748_5300_8: - ligand_a: lig_CHEMBL3402747_3400_7 - ligand_b: lig_CHEMBL3402748_5300_8 - name: edge_CHEMBL3402747_3400_7_CHEMBL3402748_5300_8 -edge_CHEMBL3402747_3400_7_CHEMBL3402751_2100_11: - ligand_a: lig_CHEMBL3402747_3400_7 - ligand_b: lig_CHEMBL3402751_2100_11 - name: edge_CHEMBL3402747_3400_7_CHEMBL3402751_2100_11 -edge_CHEMBL3402748_5300_8_CHEMBL3402751_2100_11: - ligand_a: lig_CHEMBL3402748_5300_8 - ligand_b: lig_CHEMBL3402751_2100_11 - name: edge_CHEMBL3402748_5300_8_CHEMBL3402751_2100_11 -edge_CHEMBL3402749_500_9_CHEMBL3402747_3400_7: - ligand_a: lig_CHEMBL3402749_500_9 - ligand_b: lig_CHEMBL3402747_3400_7 - name: edge_CHEMBL3402749_500_9_CHEMBL3402747_3400_7 -edge_CHEMBL3402749_500_9_CHEMBL3402748_5300_8: - ligand_a: lig_CHEMBL3402749_500_9 - ligand_b: lig_CHEMBL3402748_5300_8 - name: edge_CHEMBL3402749_500_9_CHEMBL3402748_5300_8 -edge_CHEMBL3402749_500_9_CHEMBL3402751_2100_11: - ligand_a: lig_CHEMBL3402749_500_9 - ligand_b: lig_CHEMBL3402751_2100_11 - name: edge_CHEMBL3402749_500_9_CHEMBL3402751_2100_11 -edge_CHEMBL3402749_500_9_CHEMBL3402754_40_14: - ligand_a: lig_CHEMBL3402749_500_9 - ligand_b: lig_CHEMBL3402754_40_14 - name: edge_CHEMBL3402749_500_9_CHEMBL3402754_40_14 -edge_CHEMBL3402750_400_10_CHEMBL3402747_3400_7: - ligand_a: lig_CHEMBL3402750_400_10 - ligand_b: lig_CHEMBL3402747_3400_7 - name: edge_CHEMBL3402750_400_10_CHEMBL3402747_3400_7 -edge_CHEMBL3402750_400_10_CHEMBL3402748_5300_8: - ligand_a: lig_CHEMBL3402750_400_10 - ligand_b: lig_CHEMBL3402748_5300_8 - name: edge_CHEMBL3402750_400_10_CHEMBL3402748_5300_8 -edge_CHEMBL3402750_400_10_CHEMBL3402749_500_9: - ligand_a: lig_CHEMBL3402750_400_10 - ligand_b: lig_CHEMBL3402749_500_9 - name: edge_CHEMBL3402750_400_10_CHEMBL3402749_500_9 -edge_CHEMBL3402752_30000_12_CHEMBL3402744_300_4: - ligand_a: lig_CHEMBL3402752_30000_12 - ligand_b: lig_CHEMBL3402744_300_4 - name: edge_CHEMBL3402752_30000_12_CHEMBL3402744_300_4 -edge_CHEMBL3402752_30000_12_CHEMBL3402747_3400_7: - ligand_a: lig_CHEMBL3402752_30000_12 - ligand_b: lig_CHEMBL3402747_3400_7 - name: edge_CHEMBL3402752_30000_12_CHEMBL3402747_3400_7 -edge_CHEMBL3402752_30000_12_CHEMBL3402748_5300_8: - ligand_a: lig_CHEMBL3402752_30000_12 - ligand_b: lig_CHEMBL3402748_5300_8 - name: edge_CHEMBL3402752_30000_12_CHEMBL3402748_5300_8 -edge_CHEMBL3402752_30000_12_CHEMBL3402749_500_9: - ligand_a: lig_CHEMBL3402752_30000_12 - ligand_b: lig_CHEMBL3402749_500_9 - name: edge_CHEMBL3402752_30000_12_CHEMBL3402749_500_9 -edge_CHEMBL3402752_30000_12_CHEMBL3402754_40_14: - ligand_a: lig_CHEMBL3402752_30000_12 - ligand_b: lig_CHEMBL3402754_40_14 - name: edge_CHEMBL3402752_30000_12_CHEMBL3402754_40_14 -edge_CHEMBL3402752_30000_12_CHEMBL3402755_4200_15: - ligand_a: lig_CHEMBL3402752_30000_12 - ligand_b: lig_CHEMBL3402755_4200_15 - name: edge_CHEMBL3402752_30000_12_CHEMBL3402755_4200_15 -edge_CHEMBL3402753_200_13_CHEMBL3402748_5300_8: - ligand_a: lig_CHEMBL3402753_200_13 - ligand_b: lig_CHEMBL3402748_5300_8 - name: edge_CHEMBL3402753_200_13_CHEMBL3402748_5300_8 -edge_CHEMBL3402753_200_13_CHEMBL3402754_40_14: - ligand_a: lig_CHEMBL3402753_200_13 - ligand_b: lig_CHEMBL3402754_40_14 - name: edge_CHEMBL3402753_200_13_CHEMBL3402754_40_14 -edge_CHEMBL3402754_40_14_CHEMBL3402751_2100_11: - ligand_a: lig_CHEMBL3402754_40_14 - ligand_b: lig_CHEMBL3402751_2100_11 - name: edge_CHEMBL3402754_40_14_CHEMBL3402751_2100_11 -edge_CHEMBL3402754_40_14_CHEMBL3402761_1_21: - ligand_a: lig_CHEMBL3402754_40_14 - ligand_b: lig_CHEMBL3402761_1_21 - name: edge_CHEMBL3402754_40_14_CHEMBL3402761_1_21 -edge_CHEMBL3402755_4200_15_CHEMBL3402753_200_13: - ligand_a: lig_CHEMBL3402755_4200_15 - ligand_b: lig_CHEMBL3402753_200_13 - name: edge_CHEMBL3402755_4200_15_CHEMBL3402753_200_13 -edge_CHEMBL3402755_4200_15_CHEMBL3402754_40_14: - ligand_a: lig_CHEMBL3402755_4200_15 - ligand_b: lig_CHEMBL3402754_40_14 - name: edge_CHEMBL3402755_4200_15_CHEMBL3402754_40_14 -edge_CHEMBL3402755_4200_15_CHEMBL3402761_1_21: - ligand_a: lig_CHEMBL3402755_4200_15 - ligand_b: lig_CHEMBL3402761_1_21 - name: edge_CHEMBL3402755_4200_15_CHEMBL3402761_1_21 diff --git a/data/cmet/03_edges/01_perses_openfe.yaml b/data/cmet/03_edges/01_perses_openfe.yaml new file mode 100644 index 000000000..ebcfead03 --- /dev/null +++ b/data/cmet/03_edges/01_perses_openfe.yaml @@ -0,0 +1,28 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_CHEMBL3402761_1_21_lig_CHEMBL3402749_500_9: + ligand_a: lig_CHEMBL3402761_1_21 + ligand_b: lig_CHEMBL3402749_500_9 + atom mapping: (0, 37) (1, 36) (2, 34) (3, 35) (4, 22) (5, 23) (6, 32) (7, 33) + (8, 30) (10, 28) (11, 29) (12, 26) (13, 27) (15, 24) (16, 25) (17, 21) (18, + 20) (19, 17) (20, 18) (21, 19) (22, 16) (23, 14) (24, 15) (25, 12) (26, 13) + (27, 10) (28, 11) (29, 9) (59, 40) (60, 41) (61, 38) (62, 39) + score: '0.675' + edge_lig_CHEMBL3402744_300_4_lig_CHEMBL3402761_1_21: + ligand_a: lig_CHEMBL3402744_300_4 + ligand_b: lig_CHEMBL3402761_1_21 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 15) (7, 16) (8, 12) + (9, 13) (10, 10) (11, 11) (12, 8) (14, 6) (15, 7) (16, 17) (17, 18) (18, 19) + (19, 20) (20, 21) (21, 22) (22, 59) (23, 60) (24, 29) (26, 27) (27, 28) (28, + 25) (38, 23) (39, 24) (40, 61) (41, 62) + score: '0.671' + edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402761_1_21: + ligand_a: lig_CHEMBL3402745_200_5 + ligand_b: lig_CHEMBL3402761_1_21 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 15) (7, 16) (8, 12) + (9, 13) (10, 10) (11, 11) (12, 8) (14, 6) (15, 7) (16, 17) (17, 18) (18, 19) + (19, 20) (20, 21) (21, 22) (22, 59) (23, 60) (24, 29) (26, 27) (27, 28) (28, + 25) (41, 23) (42, 24) (43, 61) (44, 62) + score: '0.648' diff --git a/data/cmet/03_edges/nohup.out b/data/cmet/03_edges/nohup.out new file mode 100644 index 000000000..023250f71 --- /dev/null +++ b/data/cmet/03_edges/nohup.out @@ -0,0 +1,12 @@ +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. +lig_CHEMBL3402761_1_21_lig_CHEMBL3402749_500_9 exceeds 1 A pairwise distance +lig_CHEMBL3402744_300_4_lig_CHEMBL3402761_1_21 exceeds 1 A pairwise distance +lig_CHEMBL3402745_200_5_lig_CHEMBL3402761_1_21 exceeds 1 A pairwise distance diff --git a/data/eg5/00_data/edges.yml b/data/eg5/00_data/edges.yml deleted file mode 100644 index 051593ef2..000000000 --- a/data/eg5/00_data/edges.yml +++ /dev/null @@ -1,260 +0,0 @@ -edge_CHEMBL1077204_CHEMBL1083836: - ligand_a: lig_CHEMBL1077204 - ligand_b: lig_CHEMBL1083836 - name: edge_CHEMBL1077204_CHEMBL1083836 -edge_CHEMBL1077204_CHEMBL1084143: - ligand_a: lig_CHEMBL1077204 - ligand_b: lig_CHEMBL1084143 - name: edge_CHEMBL1077204_CHEMBL1084143 -edge_CHEMBL1077204_CHEMBL1084676: - ligand_a: lig_CHEMBL1077204 - ligand_b: lig_CHEMBL1084676 - name: edge_CHEMBL1077204_CHEMBL1084676 -edge_CHEMBL1077227_CHEMBL1078998: - ligand_a: lig_CHEMBL1077227 - ligand_b: lig_CHEMBL1078998 - name: edge_CHEMBL1077227_CHEMBL1078998 -edge_CHEMBL1077227_CHEMBL1084935: - ligand_a: lig_CHEMBL1077227 - ligand_b: lig_CHEMBL1084935 - name: edge_CHEMBL1077227_CHEMBL1084935 -edge_CHEMBL1077227_CHEMBL1085666: - ligand_a: lig_CHEMBL1077227 - ligand_b: lig_CHEMBL1085666 - name: edge_CHEMBL1077227_CHEMBL1085666 -edge_CHEMBL1077227_CHEMBL1086410: - ligand_a: lig_CHEMBL1077227 - ligand_b: lig_CHEMBL1086410 - name: edge_CHEMBL1077227_CHEMBL1086410 -edge_CHEMBL1078691_CHEMBL1089056: - ligand_a: lig_CHEMBL1078691 - ligand_b: lig_CHEMBL1089056 - name: edge_CHEMBL1078691_CHEMBL1089056 -edge_CHEMBL1078691_CHEMBL1093088: - ligand_a: lig_CHEMBL1078691 - ligand_b: lig_CHEMBL1093088 - name: edge_CHEMBL1078691_CHEMBL1093088 -edge_CHEMBL1078774_CHEMBL1088740: - ligand_a: lig_CHEMBL1078774 - ligand_b: lig_CHEMBL1088740 - name: edge_CHEMBL1078774_CHEMBL1088740 -edge_CHEMBL1078774_CHEMBL1089056: - ligand_a: lig_CHEMBL1078774 - ligand_b: lig_CHEMBL1089056 - name: edge_CHEMBL1078774_CHEMBL1089056 -edge_CHEMBL1082248_CHEMBL1083517: - ligand_a: lig_CHEMBL1082248 - ligand_b: lig_CHEMBL1083517 - name: edge_CHEMBL1082248_CHEMBL1083517 -edge_CHEMBL1082248_CHEMBL1083836: - ligand_a: lig_CHEMBL1082248 - ligand_b: lig_CHEMBL1083836 - name: edge_CHEMBL1082248_CHEMBL1083836 -edge_CHEMBL1082248_CHEMBL1084143: - ligand_a: lig_CHEMBL1082248 - ligand_b: lig_CHEMBL1084143 - name: edge_CHEMBL1082248_CHEMBL1084143 -edge_CHEMBL1082248_CHEMBL1084678: - ligand_a: lig_CHEMBL1082248 - ligand_b: lig_CHEMBL1084678 - name: edge_CHEMBL1082248_CHEMBL1084678 -edge_CHEMBL1082248_CHEMBL1086410: - ligand_a: lig_CHEMBL1082248 - ligand_b: lig_CHEMBL1086410 - name: edge_CHEMBL1082248_CHEMBL1086410 -edge_CHEMBL1082248_CHEMBL1096002: - ligand_a: lig_CHEMBL1082248 - ligand_b: lig_CHEMBL1096002 - name: edge_CHEMBL1082248_CHEMBL1096002 -edge_CHEMBL1082249_CHEMBL1077227: - ligand_a: lig_CHEMBL1082249 - ligand_b: lig_CHEMBL1077227 - name: edge_CHEMBL1082249_CHEMBL1077227 -edge_CHEMBL1082249_CHEMBL1082248: - ligand_a: lig_CHEMBL1082249 - ligand_b: lig_CHEMBL1082248 - name: edge_CHEMBL1082249_CHEMBL1082248 -edge_CHEMBL1082249_CHEMBL1086409: - ligand_a: lig_CHEMBL1082249 - ligand_b: lig_CHEMBL1086409 - name: edge_CHEMBL1082249_CHEMBL1086409 -edge_CHEMBL1082249_CHEMBL1096003: - ligand_a: lig_CHEMBL1082249 - ligand_b: lig_CHEMBL1096003 - name: edge_CHEMBL1082249_CHEMBL1096003 -edge_CHEMBL1083517_CHEMBL1085666: - ligand_a: lig_CHEMBL1083517 - ligand_b: lig_CHEMBL1085666 - name: edge_CHEMBL1083517_CHEMBL1085666 -edge_CHEMBL1083836_CHEMBL1085666: - ligand_a: lig_CHEMBL1083836 - ligand_b: lig_CHEMBL1085666 - name: edge_CHEMBL1083836_CHEMBL1085666 -edge_CHEMBL1083836_CHEMBL1096002: - ligand_a: lig_CHEMBL1083836 - ligand_b: lig_CHEMBL1096002 - name: edge_CHEMBL1083836_CHEMBL1096002 -edge_CHEMBL1084115_CHEMBL1078998: - ligand_a: lig_CHEMBL1084115 - ligand_b: lig_CHEMBL1078998 - name: edge_CHEMBL1084115_CHEMBL1078998 -edge_CHEMBL1084115_CHEMBL1088740: - ligand_a: lig_CHEMBL1084115 - ligand_b: lig_CHEMBL1088740 - name: edge_CHEMBL1084115_CHEMBL1088740 -edge_CHEMBL1084115_CHEMBL1089056: - ligand_a: lig_CHEMBL1084115 - ligand_b: lig_CHEMBL1089056 - name: edge_CHEMBL1084115_CHEMBL1089056 -edge_CHEMBL1084431_CHEMBL1083517: - ligand_a: lig_CHEMBL1084431 - ligand_b: lig_CHEMBL1083517 - name: edge_CHEMBL1084431_CHEMBL1083517 -edge_CHEMBL1084431_CHEMBL1085666: - ligand_a: lig_CHEMBL1084431 - ligand_b: lig_CHEMBL1085666 - name: edge_CHEMBL1084431_CHEMBL1085666 -edge_CHEMBL1084431_CHEMBL1096002: - ligand_a: lig_CHEMBL1084431 - ligand_b: lig_CHEMBL1096002 - name: edge_CHEMBL1084431_CHEMBL1096002 -edge_CHEMBL1084677_CHEMBL1083836: - ligand_a: lig_CHEMBL1084677 - ligand_b: lig_CHEMBL1083836 - name: edge_CHEMBL1084677_CHEMBL1083836 -edge_CHEMBL1084677_CHEMBL1084676: - ligand_a: lig_CHEMBL1084677 - ligand_b: lig_CHEMBL1084676 - name: edge_CHEMBL1084677_CHEMBL1084676 -edge_CHEMBL1084677_CHEMBL1085692: - ligand_a: lig_CHEMBL1084677 - ligand_b: lig_CHEMBL1085692 - name: edge_CHEMBL1084677_CHEMBL1085692 -edge_CHEMBL1084677_CHEMBL1096003: - ligand_a: lig_CHEMBL1084677 - ligand_b: lig_CHEMBL1096003 - name: edge_CHEMBL1084677_CHEMBL1096003 -edge_CHEMBL1084678_CHEMBL1077204: - ligand_a: lig_CHEMBL1084678 - ligand_b: lig_CHEMBL1077204 - name: edge_CHEMBL1084678_CHEMBL1077204 -edge_CHEMBL1084678_CHEMBL1084143: - ligand_a: lig_CHEMBL1084678 - ligand_b: lig_CHEMBL1084143 - name: edge_CHEMBL1084678_CHEMBL1084143 -edge_CHEMBL1084678_CHEMBL1084431: - ligand_a: lig_CHEMBL1084678 - ligand_b: lig_CHEMBL1084431 - name: edge_CHEMBL1084678_CHEMBL1084431 -edge_CHEMBL1084678_CHEMBL1084676: - ligand_a: lig_CHEMBL1084678 - ligand_b: lig_CHEMBL1084676 - name: edge_CHEMBL1084678_CHEMBL1084676 -edge_CHEMBL1084678_CHEMBL1084677: - ligand_a: lig_CHEMBL1084678 - ligand_b: lig_CHEMBL1084677 - name: edge_CHEMBL1084678_CHEMBL1084677 -edge_CHEMBL1084678_CHEMBL1084935: - ligand_a: lig_CHEMBL1084678 - ligand_b: lig_CHEMBL1084935 - name: edge_CHEMBL1084678_CHEMBL1084935 -edge_CHEMBL1085692_CHEMBL1084676: - ligand_a: lig_CHEMBL1085692 - ligand_b: lig_CHEMBL1084676 - name: edge_CHEMBL1085692_CHEMBL1084676 -edge_CHEMBL1085692_CHEMBL1096002: - ligand_a: lig_CHEMBL1085692 - ligand_b: lig_CHEMBL1096002 - name: edge_CHEMBL1085692_CHEMBL1096002 -edge_CHEMBL1085895_CHEMBL1078998: - ligand_a: lig_CHEMBL1085895 - ligand_b: lig_CHEMBL1078998 - name: edge_CHEMBL1085895_CHEMBL1078998 -edge_CHEMBL1085895_CHEMBL1088740: - ligand_a: lig_CHEMBL1085895 - ligand_b: lig_CHEMBL1088740 - name: edge_CHEMBL1085895_CHEMBL1088740 -edge_CHEMBL1086409_CHEMBL1082248: - ligand_a: lig_CHEMBL1086409 - ligand_b: lig_CHEMBL1082248 - name: edge_CHEMBL1086409_CHEMBL1082248 -edge_CHEMBL1086409_CHEMBL1083517: - ligand_a: lig_CHEMBL1086409 - ligand_b: lig_CHEMBL1083517 - name: edge_CHEMBL1086409_CHEMBL1083517 -edge_CHEMBL1086409_CHEMBL1084676: - ligand_a: lig_CHEMBL1086409 - ligand_b: lig_CHEMBL1084676 - name: edge_CHEMBL1086409_CHEMBL1084676 -edge_CHEMBL1086409_CHEMBL1084678: - ligand_a: lig_CHEMBL1086409 - ligand_b: lig_CHEMBL1084678 - name: edge_CHEMBL1086409_CHEMBL1084678 -edge_CHEMBL1086409_CHEMBL1085666: - ligand_a: lig_CHEMBL1086409 - ligand_b: lig_CHEMBL1085666 - name: edge_CHEMBL1086409_CHEMBL1085666 -edge_CHEMBL1086409_CHEMBL1086410: - ligand_a: lig_CHEMBL1086409 - ligand_b: lig_CHEMBL1086410 - name: edge_CHEMBL1086409_CHEMBL1086410 -edge_CHEMBL1086410_CHEMBL1084935: - ligand_a: lig_CHEMBL1086410 - ligand_b: lig_CHEMBL1084935 - name: edge_CHEMBL1086410_CHEMBL1084935 -edge_CHEMBL1086410_CHEMBL1089056: - ligand_a: lig_CHEMBL1086410 - ligand_b: lig_CHEMBL1089056 - name: edge_CHEMBL1086410_CHEMBL1089056 -edge_CHEMBL1086410_CHEMBL1096002: - ligand_a: lig_CHEMBL1086410 - ligand_b: lig_CHEMBL1096002 - name: edge_CHEMBL1086410_CHEMBL1096002 -edge_CHEMBL1089056_CHEMBL1078998: - ligand_a: lig_CHEMBL1089056 - ligand_b: lig_CHEMBL1078998 - name: edge_CHEMBL1089056_CHEMBL1078998 -edge_CHEMBL1089056_CHEMBL1088740: - ligand_a: lig_CHEMBL1089056 - ligand_b: lig_CHEMBL1088740 - name: edge_CHEMBL1089056_CHEMBL1088740 -edge_CHEMBL1089393_CHEMBL1085895: - ligand_a: lig_CHEMBL1089393 - ligand_b: lig_CHEMBL1085895 - name: edge_CHEMBL1089393_CHEMBL1085895 -edge_CHEMBL1089393_CHEMBL1088740: - ligand_a: lig_CHEMBL1089393 - ligand_b: lig_CHEMBL1088740 - name: edge_CHEMBL1089393_CHEMBL1088740 -edge_CHEMBL1089393_CHEMBL1093088: - ligand_a: lig_CHEMBL1089393 - ligand_b: lig_CHEMBL1093088 - name: edge_CHEMBL1089393_CHEMBL1093088 -edge_CHEMBL1093087_CHEMBL1083517: - ligand_a: lig_CHEMBL1093087 - ligand_b: lig_CHEMBL1083517 - name: edge_CHEMBL1093087_CHEMBL1083517 -edge_CHEMBL1093087_CHEMBL1084678: - ligand_a: lig_CHEMBL1093087 - ligand_b: lig_CHEMBL1084678 - name: edge_CHEMBL1093087_CHEMBL1084678 -edge_CHEMBL1093087_CHEMBL1086409: - ligand_a: lig_CHEMBL1093087 - ligand_b: lig_CHEMBL1086409 - name: edge_CHEMBL1093087_CHEMBL1086409 -edge_CHEMBL1093087_CHEMBL1096003: - ligand_a: lig_CHEMBL1093087 - ligand_b: lig_CHEMBL1096003 - name: edge_CHEMBL1093087_CHEMBL1096003 -edge_CHEMBL1093088_CHEMBL1088740: - ligand_a: lig_CHEMBL1093088 - ligand_b: lig_CHEMBL1088740 - name: edge_CHEMBL1093088_CHEMBL1088740 -edge_CHEMBL1096002_CHEMBL1084935: - ligand_a: lig_CHEMBL1096002 - ligand_b: lig_CHEMBL1084935 - name: edge_CHEMBL1096002_CHEMBL1084935 -edge_CHEMBL1096003_CHEMBL1084143: - ligand_a: lig_CHEMBL1096003 - ligand_b: lig_CHEMBL1084143 - name: edge_CHEMBL1096003_CHEMBL1084143 diff --git a/data/eg5/03_edges/nohup.out b/data/eg5/03_edges/nohup.out new file mode 100644 index 000000000..386a103af --- /dev/null +++ b/data/eg5/03_edges/nohup.out @@ -0,0 +1,9 @@ +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. diff --git a/data/hif2a/00_data/edges.yml b/data/hif2a/00_data/edges.yml deleted file mode 100644 index 1b22a5f4c..000000000 --- a/data/hif2a/00_data/edges.yml +++ /dev/null @@ -1,368 +0,0 @@ -edge_155_84: - ligand_a: lig_155 - ligand_b: lig_84 - name: edge_155_84 -edge_156_164: - ligand_a: lig_156 - ligand_b: lig_164 - name: edge_156_164 -edge_156_165: - ligand_a: lig_156 - ligand_b: lig_165 - name: edge_156_165 -edge_156_167: - ligand_a: lig_156 - ligand_b: lig_167 - name: edge_156_167 -edge_156_42: - ligand_a: lig_156 - ligand_b: lig_42 - name: edge_156_42 -edge_15_25: - ligand_a: lig_15 - ligand_b: lig_25 - name: edge_15_25 -edge_164_124: - ligand_a: lig_164 - ligand_b: lig_124 - name: edge_164_124 -edge_164_163: - ligand_a: lig_164 - ligand_b: lig_163 - name: edge_164_163 -edge_164_25: - ligand_a: lig_164 - ligand_b: lig_25 - name: edge_164_25 -edge_165_163: - ligand_a: lig_165 - ligand_b: lig_163 - name: edge_165_163 -edge_165_252: - ligand_a: lig_165 - ligand_b: lig_252 - name: edge_165_252 -edge_165_336: - ligand_a: lig_165 - ligand_b: lig_336 - name: edge_165_336 -edge_165_42: - ligand_a: lig_165 - ligand_b: lig_42 - name: edge_165_42 -edge_167_155: - ligand_a: lig_167 - ligand_b: lig_155 - name: edge_167_155 -edge_167_165: - ligand_a: lig_167 - ligand_b: lig_165 - name: edge_167_165 -edge_167_50: - ligand_a: lig_167 - ligand_b: lig_50 - name: edge_167_50 -edge_1_15: - ligand_a: lig_1 - ligand_b: lig_15 - name: edge_1_15 -edge_1_155: - ligand_a: lig_1 - ligand_b: lig_155 - name: edge_1_155 -edge_1_254: - ligand_a: lig_1 - ligand_b: lig_254 - name: edge_1_254 -edge_1_256: - ligand_a: lig_1 - ligand_b: lig_256 - name: edge_1_256 -edge_1_7a: - ligand_a: lig_1 - ligand_b: lig_7a - name: edge_1_7a -edge_206_23: - ligand_a: lig_206 - ligand_b: lig_23 - name: edge_206_23 -edge_206_256: - ligand_a: lig_206 - ligand_b: lig_256 - name: edge_206_256 -edge_206_42: - ligand_a: lig_206 - ligand_b: lig_42 - name: edge_206_42 -edge_206_57: - ligand_a: lig_206 - ligand_b: lig_57 - name: edge_206_57 -edge_215_15: - ligand_a: lig_215 - ligand_b: lig_15 - name: edge_215_15 -edge_215_163: - ligand_a: lig_215 - ligand_b: lig_163 - name: edge_215_163 -edge_215_252: - ligand_a: lig_215 - ligand_b: lig_252 - name: edge_215_252 -edge_224_231: - ligand_a: lig_224 - ligand_b: lig_231 - name: edge_224_231 -edge_227_15: - ligand_a: lig_227 - ligand_b: lig_15 - name: edge_227_15 -edge_227_167: - ligand_a: lig_227 - ligand_b: lig_167 - name: edge_227_167 -edge_227_231: - ligand_a: lig_227 - ligand_b: lig_231 - name: edge_227_231 -edge_234_227: - ligand_a: lig_234 - ligand_b: lig_227 - name: edge_234_227 -edge_234_289: - ligand_a: lig_234 - ligand_b: lig_289 - name: edge_234_289 -edge_235_1: - ligand_a: lig_235 - ligand_b: lig_1 - name: edge_235_1 -edge_235_54: - ligand_a: lig_235 - ligand_b: lig_54 - name: edge_235_54 -edge_237_227: - ligand_a: lig_237 - ligand_b: lig_227 - name: edge_237_227 -edge_237_254: - ligand_a: lig_237 - ligand_b: lig_254 - name: edge_237_254 -edge_237_290: - ligand_a: lig_237 - ligand_b: lig_290 - name: edge_237_290 -edge_237_31: - ligand_a: lig_237 - ligand_b: lig_31 - name: edge_237_31 -edge_237_336: - ligand_a: lig_237 - ligand_b: lig_336 - name: edge_237_336 -edge_237_41: - ligand_a: lig_237 - ligand_b: lig_41 - name: edge_237_41 -edge_23_15: - ligand_a: lig_23 - ligand_b: lig_15 - name: edge_23_15 -edge_251_15: - ligand_a: lig_251 - ligand_b: lig_15 - name: edge_251_15 -edge_251_25: - ligand_a: lig_251 - ligand_b: lig_25 - name: edge_251_25 -edge_252_124: - ligand_a: lig_252 - ligand_b: lig_124 - name: edge_252_124 -edge_252_155: - ligand_a: lig_252 - ligand_b: lig_155 - name: edge_252_155 -edge_252_231: - ligand_a: lig_252 - ligand_b: lig_231 - name: edge_252_231 -edge_252_290: - ligand_a: lig_252 - ligand_b: lig_290 - name: edge_252_290 -edge_252_336: - ligand_a: lig_252 - ligand_b: lig_336 - name: edge_252_336 -edge_254_251: - ligand_a: lig_254 - ligand_b: lig_251 - name: edge_254_251 -edge_254_50: - ligand_a: lig_254 - ligand_b: lig_50 - name: edge_254_50 -edge_266_156: - ligand_a: lig_266 - ligand_b: lig_156 - name: edge_266_156 -edge_266_165: - ligand_a: lig_266 - ligand_b: lig_165 - name: edge_266_165 -edge_266_254: - ligand_a: lig_266 - ligand_b: lig_254 - name: edge_266_254 -edge_266_84: - ligand_a: lig_266 - ligand_b: lig_84 - name: edge_266_84 -edge_289_224: - ligand_a: lig_289 - ligand_b: lig_224 - name: edge_289_224 -edge_289_35: - ligand_a: lig_289 - ligand_b: lig_35 - name: edge_289_35 -edge_290_23: - ligand_a: lig_290 - ligand_b: lig_23 - name: edge_290_23 -edge_290_256: - ligand_a: lig_290 - ligand_b: lig_256 - name: edge_290_256 -edge_290_7a: - ligand_a: lig_290 - ligand_b: lig_7a - name: edge_290_7a -edge_290_84: - ligand_a: lig_290 - ligand_b: lig_84 - name: edge_290_84 -edge_30_25: - ligand_a: lig_30 - ligand_b: lig_25 - name: edge_30_25 -edge_30_251: - ligand_a: lig_30 - ligand_b: lig_251 - name: edge_30_251 -edge_30_42: - ligand_a: lig_30 - ligand_b: lig_42 - name: edge_30_42 -edge_30_84: - ligand_a: lig_30 - ligand_b: lig_84 - name: edge_30_84 -edge_31_61: - ligand_a: lig_31 - ligand_b: lig_61 - name: edge_31_61 -edge_31_7a: - ligand_a: lig_31 - ligand_b: lig_7a - name: edge_31_7a -edge_336_251: - ligand_a: lig_336 - ligand_b: lig_251 - name: edge_336_251 -edge_338_163: - ligand_a: lig_338 - ligand_b: lig_163 - name: edge_338_163 -edge_338_165: - ligand_a: lig_338 - ligand_b: lig_165 - name: edge_338_165 -edge_338_215: - ligand_a: lig_338 - ligand_b: lig_215 - name: edge_338_215 -edge_35_7a: - ligand_a: lig_35 - ligand_b: lig_7a - name: edge_35_7a -edge_35_84: - ligand_a: lig_35 - ligand_b: lig_84 - name: edge_35_84 -edge_41_7b: - ligand_a: lig_41 - ligand_b: lig_7b - name: edge_41_7b -edge_42_164: - ligand_a: lig_42 - ligand_b: lig_164 - name: edge_42_164 -edge_43_155: - ligand_a: lig_43 - ligand_b: lig_155 - name: edge_43_155 -edge_43_215: - ligand_a: lig_43 - ligand_b: lig_215 - name: edge_43_215 -edge_43_235: - ligand_a: lig_43 - ligand_b: lig_235 - name: edge_43_235 -edge_43_25: - ligand_a: lig_43 - ligand_b: lig_25 - name: edge_43_25 -edge_43_54: - ligand_a: lig_43 - ligand_b: lig_54 - name: edge_43_54 -edge_54_124: - ligand_a: lig_54 - ligand_b: lig_124 - name: edge_54_124 -edge_54_251: - ligand_a: lig_54 - ligand_b: lig_251 - name: edge_54_251 -edge_57_231: - ligand_a: lig_57 - ligand_b: lig_231 - name: edge_57_231 -edge_61_251: - ligand_a: lig_61 - ligand_b: lig_251 - name: edge_61_251 -edge_67_165: - ligand_a: lig_67 - ligand_b: lig_165 - name: edge_67_165 -edge_67_256: - ligand_a: lig_67 - ligand_b: lig_256 - name: edge_67_256 -edge_7a_224: - ligand_a: lig_7a - ligand_b: lig_224 - name: edge_7a_224 -edge_7a_23: - ligand_a: lig_7a - ligand_b: lig_23 - name: edge_7a_23 -edge_7b_231: - ligand_a: lig_7b - ligand_b: lig_231 - name: edge_7b_231 -edge_7b_42: - ligand_a: lig_7b - ligand_b: lig_42 - name: edge_7b_42 -edge_84_15: - ligand_a: lig_84 - ligand_b: lig_15 - name: edge_84_15 diff --git a/data/hif2a/03_edges/01_perses_openfe.yaml b/data/hif2a/03_edges/01_perses_openfe.yaml new file mode 100644 index 000000000..666c808c4 --- /dev/null +++ b/data/hif2a/03_edges/01_perses_openfe.yaml @@ -0,0 +1,210 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_54_lig_235: + ligand_a: lig_54 + ligand_b: lig_235 + atom mapping: (12, 7) (13, 8) (14, 9) (15, 10) (16, 11) (18, 12) (19, 13) (20, + 14) (21, 15) (22, 17) (23, 18) + score: '0.338' + edge_lig_163_lig_54: + ligand_a: lig_163 + ligand_b: lig_54 + atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (12, 21) (13, 18) (14, + 19) (15, 16) (16, 17) (18, 14) (19, 15) + score: '0.367' + edge_lig_50_lig_224: + ligand_a: lig_50 + ligand_b: lig_224 + atom mapping: (14, 24) (15, 25) (16, 26) (17, 27) + score: '0.098' + edge_lig_67_lig_124: + ligand_a: lig_67 + ligand_b: lig_124 + atom mapping: (7, 7) (8, 8) (9, 9) (10, 10) (11, 11) (13, 13) (15, 21) (17, 23) + score: '0.311' + edge_lig_290_lig_54: + ligand_a: lig_290 + ligand_b: lig_54 + atom mapping: (0, 19) (1, 18) (2, 16) (3, 17) (4, 14) (5, 15) (6, 13) (7, 12) + (34, 22) (35, 23) (36, 20) (37, 21) + score: '0.359' + edge_lig_256_lig_43: + ligand_a: lig_256 + ligand_b: lig_43 + atom mapping: (7, 9) (8, 10) (9, 11) (10, 12) (11, 13) (13, 15) (14, 16) (15, + 17) (16, 18) (17, 20) (18, 21) + score: '0.357' + edge_lig_215_lig_54: + ligand_a: lig_215 + ligand_b: lig_54 + atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (12, 21) (13, 18) (14, + 19) (15, 16) (16, 17) (18, 14) (19, 15) + score: '0.364' + edge_lig_61_lig_31: + ligand_a: lig_61 + ligand_b: lig_31 + atom mapping: (7, 10) (8, 9) (9, 7) (10, 8) (11, 4) (12, 5) (13, 2) (14, 3) (15, + 1) (17, 32) (18, 33) + score: '0.360' + edge_lig_167_lig_54: + ligand_a: lig_167 + ligand_b: lig_54 + atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (12, 21) (13, 18) (14, + 19) (15, 16) (16, 17) (18, 14) (19, 15) + score: '0.364' + edge_lig_43_lig_224: + ligand_a: lig_43 + ligand_b: lig_224 + atom mapping: (27, 24) (28, 25) (29, 26) (30, 27) (32, 29) (33, 30) + score: '0.145' + edge_lig_35_lig_224: + ligand_a: lig_35 + ligand_b: lig_224 + atom mapping: (27, 24) (28, 25) (29, 26) (30, 27) (32, 29) (33, 30) + score: '0.145' + edge_lig_227_lig_54: + ligand_a: lig_227 + ligand_b: lig_54 + atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (12, 21) (13, 18) (14, + 19) (15, 16) (16, 17) (18, 14) (19, 15) + score: '0.361' + edge_lig_31_lig_224: + ligand_a: lig_31 + ligand_b: lig_224 + atom mapping: (17, 24) (18, 26) (19, 25) (20, 27) (22, 29) (23, 28) + score: '0.145' + edge_lig_31_lig_25: + ligand_a: lig_31 + ligand_b: lig_25 + atom mapping: (1, 11) (2, 13) (3, 14) (4, 15) (7, 16) (8, 17) (9, 8) (10, 7) (32, + 9) (33, 10) + score: '0.331' + edge_lig_1_lig_31: + ligand_a: lig_1 + ligand_b: lig_31 + atom mapping: (7, 10) (8, 9) (9, 7) (10, 8) (11, 4) (12, 5) (13, 2) (14, 3) (15, + 1) (17, 32) (18, 33) + score: '0.357' + edge_lig_41_lig_224: + ligand_a: lig_41 + ligand_b: lig_224 + atom mapping: (26, 24) (27, 25) (28, 26) (29, 27) (31, 29) (32, 30) + score: '0.147' + edge_lig_234_lig_54: + ligand_a: lig_234 + ligand_b: lig_54 + atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (12, 21) (13, 18) (14, + 19) (15, 16) (16, 17) (18, 14) (19, 15) + score: '0.367' + edge_lig_336_lig_54: + ligand_a: lig_336 + ligand_b: lig_54 + atom mapping: (7, 12) (8, 13) (9, 14) (10, 15) (11, 16) (12, 17) (13, 18) (14, + 19) (15, 20) (16, 21) (18, 22) (19, 23) + score: '0.367' + edge_lig_84_lig_31: + ligand_a: lig_84 + ligand_b: lig_31 + atom mapping: (0, 3) (1, 2) (2, 1) (4, 32) (5, 33) (6, 9) (7, 10) (29, 7) (30, + 8) (31, 4) (32, 5) + score: '0.363' + edge_lig_42_lig_224: + ligand_a: lig_42 + ligand_b: lig_224 + atom mapping: (27, 24) (28, 26) (29, 25) (30, 27) (32, 29) (33, 30) + score: '0.145' + edge_lig_124_lig_224: + ligand_a: lig_124 + ligand_b: lig_224 + atom mapping: (14, 24) (15, 26) (16, 25) (17, 27) (18, 28) (19, 29) (20, 30) + score: '0.174' + edge_lig_231_lig_54: + ligand_a: lig_231 + ligand_b: lig_54 + atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (12, 21) (13, 18) (14, + 19) (15, 16) (16, 17) (18, 14) (19, 15) + score: '0.370' + edge_lig_206_lig_54: + ligand_a: lig_206 + ligand_b: lig_54 + atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (12, 21) (13, 18) (14, + 19) (15, 16) (16, 17) (18, 14) (19, 15) + score: '0.364' + edge_lig_30_lig_224: + ligand_a: lig_30 + ligand_b: lig_224 + atom mapping: (14, 24) (15, 26) (16, 25) (17, 27) (19, 29) (20, 28) + score: '0.152' + edge_lig_23_lig_31: + ligand_a: lig_23 + ligand_b: lig_31 + atom mapping: (7, 10) (8, 9) (9, 7) (10, 8) (11, 4) (12, 5) (13, 2) (14, 3) (15, + 1) (17, 32) (18, 33) + score: '0.355' + edge_lig_252_lig_54: + ligand_a: lig_252 + ligand_b: lig_54 + atom mapping: (7, 12) (8, 13) (9, 14) (10, 15) (11, 16) (12, 17) (13, 18) (14, + 19) (15, 20) (16, 21) (18, 22) (19, 23) + score: '0.367' + edge_lig_155_lig_54: + ligand_a: lig_155 + ligand_b: lig_54 + atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (12, 21) (13, 18) (14, + 19) (15, 16) (16, 17) (18, 14) (19, 15) + score: '0.367' + edge_lig_57_lig_54: + ligand_a: lig_57 + ligand_b: lig_54 + atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (12, 21) (13, 18) (14, + 19) (15, 16) (16, 17) (18, 14) (19, 15) + score: '0.364' + edge_lig_289_lig_54: + ligand_a: lig_289 + ligand_b: lig_54 + atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (12, 21) (13, 18) (14, + 19) (15, 16) (16, 17) (18, 14) (19, 15) + score: '0.367' + edge_lig_254_lig_54: + ligand_a: lig_254 + ligand_b: lig_54 + atom mapping: (7, 12) (8, 13) (9, 14) (10, 15) (11, 16) (12, 17) (13, 18) (14, + 19) (15, 20) (16, 21) (18, 22) (19, 23) + score: '0.364' + edge_lig_338_lig_54: + ligand_a: lig_338 + ligand_b: lig_54 + atom mapping: (7, 12) (8, 13) (9, 14) (10, 15) (11, 16) (12, 17) (13, 18) (14, + 19) (15, 20) (16, 21) (18, 22) (19, 23) + score: '0.364' + edge_lig_251_lig_43: + ligand_a: lig_251 + ligand_b: lig_43 + atom mapping: (7, 9) (8, 10) (9, 11) (10, 12) (11, 13) (13, 15) (14, 16) (15, + 17) (16, 18) (17, 20) (18, 21) + score: '0.355' + edge_lig_156_lig_54: + ligand_a: lig_156 + ligand_b: lig_54 + atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (13, 18) (14, 19) (15, + 16) (16, 17) (18, 14) (19, 15) + score: '0.346' + edge_lig_15_lig_54: + ligand_a: lig_15 + ligand_b: lig_54 + atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (12, 21) (13, 18) (14, + 19) (15, 16) (16, 17) (18, 14) (19, 15) + score: '0.361' + edge_lig_165_lig_54: + ligand_a: lig_165 + ligand_b: lig_54 + atom mapping: (0, 19) (1, 18) (2, 16) (3, 17) (4, 14) (5, 15) (6, 13) (7, 12) + (34, 22) (35, 23) (36, 20) (37, 21) + score: '0.367' + edge_lig_54_lig_224: + ligand_a: lig_54 + ligand_b: lig_224 + atom mapping: (29, 24) (30, 25) (31, 26) (32, 27) + score: '0.093' diff --git a/data/hif2a/03_edges/nohup.out b/data/hif2a/03_edges/nohup.out new file mode 100644 index 000000000..b21d476c5 --- /dev/null +++ b/data/hif2a/03_edges/nohup.out @@ -0,0 +1,36 @@ +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. +lig_163_lig_54 exceeds 1 A pairwise distance +lig_50_lig_224 exceeds 1 A pairwise distance +lig_67_lig_124 exceeds 1 A pairwise distance +lig_215_lig_54 exceeds 1 A pairwise distance +lig_61_lig_31 exceeds 1 A pairwise distance +lig_167_lig_54 exceeds 1 A pairwise distance +lig_43_lig_224 exceeds 1 A pairwise distance +lig_35_lig_224 exceeds 1 A pairwise distance +lig_227_lig_54 exceeds 1 A pairwise distance +lig_31_lig_224 exceeds 1 A pairwise distance +lig_31_lig_25 exceeds 1 A pairwise distance +lig_1_lig_31 exceeds 1 A pairwise distance +lig_41_lig_224 exceeds 1 A pairwise distance +lig_234_lig_54 exceeds 1 A pairwise distance +lig_42_lig_224 exceeds 1 A pairwise distance +lig_124_lig_224 exceeds 1 A pairwise distance +lig_231_lig_54 exceeds 1 A pairwise distance +lig_206_lig_54 exceeds 1 A pairwise distance +lig_30_lig_224 exceeds 1 A pairwise distance +lig_23_lig_31 exceeds 1 A pairwise distance +lig_155_lig_54 exceeds 1 A pairwise distance +lig_57_lig_54 exceeds 1 A pairwise distance +lig_289_lig_54 exceeds 1 A pairwise distance +lig_251_lig_43 exceeds 1 A pairwise distance +lig_156_lig_54 exceeds 1 A pairwise distance +lig_15_lig_54 exceeds 1 A pairwise distance +lig_54_lig_224 exceeds 1 A pairwise distance diff --git a/data/mcl1/00_data/edges.yml b/data/mcl1/00_data/edges.yml deleted file mode 100644 index c1002f59c..000000000 --- a/data/mcl1/00_data/edges.yml +++ /dev/null @@ -1,284 +0,0 @@ -edge_26_44: - ligand_a: lig_26 - ligand_b: lig_44 - name: edge_26_44 -edge_26_57: - ligand_a: lig_26 - ligand_b: lig_57 - name: edge_26_57 -edge_26_64: - ligand_a: lig_26 - ligand_b: lig_64 - name: edge_26_64 -edge_27_23: - ligand_a: lig_27 - ligand_b: lig_23 - name: edge_27_23 -edge_27_45: - ligand_a: lig_27 - ligand_b: lig_45 - name: edge_27_45 -edge_27_46: - ligand_a: lig_27 - ligand_b: lig_46 - name: edge_27_46 -edge_28_27: - ligand_a: lig_28 - ligand_b: lig_27 - name: edge_28_27 -edge_28_35: - ligand_a: lig_28 - ligand_b: lig_35 - name: edge_28_35 -edge_28_47: - ligand_a: lig_28 - ligand_b: lig_47 - name: edge_28_47 -edge_29_27: - ligand_a: lig_29 - ligand_b: lig_27 - name: edge_29_27 -edge_29_35: - ligand_a: lig_29 - ligand_b: lig_35 - name: edge_29_35 -edge_29_40: - ligand_a: lig_29 - ligand_b: lig_40 - name: edge_29_40 -edge_30_27: - ligand_a: lig_30 - ligand_b: lig_27 - name: edge_30_27 -edge_30_35: - ligand_a: lig_30 - ligand_b: lig_35 - name: edge_30_35 -edge_30_40: - ligand_a: lig_30 - ligand_b: lig_40 - name: edge_30_40 -edge_30_48: - ligand_a: lig_30 - ligand_b: lig_48 - name: edge_30_48 -edge_31_35: - ligand_a: lig_31 - ligand_b: lig_35 - name: edge_31_35 -edge_32_34: - ligand_a: lig_32 - ligand_b: lig_34 - name: edge_32_34 -edge_32_46: - ligand_a: lig_32 - ligand_b: lig_46 - name: edge_32_46 -edge_33_27: - ligand_a: lig_33 - ligand_b: lig_27 - name: edge_33_27 -edge_35_33: - ligand_a: lig_35 - ligand_b: lig_33 - name: edge_35_33 -edge_35_34: - ligand_a: lig_35 - ligand_b: lig_34 - name: edge_35_34 -edge_35_36: - ligand_a: lig_35 - ligand_b: lig_36 - name: edge_35_36 -edge_35_37: - ligand_a: lig_35 - ligand_b: lig_37 - name: edge_35_37 -edge_35_39: - ligand_a: lig_35 - ligand_b: lig_39 - name: edge_35_39 -edge_35_53: - ligand_a: lig_35 - ligand_b: lig_53 - name: edge_35_53 -edge_35_60: - ligand_a: lig_35 - ligand_b: lig_60 - name: edge_35_60 -edge_38_35: - ligand_a: lig_38 - ligand_b: lig_35 - name: edge_38_35 -edge_38_60: - ligand_a: lig_38 - ligand_b: lig_60 - name: edge_38_60 -edge_39_32: - ligand_a: lig_39 - ligand_b: lig_32 - name: edge_39_32 -edge_41_32: - ligand_a: lig_41 - ligand_b: lig_32 - name: edge_41_32 -edge_41_35: - ligand_a: lig_41 - ligand_b: lig_35 - name: edge_41_35 -edge_42_51: - ligand_a: lig_42 - ligand_b: lig_51 - name: edge_42_51 -edge_42_64: - ligand_a: lig_42 - ligand_b: lig_64 - name: edge_42_64 -edge_43_27: - ligand_a: lig_43 - ligand_b: lig_27 - name: edge_43_27 -edge_43_47: - ligand_a: lig_43 - ligand_b: lig_47 - name: edge_43_47 -edge_44_23: - ligand_a: lig_44 - ligand_b: lig_23 - name: edge_44_23 -edge_48_27: - ligand_a: lig_48 - ligand_b: lig_27 - name: edge_48_27 -edge_49_35: - ligand_a: lig_49 - ligand_b: lig_35 - name: edge_49_35 -edge_49_67: - ligand_a: lig_49 - ligand_b: lig_67 - name: edge_49_67 -edge_50_60: - ligand_a: lig_50 - ligand_b: lig_60 - name: edge_50_60 -edge_51_45: - ligand_a: lig_51 - ligand_b: lig_45 - name: edge_51_45 -edge_52_60: - ligand_a: lig_52 - ligand_b: lig_60 - name: edge_52_60 -edge_54_23: - ligand_a: lig_54 - ligand_b: lig_23 - name: edge_54_23 -edge_54_42: - ligand_a: lig_54 - ligand_b: lig_42 - name: edge_54_42 -edge_56_35: - ligand_a: lig_56 - ligand_b: lig_35 - name: edge_56_35 -edge_56_60: - ligand_a: lig_56 - ligand_b: lig_60 - name: edge_56_60 -edge_57_23: - ligand_a: lig_57 - ligand_b: lig_23 - name: edge_57_23 -edge_58_60: - ligand_a: lig_58 - ligand_b: lig_60 - name: edge_58_60 -edge_60_36: - ligand_a: lig_60 - ligand_b: lig_36 - name: edge_60_36 -edge_61_60: - ligand_a: lig_61 - ligand_b: lig_60 - name: edge_61_60 -edge_62_26: - ligand_a: lig_62 - ligand_b: lig_26 - name: edge_62_26 -edge_62_45: - ligand_a: lig_62 - ligand_b: lig_45 - name: edge_62_45 -edge_63_60: - ligand_a: lig_63 - ligand_b: lig_60 - name: edge_63_60 -edge_65_60: - ligand_a: lig_65 - ligand_b: lig_60 - name: edge_65_60 -edge_65_67: - ligand_a: lig_65 - ligand_b: lig_67 - name: edge_65_67 -edge_66_23: - ligand_a: lig_66 - ligand_b: lig_23 - name: edge_66_23 -edge_66_42: - ligand_a: lig_66 - ligand_b: lig_42 - name: edge_66_42 -edge_67_27: - ligand_a: lig_67 - ligand_b: lig_27 - name: edge_67_27 -edge_67_31: - ligand_a: lig_67 - ligand_b: lig_31 - name: edge_67_31 -edge_67_32: - ligand_a: lig_67 - ligand_b: lig_32 - name: edge_67_32 -edge_67_35: - ligand_a: lig_67 - ligand_b: lig_35 - name: edge_67_35 -edge_67_37: - ligand_a: lig_67 - ligand_b: lig_37 - name: edge_67_37 -edge_67_50: - ligand_a: lig_67 - ligand_b: lig_50 - name: edge_67_50 -edge_67_52: - ligand_a: lig_67 - ligand_b: lig_52 - name: edge_67_52 -edge_67_53: - ligand_a: lig_67 - ligand_b: lig_53 - name: edge_67_53 -edge_67_58: - ligand_a: lig_67 - ligand_b: lig_58 - name: edge_67_58 -edge_67_61: - ligand_a: lig_67 - ligand_b: lig_61 - name: edge_67_61 -edge_67_63: - ligand_a: lig_67 - ligand_b: lig_63 - name: edge_67_63 -edge_68_23: - ligand_a: lig_68 - ligand_b: lig_23 - name: edge_68_23 -edge_68_45: - ligand_a: lig_68 - ligand_b: lig_45 - name: edge_68_45 diff --git a/data/mcl1/03_edges/01_perses_openfe.yaml b/data/mcl1/03_edges/01_perses_openfe.yaml new file mode 100644 index 000000000..21b464bf5 --- /dev/null +++ b/data/mcl1/03_edges/01_perses_openfe.yaml @@ -0,0 +1,180 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_53_lig_43: + ligand_a: lig_53 + ligand_b: lig_43 + atom mapping: (0, 36) (1, 29) (2, 30) (3, 31) (4, 32) (5, 27) (6, 28) (7, 24) + (8, 25) (9, 26) (10, 37) (11, 38) (12, 39) (13, 40) (14, 21) (15, 23) (16, 22) + (17, 18) (18, 20) (19, 19) (20, 15) (21, 17) (22, 16) (23, 14) (41, 33) (43, + 35) + score: '0.548' + edge_lig_34_lig_47: + ligand_a: lig_34 + ligand_b: lig_47 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 17) (17, 16) (18, + 18) (19, 19) (20, 20) (21, 21) (22, 23) (23, 22) (24, 24) (39, 41) (40, 42) + score: '0.583' + edge_lig_28_lig_43: + ligand_a: lig_28 + ligand_b: lig_43 + atom mapping: (0, 35) (1, 30) (2, 31) (3, 32) (4, 27) (5, 28) (6, 29) (7, 36) + (8, 24) (9, 25) (10, 26) (11, 37) (12, 38) (13, 39) (14, 40) (15, 21) (16, 23) + (17, 22) (18, 18) (19, 19) (20, 20) (21, 15) (22, 17) (23, 16) (24, 14) (39, + 33) (40, 34) + score: '0.583' + edge_lig_56_lig_43: + ligand_a: lig_56 + ligand_b: lig_43 + atom mapping: (0, 35) (1, 30) (2, 31) (3, 32) (4, 27) (5, 28) (6, 29) (7, 36) + (8, 24) (9, 25) (10, 26) (15, 38) (16, 39) (17, 40) (18, 21) (19, 23) (20, 22) + (21, 18) (22, 19) (23, 20) (24, 15) (25, 16) (26, 17) (27, 14) (45, 33) (46, + 34) + score: '0.548' + edge_lig_37_lig_43: + ligand_a: lig_37 + ligand_b: lig_43 + atom mapping: (0, 35) (1, 30) (2, 31) (3, 32) (4, 27) (5, 28) (6, 29) (7, 36) + (8, 24) (9, 25) (10, 26) (11, 37) (12, 38) (13, 39) (14, 40) (15, 21) (16, 23) + (17, 22) (18, 18) (19, 19) (20, 20) (21, 15) (22, 17) (23, 16) (24, 14) (42, + 33) (43, 34) + score: '0.561' + edge_lig_58_lig_47: + ligand_a: lig_58 + ligand_b: lig_47 + atom mapping: (0, 7) (1, 6) (2, 1) (3, 2) (4, 3) (5, 4) (6, 5) (7, 8) (8, 9) (9, + 10) (14, 12) (15, 13) (16, 14) (17, 15) (18, 17) (19, 16) (20, 18) (21, 20) + (22, 19) (23, 21) (24, 23) (25, 22) (26, 24) (44, 41) (46, 0) + score: '0.538' + edge_lig_52_lig_47: + ligand_a: lig_52 + ligand_b: lig_47 + atom mapping: (0, 7) (1, 6) (2, 1) (3, 2) (4, 3) (5, 4) (6, 5) (7, 8) (8, 9) (9, + 10) (10, 11) (11, 12) (12, 13) (13, 14) (14, 15) (15, 17) (16, 16) (17, 18) + (18, 20) (19, 19) (20, 21) (21, 23) (22, 22) (23, 24) (38, 41) (40, 0) + score: '0.570' + edge_lig_63_lig_47: + ligand_a: lig_63 + ligand_b: lig_47 + atom mapping: (0, 7) (1, 6) (2, 1) (3, 2) (4, 3) (5, 4) (6, 5) (7, 8) (8, 9) (9, + 10) (10, 12) (11, 13) (12, 14) (13, 15) (14, 17) (15, 16) (16, 18) (17, 20) + (18, 19) (19, 21) (20, 22) (21, 23) (22, 24) (40, 41) (42, 0) + score: '0.542' + edge_lig_58_lig_46: + ligand_a: lig_58 + ligand_b: lig_46 + atom mapping: (0, 7) (1, 6) (2, 1) (3, 2) (4, 3) (5, 4) (6, 5) (7, 8) (8, 9) (9, + 10) (14, 12) (15, 13) (16, 14) (17, 15) (18, 17) (19, 16) (20, 18) (21, 20) + (22, 19) (23, 21) (24, 23) (25, 22) (26, 24) (44, 43) (46, 0) + score: '0.550' + edge_lig_58_lig_43: + ligand_a: lig_58 + ligand_b: lig_43 + atom mapping: (0, 36) (1, 29) (2, 30) (3, 31) (4, 32) (5, 27) (6, 28) (7, 24) + (8, 25) (9, 26) (14, 38) (15, 39) (16, 40) (17, 21) (18, 23) (19, 22) (20, 18) + (21, 20) (22, 19) (23, 15) (24, 17) (25, 16) (26, 14) (44, 33) (46, 35) + score: '0.531' + edge_lig_50_lig_43: + ligand_a: lig_50 + ligand_b: lig_43 + atom mapping: (0, 34) (1, 31) (2, 32) (3, 27) (4, 28) (5, 29) (6, 30) (7, 35) + (9, 24) (10, 25) (11, 26) (12, 37) (13, 38) (14, 39) (15, 40) (16, 21) (17, + 23) (18, 22) (19, 18) (20, 19) (21, 20) (22, 15) (23, 17) (24, 16) (25, 14) + (43, 33) + score: '0.548' + edge_lig_67_lig_47: + ligand_a: lig_67 + ligand_b: lig_47 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 12) (12, 13) (13, 14) (14, 15) (15, 17) (16, 16) (17, 18) (18, + 20) (19, 19) (20, 21) (21, 22) (22, 23) (23, 24) (41, 41) (42, 42) + score: '0.555' + edge_lig_58_lig_48: + ligand_a: lig_58 + ligand_b: lig_48 + atom mapping: (0, 7) (1, 6) (2, 1) (3, 2) (4, 3) (5, 4) (6, 5) (7, 8) (8, 9) (9, + 10) (14, 12) (15, 13) (16, 14) (17, 15) (18, 17) (19, 16) (20, 18) (21, 20) + (22, 19) (23, 21) (24, 23) (25, 22) (26, 24) (44, 40) (46, 0) + score: '0.573' + edge_lig_30_lig_47: + ligand_a: lig_30 + ligand_b: lig_47 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 17) (17, 16) (18, + 18) (19, 19) (20, 20) (21, 21) (22, 23) (23, 22) (24, 24) (39, 41) (40, 42) + score: '0.583' + edge_lig_31_lig_47: + ligand_a: lig_31 + ligand_b: lig_47 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 17) (17, 16) (18, + 18) (19, 19) (20, 20) (21, 21) (22, 23) (23, 22) (24, 24) (39, 41) (40, 42) + score: '0.583' + edge_lig_49_lig_47: + ligand_a: lig_49 + ligand_b: lig_47 + atom mapping: (0, 42) (1, 2) (2, 3) (3, 4) (4, 5) (5, 6) (6, 1) (7, 0) (9, 8) + (10, 9) (11, 10) (12, 11) (13, 12) (14, 13) (15, 14) (16, 15) (17, 17) (18, + 16) (19, 18) (20, 19) (21, 20) (22, 21) (23, 23) (24, 22) (25, 24) (40, 41) + score: '0.570' + edge_lig_27_lig_47: + ligand_a: lig_27 + ligand_b: lig_47 + atom mapping: (9, 24) (10, 21) (11, 22) (12, 23) (13, 18) (14, 19) (15, 20) (16, + 15) (17, 16) (18, 17) (19, 8) (20, 9) (21, 10) (22, 4) (23, 5) (24, 6) (25, + 1) (26, 2) (27, 3) (28, 41) (29, 42) (30, 0) (31, 7) (32, 11) (33, 12) (34, + 13) (35, 14) + score: '0.608' + edge_lig_32_lig_47: + ligand_a: lig_32 + ligand_b: lig_47 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 17) (17, 16) (18, + 18) (19, 19) (20, 20) (21, 21) (22, 23) (23, 22) (24, 24) (39, 41) (40, 42) + score: '0.583' + edge_lig_65_lig_47: + ligand_a: lig_65 + ligand_b: lig_47 + atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 42) (9, 10) + (10, 9) (11, 8) (12, 15) (13, 16) (14, 17) (15, 18) (16, 20) (17, 19) (18, 21) + (19, 22) (20, 23) (21, 24) (39, 12) (40, 13) (41, 14) (42, 7) + score: '0.542' + edge_lig_35_lig_47: + ligand_a: lig_35 + ligand_b: lig_47 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 17) (17, 16) (18, + 18) (19, 19) (20, 20) (21, 21) (22, 23) (23, 22) (24, 24) (39, 41) (40, 42) + score: '0.583' + edge_lig_61_lig_47: + ligand_a: lig_61 + ligand_b: lig_47 + atom mapping: (0, 42) (1, 2) (2, 3) (3, 4) (4, 5) (5, 6) (6, 1) (7, 0) (9, 8) + (10, 9) (11, 10) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, + 18) (19, 20) (20, 19) (21, 21) (22, 22) (23, 23) (24, 24) (42, 41) + score: '0.542' + edge_lig_33_lig_43: + ligand_a: lig_33 + ligand_b: lig_43 + atom mapping: (0, 35) (1, 30) (2, 31) (3, 32) (4, 27) (5, 28) (6, 29) (7, 36) + (8, 24) (9, 25) (10, 26) (11, 37) (12, 38) (13, 39) (14, 40) (15, 21) (16, 23) + (17, 22) (18, 18) (19, 19) (20, 20) (21, 15) (22, 17) (23, 16) (24, 14) (36, + 33) (37, 34) + score: '0.608' + edge_lig_60_lig_47: + ligand_a: lig_60 + ligand_b: lig_47 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 12) (12, 13) (13, 14) (14, 15) (15, 17) (16, 16) (17, 18) (18, + 20) (19, 19) (20, 21) (21, 22) (22, 23) (23, 24) (41, 41) (42, 42) + score: '0.555' + edge_lig_36_lig_43: + ligand_a: lig_36 + ligand_b: lig_43 + atom mapping: (0, 35) (1, 30) (2, 31) (3, 32) (4, 27) (5, 28) (6, 29) (7, 36) + (8, 24) (9, 25) (10, 26) (11, 37) (12, 38) (13, 39) (14, 40) (15, 21) (16, 23) + (17, 22) (18, 18) (19, 19) (20, 20) (21, 15) (22, 17) (23, 16) (24, 14) (42, + 33) (43, 34) + score: '0.561' diff --git a/data/mcl1/03_edges/nohup.out b/data/mcl1/03_edges/nohup.out new file mode 100644 index 000000000..6ab1627ad --- /dev/null +++ b/data/mcl1/03_edges/nohup.out @@ -0,0 +1,31 @@ +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. +lig_34_lig_47 exceeds 1 A pairwise distance +lig_28_lig_43 exceeds 1 A pairwise distance +lig_56_lig_43 exceeds 1 A pairwise distance +lig_37_lig_43 exceeds 1 A pairwise distance +lig_58_lig_47 exceeds 1 A pairwise distance +lig_52_lig_47 exceeds 1 A pairwise distance +lig_63_lig_47 exceeds 1 A pairwise distance +lig_58_lig_46 exceeds 1 A pairwise distance +lig_50_lig_43 exceeds 1 A pairwise distance +lig_67_lig_47 exceeds 1 A pairwise distance +lig_58_lig_48 exceeds 1 A pairwise distance +lig_30_lig_47 exceeds 1 A pairwise distance +lig_31_lig_47 exceeds 1 A pairwise distance +lig_49_lig_47 exceeds 1 A pairwise distance +lig_27_lig_47 exceeds 1 A pairwise distance +lig_32_lig_47 exceeds 1 A pairwise distance +lig_65_lig_47 exceeds 1 A pairwise distance +lig_35_lig_47 exceeds 1 A pairwise distance +lig_61_lig_47 exceeds 1 A pairwise distance +lig_33_lig_43 exceeds 1 A pairwise distance +lig_60_lig_47 exceeds 1 A pairwise distance +lig_36_lig_43 exceeds 1 A pairwise distance diff --git a/data/p38/00_data/edges.yml b/data/p38/00_data/edges.yml deleted file mode 100644 index ddc88af65..000000000 --- a/data/p38/00_data/edges.yml +++ /dev/null @@ -1,224 +0,0 @@ -edge_p38a_2aa_p38a_2bb: - ligand_a: lig_p38a_2aa - ligand_b: lig_p38a_2bb - name: edge_p38a_2aa_p38a_2bb -edge_p38a_2aa_p38a_3flw: - ligand_a: lig_p38a_2aa - ligand_b: lig_p38a_3flw - name: edge_p38a_2aa_p38a_3flw -edge_p38a_2e_p38a_2j: - ligand_a: lig_p38a_2e - ligand_b: lig_p38a_2j - name: edge_p38a_2e_p38a_2j -edge_p38a_2ee_p38a_2j: - ligand_a: lig_p38a_2ee - ligand_b: lig_p38a_2j - name: edge_p38a_2ee_p38a_2j -edge_p38a_2ee_p38a_3fln: - ligand_a: lig_p38a_2ee - ligand_b: lig_p38a_3fln - name: edge_p38a_2ee_p38a_3fln -edge_p38a_2g_p38a_2c: - ligand_a: lig_p38a_2g - ligand_b: lig_p38a_2c - name: edge_p38a_2g_p38a_2c -edge_p38a_2g_p38a_2f: - ligand_a: lig_p38a_2g - ligand_b: lig_p38a_2f - name: edge_p38a_2g_p38a_2f -edge_p38a_2g_p38a_2h: - ligand_a: lig_p38a_2g - ligand_b: lig_p38a_2h - name: edge_p38a_2g_p38a_2h -edge_p38a_2g_p38a_2i: - ligand_a: lig_p38a_2g - ligand_b: lig_p38a_2i - name: edge_p38a_2g_p38a_2i -edge_p38a_2gg_p38a_2j: - ligand_a: lig_p38a_2gg - ligand_b: lig_p38a_2j - name: edge_p38a_2gg_p38a_2j -edge_p38a_2j_p38a_2f: - ligand_a: lig_p38a_2j - ligand_b: lig_p38a_2f - name: edge_p38a_2j_p38a_2f -edge_p38a_2j_p38a_2ff: - ligand_a: lig_p38a_2j - ligand_b: lig_p38a_2ff - name: edge_p38a_2j_p38a_2ff -edge_p38a_2j_p38a_2h: - ligand_a: lig_p38a_2j - ligand_b: lig_p38a_2h - name: edge_p38a_2j_p38a_2h -edge_p38a_2j_p38a_2q: - ligand_a: lig_p38a_2j - ligand_b: lig_p38a_2q - name: edge_p38a_2j_p38a_2q -edge_p38a_2j_p38a_2r: - ligand_a: lig_p38a_2j - ligand_b: lig_p38a_2r - name: edge_p38a_2j_p38a_2r -edge_p38a_2l_p38a_2j: - ligand_a: lig_p38a_2l - ligand_b: lig_p38a_2j - name: edge_p38a_2l_p38a_2j -edge_p38a_2l_p38a_2n: - ligand_a: lig_p38a_2l - ligand_b: lig_p38a_2n - name: edge_p38a_2l_p38a_2n -edge_p38a_2l_p38a_2o: - ligand_a: lig_p38a_2l - ligand_b: lig_p38a_2o - name: edge_p38a_2l_p38a_2o -edge_p38a_2l_p38a_2p: - ligand_a: lig_p38a_2l - ligand_b: lig_p38a_2p - name: edge_p38a_2l_p38a_2p -edge_p38a_2m_p38a_2j: - ligand_a: lig_p38a_2m - ligand_b: lig_p38a_2j - name: edge_p38a_2m_p38a_2j -edge_p38a_2m_p38a_2k: - ligand_a: lig_p38a_2m - ligand_b: lig_p38a_2k - name: edge_p38a_2m_p38a_2k -edge_p38a_2s_p38a_2l: - ligand_a: lig_p38a_2s - ligand_b: lig_p38a_2l - name: edge_p38a_2s_p38a_2l -edge_p38a_2t_p38a_2j: - ligand_a: lig_p38a_2t - ligand_b: lig_p38a_2j - name: edge_p38a_2t_p38a_2j -edge_p38a_2u_p38a_2k: - ligand_a: lig_p38a_2u - ligand_b: lig_p38a_2k - name: edge_p38a_2u_p38a_2k -edge_p38a_2u_p38a_2q: - ligand_a: lig_p38a_2u - ligand_b: lig_p38a_2q - name: edge_p38a_2u_p38a_2q -edge_p38a_2v_p38a_2bb: - ligand_a: lig_p38a_2v - ligand_b: lig_p38a_2bb - name: edge_p38a_2v_p38a_2bb -edge_p38a_2v_p38a_2j: - ligand_a: lig_p38a_2v - ligand_b: lig_p38a_2j - name: edge_p38a_2v_p38a_2j -edge_p38a_2v_p38a_2x: - ligand_a: lig_p38a_2v - ligand_b: lig_p38a_2x - name: edge_p38a_2v_p38a_2x -edge_p38a_2v_p38a_2y: - ligand_a: lig_p38a_2v - ligand_b: lig_p38a_2y - name: edge_p38a_2v_p38a_2y -edge_p38a_2v_p38a_3fln: - ligand_a: lig_p38a_2v - ligand_b: lig_p38a_3fln - name: edge_p38a_2v_p38a_3fln -edge_p38a_2v_p38a_3fly: - ligand_a: lig_p38a_2v - ligand_b: lig_p38a_3fly - name: edge_p38a_2v_p38a_3fly -edge_p38a_2v_p38a_3fmh: - ligand_a: lig_p38a_2v - ligand_b: lig_p38a_3fmh - name: edge_p38a_2v_p38a_3fmh -edge_p38a_2v_p38a_3fmk: - ligand_a: lig_p38a_2v - ligand_b: lig_p38a_3fmk - name: edge_p38a_2v_p38a_3fmk -edge_p38a_2z_p38a_2aa: - ligand_a: lig_p38a_2z - ligand_b: lig_p38a_2aa - name: edge_p38a_2z_p38a_2aa -edge_p38a_2z_p38a_2y: - ligand_a: lig_p38a_2z - ligand_b: lig_p38a_2y - name: edge_p38a_2z_p38a_2y -edge_p38a_2z_p38a_3flq: - ligand_a: lig_p38a_2z - ligand_b: lig_p38a_3flq - name: edge_p38a_2z_p38a_3flq -edge_p38a_2z_p38a_3flw: - ligand_a: lig_p38a_2z - ligand_b: lig_p38a_3flw - name: edge_p38a_2z_p38a_3flw -edge_p38a_2z_p38a_3fmk: - ligand_a: lig_p38a_2z - ligand_b: lig_p38a_3fmk - name: edge_p38a_2z_p38a_3fmk -edge_p38a_3fln_p38a_2e: - ligand_a: lig_p38a_3fln - ligand_b: lig_p38a_2e - name: edge_p38a_3fln_p38a_2e -edge_p38a_3fln_p38a_2ff: - ligand_a: lig_p38a_3fln - ligand_b: lig_p38a_2ff - name: edge_p38a_3fln_p38a_2ff -edge_p38a_3fln_p38a_2g: - ligand_a: lig_p38a_3fln - ligand_b: lig_p38a_2g - name: edge_p38a_3fln_p38a_2g -edge_p38a_3fln_p38a_2gg: - ligand_a: lig_p38a_3fln - ligand_b: lig_p38a_2gg - name: edge_p38a_3fln_p38a_2gg -edge_p38a_3fln_p38a_2i: - ligand_a: lig_p38a_3fln - ligand_b: lig_p38a_2i - name: edge_p38a_3fln_p38a_2i -edge_p38a_3fln_p38a_2k: - ligand_a: lig_p38a_3fln - ligand_b: lig_p38a_2k - name: edge_p38a_3fln_p38a_2k -edge_p38a_3fln_p38a_2n: - ligand_a: lig_p38a_3fln - ligand_b: lig_p38a_2n - name: edge_p38a_3fln_p38a_2n -edge_p38a_3fln_p38a_2o: - ligand_a: lig_p38a_3fln - ligand_b: lig_p38a_2o - name: edge_p38a_3fln_p38a_2o -edge_p38a_3fln_p38a_2p: - ligand_a: lig_p38a_3fln - ligand_b: lig_p38a_2p - name: edge_p38a_3fln_p38a_2p -edge_p38a_3fln_p38a_2r: - ligand_a: lig_p38a_3fln - ligand_b: lig_p38a_2r - name: edge_p38a_3fln_p38a_2r -edge_p38a_3fln_p38a_2s: - ligand_a: lig_p38a_3fln - ligand_b: lig_p38a_2s - name: edge_p38a_3fln_p38a_2s -edge_p38a_3fln_p38a_2t: - ligand_a: lig_p38a_3fln - ligand_b: lig_p38a_2t - name: edge_p38a_3fln_p38a_2t -edge_p38a_3fln_p38a_3flz: - ligand_a: lig_p38a_3fln - ligand_b: lig_p38a_3flz - name: edge_p38a_3fln_p38a_3flz -edge_p38a_3fly_p38a_2x: - ligand_a: lig_p38a_3fly - ligand_b: lig_p38a_2x - name: edge_p38a_3fly_p38a_2x -edge_p38a_3fly_p38a_3flq: - ligand_a: lig_p38a_3fly - ligand_b: lig_p38a_3flq - name: edge_p38a_3fly_p38a_3flq -edge_p38a_3fly_p38a_3fmh: - ligand_a: lig_p38a_3fly - ligand_b: lig_p38a_3fmh - name: edge_p38a_3fly_p38a_3fmh -edge_p38a_3flz_p38a_2c: - ligand_a: lig_p38a_3flz - ligand_b: lig_p38a_2c - name: edge_p38a_3flz_p38a_2c -edge_p38a_3flz_p38a_2g: - ligand_a: lig_p38a_3flz - ligand_b: lig_p38a_2g - name: edge_p38a_3flz_p38a_2g diff --git a/data/p38/03_edges/01_perses_openfe.yaml b/data/p38/03_edges/01_perses_openfe.yaml new file mode 100644 index 000000000..06e33b1e2 --- /dev/null +++ b/data/p38/03_edges/01_perses_openfe.yaml @@ -0,0 +1,225 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_p38a_3flw_lig_p38a_2gg: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2gg + atom mapping: (10, 4) (12, 3) (13, 2) (14, 1) (15, 0) (16, 25) (17, 24) (18, 23) + (19, 43) (20, 44) (21, 47) (22, 46) (23, 45) (24, 41) (25, 42) (26, 28) (27, + 29) (28, 30) (29, 39) (31, 37) (32, 38) (33, 35) (34, 36) (35, 33) (36, 34) + (37, 31) (39, 26) (40, 27) + score: '0.670' + edge_lig_p38a_3flw_lig_p38a_2j: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2j + atom mapping: (10, 4) (11, 5) (12, 3) (13, 2) (14, 1) (15, 0) (16, 23) (17, 22) + (18, 21) (19, 43) (20, 44) (21, 45) (22, 46) (23, 47) (24, 41) (25, 42) (26, + 26) (27, 27) (28, 30) (29, 31) (31, 33) (32, 34) (33, 35) (34, 36) (35, 37) + (36, 38) (37, 39) (39, 24) (40, 25) + score: '0.686' + edge_lig_p38a_3flw_lig_p38a_2m: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2m + atom mapping: (10, 4) (12, 3) (13, 2) (14, 1) (15, 0) (16, 23) (17, 22) (18, 21) + (19, 41) (24, 39) (25, 40) (26, 26) (27, 27) (28, 28) (29, 37) (31, 35) (32, + 36) (33, 33) (34, 34) (35, 31) (36, 32) (37, 29) (39, 24) (40, 25) + score: '0.598' + edge_lig_p38a_3fmh_lig_p38a_2g: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_2g + atom mapping: (9, 4) (11, 3) (12, 2) (13, 1) (14, 0) (15, 23) (16, 22) (17, 21) + (18, 41) (19, 42) (20, 43) (21, 44) (22, 45) (23, 39) (24, 40) (25, 26) (26, + 27) (27, 28) (28, 37) (30, 35) (31, 36) (32, 33) (34, 31) (35, 32) (36, 29) + (38, 24) (39, 25) + score: '0.668' + edge_lig_p38a_3flw_lig_p38a_2i: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2i + atom mapping: (10, 4) (11, 5) (12, 3) (13, 2) (14, 1) (15, 0) (16, 23) (17, 22) + (18, 21) (19, 43) (20, 44) (21, 45) (22, 46) (23, 47) (24, 41) (25, 42) (26, + 26) (27, 27) (28, 30) (29, 31) (31, 33) (32, 34) (33, 35) (35, 37) (36, 38) + (37, 39) (39, 24) (40, 25) + score: '0.667' + edge_lig_p38a_2z_lig_p38a_2m: + ligand_a: lig_p38a_2z + ligand_b: lig_p38a_2m + atom mapping: (6, 4) (7, 5) (8, 3) (9, 21) (10, 22) (11, 23) (12, 1) (13, 0) (14, + 2) (15, 24) (16, 25) (17, 26) (18, 27) (19, 28) (20, 37) (22, 35) (23, 36) (24, + 33) (25, 34) (26, 31) (27, 32) (28, 29) (30, 39) (31, 40) (32, 41) + score: '0.641' + edge_lig_p38a_3flw_lig_p38a_2p: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2p + atom mapping: (10, 4) (12, 3) (13, 2) (14, 1) (15, 0) (16, 23) (17, 22) (18, 21) + (19, 41) (20, 42) (22, 44) (23, 43) (24, 39) (25, 40) (26, 26) (27, 27) (28, + 28) (29, 37) (31, 35) (32, 36) (33, 33) (34, 34) (35, 31) (36, 32) (37, 29) + (39, 24) (40, 25) + score: '0.634' + edge_lig_p38a_3flw_lig_p38a_2ff: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2ff + atom mapping: (10, 12) (12, 14) (13, 20) (14, 18) (15, 19) (16, 17) (17, 16) (18, + 15) (19, 38) (20, 39) (21, 42) (22, 41) (23, 40) (24, 36) (25, 37) (26, 23) + (27, 24) (28, 25) (29, 34) (31, 32) (32, 33) (33, 30) (34, 31) (35, 28) (36, + 29) (37, 26) (39, 21) (40, 22) + score: '0.665' + edge_lig_p38a_2v_lig_p38a_2m: + ligand_a: lig_p38a_2v + ligand_b: lig_p38a_2m + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (10, 21) (11, 22) (12, 23) (13, + 24) (14, 25) (15, 26) (16, 27) (17, 28) (18, 37) (20, 35) (21, 36) (22, 33) + (23, 34) (24, 31) (25, 32) (26, 29) (28, 39) (29, 40) (30, 41) + score: '0.718' + edge_lig_p38a_3fmk_lig_p38a_2m: + ligand_a: lig_p38a_3fmk + ligand_b: lig_p38a_2m + atom mapping: (9, 4) (11, 3) (12, 2) (13, 1) (14, 0) (15, 23) (16, 22) (17, 21) + (18, 41) (23, 39) (24, 40) (25, 26) (26, 27) (27, 28) (28, 37) (30, 35) (31, + 36) (32, 33) (33, 34) (34, 31) (35, 32) (36, 29) (38, 24) (39, 25) + score: '0.620' + edge_lig_p38a_3flw_lig_p38a_2t: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2t + atom mapping: (10, 4) (12, 3) (13, 2) (14, 1) (15, 0) (16, 23) (17, 22) (18, 21) + (19, 41) (20, 42) (22, 44) (23, 43) (24, 39) (25, 40) (26, 26) (27, 27) (28, + 28) (29, 37) (31, 35) (32, 36) (33, 33) (34, 34) (35, 31) (36, 32) (37, 29) + (39, 24) (40, 25) + score: '0.665' + edge_lig_p38a_3fmh_lig_p38a_2k: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_2k + atom mapping: (9, 4) (11, 3) (12, 2) (13, 1) (14, 0) (15, 23) (16, 22) (17, 21) + (18, 41) (23, 39) (24, 40) (25, 26) (26, 27) (27, 28) (28, 37) (30, 35) (31, + 36) (32, 33) (33, 34) (34, 31) (35, 32) (36, 29) (38, 24) (39, 25) + score: '0.654' + edge_lig_p38a_3fmh_lig_p38a_3fln: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_3fln + atom mapping: (9, 4) (11, 3) (12, 2) (13, 1) (14, 0) (15, 23) (16, 22) (17, 21) + (18, 41) (19, 42) (20, 43) (21, 44) (22, 45) (23, 39) (24, 40) (25, 26) (26, + 27) (27, 28) (28, 37) (30, 35) (31, 36) (32, 33) (33, 34) (34, 31) (35, 32) + (36, 29) (38, 24) (39, 25) + score: '0.686' + edge_lig_p38a_3fmh_lig_p38a_2e: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_2e + atom mapping: (9, 4) (11, 3) (12, 2) (13, 1) (14, 0) (15, 23) (16, 22) (17, 21) + (18, 41) (19, 42) (20, 43) (21, 44) (22, 45) (23, 39) (24, 40) (25, 26) (26, + 27) (27, 28) (28, 37) (30, 35) (31, 36) (32, 33) (33, 34) (34, 31) (35, 32) + (36, 29) (37, 30) (38, 24) (39, 25) + score: '0.699' + edge_lig_p38a_3flw_lig_p38a_2n: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2n + atom mapping: (10, 33) (11, 34) (12, 32) (13, 50) (14, 51) (15, 52) (16, 29) (17, + 30) (18, 31) (19, 11) (20, 8) (22, 9) (23, 10) (24, 12) (25, 13) (26, 14) (27, + 15) (28, 16) (29, 17) (31, 19) (32, 20) (33, 21) (34, 22) (35, 23) (36, 24) + (37, 25) (39, 27) (40, 28) + score: '0.657' + edge_lig_p38a_2s_lig_p38a_3flw: + ligand_a: lig_p38a_2s + ligand_b: lig_p38a_3flw + atom mapping: (9, 20) (10, 23) (11, 22) (12, 19) (13, 24) (14, 25) (15, 26) (16, + 27) (17, 28) (18, 29) (20, 31) (21, 32) (22, 33) (23, 34) (24, 35) (25, 36) + (26, 37) (28, 39) (29, 40) (30, 16) (31, 17) (32, 18) (33, 12) (34, 10) (51, + 13) (52, 14) (53, 15) + score: '0.641' + edge_lig_p38a_2x_lig_p38a_2m: + ligand_a: lig_p38a_2x + ligand_b: lig_p38a_2m + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (18, 21) (19, 22) (20, + 23) (21, 24) (22, 25) (23, 26) (24, 27) (25, 28) (26, 37) (28, 35) (29, 36) + (30, 33) (31, 34) (32, 31) (33, 32) (34, 29) (36, 39) (37, 40) (38, 41) + score: '0.657' + edge_lig_p38a_2y_lig_p38a_2m: + ligand_a: lig_p38a_2y + ligand_b: lig_p38a_2m + atom mapping: (14, 4) (15, 5) (16, 3) (17, 21) (18, 22) (19, 23) (20, 1) (21, + 0) (22, 2) (23, 24) (24, 25) (25, 26) (26, 27) (27, 28) (28, 37) (30, 35) (31, + 36) (32, 33) (33, 34) (34, 31) (35, 32) (36, 29) (38, 39) (39, 40) (40, 41) + score: '0.641' + edge_lig_p38a_3fly_lig_p38a_2m: + ligand_a: lig_p38a_3fly + ligand_b: lig_p38a_2m + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (16, 21) (17, 22) (18, 23) (19, + 24) (20, 25) (21, 26) (22, 27) (23, 28) (24, 37) (26, 35) (27, 36) (28, 33) + (29, 34) (30, 31) (31, 32) (32, 29) (34, 39) (35, 40) (36, 41) + score: '0.661' + edge_lig_p38a_3flw_lig_p38a_2r: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2r + atom mapping: (10, 36) (12, 35) (13, 53) (14, 54) (15, 55) (16, 32) (17, 33) (18, + 34) (19, 14) (20, 11) (21, 13) (22, 12) (24, 15) (25, 16) (26, 17) (27, 18) + (28, 19) (29, 28) (31, 26) (32, 27) (33, 24) (34, 25) (35, 22) (36, 23) (37, + 20) (39, 30) (40, 31) + score: '0.641' + edge_lig_p38a_3fmh_lig_p38a_2f: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_2f + atom mapping: (9, 4) (11, 3) (12, 2) (13, 1) (14, 0) (15, 23) (16, 22) (17, 21) + (18, 41) (19, 42) (20, 43) (21, 44) (22, 45) (23, 39) (24, 40) (25, 26) (26, + 27) (27, 28) (28, 37) (30, 35) (32, 33) (34, 31) (35, 32) (36, 29) (37, 30) + (38, 24) (39, 25) + score: '0.668' + edge_lig_p38a_3flw_lig_p38a_2o: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2o + atom mapping: (10, 4) (12, 3) (13, 2) (14, 1) (15, 0) (16, 23) (17, 22) (18, 21) + (19, 41) (20, 42) (22, 44) (23, 43) (24, 39) (25, 40) (26, 26) (27, 27) (28, + 28) (29, 37) (31, 35) (32, 36) (33, 33) (34, 34) (35, 31) (36, 32) (37, 29) + (39, 24) (40, 25) + score: '0.638' + edge_lig_p38a_3flw_lig_p38a_2ee: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2ee + atom mapping: (10, 4) (12, 3) (13, 2) (14, 1) (15, 0) (16, 29) (17, 28) (18, 27) + (19, 47) (20, 48) (21, 51) (22, 50) (23, 49) (24, 45) (25, 46) (26, 32) (27, + 33) (28, 34) (29, 43) (31, 41) (32, 42) (33, 39) (34, 40) (35, 37) (36, 38) + (37, 35) (39, 30) (40, 31) + score: '0.657' + edge_lig_p38a_3flw_lig_p38a_2l: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2l + atom mapping: (10, 4) (12, 3) (13, 2) (14, 1) (15, 0) (16, 23) (17, 22) (18, 21) + (19, 41) (20, 42) (22, 44) (23, 43) (24, 39) (25, 40) (26, 26) (27, 27) (28, + 28) (29, 37) (31, 35) (32, 36) (33, 33) (34, 34) (35, 31) (36, 32) (37, 29) + (39, 24) (40, 25) + score: '0.653' + edge_lig_p38a_3fmh_lig_p38a_2h: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_2h + atom mapping: (9, 4) (10, 5) (11, 3) (12, 2) (13, 1) (14, 0) (15, 23) (16, 22) + (17, 21) (18, 41) (19, 42) (20, 43) (21, 44) (22, 45) (23, 39) (24, 40) (25, + 26) (26, 27) (27, 28) (28, 29) (30, 31) (31, 32) (32, 33) (34, 35) (35, 36) + (36, 37) (38, 24) (39, 25) + score: '0.680' + edge_lig_p38a_2bb_lig_p38a_2m: + ligand_a: lig_p38a_2bb + ligand_b: lig_p38a_2m + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (19, 21) (20, 22) (21, 23) (22, + 24) (23, 25) (24, 26) (25, 27) (26, 28) (27, 37) (29, 35) (30, 36) (31, 33) + (32, 34) (33, 31) (34, 32) (35, 29) (37, 39) (38, 40) (39, 41) + score: '0.636' + edge_lig_p38a_2aa_lig_p38a_2m: + ligand_a: lig_p38a_2aa + ligand_b: lig_p38a_2m + atom mapping: (7, 4) (9, 3) (10, 21) (11, 22) (12, 23) (13, 1) (14, 0) (15, 2) + (16, 24) (17, 25) (18, 26) (19, 27) (20, 28) (21, 37) (23, 35) (24, 36) (25, + 33) (26, 34) (27, 31) (28, 32) (29, 29) (31, 39) (32, 40) (33, 41) + score: '0.644' + edge_lig_p38a_3fmh_lig_p38a_3flz: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_3flz + atom mapping: (9, 4) (11, 3) (12, 2) (13, 1) (14, 0) (15, 23) (16, 22) (17, 21) + (18, 41) (19, 42) (20, 43) (21, 44) (22, 45) (23, 39) (24, 40) (25, 26) (26, + 27) (27, 28) (28, 37) (30, 35) (31, 36) (32, 33) (34, 31) (35, 32) (36, 29) + (37, 30) (38, 24) (39, 25) + score: '0.680' + edge_lig_p38a_3fmh_lig_p38a_2m: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_2m + atom mapping: (9, 4) (11, 3) (12, 2) (13, 1) (14, 0) (15, 23) (16, 22) (17, 21) + (18, 41) (23, 39) (24, 40) (25, 26) (26, 27) (27, 28) (28, 37) (30, 35) (31, + 36) (32, 33) (33, 34) (34, 31) (35, 32) (36, 29) (38, 24) (39, 25) + score: '0.620' diff --git a/data/p38/03_edges/nohup.out b/data/p38/03_edges/nohup.out new file mode 100644 index 000000000..b0a937e5b --- /dev/null +++ b/data/p38/03_edges/nohup.out @@ -0,0 +1,39 @@ +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. +lig_p38a_3flw_lig_p38a_2gg exceeds 1 A pairwise distance +lig_p38a_3flw_lig_p38a_2j exceeds 1 A pairwise distance +lig_p38a_3flw_lig_p38a_2m exceeds 1 A pairwise distance +lig_p38a_3fmh_lig_p38a_2g exceeds 1 A pairwise distance +lig_p38a_3flw_lig_p38a_2i exceeds 1 A pairwise distance +lig_p38a_2z_lig_p38a_2m exceeds 1 A pairwise distance +lig_p38a_3flw_lig_p38a_2p exceeds 1 A pairwise distance +lig_p38a_3flw_lig_p38a_2ff exceeds 1 A pairwise distance +lig_p38a_3flw_lig_p38a_2ff exceeds 1 A pairwise distance +lig_p38a_2v_lig_p38a_2m exceeds 1 A pairwise distance +lig_p38a_3fmk_lig_p38a_2m exceeds 1 A pairwise distance +lig_p38a_3flw_lig_p38a_2t exceeds 1 A pairwise distance +lig_p38a_3fmh_lig_p38a_2k exceeds 1 A pairwise distance +lig_p38a_3fmh_lig_p38a_3fln exceeds 1 A pairwise distance +lig_p38a_3fmh_lig_p38a_2e exceeds 1 A pairwise distance +lig_p38a_3flw_lig_p38a_2n exceeds 1 A pairwise distance +lig_p38a_2s_lig_p38a_3flw exceeds 1 A pairwise distance +lig_p38a_2x_lig_p38a_2m exceeds 1 A pairwise distance +lig_p38a_2y_lig_p38a_2m exceeds 1 A pairwise distance +lig_p38a_3fly_lig_p38a_2m exceeds 1 A pairwise distance +lig_p38a_3flw_lig_p38a_2r exceeds 1 A pairwise distance +lig_p38a_3fmh_lig_p38a_2f exceeds 1 A pairwise distance +lig_p38a_3flw_lig_p38a_2o exceeds 1 A pairwise distance +lig_p38a_3flw_lig_p38a_2ee exceeds 1 A pairwise distance +lig_p38a_3flw_lig_p38a_2l exceeds 1 A pairwise distance +lig_p38a_3fmh_lig_p38a_2h exceeds 1 A pairwise distance +lig_p38a_2bb_lig_p38a_2m exceeds 1 A pairwise distance +lig_p38a_2aa_lig_p38a_2m exceeds 1 A pairwise distance +lig_p38a_3fmh_lig_p38a_3flz exceeds 1 A pairwise distance +lig_p38a_3fmh_lig_p38a_2m exceeds 1 A pairwise distance diff --git a/data/pde2/00_data/edges.yml b/data/pde2/00_data/edges.yml deleted file mode 100644 index 7327dcec1..000000000 --- a/data/pde2/00_data/edges.yml +++ /dev/null @@ -1,136 +0,0 @@ -edge_43249674_48022468: - ligand_a: lig_43249674 - ligand_b: lig_48022468 - name: edge_43249674_48022468 -edge_43249674_49175789: - ligand_a: lig_43249674 - ligand_b: lig_49175789 - name: edge_43249674_49175789 -edge_48009208_43249674: - ligand_a: lig_48009208 - ligand_b: lig_43249674 - name: edge_48009208_43249674 -edge_48009208_49137374: - ligand_a: lig_48009208 - ligand_b: lig_49137374 - name: edge_48009208_49137374 -edge_48168913_48022468: - ligand_a: lig_48168913 - ligand_b: lig_48022468 - name: edge_48168913_48022468 -edge_48168913_48271249: - ligand_a: lig_48168913 - ligand_b: lig_48271249 - name: edge_48168913_48271249 -edge_48168913_49585367: - ligand_a: lig_48168913 - ligand_b: lig_49585367 - name: edge_48168913_49585367 -edge_49072088_48271249: - ligand_a: lig_49072088 - ligand_b: lig_48271249 - name: edge_49072088_48271249 -edge_49137374_48271249: - ligand_a: lig_49137374 - ligand_b: lig_48271249 - name: edge_49137374_48271249 -edge_49175789_49072088: - ligand_a: lig_49175789 - ligand_b: lig_49072088 - name: edge_49175789_49072088 -edge_49175828_49580115: - ligand_a: lig_49175828 - ligand_b: lig_49580115 - name: edge_49175828_49580115 -edge_49220392_49137530: - ligand_a: lig_49220392 - ligand_b: lig_49137530 - name: edge_49220392_49137530 -edge_49220392_49175828: - ligand_a: lig_49220392 - ligand_b: lig_49175828 - name: edge_49220392_49175828 -edge_49220548_49137374: - ligand_a: lig_49220548 - ligand_b: lig_49137374 - name: edge_49220548_49137374 -edge_49220548_49220392: - ligand_a: lig_49220548 - ligand_b: lig_49220392 - name: edge_49220548_49220392 -edge_49220548_49580115: - ligand_a: lig_49220548 - ligand_b: lig_49580115 - name: edge_49220548_49580115 -edge_49220548_49932129: - ligand_a: lig_49220548 - ligand_b: lig_49932129 - name: edge_49220548_49932129 -edge_49396360_49137530: - ligand_a: lig_49396360 - ligand_b: lig_49137530 - name: edge_49396360_49137530 -edge_49396360_49175828: - ligand_a: lig_49396360 - ligand_b: lig_49175828 - name: edge_49396360_49175828 -edge_49396360_49220548: - ligand_a: lig_49396360 - ligand_b: lig_49220548 - name: edge_49396360_49220548 -edge_49396360_49582390: - ligand_a: lig_49396360 - ligand_b: lig_49582390 - name: edge_49396360_49582390 -edge_49582468_49137530: - ligand_a: lig_49582468 - ligand_b: lig_49137530 - name: edge_49582468_49137530 -edge_49582468_49932129: - ligand_a: lig_49582468 - ligand_b: lig_49932129 - name: edge_49582468_49932129 -edge_49585367_49137530: - ligand_a: lig_49585367 - ligand_b: lig_49137530 - name: edge_49585367_49137530 -edge_49932714_49137530: - ligand_a: lig_49932714 - ligand_b: lig_49137530 - name: edge_49932714_49137530 -edge_49932714_49175789: - ligand_a: lig_49932714 - ligand_b: lig_49175789 - name: edge_49932714_49175789 -edge_49932714_49580115: - ligand_a: lig_49932714 - ligand_b: lig_49580115 - name: edge_49932714_49580115 -edge_49932714_49582390: - ligand_a: lig_49932714 - ligand_b: lig_49582390 - name: edge_49932714_49582390 -edge_49932714_49582468: - ligand_a: lig_49932714 - ligand_b: lig_49582468 - name: edge_49932714_49582468 -edge_50107616_48271249: - ligand_a: lig_50107616 - ligand_b: lig_48271249 - name: edge_50107616_48271249 -edge_50107616_49582390: - ligand_a: lig_50107616 - ligand_b: lig_49582390 - name: edge_50107616_49582390 -edge_50107616_49585367: - ligand_a: lig_50107616 - ligand_b: lig_49585367 - name: edge_50107616_49585367 -edge_50181001_49137530: - ligand_a: lig_50181001 - ligand_b: lig_49137530 - name: edge_50181001_49137530 -edge_50181001_49582390: - ligand_a: lig_50181001 - ligand_b: lig_49582390 - name: edge_50181001_49582390 diff --git a/data/pde2/03_edges/01_perses_openfe.yaml b/data/pde2/03_edges/01_perses_openfe.yaml new file mode 100644 index 000000000..43e7cfdbd --- /dev/null +++ b/data/pde2/03_edges/01_perses_openfe.yaml @@ -0,0 +1,202 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_48271249_lig_48168913: + ligand_a: lig_48271249 + ligand_b: lig_48168913 + atom mapping: (0, 20) (1, 19) (2, 10) (3, 9) (4, 8) (5, 7) (6, 11) (7, 12) (8, + 13) (9, 14) (10, 15) (11, 16) (12, 17) (13, 18) (14, 21) (15, 22) (16, 23) (17, + 24) (18, 25) (19, 26) (20, 27) (21, 2) (22, 3) (23, 4) (24, 5) (25, 6) (26, + 1) (29, 37) (30, 38) (31, 39) (32, 34) (33, 35) (34, 36) (35, 41) (36, 40) (37, + 42) (38, 43) (39, 45) (40, 44) (41, 46) (42, 47) (43, 49) (44, 48) (45, 31) + (46, 33) + score: '0.929' + edge_lig_49582390_lig_49175789: + ligand_a: lig_49582390 + ligand_b: lig_49175789 + atom mapping: (0, 24) (1, 23) (2, 14) (3, 13) (4, 12) (5, 11) (6, 15) (7, 16) + (8, 17) (9, 18) (10, 19) (11, 20) (12, 21) (13, 22) (14, 25) (15, 26) (16, 27) + (17, 28) (18, 29) (19, 30) (20, 31) (21, 9) (22, 10) (23, 5) (24, 6) (25, 7) + (26, 8) (27, 4) (28, 3) (32, 48) (33, 49) (34, 50) (35, 45) (36, 46) (37, 47) + (38, 52) (39, 51) (40, 53) (41, 54) (42, 56) (43, 55) (44, 57) (45, 58) (46, + 60) (47, 59) (48, 44) (49, 42) (52, 41) + score: '0.861' + edge_lig_49582390_lig_49220392: + ligand_a: lig_49582390 + ligand_b: lig_49220392 + atom mapping: (0, 22) (1, 21) (2, 12) (3, 11) (4, 10) (5, 9) (6, 13) (7, 14) (8, + 15) (9, 16) (10, 17) (11, 18) (12, 19) (13, 20) (14, 23) (15, 24) (16, 25) (17, + 26) (18, 27) (19, 28) (20, 29) (21, 7) (22, 8) (23, 3) (24, 4) (25, 5) (26, + 6) (27, 2) (28, 1) (32, 42) (33, 43) (34, 44) (35, 39) (36, 40) (37, 41) (38, + 46) (39, 45) (40, 47) (41, 48) (42, 50) (43, 49) (44, 51) (45, 52) (46, 54) + (47, 53) (48, 38) (49, 36) (52, 35) + score: '0.894' + edge_lig_49582390_lig_49585367: + ligand_a: lig_49582390 + ligand_b: lig_49585367 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, + 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 24) (25, 25) (26, 26) + (27, 27) (28, 28) (32, 32) (33, 33) (34, 34) (35, 35) (36, 36) (37, 37) (38, + 39) (39, 38) (40, 40) (41, 41) (42, 43) (43, 42) (44, 44) (45, 45) (46, 47) + (47, 46) (48, 48) (49, 49) (50, 50) (52, 52) + score: '0.877' + edge_lig_49582390_lig_49396360: + ligand_a: lig_49582390 + ligand_b: lig_49396360 + atom mapping: (0, 23) (1, 22) (2, 13) (3, 12) (4, 11) (5, 10) (6, 14) (7, 15) + (8, 16) (9, 17) (10, 18) (11, 19) (12, 20) (13, 21) (14, 24) (15, 25) (16, 26) + (17, 27) (18, 28) (19, 29) (20, 30) (21, 6) (22, 5) (23, 4) (24, 9) (25, 8) + (26, 7) (27, 3) (28, 2) (32, 44) (33, 45) (34, 46) (35, 41) (36, 42) (37, 43) + (38, 48) (39, 47) (40, 49) (41, 50) (42, 52) (43, 51) (44, 53) (45, 54) (46, + 56) (47, 55) (48, 38) (49, 40) (50, 39) (52, 36) + score: '0.886' + edge_lig_50181001_lig_48168913: + ligand_a: lig_50181001 + ligand_b: lig_48168913 + atom mapping: (5, 4) (6, 3) (7, 2) (8, 1) (9, 6) (10, 5) (12, 7) (13, 8) (14, + 9) (15, 10) (16, 11) (17, 12) (18, 13) (19, 14) (20, 15) (21, 16) (22, 17) (23, + 18) (24, 19) (25, 20) (26, 21) (27, 22) (28, 27) (29, 26) (30, 25) (31, 24) + (32, 23) (42, 31) (44, 34) (45, 35) (46, 36) (47, 37) (48, 38) (49, 39) (50, + 40) (51, 41) (52, 49) (53, 48) (54, 47) (55, 46) (56, 44) (57, 45) (58, 42) + (59, 43) + score: '0.895' + edge_lig_49582390_lig_49932129: + ligand_a: lig_49582390 + ligand_b: lig_49932129 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, + 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 24) (25, 25) (26, 26) + (27, 27) (28, 28) (32, 31) (33, 32) (34, 33) (35, 34) (36, 35) (37, 36) (38, + 38) (39, 37) (40, 39) (41, 40) (42, 42) (43, 41) (44, 43) (45, 44) (46, 46) + (47, 45) (48, 47) (49, 48) (50, 49) (52, 52) + score: '0.886' + edge_lig_49582390_lig_49932714: + ligand_a: lig_49582390 + ligand_b: lig_49932714 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, + 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 24) (25, 25) (26, 26) + (27, 27) (28, 28) (32, 32) (33, 33) (34, 34) (35, 35) (36, 36) (37, 37) (38, + 39) (39, 38) (40, 40) (41, 41) (42, 43) (43, 42) (44, 44) (45, 45) (46, 47) + (47, 46) (48, 48) (49, 49) (50, 50) (52, 51) + score: '0.886' + edge_lig_50181001_lig_43249674: + ligand_a: lig_50181001 + ligand_b: lig_43249674 + atom mapping: (5, 23) (6, 22) (7, 21) (8, 26) (9, 25) (10, 24) (12, 5) (13, 4) + (14, 3) (15, 2) (16, 6) (17, 7) (18, 8) (19, 9) (20, 10) (21, 11) (22, 12) (23, + 13) (24, 1) (25, 0) (26, 14) (27, 15) (28, 20) (29, 19) (30, 18) (31, 17) (32, + 16) (42, 44) (44, 31) (45, 32) (46, 33) (47, 28) (48, 29) (49, 30) (50, 34) + (51, 35) (52, 43) (53, 42) (54, 41) (55, 40) (56, 38) (57, 39) (58, 36) (59, + 37) + score: '0.917' + edge_lig_49582390_lig_50107616: + ligand_a: lig_49582390 + ligand_b: lig_50107616 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, + 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 24) (25, 25) (26, 26) + (27, 27) (28, 28) (32, 32) (33, 33) (34, 34) (35, 35) (36, 36) (37, 37) (38, + 39) (39, 38) (40, 40) (41, 41) (42, 43) (43, 42) (44, 44) (45, 45) (46, 47) + (47, 46) (48, 48) (49, 49) (50, 50) (52, 54) + score: '0.877' + edge_lig_49582390_lig_49580115: + ligand_a: lig_49582390 + ligand_b: lig_49580115 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, + 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 24) (25, 25) (26, 26) + (27, 27) (28, 28) (32, 31) (33, 32) (34, 33) (35, 34) (36, 35) (37, 36) (38, + 38) (39, 37) (40, 39) (41, 40) (42, 42) (43, 41) (44, 43) (45, 44) (46, 46) + (47, 45) (48, 47) (49, 48) (50, 49) (52, 51) + score: '0.915' + edge_lig_50181001_lig_48022468: + ligand_a: lig_50181001 + ligand_b: lig_48022468 + atom mapping: (5, 23) (6, 22) (7, 21) (8, 26) (9, 25) (10, 24) (12, 5) (13, 4) + (14, 3) (15, 2) (16, 6) (17, 7) (18, 8) (19, 9) (20, 10) (21, 11) (22, 12) (23, + 13) (24, 1) (25, 0) (26, 14) (27, 15) (28, 20) (29, 19) (30, 18) (31, 17) (32, + 16) (44, 32) (45, 33) (46, 34) (47, 29) (48, 30) (49, 31) (50, 35) (51, 36) + (52, 44) (53, 43) (54, 42) (55, 41) (56, 39) (57, 40) (58, 37) (59, 38) + score: '0.905' + edge_lig_49137374_lig_48168913: + ligand_a: lig_49137374 + ligand_b: lig_48168913 + atom mapping: (0, 20) (1, 19) (2, 10) (3, 9) (4, 8) (5, 7) (6, 11) (7, 12) (8, + 13) (9, 14) (10, 15) (11, 16) (12, 17) (13, 18) (14, 21) (15, 22) (16, 27) (17, + 26) (18, 25) (19, 24) (20, 23) (21, 2) (22, 1) (23, 6) (24, 5) (25, 4) (26, + 3) (30, 37) (31, 38) (32, 39) (33, 34) (34, 35) (35, 36) (36, 41) (37, 40) (38, + 48) (39, 49) (40, 47) (41, 46) (42, 44) (43, 45) (44, 43) (45, 42) (47, 33) + (48, 32) + score: '0.923' + edge_lig_49582390_lig_49137530: + ligand_a: lig_49582390 + ligand_b: lig_49137530 + atom mapping: (0, 24) (1, 23) (2, 14) (3, 13) (4, 12) (5, 11) (6, 15) (7, 16) + (8, 17) (9, 18) (10, 19) (11, 20) (12, 21) (13, 22) (14, 25) (15, 26) (16, 27) + (17, 28) (18, 29) (19, 30) (20, 31) (21, 7) (22, 6) (23, 5) (24, 10) (25, 9) + (26, 8) (27, 4) (28, 3) (32, 47) (33, 48) (34, 49) (35, 44) (36, 45) (37, 46) + (38, 51) (39, 50) (40, 52) (41, 53) (42, 55) (43, 54) (44, 56) (45, 57) (46, + 59) (47, 58) (48, 41) (49, 43) (50, 42) (52, 39) + score: '0.877' + edge_lig_49582390_lig_49220548: + ligand_a: lig_49582390 + ligand_b: lig_49220548 + atom mapping: (0, 23) (1, 22) (2, 13) (3, 12) (4, 11) (5, 10) (6, 14) (7, 15) + (8, 16) (9, 17) (10, 18) (11, 19) (12, 20) (13, 21) (14, 24) (15, 25) (16, 26) + (17, 27) (18, 28) (19, 29) (20, 30) (21, 8) (22, 9) (23, 4) (24, 5) (25, 6) + (26, 7) (27, 3) (28, 2) (32, 45) (33, 46) (34, 47) (35, 42) (36, 43) (37, 44) + (38, 49) (39, 48) (40, 50) (41, 51) (42, 53) (43, 52) (44, 54) (45, 55) (46, + 57) (47, 56) (48, 41) (49, 39) (52, 37) + score: '0.866' + edge_lig_49582390_lig_50181001: + ligand_a: lig_49582390 + ligand_b: lig_50181001 + atom mapping: (0, 25) (1, 24) (2, 15) (3, 14) (4, 13) (5, 12) (6, 16) (7, 17) + (8, 18) (9, 19) (10, 20) (11, 21) (12, 22) (13, 23) (14, 26) (15, 27) (16, 28) + (17, 29) (18, 30) (19, 31) (20, 32) (21, 7) (22, 6) (23, 5) (24, 10) (25, 9) + (26, 8) (27, 4) (28, 3) (32, 47) (33, 48) (34, 49) (35, 44) (36, 45) (37, 46) + (38, 51) (39, 50) (40, 52) (41, 53) (42, 55) (43, 54) (44, 56) (45, 57) (46, + 59) (47, 58) (48, 42) (50, 43) (52, 40) + score: '0.861' + edge_lig_49582390_lig_49582468: + ligand_a: lig_49582390 + ligand_b: lig_49582468 + atom mapping: (0, 23) (1, 22) (2, 13) (3, 12) (4, 11) (5, 10) (6, 14) (7, 15) + (8, 16) (9, 17) (10, 18) (11, 19) (12, 20) (13, 21) (14, 24) (15, 25) (16, 26) + (17, 27) (18, 28) (19, 29) (20, 30) (21, 6) (22, 5) (23, 4) (24, 9) (25, 8) + (26, 7) (27, 3) (28, 2) (32, 46) (33, 45) (34, 44) (35, 41) (36, 42) (37, 43) + (38, 47) (39, 48) (40, 49) (41, 50) (42, 52) (43, 51) (44, 53) (45, 54) (46, + 56) (47, 55) (48, 38) (49, 40) (50, 39) + score: '0.875' + edge_lig_49582390_lig_49072088: + ligand_a: lig_49582390 + ligand_b: lig_49072088 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, + 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 24) (25, 25) (26, 26) + (27, 27) (28, 28) (32, 31) (33, 32) (34, 33) (35, 34) (36, 35) (37, 36) (38, + 38) (39, 37) (40, 39) (41, 40) (42, 42) (43, 41) (44, 43) (45, 44) (46, 46) + (47, 45) (48, 47) (49, 48) (50, 49) + score: '0.875' + edge_lig_49582390_lig_49175828: + ligand_a: lig_49582390 + ligand_b: lig_49175828 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, + 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 24) (25, 25) (26, 26) + (27, 28) (28, 29) (32, 32) (33, 33) (34, 34) (35, 35) (36, 36) (37, 37) (38, + 39) (39, 38) (40, 40) (41, 41) (42, 43) (43, 42) (44, 44) (45, 45) (46, 47) + (47, 46) (48, 48) (49, 49) + score: '0.855' + edge_lig_49582390_lig_48009208: + ligand_a: lig_49582390 + ligand_b: lig_48009208 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, + 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 24) (25, 25) (26, 26) + (32, 29) (33, 30) (34, 31) (35, 32) (36, 33) (37, 34) (38, 36) (39, 35) (40, + 37) (41, 38) (42, 40) (43, 39) (44, 41) (45, 42) (46, 44) (47, 43) (48, 45) + score: '0.909' diff --git a/data/pde2/03_edges/nohup.out b/data/pde2/03_edges/nohup.out new file mode 100644 index 000000000..7f1311d96 --- /dev/null +++ b/data/pde2/03_edges/nohup.out @@ -0,0 +1,29 @@ +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. +lig_48271249_lig_48168913 exceeds 1 A pairwise distance +lig_49582390_lig_49175789 exceeds 1 A pairwise distance +lig_49582390_lig_49220392 exceeds 1 A pairwise distance +lig_49582390_lig_49585367 exceeds 1 A pairwise distance +lig_49582390_lig_49396360 exceeds 1 A pairwise distance +lig_50181001_lig_48168913 exceeds 1 A pairwise distance +lig_49582390_lig_49932129 exceeds 1 A pairwise distance +lig_49582390_lig_49932714 exceeds 1 A pairwise distance +lig_50181001_lig_43249674 exceeds 1 A pairwise distance +lig_49582390_lig_50107616 exceeds 1 A pairwise distance +lig_49582390_lig_49580115 exceeds 1 A pairwise distance +lig_50181001_lig_48022468 exceeds 1 A pairwise distance +lig_49137374_lig_48168913 exceeds 1 A pairwise distance +lig_49582390_lig_49137530 exceeds 1 A pairwise distance +lig_49582390_lig_49220548 exceeds 1 A pairwise distance +lig_49582390_lig_50181001 exceeds 1 A pairwise distance +lig_49582390_lig_49582468 exceeds 1 A pairwise distance +lig_49582390_lig_49072088 exceeds 1 A pairwise distance +lig_49582390_lig_49175828 exceeds 1 A pairwise distance +lig_49582390_lig_48009208 exceeds 1 A pairwise distance diff --git a/data/pfkfb3/00_data/edges.yml b/data/pfkfb3/00_data/edges.yml deleted file mode 100644 index af9dcf05a..000000000 --- a/data/pfkfb3/00_data/edges.yml +++ /dev/null @@ -1,264 +0,0 @@ -edge_19_37: - ligand_a: lig_19 - ligand_b: lig_37 - name: edge_19_37 -edge_19_70: - ligand_a: lig_19 - ligand_b: lig_70 - name: edge_19_70 -edge_20_39: - ligand_a: lig_20 - ligand_b: lig_39 - name: edge_20_39 -edge_20_42: - ligand_a: lig_20 - ligand_b: lig_42 - name: edge_20_42 -edge_24_34: - ligand_a: lig_24 - ligand_b: lig_34 - name: edge_24_34 -edge_24_69: - ligand_a: lig_24 - ligand_b: lig_69 - name: edge_24_69 -edge_24_70: - ligand_a: lig_24 - ligand_b: lig_70 - name: edge_24_70 -edge_26_69: - ligand_a: lig_26 - ligand_b: lig_69 - name: edge_26_69 -edge_26_70: - ligand_a: lig_26 - ligand_b: lig_70 - name: edge_26_70 -edge_29_23: - ligand_a: lig_29 - ligand_b: lig_23 - name: edge_29_23 -edge_29_54: - ligand_a: lig_29 - ligand_b: lig_54 - name: edge_29_54 -edge_29_63: - ligand_a: lig_29 - ligand_b: lig_63 - name: edge_29_63 -edge_29_70: - ligand_a: lig_29 - ligand_b: lig_70 - name: edge_29_70 -edge_30_56: - ligand_a: lig_30 - ligand_b: lig_56 - name: edge_30_56 -edge_30_70: - ligand_a: lig_30 - ligand_b: lig_70 - name: edge_30_70 -edge_31_19: - ligand_a: lig_31 - ligand_b: lig_19 - name: edge_31_19 -edge_33_23: - ligand_a: lig_33 - ligand_b: lig_23 - name: edge_33_23 -edge_33_36: - ligand_a: lig_33 - ligand_b: lig_36 - name: edge_33_36 -edge_33_70: - ligand_a: lig_33 - ligand_b: lig_70 - name: edge_33_70 -edge_35_69: - ligand_a: lig_35 - ligand_b: lig_69 - name: edge_35_69 -edge_38_26: - ligand_a: lig_38 - ligand_b: lig_26 - name: edge_38_26 -edge_38_39: - ligand_a: lig_38 - ligand_b: lig_39 - name: edge_38_39 -edge_38_41: - ligand_a: lig_38 - ligand_b: lig_41 - name: edge_38_41 -edge_39_37: - ligand_a: lig_39 - ligand_b: lig_37 - name: edge_39_37 -edge_41_44: - ligand_a: lig_41 - ligand_b: lig_44 - name: edge_41_44 -edge_43_44: - ligand_a: lig_43 - ligand_b: lig_44 - name: edge_43_44 -edge_43_48: - ligand_a: lig_43 - ligand_b: lig_48 - name: edge_43_48 -edge_44_68: - ligand_a: lig_44 - ligand_b: lig_68 - name: edge_44_68 -edge_47_20: - ligand_a: lig_47 - ligand_b: lig_20 - name: edge_47_20 -edge_47_46: - ligand_a: lig_47 - ligand_b: lig_46 - name: edge_47_46 -edge_48_20: - ligand_a: lig_48 - ligand_b: lig_20 - name: edge_48_20 -edge_48_47: - ligand_a: lig_48 - ligand_b: lig_47 - name: edge_48_47 -edge_49_42: - ligand_a: lig_49 - ligand_b: lig_42 - name: edge_49_42 -edge_49_44: - ligand_a: lig_49 - ligand_b: lig_44 - name: edge_49_44 -edge_49_58: - ligand_a: lig_49 - ligand_b: lig_58 - name: edge_49_58 -edge_52_19: - ligand_a: lig_52 - ligand_b: lig_19 - name: edge_52_19 -edge_52_46: - ligand_a: lig_52 - ligand_b: lig_46 - name: edge_52_46 -edge_52_53: - ligand_a: lig_52 - ligand_b: lig_53 - name: edge_52_53 -edge_54_36: - ligand_a: lig_54 - ligand_b: lig_36 - name: edge_54_36 -edge_54_70: - ligand_a: lig_54 - ligand_b: lig_70 - name: edge_54_70 -edge_55_23: - ligand_a: lig_55 - ligand_b: lig_23 - name: edge_55_23 -edge_55_63: - ligand_a: lig_55 - ligand_b: lig_63 - name: edge_55_63 -edge_56_69: - ligand_a: lig_56 - ligand_b: lig_69 - name: edge_56_69 -edge_57_70: - ligand_a: lig_57 - ligand_b: lig_70 - name: edge_57_70 -edge_58_60: - ligand_a: lig_58 - ligand_b: lig_60 - name: edge_58_60 -edge_58_63: - ligand_a: lig_58 - ligand_b: lig_63 - name: edge_58_63 -edge_58_68: - ligand_a: lig_58 - ligand_b: lig_68 - name: edge_58_68 -edge_59_35: - ligand_a: lig_59 - ligand_b: lig_35 - name: edge_59_35 -edge_59_47: - ligand_a: lig_59 - ligand_b: lig_47 - name: edge_59_47 -edge_59_52: - ligand_a: lig_59 - ligand_b: lig_52 - name: edge_59_52 -edge_62_31: - ligand_a: lig_62 - ligand_b: lig_31 - name: edge_62_31 -edge_62_70: - ligand_a: lig_62 - ligand_b: lig_70 - name: edge_62_70 -edge_63_36: - ligand_a: lig_63 - ligand_b: lig_36 - name: edge_63_36 -edge_65_20: - ligand_a: lig_65 - ligand_b: lig_20 - name: edge_65_20 -edge_65_34: - ligand_a: lig_65 - ligand_b: lig_34 - name: edge_65_34 -edge_65_63: - ligand_a: lig_65 - ligand_b: lig_63 - name: edge_65_63 -edge_65_64: - ligand_a: lig_65 - ligand_b: lig_64 - name: edge_65_64 -edge_65_70: - ligand_a: lig_65 - ligand_b: lig_70 - name: edge_65_70 -edge_67_56: - ligand_a: lig_67 - ligand_b: lig_56 - name: edge_67_56 -edge_67_57: - ligand_a: lig_67 - ligand_b: lig_57 - name: edge_67_57 -edge_67_64: - ligand_a: lig_67 - ligand_b: lig_64 - name: edge_67_64 -edge_68_53: - ligand_a: lig_68 - ligand_b: lig_53 - name: edge_68_53 -edge_68_70: - ligand_a: lig_68 - ligand_b: lig_70 - name: edge_68_70 -edge_69_23: - ligand_a: lig_69 - ligand_b: lig_23 - name: edge_69_23 -edge_69_53: - ligand_a: lig_69 - ligand_b: lig_53 - name: edge_69_53 -edge_69_60: - ligand_a: lig_69 - ligand_b: lig_60 - name: edge_69_60 diff --git a/data/pfkfb3/03_edges/01_perses_openfe.yaml b/data/pfkfb3/03_edges/01_perses_openfe.yaml new file mode 100644 index 000000000..2527ce342 --- /dev/null +++ b/data/pfkfb3/03_edges/01_perses_openfe.yaml @@ -0,0 +1,279 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_29_lig_38: + ligand_a: lig_29 + ligand_b: lig_38 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 49) (5, 50) (6, 30) (7, 31) (8, + 32) (9, 33) (10, 41) (11, 42) (12, 44) (13, 43) (14, 45) (15, 46) (16, 47) (17, + 48) (18, 39) (19, 40) (20, 37) (21, 38) (22, 36) (24, 34) (25, 35) (26, 28) + (27, 29) (28, 8) (47, 4) (48, 5) (49, 6) (50, 7) + score: '0.656' + edge_lig_19_lig_41: + ligand_a: lig_19 + ligand_b: lig_41 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 45) (5, 46) (6, 26) (7, 27) (8, + 28) (9, 29) (10, 30) (11, 31) (12, 32) (14, 33) (15, 34) (16, 35) (17, 36) (18, + 37) (20, 24) (21, 25) (22, 8) (41, 4) (42, 5) (43, 6) (44, 7) + score: '0.595' + edge_lig_58_lig_59: + ligand_a: lig_58 + ligand_b: lig_59 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (25, + 26) (26, 27) (27, 28) (28, 29) (29, 30) (30, 31) (31, 32) (32, 33) (33, 34) + (34, 35) (35, 36) (36, 37) (37, 38) (38, 39) (39, 40) (40, 42) (41, 41) (42, + 43) (43, 44) (44, 45) (45, 46) (46, 47) (47, 48) + score: '0.674' + edge_lig_24_lig_38: + ligand_a: lig_24 + ligand_b: lig_38 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, + 28) (28, 29) (29, 30) (30, 31) (31, 32) (32, 33) (33, 41) (35, 39) (36, 40) + (37, 37) (38, 38) (39, 36) (41, 34) (44, 49) (45, 50) + score: '0.584' + edge_lig_46_lig_24: + ligand_a: lig_46 + ligand_b: lig_24 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (23, + 27) (24, 28) (25, 29) (26, 30) (27, 31) (28, 32) (29, 41) (31, 39) (32, 37) + (33, 38) (34, 35) (35, 36) (36, 33) (44, 44) (45, 45) + score: '0.580' + edge_lig_24_lig_42: + ligand_a: lig_24 + ligand_b: lig_42 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, + 24) (28, 25) (29, 26) (30, 27) (31, 28) (32, 29) (33, 37) (35, 35) (36, 36) + (37, 33) (38, 34) (39, 32) (41, 30) (44, 45) (45, 46) + score: '0.587' + edge_lig_56_lig_38: + ligand_a: lig_56 + ligand_b: lig_38 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (30, + 28) (31, 29) (32, 30) (33, 31) (34, 32) (35, 33) (36, 34) (37, 35) (38, 36) + (39, 37) (40, 38) (41, 39) (42, 40) (43, 41) (44, 42) (45, 43) (46, 44) (47, + 45) (48, 46) (49, 47) (50, 48) (51, 49) (52, 50) + score: '0.652' + edge_lig_38_lig_36: + ligand_a: lig_38 + ligand_b: lig_36 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (28, + 27) (29, 28) (30, 29) (31, 30) (33, 31) (34, 45) (35, 46) (36, 44) (37, 42) + (38, 43) (39, 40) (40, 41) (41, 32) (42, 33) (43, 35) (44, 34) (45, 36) (46, + 39) (47, 38) (48, 37) (49, 51) (50, 52) + score: '0.642' + edge_lig_69_lig_24: + ligand_a: lig_69 + ligand_b: lig_24 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (26, + 27) (27, 28) (28, 29) (29, 30) (30, 31) (31, 32) (32, 33) (40, 35) (41, 36) + (42, 37) (43, 38) (44, 39) (45, 41) (47, 44) (48, 45) + score: '0.580' + edge_lig_24_lig_43: + ligand_a: lig_24 + ligand_b: lig_43 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, + 20) (28, 21) (29, 22) (30, 23) (31, 24) (32, 25) (33, 33) (35, 31) (36, 32) + (37, 29) (38, 30) (39, 28) (41, 26) (44, 41) (45, 42) + score: '0.608' + edge_lig_26_lig_59: + ligand_a: lig_26 + ligand_b: lig_59 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, + 26) (28, 27) (29, 28) (30, 29) (31, 30) (32, 31) (33, 39) (34, 40) (35, 41) + (36, 43) (39, 37) (40, 38) (41, 35) (42, 36) (43, 34) (45, 32) (46, 33) (47, + 47) (48, 48) + score: '0.618' + edge_lig_41_lig_64: + ligand_a: lig_41 + ligand_b: lig_64 + atom mapping: (0, 39) (1, 38) (2, 40) (3, 33) (4, 34) (5, 35) (6, 36) (7, 37) + (8, 9) (24, 10) (25, 11) (26, 12) (27, 13) (28, 14) (29, 15) (30, 29) (31, 30) + (32, 28) (33, 26) (34, 27) (35, 24) (36, 25) (37, 16) (38, 17) (39, 19) (40, + 18) (41, 20) (42, 23) (43, 22) (44, 21) (45, 31) (46, 32) + score: '0.696' + edge_lig_38_lig_37: + ligand_a: lig_38 + ligand_b: lig_37 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (28, + 27) (29, 28) (30, 29) (31, 30) (32, 31) (33, 32) (34, 33) (35, 34) (36, 35) + (37, 36) (38, 37) (39, 38) (40, 39) (41, 40) (42, 41) (44, 42) (45, 43) (49, + 60) (50, 61) + score: '0.578' + edge_lig_24_lig_49: + ligand_a: lig_24 + ligand_b: lig_49 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, + 22) (28, 23) (29, 24) (30, 25) (31, 26) (32, 27) (33, 35) (35, 33) (36, 34) + (37, 31) (38, 32) (39, 30) (41, 28) (44, 43) (45, 44) + score: '0.594' + edge_lig_59_lig_31: + ligand_a: lig_59 + ligand_b: lig_31 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 44) (5, 45) (6, 46) (7, 47) (8, + 25) (26, 23) (27, 24) (28, 6) (29, 7) (30, 8) (31, 9) (32, 10) (33, 11) (34, + 12) (35, 13) (36, 14) (37, 15) (38, 16) (39, 17) (40, 18) (43, 19) (44, 22) + (45, 21) (46, 20) (47, 4) (48, 5) + score: '0.642' + edge_lig_24_lig_41: + ligand_a: lig_24 + ligand_b: lig_41 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, + 24) (28, 25) (29, 26) (30, 27) (31, 28) (32, 29) (33, 37) (35, 35) (36, 36) + (37, 33) (38, 34) (39, 32) (41, 30) (44, 45) (45, 46) + score: '0.577' + edge_lig_34_lig_59: + ligand_a: lig_34 + ligand_b: lig_59 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, + 26) (28, 27) (29, 28) (30, 29) (31, 30) (32, 31) (33, 39) (34, 40) (35, 41) + (36, 43) (39, 37) (40, 38) (41, 35) (42, 36) (43, 34) (44, 32) (45, 33) (46, + 47) (47, 48) + score: '0.625' + edge_lig_54_lig_38: + ligand_a: lig_54 + ligand_b: lig_38 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 49) (5, 50) (6, 30) (7, 31) (8, + 32) (9, 33) (10, 34) (11, 35) (12, 36) (13, 37) (14, 38) (15, 39) (16, 40) (17, + 41) (18, 42) (19, 44) (20, 43) (21, 45) (22, 48) (23, 47) (24, 46) (25, 28) + (26, 29) (27, 8) (52, 4) (53, 5) (54, 6) (55, 7) + score: '0.649' + edge_lig_24_lig_59: + ligand_a: lig_24 + ligand_b: lig_59 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, + 26) (28, 27) (29, 28) (30, 29) (31, 30) (32, 31) (33, 39) (35, 37) (36, 38) + (37, 35) (38, 36) (39, 34) (41, 32) (44, 47) (45, 48) + score: '0.578' + edge_lig_24_lig_39: + ligand_a: lig_24 + ligand_b: lig_39 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, + 22) (28, 23) (29, 24) (30, 25) (31, 26) (32, 27) (33, 35) (35, 33) (36, 34) + (37, 31) (38, 32) (39, 30) (41, 28) (44, 43) (45, 44) + score: '0.594' + edge_lig_24_lig_65: + ligand_a: lig_24 + ligand_b: lig_65 + atom mapping: (0, 37) (1, 36) (2, 38) (3, 31) (4, 32) (5, 33) (6, 34) (7, 35) + (8, 7) (27, 8) (28, 9) (29, 10) (30, 11) (31, 12) (32, 13) (33, 21) (35, 19) + (36, 20) (37, 17) (38, 18) (39, 16) (41, 14) (44, 29) (45, 30) + score: '0.590' + edge_lig_67_lig_24: + ligand_a: lig_67 + ligand_b: lig_24 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (24, + 27) (25, 28) (26, 29) (27, 30) (28, 31) (29, 32) (30, 41) (32, 39) (33, 37) + (34, 38) (35, 35) (36, 36) (37, 33) (45, 44) (46, 45) + score: '0.580' + edge_lig_24_lig_20: + ligand_a: lig_24 + ligand_b: lig_20 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, + 24) (28, 25) (29, 26) (30, 27) (31, 28) (32, 29) (33, 37) (35, 35) (36, 36) + (37, 33) (38, 34) (39, 32) (41, 30) (44, 45) (45, 46) + score: '0.587' + edge_lig_55_lig_38: + ligand_a: lig_55 + ligand_b: lig_38 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 49) (5, 50) (6, 30) (7, 31) (8, + 32) (9, 33) (10, 34) (11, 35) (12, 36) (13, 37) (14, 38) (15, 39) (16, 40) (17, + 41) (18, 42) (19, 44) (20, 43) (21, 45) (22, 48) (23, 47) (24, 46) (25, 28) + (26, 29) (27, 8) (46, 4) (47, 5) (48, 6) (49, 7) + score: '0.659' + edge_lig_35_lig_38: + ligand_a: lig_35 + ligand_b: lig_38 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 49) (5, 50) (6, 30) (7, 31) (8, + 32) (9, 33) (10, 41) (11, 42) (12, 44) (13, 43) (14, 45) (15, 46) (16, 47) (17, + 48) (18, 39) (19, 40) (20, 37) (21, 38) (22, 36) (23, 34) (24, 35) (25, 28) + (26, 29) (27, 8) (46, 4) (47, 5) (48, 6) (49, 7) + score: '0.663' + edge_lig_24_lig_47: + ligand_a: lig_24 + ligand_b: lig_47 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 45) (5, 46) (6, 47) (7, 48) (8, + 27) (27, 25) (28, 26) (29, 6) (30, 7) (31, 8) (32, 9) (33, 17) (35, 15) (36, + 16) (37, 13) (38, 14) (39, 12) (41, 10) (44, 4) (45, 5) + score: '0.587' + edge_lig_33_lig_41: + ligand_a: lig_33 + ligand_b: lig_41 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 45) (5, 46) (6, 26) (7, 27) (8, + 28) (9, 29) (10, 37) (11, 38) (13, 35) (14, 36) (15, 33) (16, 34) (17, 32) (18, + 30) (19, 31) (20, 24) (21, 25) (22, 8) (41, 4) (42, 5) (43, 6) (44, 7) + score: '0.612' + edge_lig_24_lig_63: + ligand_a: lig_24 + ligand_b: lig_63 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, + 21) (28, 22) (29, 23) (30, 24) (31, 25) (32, 26) (33, 27) (35, 35) (36, 36) + (37, 37) (38, 38) (39, 39) (41, 40) (44, 42) (45, 43) + score: '0.597' + edge_lig_57_lig_38: + ligand_a: lig_57 + ligand_b: lig_38 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, + 28) (28, 29) (29, 30) (30, 31) (31, 32) (32, 33) (33, 34) (34, 35) (35, 36) + (36, 37) (37, 38) (38, 39) (39, 40) (40, 41) (41, 42) (42, 44) (43, 43) (44, + 45) (45, 48) (46, 47) (47, 46) (48, 49) (49, 50) + score: '0.656' + edge_lig_70_lig_24: + ligand_a: lig_70 + ligand_b: lig_24 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (26, + 27) (27, 28) (28, 29) (29, 30) (30, 31) (31, 32) (32, 33) (40, 35) (41, 36) + (42, 37) (43, 38) (44, 39) (45, 41) (47, 44) (48, 45) + score: '0.580' + edge_lig_24_lig_44: + ligand_a: lig_24 + ligand_b: lig_44 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, + 20) (28, 21) (29, 22) (30, 23) (31, 24) (32, 25) (33, 33) (35, 31) (36, 32) + (37, 29) (38, 30) (39, 28) (41, 26) (44, 41) (45, 42) + score: '0.608' + edge_lig_53_lig_38: + ligand_a: lig_53 + ligand_b: lig_38 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (33, + 28) (34, 29) (35, 30) (36, 31) (37, 32) (38, 33) (39, 34) (40, 35) (41, 36) + (42, 37) (43, 38) (44, 39) (45, 40) (46, 41) (47, 42) (48, 44) (49, 43) (50, + 45) (51, 48) (52, 47) (53, 46) (54, 49) (55, 50) + score: '0.649' + edge_lig_24_lig_48: + ligand_a: lig_24 + ligand_b: lig_48 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, + 24) (28, 25) (29, 26) (30, 27) (31, 28) (32, 29) (33, 37) (35, 35) (36, 36) + (37, 33) (38, 34) (39, 32) (41, 30) (44, 45) (45, 46) + score: '0.587' + edge_lig_59_lig_30: + ligand_a: lig_59 + ligand_b: lig_30 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 44) (5, 45) (6, 46) (7, 47) (8, + 25) (26, 23) (27, 24) (28, 6) (29, 7) (30, 8) (31, 9) (32, 21) (33, 22) (34, + 19) (35, 17) (36, 18) (37, 16) (39, 10) (40, 11) (43, 12) (44, 15) (45, 14) + (46, 13) (47, 4) (48, 5) + score: '0.631' + edge_lig_41_lig_23: + ligand_a: lig_41 + ligand_b: lig_23 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 40) (5, 41) (6, 42) (7, 43) (8, + 21) (24, 19) (25, 20) (26, 6) (27, 7) (28, 8) (29, 9) (30, 10) (31, 11) (32, + 12) (33, 13) (34, 14) (35, 15) (36, 16) (37, 17) (45, 4) (46, 5) + score: '0.602' + edge_lig_52_lig_38: + ligand_a: lig_52 + ligand_b: lig_38 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (30, + 28) (31, 29) (32, 30) (33, 31) (34, 32) (35, 33) (36, 34) (37, 35) (38, 36) + (39, 37) (40, 38) (41, 39) (42, 40) (43, 41) (44, 42) (45, 44) (46, 43) (47, + 45) (48, 48) (49, 47) (50, 46) (51, 49) (52, 50) + score: '0.652' + edge_lig_24_lig_62: + ligand_a: lig_24 + ligand_b: lig_62 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, + 21) (28, 22) (29, 23) (30, 24) (31, 25) (32, 26) (33, 27) (35, 35) (36, 36) + (37, 37) (38, 38) (39, 39) (41, 40) (44, 42) (45, 43) + score: '0.597' diff --git a/data/pfkfb3/03_edges/nohup.out b/data/pfkfb3/03_edges/nohup.out new file mode 100644 index 000000000..99d2f26e2 --- /dev/null +++ b/data/pfkfb3/03_edges/nohup.out @@ -0,0 +1,45 @@ +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. +lig_29_lig_38 exceeds 1 A pairwise distance +lig_19_lig_41 exceeds 1 A pairwise distance +lig_58_lig_59 exceeds 1 A pairwise distance +lig_24_lig_38 exceeds 1 A pairwise distance +lig_46_lig_24 exceeds 1 A pairwise distance +lig_24_lig_42 exceeds 1 A pairwise distance +lig_56_lig_38 exceeds 1 A pairwise distance +lig_38_lig_36 exceeds 1 A pairwise distance +lig_69_lig_24 exceeds 1 A pairwise distance +lig_24_lig_43 exceeds 1 A pairwise distance +lig_26_lig_59 exceeds 1 A pairwise distance +lig_41_lig_64 exceeds 1 A pairwise distance +lig_38_lig_37 exceeds 1 A pairwise distance +lig_24_lig_49 exceeds 1 A pairwise distance +lig_59_lig_31 exceeds 1 A pairwise distance +lig_24_lig_41 exceeds 1 A pairwise distance +lig_34_lig_59 exceeds 1 A pairwise distance +lig_54_lig_38 exceeds 1 A pairwise distance +lig_24_lig_59 exceeds 1 A pairwise distance +lig_24_lig_39 exceeds 1 A pairwise distance +lig_24_lig_65 exceeds 1 A pairwise distance +lig_67_lig_24 exceeds 1 A pairwise distance +lig_24_lig_20 exceeds 1 A pairwise distance +lig_55_lig_38 exceeds 1 A pairwise distance +lig_35_lig_38 exceeds 1 A pairwise distance +lig_24_lig_47 exceeds 1 A pairwise distance +lig_24_lig_63 exceeds 1 A pairwise distance +lig_57_lig_38 exceeds 1 A pairwise distance +lig_70_lig_24 exceeds 1 A pairwise distance +lig_24_lig_44 exceeds 1 A pairwise distance +lig_53_lig_38 exceeds 1 A pairwise distance +lig_24_lig_48 exceeds 1 A pairwise distance +lig_59_lig_30 exceeds 1 A pairwise distance +lig_41_lig_23 exceeds 1 A pairwise distance +lig_52_lig_38 exceeds 1 A pairwise distance +lig_24_lig_62 exceeds 1 A pairwise distance diff --git a/data/ptp1b/00_data/edges.yml b/data/ptp1b/00_data/edges.yml deleted file mode 100644 index fbfe76e05..000000000 --- a/data/ptp1b/00_data/edges.yml +++ /dev/null @@ -1,196 +0,0 @@ -edge_20667_2qbp_23479: - ligand_a: lig_20667_2qbp - ligand_b: lig_23479 - name: edge_20667_2qbp_23479 -edge_20667_2qbp_23482: - ligand_a: lig_20667_2qbp - ligand_b: lig_23482 - name: edge_20667_2qbp_23482 -edge_20667_2qbp_23484: - ligand_a: lig_20667_2qbp - ligand_b: lig_23484 - name: edge_20667_2qbp_23484 -edge_20667_2qbp_23485: - ligand_a: lig_20667_2qbp - ligand_b: lig_23485 - name: edge_20667_2qbp_23485 -edge_20667_2qbp_23486: - ligand_a: lig_20667_2qbp - ligand_b: lig_23486 - name: edge_20667_2qbp_23486 -edge_20669_2qbr_23466: - ligand_a: lig_20669_2qbr - ligand_b: lig_23466 - name: edge_20669_2qbr_23466 -edge_20669_2qbr_23472: - ligand_a: lig_20669_2qbr - ligand_b: lig_23472 - name: edge_20669_2qbr_23472 -edge_20670_2qbs_23330_2qbq: - ligand_a: lig_20670_2qbs - ligand_b: lig_23330_2qbq - name: edge_20670_2qbs_23330_2qbq -edge_20670_2qbs_23466: - ligand_a: lig_20670_2qbs - ligand_b: lig_23466 - name: edge_20670_2qbs_23466 -edge_20670_2qbs_23477: - ligand_a: lig_20670_2qbs - ligand_b: lig_23477 - name: edge_20670_2qbs_23477 -edge_20670_2qbs_23479: - ligand_a: lig_20670_2qbs - ligand_b: lig_23479 - name: edge_20670_2qbs_23479 -edge_20670_2qbs_23482: - ligand_a: lig_20670_2qbs - ligand_b: lig_23482 - name: edge_20670_2qbs_23482 -edge_20670_2qbs_23483: - ligand_a: lig_20670_2qbs - ligand_b: lig_23483 - name: edge_20670_2qbs_23483 -edge_23466_23475: - ligand_a: lig_23466 - ligand_b: lig_23475 - name: edge_23466_23475 -edge_23467_23466: - ligand_a: lig_23467 - ligand_b: lig_23466 - name: edge_23467_23466 -edge_23467_23468: - ligand_a: lig_23467 - ligand_b: lig_23468 - name: edge_23467_23468 -edge_23467_23469: - ligand_a: lig_23467 - ligand_b: lig_23469 - name: edge_23467_23469 -edge_23467_23470: - ligand_a: lig_23467 - ligand_b: lig_23470 - name: edge_23467_23470 -edge_23467_23473: - ligand_a: lig_23467 - ligand_b: lig_23473 - name: edge_23467_23473 -edge_23467_23474: - ligand_a: lig_23467 - ligand_b: lig_23474 - name: edge_23467_23474 -edge_23467_23475: - ligand_a: lig_23467 - ligand_b: lig_23475 - name: edge_23467_23475 -edge_23467_23476: - ligand_a: lig_23467 - ligand_b: lig_23476 - name: edge_23467_23476 -edge_23469_20669_2qbr: - ligand_a: lig_23469 - ligand_b: lig_20669_2qbr - name: edge_23469_20669_2qbr -edge_23469_23472: - ligand_a: lig_23469 - ligand_b: lig_23472 - name: edge_23469_23472 -edge_23471_23466: - ligand_a: lig_23471 - ligand_b: lig_23466 - name: edge_23471_23466 -edge_23471_23468: - ligand_a: lig_23471 - ligand_b: lig_23468 - name: edge_23471_23468 -edge_23471_23470: - ligand_a: lig_23471 - ligand_b: lig_23470 - name: edge_23471_23470 -edge_23473_20669_2qbr: - ligand_a: lig_23473 - ligand_b: lig_20669_2qbr - name: edge_23473_20669_2qbr -edge_23474_23466: - ligand_a: lig_23474 - ligand_b: lig_23466 - name: edge_23474_23466 -edge_23476_23466: - ligand_a: lig_23476 - ligand_b: lig_23466 - name: edge_23476_23466 -edge_23477_23330_2qbq: - ligand_a: lig_23477 - ligand_b: lig_23330_2qbq - name: edge_23477_23330_2qbq -edge_23477_23466: - ligand_a: lig_23477 - ligand_b: lig_23466 - name: edge_23477_23466 -edge_23477_23467: - ligand_a: lig_23477 - ligand_b: lig_23467 - name: edge_23477_23467 -edge_23477_23479: - ligand_a: lig_23477 - ligand_b: lig_23479 - name: edge_23477_23479 -edge_23477_23482: - ligand_a: lig_23477 - ligand_b: lig_23482 - name: edge_23477_23482 -edge_23477_23483: - ligand_a: lig_23477 - ligand_b: lig_23483 - name: edge_23477_23483 -edge_23480_23479: - ligand_a: lig_23480 - ligand_b: lig_23479 - name: edge_23480_23479 -edge_23480_23482: - ligand_a: lig_23480 - ligand_b: lig_23482 - name: edge_23480_23482 -edge_23482_23479: - ligand_a: lig_23482 - ligand_b: lig_23479 - name: edge_23482_23479 -edge_23482_23485: - ligand_a: lig_23482 - ligand_b: lig_23485 - name: edge_23482_23485 -edge_23482_23486: - ligand_a: lig_23482 - ligand_b: lig_23486 - name: edge_23482_23486 -edge_23483_23479: - ligand_a: lig_23483 - ligand_b: lig_23479 - name: edge_23483_23479 -edge_23484_23479: - ligand_a: lig_23484 - ligand_b: lig_23479 - name: edge_23484_23479 -edge_23484_23482: - ligand_a: lig_23484 - ligand_b: lig_23482 - name: edge_23484_23482 -edge_23484_23485: - ligand_a: lig_23484 - ligand_b: lig_23485 - name: edge_23484_23485 -edge_23484_23486: - ligand_a: lig_23484 - ligand_b: lig_23486 - name: edge_23484_23486 -edge_23485_23479: - ligand_a: lig_23485 - ligand_b: lig_23479 - name: edge_23485_23479 -edge_23486_23479: - ligand_a: lig_23486 - ligand_b: lig_23479 - name: edge_23486_23479 -edge_23486_23485: - ligand_a: lig_23486 - ligand_b: lig_23485 - name: edge_23486_23485 diff --git a/data/ptp1b/03_edges/01_perses_openfe.yaml b/data/ptp1b/03_edges/01_perses_openfe.yaml new file mode 100644 index 000000000..10697030b --- /dev/null +++ b/data/ptp1b/03_edges/01_perses_openfe.yaml @@ -0,0 +1,172 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_23480_lig_23485: + ligand_a: lig_23480 + ligand_b: lig_23485 + atom mapping: (0, 62) (1, 2) (2, 1) (3, 6) (4, 5) (5, 4) (6, 3) (7, 61) (8, 9) + (10, 12) (13, 15) (14, 20) (15, 19) (16, 18) (17, 17) (18, 16) (19, 59) (20, + 60) (21, 58) (22, 57) (23, 26) (30, 23) (31, 24) (32, 22) (33, 21) (35, 8) (52, + 0) + score: '0.488' + edge_lig_23484_lig_23475: + ligand_a: lig_23484 + ligand_b: lig_23475 + atom mapping: (26, 8) (27, 9) (28, 5) (29, 6) (30, 1) (31, 2) (32, 3) (33, 4) + (34, 24) (35, 25) (36, 26) (37, 27) (38, 28) (39, 29) (40, 30) (41, 31) (42, + 32) (43, 33) (44, 34) (45, 36) (46, 35) (47, 37) (48, 38) (49, 39) (51, 41) + (52, 0) (53, 7) + score: '0.586' + edge_lig_23466_lig_23483: + ligand_a: lig_23466 + ligand_b: lig_23483 + atom mapping: (0, 49) (1, 27) (2, 28) (3, 29) (4, 30) (5, 25) (6, 26) (7, 50) + (8, 23) (10, 24) (11, 31) (12, 32) (13, 33) (14, 34) (15, 35) (16, 36) (17, + 37) (18, 38) (19, 39) (20, 40) (21, 41) (22, 42) (23, 43) (24, 44) (25, 45) + (26, 46) (27, 47) (28, 48) + score: '0.725' + edge_lig_23484_lig_23472: + ligand_a: lig_23484 + ligand_b: lig_23472 + atom mapping: (26, 8) (28, 5) (29, 6) (30, 1) (31, 2) (32, 3) (33, 4) (34, 24) + (35, 25) (36, 26) (37, 27) (38, 28) (39, 29) (40, 30) (41, 31) (42, 32) (43, + 33) (44, 34) (45, 36) (46, 35) (47, 37) (48, 38) (49, 39) (51, 41) (52, 0) (53, + 7) + score: '0.574' + edge_lig_20667_2qbp_lig_23480: + ligand_a: lig_20667_2qbp + ligand_b: lig_23480 + atom mapping: (0, 52) (1, 2) (2, 1) (3, 6) (4, 5) (5, 4) (6, 3) (8, 35) (9, 8) + (12, 10) (15, 13) (16, 18) (17, 17) (18, 16) (19, 15) (20, 14) (21, 33) (22, + 32) (23, 30) (24, 31) (26, 23) (54, 22) (55, 21) (56, 19) (57, 20) (58, 7) (59, + 0) + score: '0.488' + edge_lig_23484_lig_23468: + ligand_a: lig_23484 + ligand_b: lig_23468 + atom mapping: (26, 8) (28, 5) (29, 6) (30, 1) (31, 2) (32, 3) (33, 4) (34, 19) + (35, 20) (36, 21) (37, 22) (38, 23) (39, 24) (40, 25) (41, 26) (42, 27) (43, + 28) (44, 29) (45, 31) (46, 30) (47, 32) (48, 33) (49, 34) (51, 36) (52, 0) (53, + 7) + score: '0.612' + edge_lig_23477_lig_23472: + ligand_a: lig_23477 + ligand_b: lig_23472 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (25, + 24) (26, 25) (27, 26) (28, 27) (29, 28) (30, 29) (31, 30) (32, 31) (33, 32) + (34, 33) (35, 34) (36, 35) (37, 36) (38, 37) (39, 38) (40, 39) (41, 40) (42, + 41) + score: '0.632' + edge_lig_20670_2qbs_lig_23472: + ligand_a: lig_20670_2qbs + ligand_b: lig_23472 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, + 24) (28, 25) (29, 26) (30, 27) (31, 28) (32, 29) (33, 30) (34, 31) (35, 32) + (36, 33) (37, 34) (38, 35) (39, 36) (40, 37) (41, 38) (42, 39) (43, 40) (44, + 41) + score: '0.632' + edge_lig_23484_lig_23469: + ligand_a: lig_23484 + ligand_b: lig_23469 + atom mapping: (26, 11) (28, 13) (29, 14) (30, 15) (31, 16) (32, 17) (33, 18) (34, + 19) (35, 20) (36, 21) (37, 22) (38, 23) (39, 24) (40, 25) (41, 26) (42, 27) + (43, 28) (44, 29) (45, 31) (46, 30) (47, 32) (48, 33) (49, 34) (51, 36) (52, + 37) (53, 38) + score: '0.581' + edge_lig_23484_lig_23476: + ligand_a: lig_23484 + ligand_b: lig_23476 + atom mapping: (26, 8) (27, 9) (28, 5) (29, 6) (30, 1) (31, 2) (32, 3) (33, 4) + (34, 30) (35, 31) (36, 32) (37, 33) (38, 34) (39, 35) (40, 36) (41, 37) (42, + 38) (43, 39) (44, 40) (45, 41) (46, 42) (47, 43) (48, 44) (49, 45) (51, 47) + (52, 0) (53, 7) + score: '0.545' + edge_lig_23482_lig_23480: + ligand_a: lig_23482 + ligand_b: lig_23480 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (32, + 35) (33, 36) (34, 37) (35, 38) (36, 39) (37, 40) (38, 41) (39, 42) (40, 43) + (41, 44) (42, 45) (43, 46) (44, 47) (45, 48) (46, 49) (47, 50) (48, 51) (49, + 52) + score: '0.602' + edge_lig_23471_lig_23483: + ligand_a: lig_23471 + ligand_b: lig_23483 + atom mapping: (0, 49) (1, 27) (2, 28) (3, 29) (4, 30) (5, 25) (6, 26) (7, 50) + (8, 23) (17, 31) (18, 32) (19, 33) (20, 34) (21, 35) (22, 36) (23, 37) (24, + 38) (25, 39) (26, 40) (27, 41) (28, 43) (29, 42) (30, 44) (31, 45) (32, 46) + (33, 47) (34, 48) + score: '0.650' + edge_lig_23484_lig_20669_2qbr: + ligand_a: lig_23484 + ligand_b: lig_20669_2qbr + atom mapping: (26, 12) (28, 14) (29, 15) (30, 16) (31, 17) (32, 18) (33, 19) (34, + 20) (35, 21) (36, 22) (37, 23) (38, 24) (39, 25) (40, 26) (41, 27) (42, 28) + (43, 29) (44, 30) (45, 32) (46, 31) (47, 33) (48, 34) (49, 35) (51, 37) (52, + 38) (53, 39) + score: '0.574' + edge_lig_23480_lig_23483: + ligand_a: lig_23480 + ligand_b: lig_23483 + atom mapping: (0, 49) (1, 27) (2, 28) (3, 29) (4, 30) (5, 25) (6, 26) (7, 50) + (8, 23) (35, 31) (36, 32) (37, 33) (38, 34) (39, 35) (40, 36) (41, 37) (42, + 38) (43, 39) (44, 40) (45, 41) (46, 43) (47, 42) (48, 44) (49, 45) (50, 46) + (51, 47) (52, 48) + score: '0.520' + edge_lig_23484_lig_23470: + ligand_a: lig_23484 + ligand_b: lig_23470 + atom mapping: (26, 8) (28, 5) (29, 6) (30, 1) (31, 2) (32, 3) (33, 4) (34, 24) + (35, 25) (36, 26) (37, 27) (38, 28) (39, 29) (40, 30) (41, 31) (42, 32) (43, + 33) (44, 34) (45, 36) (46, 35) (47, 37) (48, 38) (49, 39) (51, 41) (52, 0) (53, + 7) + score: '0.574' + edge_lig_23484_lig_23480: + ligand_a: lig_23484 + ligand_b: lig_23480 + atom mapping: (0, 52) (1, 2) (2, 1) (3, 6) (4, 5) (5, 4) (6, 3) (8, 35) (9, 8) + (12, 10) (15, 13) (16, 14) (17, 15) (18, 16) (19, 17) (20, 18) (21, 20) (22, + 19) (23, 22) (24, 21) (26, 23) (54, 30) (55, 31) (56, 32) (57, 33) (58, 7) (59, + 0) + score: '0.491' + edge_lig_23474_lig_23486: + ligand_a: lig_23474 + ligand_b: lig_23486 + atom mapping: (0, 7) (1, 6) (2, 1) (3, 2) (4, 3) (5, 4) (6, 5) (7, 8) (8, 9) (10, + 12) (13, 15) (14, 20) (15, 19) (16, 18) (17, 17) (18, 16) (19, 56) (20, 57) + (21, 55) (22, 54) (24, 25) (25, 23) (26, 24) (27, 22) (28, 21) (30, 58) (47, + 0) + score: '0.511' + edge_lig_23473_lig_23484: + ligand_a: lig_23473 + ligand_b: lig_23484 + atom mapping: (12, 26) (13, 28) (14, 29) (15, 30) (16, 31) (17, 32) (18, 33) (19, + 34) (20, 35) (21, 36) (22, 37) (23, 38) (24, 39) (25, 40) (26, 41) (27, 42) + (28, 43) (29, 44) (30, 46) (31, 45) (32, 47) (33, 48) (34, 49) (36, 51) (37, + 52) (38, 53) + score: '0.581' + edge_lig_23479_lig_23480: + ligand_a: lig_23479 + ligand_b: lig_23480 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (31, + 35) (32, 36) (33, 37) (34, 38) (35, 39) (36, 40) (37, 41) (38, 42) (39, 43) + (40, 44) (41, 45) (42, 46) (43, 47) (44, 48) (45, 49) (46, 50) (47, 51) (48, + 52) + score: '0.610' + edge_lig_23467_lig_23486: + ligand_a: lig_23467 + ligand_b: lig_23486 + atom mapping: (0, 52) (1, 30) (2, 31) (3, 32) (4, 33) (5, 28) (6, 29) (7, 53) + (8, 26) (13, 34) (14, 35) (15, 36) (16, 37) (17, 38) (18, 39) (19, 40) (20, + 41) (21, 42) (22, 43) (23, 44) (24, 46) (25, 45) (26, 47) (27, 48) (28, 49) + (29, 50) (30, 51) + score: '0.684' + edge_lig_23480_lig_23486: + ligand_a: lig_23480 + ligand_b: lig_23486 + atom mapping: (0, 7) (1, 6) (2, 1) (3, 2) (4, 3) (5, 4) (6, 5) (7, 8) (8, 9) (10, + 12) (13, 15) (14, 20) (15, 19) (16, 18) (17, 17) (18, 16) (19, 56) (20, 57) + (21, 55) (22, 54) (23, 26) (30, 23) (31, 24) (32, 22) (33, 21) (35, 58) (52, + 0) + score: '0.488' diff --git a/data/ptp1b/03_edges/nohup.out b/data/ptp1b/03_edges/nohup.out new file mode 100644 index 000000000..8bf8e8274 --- /dev/null +++ b/data/ptp1b/03_edges/nohup.out @@ -0,0 +1,24 @@ +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. +lig_23480_lig_23485 exceeds 1 A pairwise distance +lig_23484_lig_23475 exceeds 1 A pairwise distance +lig_23484_lig_23472 exceeds 1 A pairwise distance +lig_20667_2qbp_lig_23480 exceeds 1 A pairwise distance +lig_23484_lig_23469 exceeds 1 A pairwise distance +lig_23471_lig_23483 exceeds 1 A pairwise distance +lig_23484_lig_20669_2qbr exceeds 1 A pairwise distance +lig_23480_lig_23483 exceeds 1 A pairwise distance +lig_23484_lig_23470 exceeds 1 A pairwise distance +lig_23484_lig_23480 exceeds 1 A pairwise distance +lig_23474_lig_23486 exceeds 1 A pairwise distance +lig_23473_lig_23484 exceeds 1 A pairwise distance +lig_23479_lig_23480 exceeds 1 A pairwise distance +lig_23467_lig_23486 exceeds 1 A pairwise distance +lig_23480_lig_23486 exceeds 1 A pairwise distance diff --git a/data/shp2/00_data/edges.yml b/data/shp2/00_data/edges.yml deleted file mode 100644 index d9b03b408..000000000 --- a/data/shp2/00_data/edges.yml +++ /dev/null @@ -1,224 +0,0 @@ -edge_10_E30: - ligand_a: lig_10 - ligand_b: lig_E30 - name: edge_10_E30 -edge_11_4: - ligand_a: lig_11 - ligand_b: lig_4 - name: edge_11_4 -edge_11_7: - ligand_a: lig_11 - ligand_b: lig_7 - name: edge_11_7 -edge_11_E25: - ligand_a: lig_11 - ligand_b: lig_E25 - name: edge_11_E25 -edge_11_E6: - ligand_a: lig_11 - ligand_b: lig_E6 - name: edge_11_E6 -edge_3_E3: - ligand_a: lig_3 - ligand_b: lig_E3 - name: edge_3_E3 -edge_3_E9: - ligand_a: lig_3 - ligand_b: lig_E9 - name: edge_3_E9 -edge_4_E27: - ligand_a: lig_4 - ligand_b: lig_E27 - name: edge_4_E27 -edge_4_E5: - ligand_a: lig_4 - ligand_b: lig_E5 - name: edge_4_E5 -edge_4_SHP836-2: - ligand_a: lig_4 - ligand_b: lig_SHP836-2 - name: edge_4_SHP836-2 -edge_7_10: - ligand_a: lig_7 - ligand_b: lig_10 - name: edge_7_10 -edge_E14_6: - ligand_a: lig_E14 - ligand_b: lig_6 - name: edge_E14_6 -edge_E14_7: - ligand_a: lig_E14 - ligand_b: lig_7 - name: edge_E14_7 -edge_E1_6: - ligand_a: lig_E1 - ligand_b: lig_6 - name: edge_E1_6 -edge_E1_7: - ligand_a: lig_E1 - ligand_b: lig_7 - name: edge_E1_7 -edge_E1_E24: - ligand_a: lig_E1 - ligand_b: lig_E24 - name: edge_E1_E24 -edge_E1_E3: - ligand_a: lig_E1 - ligand_b: lig_E3 - name: edge_E1_E3 -edge_E1_E4: - ligand_a: lig_E1 - ligand_b: lig_E4 - name: edge_E1_E4 -edge_E22_7: - ligand_a: lig_E22 - ligand_b: lig_7 - name: edge_E22_7 -edge_E22_E23: - ligand_a: lig_E22 - ligand_b: lig_E23 - name: edge_E22_E23 -edge_E24_E23: - ligand_a: lig_E24 - ligand_b: lig_E23 - name: edge_E24_E23 -edge_E24_E28: - ligand_a: lig_E24 - ligand_b: lig_E28 - name: edge_E24_E28 -edge_E24_E30: - ligand_a: lig_E24 - ligand_b: lig_E30 - name: edge_E24_E30 -edge_E25_E3: - ligand_a: lig_E25 - ligand_b: lig_E3 - name: edge_E25_E3 -edge_E26_E25: - ligand_a: lig_E26 - ligand_b: lig_E25 - name: edge_E26_E25 -edge_E26_E6: - ligand_a: lig_E26 - ligand_b: lig_E6 - name: edge_E26_E6 -edge_E26_SHP836-2: - ligand_a: lig_E26 - ligand_b: lig_SHP836-2 - name: edge_E26_SHP836-2 -edge_E27_E4: - ligand_a: lig_E27 - ligand_b: lig_E4 - name: edge_E27_E4 -edge_E28_6: - ligand_a: lig_E28 - ligand_b: lig_6 - name: edge_E28_6 -edge_E29_11: - ligand_a: lig_E29 - ligand_b: lig_11 - name: edge_E29_11 -edge_E29_E9: - ligand_a: lig_E29 - ligand_b: lig_E9 - name: edge_E29_E9 -edge_E2_E1: - ligand_a: lig_E2 - ligand_b: lig_E1 - name: edge_E2_E1 -edge_E2_E23: - ligand_a: lig_E2 - ligand_b: lig_E23 - name: edge_E2_E23 -edge_E2_E4: - ligand_a: lig_E2 - ligand_b: lig_E4 - name: edge_E2_E4 -edge_E4_E3: - ligand_a: lig_E4 - ligand_b: lig_E3 - name: edge_E4_E3 -edge_E6_6: - ligand_a: lig_E6 - ligand_b: lig_6 - name: edge_E6_6 -edge_E6_E25: - ligand_a: lig_E6 - ligand_b: lig_E25 - name: edge_E6_E25 -edge_E6_E8: - ligand_a: lig_E6 - ligand_b: lig_E8 - name: edge_E6_E8 -edge_E8_E30: - ligand_a: lig_E8 - ligand_b: lig_E30 - name: edge_E8_E30 -edge_E8_E4: - ligand_a: lig_E8 - ligand_b: lig_E4 - name: edge_E8_E4 -edge_E9_E30: - ligand_a: lig_E9 - ligand_b: lig_E30 - name: edge_E9_E30 -edge_SHP099-1_10: - ligand_a: lig_SHP099-1 - ligand_b: lig_10 - name: edge_SHP099-1_10 -edge_SHP099-1_E1: - ligand_a: lig_SHP099-1 - ligand_b: lig_E1 - name: edge_SHP099-1_E1 -edge_SHP099-1_E14: - ligand_a: lig_SHP099-1 - ligand_b: lig_E14 - name: edge_SHP099-1_E14 -edge_SHP099-1_E2: - ligand_a: lig_SHP099-1 - ligand_b: lig_E2 - name: edge_SHP099-1_E2 -edge_SHP099-1_E22: - ligand_a: lig_SHP099-1 - ligand_b: lig_E22 - name: edge_SHP099-1_E22 -edge_SHP099-1_E23: - ligand_a: lig_SHP099-1 - ligand_b: lig_E23 - name: edge_SHP099-1_E23 -edge_SHP099-1_E24: - ligand_a: lig_SHP099-1 - ligand_b: lig_E24 - name: edge_SHP099-1_E24 -edge_SHP099-1_E25: - ligand_a: lig_SHP099-1 - ligand_b: lig_E25 - name: edge_SHP099-1_E25 -edge_SHP099-1_E26: - ligand_a: lig_SHP099-1 - ligand_b: lig_E26 - name: edge_SHP099-1_E26 -edge_SHP099-1_E28: - ligand_a: lig_SHP099-1 - ligand_b: lig_E28 - name: edge_SHP099-1_E28 -edge_SHP099-1_E30: - ligand_a: lig_SHP099-1 - ligand_b: lig_E30 - name: edge_SHP099-1_E30 -edge_SHP099-1_E5: - ligand_a: lig_SHP099-1 - ligand_b: lig_E5 - name: edge_SHP099-1_E5 -edge_SHP099-1_E8: - ligand_a: lig_SHP099-1 - ligand_b: lig_E8 - name: edge_SHP099-1_E8 -edge_SHP836-2_E27: - ligand_a: lig_SHP836-2 - ligand_b: lig_E27 - name: edge_SHP836-2_E27 -edge_SHP836-2_E5: - ligand_a: lig_SHP836-2 - ligand_b: lig_E5 - name: edge_SHP836-2_E5 diff --git a/data/shp2/03_edges/01_perses_openfe.yaml b/data/shp2/03_edges/01_perses_openfe.yaml new file mode 100644 index 000000000..c67260f39 --- /dev/null +++ b/data/shp2/03_edges/01_perses_openfe.yaml @@ -0,0 +1,153 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_7_lig_E28: + ligand_a: lig_7 + ligand_b: lig_E28 + atom mapping: (1, 16) (2, 17) (3, 19) (4, 20) (5, 21) (6, 23) (7, 22) (8, 24) + (9, 26) (10, 25) (11, 27) (13, 28) (22, 35) (23, 37) (24, 36) (25, 38) (26, + 40) (27, 39) (28, 41) (29, 42) (30, 43) (31, 44) (32, 45) (33, 15) + score: '0.534' + edge_lig_SHP836-2_lig_E28: + ligand_a: lig_SHP836-2 + ligand_b: lig_E28 + atom mapping: (1, 16) (2, 17) (3, 19) (4, 20) (5, 38) (6, 40) (7, 39) (8, 35) + (9, 36) (14, 27) (16, 24) (17, 25) (22, 21) (23, 23) (24, 22) (25, 41) (26, + 42) (27, 43) (28, 45) (29, 44) (30, 15) + score: '0.508' + edge_lig_E14_lig_E3: + ligand_a: lig_E14 + ligand_b: lig_E3 + atom mapping: (1, 9) (2, 7) (3, 6) (15, 33) (16, 34) (17, 35) (18, 36) (19, 32) + (20, 10) + score: '0.292' + edge_lig_E14_lig_E26: + ligand_a: lig_E14 + ligand_b: lig_E26 + atom mapping: (1, 11) (2, 10) (3, 9) (4, 8) (5, 6) (7, 4) (9, 2) (10, 3) (11, + 1) (13, 44) (15, 40) (16, 41) (17, 43) (18, 42) (19, 39) (20, 17) + score: '0.529' + edge_lig_E14_lig_E28: + ligand_a: lig_E14 + ligand_b: lig_E28 + atom mapping: (0, 18) (1, 17) (2, 16) (3, 15) (15, 42) (16, 43) (17, 44) (18, + 45) (19, 41) (20, 19) + score: '0.296' + edge_lig_E14_lig_E4: + ligand_a: lig_E14 + ligand_b: lig_E4 + atom mapping: (1, 6) (2, 4) (3, 3) (15, 30) (16, 31) (17, 32) (18, 33) (19, 29) + (20, 7) + score: '0.292' + edge_lig_E14_lig_E23: + ligand_a: lig_E14 + ligand_b: lig_E23 + atom mapping: (1, 11) (2, 10) (3, 9) (4, 8) (5, 6) (7, 4) (9, 2) (10, 3) (11, + 1) (13, 40) (15, 36) (16, 37) (17, 39) (18, 38) (19, 35) (20, 13) + score: '0.536' + edge_lig_E14_lig_E24: + ligand_a: lig_E14 + ligand_b: lig_E24 + atom mapping: (1, 11) (2, 10) (3, 9) (4, 8) (5, 6) (7, 4) (9, 2) (10, 3) (11, + 1) (13, 43) (15, 39) (16, 40) (17, 42) (18, 41) (19, 38) (20, 16) + score: '0.536' + edge_lig_E14_lig_SHP099-1: + ligand_a: lig_E14 + ligand_b: lig_SHP099-1 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 13) (7, 11) (9, 9) (10, 10) + (11, 7) (13, 5) (15, 15) (16, 16) (17, 18) (18, 17) (19, 19) (20, 20) + score: '0.555' + edge_lig_E28_lig_E5: + ligand_a: lig_E28 + ligand_b: lig_E5 + atom mapping: (15, 30) (16, 1) (17, 2) (19, 3) (20, 4) (21, 5) (22, 6) (23, 7) + (24, 8) (25, 9) (26, 10) (27, 11) (28, 16) (32, 12) (35, 19) (36, 21) (37, 20) + (38, 22) (39, 24) (40, 23) (41, 25) (42, 26) (43, 27) (44, 29) (45, 28) + score: '0.543' + edge_lig_E14_lig_E30: + ligand_a: lig_E14 + ligand_b: lig_E30 + atom mapping: (1, 11) (2, 10) (3, 9) (4, 8) (5, 6) (7, 4) (9, 2) (10, 3) (11, + 1) (13, 39) (15, 35) (16, 36) (17, 38) (18, 37) (19, 34) (20, 12) + score: '0.540' + edge_lig_E14_lig_E1: + ligand_a: lig_E14 + ligand_b: lig_E1 + atom mapping: (1, 2) (2, 1) (3, 30) (4, 31) (5, 40) (7, 38) (9, 36) (10, 37) (11, + 34) (13, 32) (15, 26) (16, 27) (17, 29) (18, 28) (19, 25) (20, 3) + score: '0.540' + edge_lig_E14_lig_E25: + ligand_a: lig_E14 + ligand_b: lig_E25 + atom mapping: (1, 11) (2, 10) (3, 9) (4, 8) (5, 6) (7, 4) (9, 2) (10, 3) (11, + 1) (13, 41) (15, 37) (16, 38) (17, 40) (18, 39) (19, 36) (20, 14) + score: '0.532' + edge_lig_E14_lig_11: + ligand_a: lig_E14 + ligand_b: lig_11 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 13) (7, 11) (9, 9) (10, 10) + (11, 7) (13, 5) (15, 15) (16, 16) (18, 17) (19, 22) (20, 23) + score: '0.536' + edge_lig_E4_lig_E27: + ligand_a: lig_E4 + ligand_b: lig_E27 + atom mapping: (3, 3) (4, 2) (6, 1) (7, 20) (8, 21) (9, 39) (10, 41) (11, 40) (12, + 33) (14, 34) (15, 31) (23, 25) (25, 26) (26, 22) (27, 24) (28, 23) (29, 19) + (30, 15) (31, 16) (32, 18) (33, 17) + score: '0.520' + edge_lig_3_lig_E28: + ligand_a: lig_3 + ligand_b: lig_E28 + atom mapping: (1, 16) (2, 17) (3, 19) (4, 20) (5, 38) (6, 40) (7, 39) (8, 35) + (9, 36) (14, 27) (16, 24) (17, 25) (22, 21) (23, 23) (24, 22) (25, 41) (26, + 42) (27, 43) (28, 45) (29, 44) (30, 15) + score: '0.508' + edge_lig_E14_lig_E2: + ligand_a: lig_E14 + ligand_b: lig_E2 + atom mapping: (1, 2) (2, 1) (3, 30) (4, 31) (5, 43) (7, 38) (9, 36) (10, 37) (11, + 34) (13, 32) (15, 26) (16, 27) (17, 29) (18, 28) (19, 25) (20, 3) + score: '0.540' + edge_lig_E14_lig_10: + ligand_a: lig_E14 + ligand_b: lig_10 + atom mapping: (0, 26) (1, 25) (2, 27) (3, 28) (4, 29) (5, 38) (7, 36) (9, 34) + (10, 35) (11, 32) (13, 30) (15, 1) (19, 2) (20, 3) + score: '0.507' + edge_lig_E8_lig_E14: + ligand_a: lig_E8 + ligand_b: lig_E14 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 13) (7, 11) (9, 9) (10, 10) + (11, 7) (13, 5) (15, 15) (16, 16) (17, 17) (18, 18) (19, 19) (20, 20) + score: '0.551' + edge_lig_E14_lig_E22: + ligand_a: lig_E14 + ligand_b: lig_E22 + atom mapping: (1, 11) (2, 10) (3, 9) (4, 8) (5, 6) (7, 4) (9, 2) (10, 3) (11, + 1) (13, 40) (15, 36) (16, 37) (17, 39) (18, 38) (19, 35) (20, 13) + score: '0.536' + edge_lig_6_lig_E14: + ligand_a: lig_6 + ligand_b: lig_E14 + atom mapping: (1, 2) (2, 1) (3, 20) (22, 19) (23, 15) (24, 16) (25, 18) (26, 17) + (27, 3) (28, 4) (29, 13) (31, 11) (33, 9) (34, 10) (35, 7) (37, 5) + score: '0.544' + edge_lig_E14_lig_E29: + ligand_a: lig_E14 + ligand_b: lig_E29 + atom mapping: (0, 6) (1, 5) (2, 4) (3, 3) (15, 30) (16, 31) (17, 32) (18, 33) + (19, 29) (20, 7) + score: '0.305' + edge_lig_E9_lig_E14: + ligand_a: lig_E9 + ligand_b: lig_E14 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 13) (7, 11) (9, 9) (10, 10) + (11, 7) (13, 5) (15, 15) (16, 16) (17, 18) (18, 17) (19, 19) (20, 20) + score: '0.555' + edge_lig_E14_lig_E6: + ligand_a: lig_E14 + ligand_b: lig_E6 + atom mapping: (1, 13) (2, 11) (3, 10) (4, 9) (5, 7) (7, 5) (9, 3) (10, 4) (11, + 2) (12, 1) (13, 41) (15, 37) (16, 38) (17, 40) (18, 39) (19, 36) (20, 14) + score: '0.558' diff --git a/data/shp2/03_edges/nohup.out b/data/shp2/03_edges/nohup.out new file mode 100644 index 000000000..e8a050dde --- /dev/null +++ b/data/shp2/03_edges/nohup.out @@ -0,0 +1,29 @@ +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. +lig_7_lig_E28 exceeds 1 A pairwise distance +lig_SHP836-2_lig_E28 exceeds 1 A pairwise distance +lig_E14_lig_E26 exceeds 1 A pairwise distance +lig_E14_lig_E23 exceeds 1 A pairwise distance +lig_E14_lig_E24 exceeds 1 A pairwise distance +lig_E14_lig_SHP099-1 exceeds 1 A pairwise distance +lig_E28_lig_E5 exceeds 1 A pairwise distance +lig_E14_lig_E30 exceeds 1 A pairwise distance +lig_E14_lig_E1 exceeds 1 A pairwise distance +lig_E14_lig_E25 exceeds 1 A pairwise distance +lig_E14_lig_11 exceeds 1 A pairwise distance +lig_E4_lig_E27 exceeds 1 A pairwise distance +lig_3_lig_E28 exceeds 1 A pairwise distance +lig_E14_lig_E2 exceeds 1 A pairwise distance +lig_E14_lig_10 exceeds 1 A pairwise distance +lig_E8_lig_E14 exceeds 1 A pairwise distance +lig_E14_lig_E22 exceeds 1 A pairwise distance +lig_6_lig_E14 exceeds 1 A pairwise distance +lig_E9_lig_E14 exceeds 1 A pairwise distance +lig_E14_lig_E6 exceeds 1 A pairwise distance diff --git a/data/syk/00_data/edges.yml b/data/syk/00_data/edges.yml deleted file mode 100644 index 01535a32e..000000000 --- a/data/syk/00_data/edges.yml +++ /dev/null @@ -1,404 +0,0 @@ -edge_CHEMBL3264995_CHEMBL3264994: - ligand_a: lig_CHEMBL3264995 - ligand_b: lig_CHEMBL3264994 - name: edge_CHEMBL3264995_CHEMBL3264994 -edge_CHEMBL3264995_CHEMBL3265001: - ligand_a: lig_CHEMBL3264995 - ligand_b: lig_CHEMBL3265001 - name: edge_CHEMBL3264995_CHEMBL3265001 -edge_CHEMBL3264997_CHEMBL3264994: - ligand_a: lig_CHEMBL3264997 - ligand_b: lig_CHEMBL3264994 - name: edge_CHEMBL3264997_CHEMBL3264994 -edge_CHEMBL3264997_CHEMBL3264995: - ligand_a: lig_CHEMBL3264997 - ligand_b: lig_CHEMBL3264995 - name: edge_CHEMBL3264997_CHEMBL3264995 -edge_CHEMBL3264998_CHEMBL3264995: - ligand_a: lig_CHEMBL3264998 - ligand_b: lig_CHEMBL3264995 - name: edge_CHEMBL3264998_CHEMBL3264995 -edge_CHEMBL3264998_CHEMBL3265001: - ligand_a: lig_CHEMBL3264998 - ligand_b: lig_CHEMBL3265001 - name: edge_CHEMBL3264998_CHEMBL3265001 -edge_CHEMBL3264999_CHEMBL3264996: - ligand_a: lig_CHEMBL3264999 - ligand_b: lig_CHEMBL3264996 - name: edge_CHEMBL3264999_CHEMBL3264996 -edge_CHEMBL3265000_CHEMBL3264994: - ligand_a: lig_CHEMBL3265000 - ligand_b: lig_CHEMBL3264994 - name: edge_CHEMBL3265000_CHEMBL3264994 -edge_CHEMBL3265000_CHEMBL3264995: - ligand_a: lig_CHEMBL3265000 - ligand_b: lig_CHEMBL3264995 - name: edge_CHEMBL3265000_CHEMBL3264995 -edge_CHEMBL3265000_CHEMBL3264997: - ligand_a: lig_CHEMBL3265000 - ligand_b: lig_CHEMBL3264997 - name: edge_CHEMBL3265000_CHEMBL3264997 -edge_CHEMBL3265002_CHEMBL3264996: - ligand_a: lig_CHEMBL3265002 - ligand_b: lig_CHEMBL3264996 - name: edge_CHEMBL3265002_CHEMBL3264996 -edge_CHEMBL3265002_CHEMBL3264999: - ligand_a: lig_CHEMBL3265002 - ligand_b: lig_CHEMBL3264999 - name: edge_CHEMBL3265002_CHEMBL3264999 -edge_CHEMBL3265002_CHEMBL3265001: - ligand_a: lig_CHEMBL3265002 - ligand_b: lig_CHEMBL3265001 - name: edge_CHEMBL3265002_CHEMBL3265001 -edge_CHEMBL3265003_CHEMBL3264999: - ligand_a: lig_CHEMBL3265003 - ligand_b: lig_CHEMBL3264999 - name: edge_CHEMBL3265003_CHEMBL3264999 -edge_CHEMBL3265004_CHEMBL3264999: - ligand_a: lig_CHEMBL3265004 - ligand_b: lig_CHEMBL3264999 - name: edge_CHEMBL3265004_CHEMBL3264999 -edge_CHEMBL3265004_CHEMBL3265001: - ligand_a: lig_CHEMBL3265004 - ligand_b: lig_CHEMBL3265001 - name: edge_CHEMBL3265004_CHEMBL3265001 -edge_CHEMBL3265004_CHEMBL3265002: - ligand_a: lig_CHEMBL3265004 - ligand_b: lig_CHEMBL3265002 - name: edge_CHEMBL3265004_CHEMBL3265002 -edge_CHEMBL3265004_CHEMBL3265003: - ligand_a: lig_CHEMBL3265004 - ligand_b: lig_CHEMBL3265003 - name: edge_CHEMBL3265004_CHEMBL3265003 -edge_CHEMBL3265006_CHEMBL3265011: - ligand_a: lig_CHEMBL3265006 - ligand_b: lig_CHEMBL3265011 - name: edge_CHEMBL3265006_CHEMBL3265011 -edge_CHEMBL3265006_CHEMBL3265026: - ligand_a: lig_CHEMBL3265006 - ligand_b: lig_CHEMBL3265026 - name: edge_CHEMBL3265006_CHEMBL3265026 -edge_CHEMBL3265008_CHEMBL3259820: - ligand_a: lig_CHEMBL3265008 - ligand_b: lig_CHEMBL3259820 - name: edge_CHEMBL3265008_CHEMBL3259820 -edge_CHEMBL3265008_CHEMBL3265005: - ligand_a: lig_CHEMBL3265008 - ligand_b: lig_CHEMBL3265005 - name: edge_CHEMBL3265008_CHEMBL3265005 -edge_CHEMBL3265008_CHEMBL3265006: - ligand_a: lig_CHEMBL3265008 - ligand_b: lig_CHEMBL3265006 - name: edge_CHEMBL3265008_CHEMBL3265006 -edge_CHEMBL3265009_CHEMBL3265003: - ligand_a: lig_CHEMBL3265009 - ligand_b: lig_CHEMBL3265003 - name: edge_CHEMBL3265009_CHEMBL3265003 -edge_CHEMBL3265009_CHEMBL3265005: - ligand_a: lig_CHEMBL3265009 - ligand_b: lig_CHEMBL3265005 - name: edge_CHEMBL3265009_CHEMBL3265005 -edge_CHEMBL3265009_CHEMBL3265006: - ligand_a: lig_CHEMBL3265009 - ligand_b: lig_CHEMBL3265006 - name: edge_CHEMBL3265009_CHEMBL3265006 -edge_CHEMBL3265009_CHEMBL3265008: - ligand_a: lig_CHEMBL3265009 - ligand_b: lig_CHEMBL3265008 - name: edge_CHEMBL3265009_CHEMBL3265008 -edge_CHEMBL3265009_CHEMBL3265020: - ligand_a: lig_CHEMBL3265009 - ligand_b: lig_CHEMBL3265020 - name: edge_CHEMBL3265009_CHEMBL3265020 -edge_CHEMBL3265010_CHEMBL3264996: - ligand_a: lig_CHEMBL3265010 - ligand_b: lig_CHEMBL3264996 - name: edge_CHEMBL3265010_CHEMBL3264996 -edge_CHEMBL3265010_CHEMBL3265011: - ligand_a: lig_CHEMBL3265010 - ligand_b: lig_CHEMBL3265011 - name: edge_CHEMBL3265010_CHEMBL3265011 -edge_CHEMBL3265012_CHEMBL3259820: - ligand_a: lig_CHEMBL3265012 - ligand_b: lig_CHEMBL3259820 - name: edge_CHEMBL3265012_CHEMBL3259820 -edge_CHEMBL3265012_CHEMBL3265002: - ligand_a: lig_CHEMBL3265012 - ligand_b: lig_CHEMBL3265002 - name: edge_CHEMBL3265012_CHEMBL3265002 -edge_CHEMBL3265012_CHEMBL3265010: - ligand_a: lig_CHEMBL3265012 - ligand_b: lig_CHEMBL3265010 - name: edge_CHEMBL3265012_CHEMBL3265010 -edge_CHEMBL3265013_CHEMBL3259820: - ligand_a: lig_CHEMBL3265013 - ligand_b: lig_CHEMBL3259820 - name: edge_CHEMBL3265013_CHEMBL3259820 -edge_CHEMBL3265013_CHEMBL3265004: - ligand_a: lig_CHEMBL3265013 - ligand_b: lig_CHEMBL3265004 - name: edge_CHEMBL3265013_CHEMBL3265004 -edge_CHEMBL3265013_CHEMBL3265012: - ligand_a: lig_CHEMBL3265013 - ligand_b: lig_CHEMBL3265012 - name: edge_CHEMBL3265013_CHEMBL3265012 -edge_CHEMBL3265013_CHEMBL3265020: - ligand_a: lig_CHEMBL3265013 - ligand_b: lig_CHEMBL3265020 - name: edge_CHEMBL3265013_CHEMBL3265020 -edge_CHEMBL3265013_CHEMBL3265023: - ligand_a: lig_CHEMBL3265013 - ligand_b: lig_CHEMBL3265023 - name: edge_CHEMBL3265013_CHEMBL3265023 -edge_CHEMBL3265014_CHEMBL3265006: - ligand_a: lig_CHEMBL3265014 - ligand_b: lig_CHEMBL3265006 - name: edge_CHEMBL3265014_CHEMBL3265006 -edge_CHEMBL3265014_CHEMBL3265022: - ligand_a: lig_CHEMBL3265014 - ligand_b: lig_CHEMBL3265022 - name: edge_CHEMBL3265014_CHEMBL3265022 -edge_CHEMBL3265014_CHEMBL3265025: - ligand_a: lig_CHEMBL3265014 - ligand_b: lig_CHEMBL3265025 - name: edge_CHEMBL3265014_CHEMBL3265025 -edge_CHEMBL3265014_CHEMBL3265028: - ligand_a: lig_CHEMBL3265014 - ligand_b: lig_CHEMBL3265028 - name: edge_CHEMBL3265014_CHEMBL3265028 -edge_CHEMBL3265015_CHEMBL3259820: - ligand_a: lig_CHEMBL3265015 - ligand_b: lig_CHEMBL3259820 - name: edge_CHEMBL3265015_CHEMBL3259820 -edge_CHEMBL3265015_CHEMBL3264999: - ligand_a: lig_CHEMBL3265015 - ligand_b: lig_CHEMBL3264999 - name: edge_CHEMBL3265015_CHEMBL3264999 -edge_CHEMBL3265015_CHEMBL3265009: - ligand_a: lig_CHEMBL3265015 - ligand_b: lig_CHEMBL3265009 - name: edge_CHEMBL3265015_CHEMBL3265009 -edge_CHEMBL3265015_CHEMBL3265011: - ligand_a: lig_CHEMBL3265015 - ligand_b: lig_CHEMBL3265011 - name: edge_CHEMBL3265015_CHEMBL3265011 -edge_CHEMBL3265015_CHEMBL3265014: - ligand_a: lig_CHEMBL3265015 - ligand_b: lig_CHEMBL3265014 - name: edge_CHEMBL3265015_CHEMBL3265014 -edge_CHEMBL3265015_CHEMBL3265017: - ligand_a: lig_CHEMBL3265015 - ligand_b: lig_CHEMBL3265017 - name: edge_CHEMBL3265015_CHEMBL3265017 -edge_CHEMBL3265016_CHEMBL3265005: - ligand_a: lig_CHEMBL3265016 - ligand_b: lig_CHEMBL3265005 - name: edge_CHEMBL3265016_CHEMBL3265005 -edge_CHEMBL3265016_CHEMBL3265020: - ligand_a: lig_CHEMBL3265016 - ligand_b: lig_CHEMBL3265020 - name: edge_CHEMBL3265016_CHEMBL3265020 -edge_CHEMBL3265017_CHEMBL3265002: - ligand_a: lig_CHEMBL3265017 - ligand_b: lig_CHEMBL3265002 - name: edge_CHEMBL3265017_CHEMBL3265002 -edge_CHEMBL3265017_CHEMBL3265016: - ligand_a: lig_CHEMBL3265017 - ligand_b: lig_CHEMBL3265016 - name: edge_CHEMBL3265017_CHEMBL3265016 -edge_CHEMBL3265017_CHEMBL3265020: - ligand_a: lig_CHEMBL3265017 - ligand_b: lig_CHEMBL3265020 - name: edge_CHEMBL3265017_CHEMBL3265020 -edge_CHEMBL3265017_CHEMBL3265024: - ligand_a: lig_CHEMBL3265017 - ligand_b: lig_CHEMBL3265024 - name: edge_CHEMBL3265017_CHEMBL3265024 -edge_CHEMBL3265017_CHEMBL3265026: - ligand_a: lig_CHEMBL3265017 - ligand_b: lig_CHEMBL3265026 - name: edge_CHEMBL3265017_CHEMBL3265026 -edge_CHEMBL3265017_CHEMBL3265027: - ligand_a: lig_CHEMBL3265017 - ligand_b: lig_CHEMBL3265027 - name: edge_CHEMBL3265017_CHEMBL3265027 -edge_CHEMBL3265017_CHEMBL3265029: - ligand_a: lig_CHEMBL3265017 - ligand_b: lig_CHEMBL3265029 - name: edge_CHEMBL3265017_CHEMBL3265029 -edge_CHEMBL3265017_CHEMBL3265032: - ligand_a: lig_CHEMBL3265017 - ligand_b: lig_CHEMBL3265032 - name: edge_CHEMBL3265017_CHEMBL3265032 -edge_CHEMBL3265018_CHEMBL3265005: - ligand_a: lig_CHEMBL3265018 - ligand_b: lig_CHEMBL3265005 - name: edge_CHEMBL3265018_CHEMBL3265005 -edge_CHEMBL3265018_CHEMBL3265011: - ligand_a: lig_CHEMBL3265018 - ligand_b: lig_CHEMBL3265011 - name: edge_CHEMBL3265018_CHEMBL3265011 -edge_CHEMBL3265018_CHEMBL3265019: - ligand_a: lig_CHEMBL3265018 - ligand_b: lig_CHEMBL3265019 - name: edge_CHEMBL3265018_CHEMBL3265019 -edge_CHEMBL3265019_CHEMBL3265005: - ligand_a: lig_CHEMBL3265019 - ligand_b: lig_CHEMBL3265005 - name: edge_CHEMBL3265019_CHEMBL3265005 -edge_CHEMBL3265020_CHEMBL3265026: - ligand_a: lig_CHEMBL3265020 - ligand_b: lig_CHEMBL3265026 - name: edge_CHEMBL3265020_CHEMBL3265026 -edge_CHEMBL3265021_CHEMBL3265011: - ligand_a: lig_CHEMBL3265021 - ligand_b: lig_CHEMBL3265011 - name: edge_CHEMBL3265021_CHEMBL3265011 -edge_CHEMBL3265021_CHEMBL3265013: - ligand_a: lig_CHEMBL3265021 - ligand_b: lig_CHEMBL3265013 - name: edge_CHEMBL3265021_CHEMBL3265013 -edge_CHEMBL3265021_CHEMBL3265017: - ligand_a: lig_CHEMBL3265021 - ligand_b: lig_CHEMBL3265017 - name: edge_CHEMBL3265021_CHEMBL3265017 -edge_CHEMBL3265021_CHEMBL3265020: - ligand_a: lig_CHEMBL3265021 - ligand_b: lig_CHEMBL3265020 - name: edge_CHEMBL3265021_CHEMBL3265020 -edge_CHEMBL3265021_CHEMBL3265022: - ligand_a: lig_CHEMBL3265021 - ligand_b: lig_CHEMBL3265022 - name: edge_CHEMBL3265021_CHEMBL3265022 -edge_CHEMBL3265021_CHEMBL3265023: - ligand_a: lig_CHEMBL3265021 - ligand_b: lig_CHEMBL3265023 - name: edge_CHEMBL3265021_CHEMBL3265023 -edge_CHEMBL3265021_CHEMBL3265024: - ligand_a: lig_CHEMBL3265021 - ligand_b: lig_CHEMBL3265024 - name: edge_CHEMBL3265021_CHEMBL3265024 -edge_CHEMBL3265021_CHEMBL3265035: - ligand_a: lig_CHEMBL3265021 - ligand_b: lig_CHEMBL3265035 - name: edge_CHEMBL3265021_CHEMBL3265035 -edge_CHEMBL3265023_CHEMBL3265020: - ligand_a: lig_CHEMBL3265023 - ligand_b: lig_CHEMBL3265020 - name: edge_CHEMBL3265023_CHEMBL3265020 -edge_CHEMBL3265023_CHEMBL3265022: - ligand_a: lig_CHEMBL3265023 - ligand_b: lig_CHEMBL3265022 - name: edge_CHEMBL3265023_CHEMBL3265022 -edge_CHEMBL3265023_CHEMBL3265028: - ligand_a: lig_CHEMBL3265023 - ligand_b: lig_CHEMBL3265028 - name: edge_CHEMBL3265023_CHEMBL3265028 -edge_CHEMBL3265024_CHEMBL3265008: - ligand_a: lig_CHEMBL3265024 - ligand_b: lig_CHEMBL3265008 - name: edge_CHEMBL3265024_CHEMBL3265008 -edge_CHEMBL3265025_CHEMBL3265008: - ligand_a: lig_CHEMBL3265025 - ligand_b: lig_CHEMBL3265008 - name: edge_CHEMBL3265025_CHEMBL3265008 -edge_CHEMBL3265025_CHEMBL3265020: - ligand_a: lig_CHEMBL3265025 - ligand_b: lig_CHEMBL3265020 - name: edge_CHEMBL3265025_CHEMBL3265020 -edge_CHEMBL3265027_CHEMBL3265010: - ligand_a: lig_CHEMBL3265027 - ligand_b: lig_CHEMBL3265010 - name: edge_CHEMBL3265027_CHEMBL3265010 -edge_CHEMBL3265027_CHEMBL3265020: - ligand_a: lig_CHEMBL3265027 - ligand_b: lig_CHEMBL3265020 - name: edge_CHEMBL3265027_CHEMBL3265020 -edge_CHEMBL3265027_CHEMBL3265030_n: - ligand_a: lig_CHEMBL3265027 - ligand_b: lig_CHEMBL3265030_n - name: edge_CHEMBL3265027_CHEMBL3265030_n -edge_CHEMBL3265027_CHEMBL3265033: - ligand_a: lig_CHEMBL3265027 - ligand_b: lig_CHEMBL3265033 - name: edge_CHEMBL3265027_CHEMBL3265033 -edge_CHEMBL3265028_CHEMBL3265027: - ligand_a: lig_CHEMBL3265028 - ligand_b: lig_CHEMBL3265027 - name: edge_CHEMBL3265028_CHEMBL3265027 -edge_CHEMBL3265028_CHEMBL3265030_n: - ligand_a: lig_CHEMBL3265028 - ligand_b: lig_CHEMBL3265030_n - name: edge_CHEMBL3265028_CHEMBL3265030_n -edge_CHEMBL3265029_CHEMBL3265016: - ligand_a: lig_CHEMBL3265029 - ligand_b: lig_CHEMBL3265016 - name: edge_CHEMBL3265029_CHEMBL3265016 -edge_CHEMBL3265029_CHEMBL3265027: - ligand_a: lig_CHEMBL3265029 - ligand_b: lig_CHEMBL3265027 - name: edge_CHEMBL3265029_CHEMBL3265027 -edge_CHEMBL3265031_CHEMBL3265024: - ligand_a: lig_CHEMBL3265031 - ligand_b: lig_CHEMBL3265024 - name: edge_CHEMBL3265031_CHEMBL3265024 -edge_CHEMBL3265031_CHEMBL3265030_n: - ligand_a: lig_CHEMBL3265031 - ligand_b: lig_CHEMBL3265030_n - name: edge_CHEMBL3265031_CHEMBL3265030_n -edge_CHEMBL3265031_CHEMBL3265037: - ligand_a: lig_CHEMBL3265031 - ligand_b: lig_CHEMBL3265037 - name: edge_CHEMBL3265031_CHEMBL3265037 -edge_CHEMBL3265032_CHEMBL3265022: - ligand_a: lig_CHEMBL3265032 - ligand_b: lig_CHEMBL3265022 - name: edge_CHEMBL3265032_CHEMBL3265022 -edge_CHEMBL3265032_CHEMBL3265027: - ligand_a: lig_CHEMBL3265032 - ligand_b: lig_CHEMBL3265027 - name: edge_CHEMBL3265032_CHEMBL3265027 -edge_CHEMBL3265032_CHEMBL3265033: - ligand_a: lig_CHEMBL3265032 - ligand_b: lig_CHEMBL3265033 - name: edge_CHEMBL3265032_CHEMBL3265033 -edge_CHEMBL3265033_CHEMBL3265022: - ligand_a: lig_CHEMBL3265033 - ligand_b: lig_CHEMBL3265022 - name: edge_CHEMBL3265033_CHEMBL3265022 -edge_CHEMBL3265034_CHEMBL3265026: - ligand_a: lig_CHEMBL3265034 - ligand_b: lig_CHEMBL3265026 - name: edge_CHEMBL3265034_CHEMBL3265026 -edge_CHEMBL3265034_CHEMBL3265027: - ligand_a: lig_CHEMBL3265034 - ligand_b: lig_CHEMBL3265027 - name: edge_CHEMBL3265034_CHEMBL3265027 -edge_CHEMBL3265034_CHEMBL3265033: - ligand_a: lig_CHEMBL3265034 - ligand_b: lig_CHEMBL3265033 - name: edge_CHEMBL3265034_CHEMBL3265033 -edge_CHEMBL3265034_CHEMBL3265037: - ligand_a: lig_CHEMBL3265034 - ligand_b: lig_CHEMBL3265037 - name: edge_CHEMBL3265034_CHEMBL3265037 -edge_CHEMBL3265035_CHEMBL3264996: - ligand_a: lig_CHEMBL3265035 - ligand_b: lig_CHEMBL3264996 - name: edge_CHEMBL3265035_CHEMBL3264996 -edge_CHEMBL3265035_CHEMBL3265024: - ligand_a: lig_CHEMBL3265035 - ligand_b: lig_CHEMBL3265024 - name: edge_CHEMBL3265035_CHEMBL3265024 -edge_CHEMBL3265036_CHEMBL3265016: - ligand_a: lig_CHEMBL3265036 - ligand_b: lig_CHEMBL3265016 - name: edge_CHEMBL3265036_CHEMBL3265016 -edge_CHEMBL3265036_CHEMBL3265029: - ligand_a: lig_CHEMBL3265036 - ligand_b: lig_CHEMBL3265029 - name: edge_CHEMBL3265036_CHEMBL3265029 -edge_CHEMBL3265037_CHEMBL3265032: - ligand_a: lig_CHEMBL3265037 - ligand_b: lig_CHEMBL3265032 - name: edge_CHEMBL3265037_CHEMBL3265032 diff --git a/data/syk/03_edges/01_perses_openfe.yaml b/data/syk/03_edges/01_perses_openfe.yaml new file mode 100644 index 000000000..43ed4f820 --- /dev/null +++ b/data/syk/03_edges/01_perses_openfe.yaml @@ -0,0 +1,312 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_CHEMBL3265001_lig_CHEMBL3265035: + ligand_a: lig_CHEMBL3265001 + ligand_b: lig_CHEMBL3265035 + atom mapping: (0, 40) (1, 39) (2, 41) (3, 42) (4, 36) (5, 37) (6, 38) (7, 17) + (8, 15) (9, 16) (10, 14) (11, 43) (12, 44) (13, 45) (14, 46) (15, 9) (16, 8) + (17, 5) (18, 7) (19, 6) (21, 10) (27, 12) (28, 13) (29, 18) (30, 19) (60, 34) + (61, 35) + score: '0.472' + edge_lig_CHEMBL3265014_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265014 + ligand_b: lig_CHEMBL3265031 + atom mapping: (0, 45) (1, 44) (2, 46) (3, 47) (4, 41) (5, 42) (6, 43) (7, 22) + (8, 20) (9, 21) (10, 19) (11, 48) (12, 49) (13, 50) (14, 51) (15, 14) (21, 15) + (27, 17) (28, 18) (29, 23) (30, 24) (50, 39) (51, 40) + score: '0.464' + edge_lig_CHEMBL3265022_lig_CHEMBL3264994: + ligand_a: lig_CHEMBL3265022 + ligand_b: lig_CHEMBL3264994 + atom mapping: (12, 34) (13, 62) (14, 63) (15, 4) (16, 5) (17, 6) (18, 1) (19, + 0) (20, 2) (21, 3) (22, 7) (23, 8) (24, 9) (25, 10) (26, 31) (27, 32) (28, 29) + (29, 30) (30, 15) (31, 16) (32, 17) (33, 20) (34, 19) (35, 18) (36, 13) (42, + 11) (43, 12) (44, 33) + score: '0.507' + edge_lig_CHEMBL3265000_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265000 + ligand_b: lig_CHEMBL3265033 + atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) + (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) + (27, 46) (28, 47) (29, 48) (30, 9) (65, 10) (66, 11) + score: '0.412' + edge_lig_CHEMBL3265001_lig_CHEMBL3265030_n: + ligand_a: lig_CHEMBL3265001 + ligand_b: lig_CHEMBL3265030_n + atom mapping: (0, 42) (1, 41) (2, 43) (3, 44) (4, 38) (5, 39) (6, 40) (7, 19) + (8, 17) (9, 18) (10, 16) (11, 45) (12, 46) (13, 47) (14, 48) (15, 11) (21, 12) + (27, 14) (28, 15) (29, 20) (30, 21) (60, 36) (61, 37) + score: '0.417' + edge_lig_CHEMBL3264995_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3264995 + ligand_b: lig_CHEMBL3265031 + atom mapping: (0, 45) (1, 44) (2, 46) (3, 47) (4, 41) (5, 42) (6, 43) (7, 22) + (8, 20) (9, 21) (10, 19) (11, 48) (12, 49) (13, 50) (14, 51) (15, 14) (21, 15) + (27, 17) (28, 18) (29, 23) (30, 24) (58, 39) (59, 40) + score: '0.404' + edge_lig_CHEMBL3265000_lig_CHEMBL3265036: + ligand_a: lig_CHEMBL3265000 + ligand_b: lig_CHEMBL3265036 + atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) + (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 45) + (27, 47) (28, 48) (29, 49) (30, 9) (65, 10) (66, 11) + score: '0.407' + edge_lig_CHEMBL3265004_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265004 + ligand_b: lig_CHEMBL3265031 + atom mapping: (26, 24) (27, 39) (28, 40) (29, 41) (30, 42) (31, 43) (32, 44) (33, + 45) (34, 46) (35, 47) (36, 22) (37, 20) (38, 21) (39, 19) (40, 17) (41, 18) + (42, 15) (43, 16) (44, 14) (50, 50) (56, 48) (57, 49) (58, 23) + score: '0.397' + edge_lig_CHEMBL3265005_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265005 + ligand_b: lig_CHEMBL3265033 + atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) + (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) + (27, 46) (28, 47) (29, 48) (30, 9) (46, 10) (47, 11) + score: '0.485' + edge_lig_CHEMBL3265016_lig_CHEMBL3264994: + ligand_a: lig_CHEMBL3265016 + ligand_b: lig_CHEMBL3264994 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, + 20) (19, 19) (20, 18) (21, 29) (27, 31) (28, 32) (29, 33) (30, 34) (46, 62) + (47, 63) + score: '0.518' + edge_lig_CHEMBL3265009_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265009 + ligand_b: lig_CHEMBL3265033 + atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) + (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) + (27, 46) (28, 47) (29, 48) (30, 9) (49, 10) (50, 11) + score: '0.469' + edge_lig_CHEMBL3264996_lig_CHEMBL3265027: + ligand_a: lig_CHEMBL3264996 + ligand_b: lig_CHEMBL3265027 + atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) + (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 29) + (27, 31) (28, 32) (29, 33) (30, 9) (62, 10) (63, 11) + score: '0.499' + edge_lig_CHEMBL3265003_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265003 + ligand_b: lig_CHEMBL3265031 + atom mapping: (24, 24) (25, 39) (26, 40) (27, 41) (28, 42) (29, 43) (30, 44) (31, + 45) (32, 46) (33, 47) (34, 22) (35, 20) (36, 21) (37, 19) (38, 17) (39, 18) + (40, 15) (41, 16) (42, 14) (48, 50) (54, 48) (55, 49) (56, 23) + score: '0.397' + edge_lig_CHEMBL3265019_lig_CHEMBL3264994: + ligand_a: lig_CHEMBL3265019 + ligand_b: lig_CHEMBL3264994 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 21) (18, + 24) (19, 23) (20, 22) (21, 29) (27, 31) (28, 32) (29, 33) (30, 34) (44, 62) + (45, 63) + score: '0.530' + edge_lig_CHEMBL3264997_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3264997 + ligand_b: lig_CHEMBL3265031 + atom mapping: (0, 45) (1, 44) (2, 46) (3, 47) (4, 41) (5, 42) (6, 43) (7, 22) + (8, 20) (9, 21) (10, 19) (11, 48) (12, 49) (13, 50) (14, 51) (15, 14) (21, 15) + (27, 17) (28, 18) (29, 23) (30, 24) (58, 39) (59, 40) + score: '0.404' + edge_lig_CHEMBL3265000_lig_CHEMBL3265034: + ligand_a: lig_CHEMBL3265000 + ligand_b: lig_CHEMBL3265034 + atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) + (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 43) + (27, 45) (28, 46) (29, 47) (30, 9) (65, 10) (66, 11) + score: '0.416' + edge_lig_CHEMBL3265001_lig_CHEMBL3265029: + ligand_a: lig_CHEMBL3265001 + ligand_b: lig_CHEMBL3265029 + atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) + (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (16, 28) + (17, 29) (18, 32) (19, 31) (20, 30) (21, 33) (27, 35) (28, 36) (29, 37) (30, + 9) (60, 10) (61, 11) + score: '0.530' + edge_lig_CHEMBL3265024_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265024 + ligand_b: lig_CHEMBL3265033 + atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) + (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) + (27, 46) (28, 47) (29, 48) (30, 9) (48, 10) (49, 11) + score: '0.474' + edge_lig_CHEMBL3265021_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265021 + ligand_b: lig_CHEMBL3265031 + atom mapping: (11, 24) (12, 39) (13, 40) (14, 41) (15, 42) (16, 43) (17, 44) (18, + 45) (19, 46) (20, 47) (21, 22) (22, 20) (23, 21) (24, 19) (25, 17) (26, 18) + (27, 15) (28, 16) (29, 14) (35, 50) (41, 48) (42, 49) (43, 23) + score: '0.491' + edge_lig_CHEMBL3265018_lig_CHEMBL3264994: + ligand_a: lig_CHEMBL3265018 + ligand_b: lig_CHEMBL3264994 + atom mapping: (9, 34) (10, 62) (11, 63) (12, 4) (13, 5) (14, 6) (15, 1) (16, 0) + (17, 2) (18, 3) (19, 7) (20, 8) (21, 9) (22, 10) (23, 11) (24, 12) (25, 13) + (26, 14) (27, 15) (28, 16) (29, 25) (30, 26) (31, 27) (32, 28) (33, 29) (39, + 31) (40, 32) (41, 33) + score: '0.524' + edge_lig_CHEMBL3265000_lig_CHEMBL3265032: + ligand_a: lig_CHEMBL3265000 + ligand_b: lig_CHEMBL3265032 + atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) + (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 42) + (27, 44) (28, 45) (29, 46) (30, 9) (65, 10) (66, 11) + score: '0.421' + edge_lig_CHEMBL3265023_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265023 + ligand_b: lig_CHEMBL3265033 + atom mapping: (14, 9) (15, 10) (16, 11) (17, 12) (18, 13) (19, 14) (20, 15) (21, + 16) (22, 17) (23, 18) (24, 19) (25, 20) (26, 21) (27, 22) (28, 23) (29, 24) + (30, 25) (31, 26) (32, 27) (38, 44) (44, 46) (45, 47) (46, 48) + score: '0.474' + edge_lig_CHEMBL3265017_lig_CHEMBL3264994: + ligand_a: lig_CHEMBL3265017 + ligand_b: lig_CHEMBL3264994 + atom mapping: (9, 34) (10, 62) (11, 63) (12, 4) (13, 5) (14, 6) (15, 1) (16, 0) + (17, 2) (18, 3) (19, 7) (20, 8) (21, 9) (22, 10) (23, 11) (24, 12) (25, 13) + (26, 14) (27, 15) (28, 16) (29, 21) (30, 24) (31, 23) (32, 22) (33, 29) (39, + 31) (40, 32) (41, 33) + score: '0.524' + edge_lig_CHEMBL3265025_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265025 + ligand_b: lig_CHEMBL3265033 + atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) + (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) + (27, 46) (28, 47) (29, 48) (30, 9) (48, 10) (49, 11) + score: '0.474' + edge_lig_CHEMBL3265028_lig_CHEMBL3264994: + ligand_a: lig_CHEMBL3265028 + ligand_b: lig_CHEMBL3264994 + atom mapping: (9, 34) (10, 62) (11, 63) (12, 4) (13, 5) (14, 6) (15, 1) (16, 0) + (17, 2) (18, 3) (19, 7) (20, 8) (21, 9) (22, 10) (23, 11) (24, 12) (25, 13) + (26, 14) (27, 15) (29, 29) (35, 31) (36, 32) (37, 33) + score: '0.479' + edge_lig_CHEMBL3265006_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265006 + ligand_b: lig_CHEMBL3265033 + atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) + (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) + (27, 46) (28, 47) (29, 48) (30, 9) (49, 10) (50, 11) + score: '0.469' + edge_lig_CHEMBL3265011_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265011 + ligand_b: lig_CHEMBL3265031 + atom mapping: (0, 45) (1, 44) (2, 46) (3, 47) (4, 41) (5, 42) (6, 43) (7, 22) + (8, 20) (9, 21) (10, 19) (11, 48) (12, 49) (13, 50) (14, 51) (15, 14) (21, 15) + (27, 17) (28, 18) (29, 23) (30, 24) (49, 39) (50, 40) + score: '0.469' + edge_lig_CHEMBL3265001_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265001 + ligand_b: lig_CHEMBL3265031 + atom mapping: (0, 45) (1, 44) (2, 46) (3, 47) (4, 41) (5, 42) (6, 43) (7, 22) + (8, 20) (9, 21) (10, 19) (11, 48) (12, 49) (13, 50) (14, 51) (15, 14) (21, 15) + (27, 17) (28, 18) (29, 23) (30, 24) (60, 39) (61, 40) + score: '0.397' + edge_lig_CHEMBL3265012_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265012 + ligand_b: lig_CHEMBL3265033 + atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) + (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) + (27, 46) (28, 47) (29, 48) (30, 9) (46, 10) (47, 11) + score: '0.485' + edge_lig_CHEMBL3265002_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265002 + ligand_b: lig_CHEMBL3265031 + atom mapping: (25, 24) (26, 39) (27, 40) (28, 41) (29, 42) (30, 43) (31, 44) (32, + 45) (33, 46) (34, 47) (35, 22) (36, 20) (37, 21) (38, 19) (39, 17) (40, 18) + (41, 15) (42, 16) (43, 14) (49, 50) (55, 48) (56, 49) (57, 23) + score: '0.397' + edge_lig_CHEMBL3265013_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265013 + ligand_b: lig_CHEMBL3265033 + atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) + (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) + (27, 46) (28, 47) (29, 48) (30, 9) (49, 10) (50, 11) + score: '0.469' + edge_lig_CHEMBL3265015_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265015 + ligand_b: lig_CHEMBL3265033 + atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) + (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) + (27, 46) (28, 47) (29, 48) (30, 9) (49, 10) (50, 11) + score: '0.469' + edge_lig_CHEMBL3265008_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265008 + ligand_b: lig_CHEMBL3265033 + atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) + (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) + (27, 46) (28, 47) (29, 48) (30, 9) (46, 10) (47, 11) + score: '0.485' + edge_lig_CHEMBL3265020_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265020 + ligand_b: lig_CHEMBL3265033 + atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) + (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) + (27, 46) (28, 47) (29, 48) (30, 9) (46, 10) (47, 11) + score: '0.485' + edge_lig_CHEMBL3265000_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265000 + ligand_b: lig_CHEMBL3265031 + atom mapping: (0, 45) (1, 44) (2, 46) (3, 47) (4, 41) (5, 42) (6, 43) (7, 22) + (8, 20) (9, 21) (10, 19) (11, 48) (12, 49) (13, 50) (14, 51) (15, 14) (21, 15) + (27, 17) (28, 18) (29, 23) (30, 24) (65, 39) (66, 40) + score: '0.397' + edge_lig_CHEMBL3264998_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3264998 + ligand_b: lig_CHEMBL3265031 + atom mapping: (0, 45) (1, 44) (2, 46) (3, 47) (4, 41) (5, 42) (6, 43) (7, 22) + (8, 20) (9, 21) (10, 19) (11, 48) (12, 49) (13, 50) (14, 51) (15, 14) (21, 15) + (27, 17) (28, 18) (29, 23) (30, 24) (61, 39) (62, 40) + score: '0.402' + edge_lig_CHEMBL3265031_lig_CHEMBL3264994: + ligand_a: lig_CHEMBL3265031 + ligand_b: lig_CHEMBL3264994 + atom mapping: (14, 15) (15, 13) (16, 14) (17, 11) (18, 12) (19, 10) (20, 8) (21, + 9) (22, 7) (23, 33) (24, 34) (39, 62) (40, 63) (41, 4) (42, 5) (43, 6) (44, + 1) (45, 0) (46, 2) (47, 3) (48, 31) (49, 32) (50, 29) (51, 30) + score: '0.414' + edge_lig_CHEMBL3265010_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265010 + ligand_b: lig_CHEMBL3265033 + atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) + (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) + (27, 46) (28, 47) (29, 48) (30, 9) (50, 10) (51, 11) + score: '0.464' + edge_lig_CHEMBL3265026_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265026 + ligand_b: lig_CHEMBL3265033 + atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) + (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) + (27, 46) (28, 47) (29, 48) (30, 9) (49, 10) (50, 11) + score: '0.469' + edge_lig_CHEMBL3259820_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3259820 + ligand_b: lig_CHEMBL3265033 + atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) + (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) + (27, 46) (28, 47) (29, 48) (30, 9) (46, 10) (47, 11) + score: '0.485' + edge_lig_CHEMBL3264996_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3264996 + ligand_b: lig_CHEMBL3265031 + atom mapping: (0, 45) (1, 44) (2, 46) (3, 47) (4, 41) (5, 42) (6, 43) (7, 22) + (8, 20) (9, 21) (10, 19) (11, 48) (12, 49) (13, 50) (14, 51) (15, 14) (21, 15) + (27, 17) (28, 18) (29, 23) (30, 24) (62, 39) (63, 40) + score: '0.402' + edge_lig_CHEMBL3265031_lig_CHEMBL3264999: + ligand_a: lig_CHEMBL3265031 + ligand_b: lig_CHEMBL3264999 + atom mapping: (14, 15) (15, 13) (16, 14) (17, 11) (18, 12) (19, 10) (20, 8) (21, + 9) (22, 7) (23, 29) (24, 30) (39, 60) (40, 61) (41, 4) (42, 5) (43, 6) (44, + 1) (45, 0) (46, 2) (47, 3) (48, 27) (49, 28) (50, 21) + score: '0.404' + edge_lig_CHEMBL3265037_lig_CHEMBL3264994: + ligand_a: lig_CHEMBL3265037 + ligand_b: lig_CHEMBL3264994 + atom mapping: (9, 34) (10, 62) (11, 63) (12, 4) (13, 5) (14, 6) (15, 1) (16, 0) + (17, 2) (18, 3) (19, 7) (20, 8) (21, 9) (22, 10) (23, 11) (24, 12) (25, 13) + (26, 14) (27, 15) (42, 29) (48, 31) (49, 32) (50, 33) + score: '0.412' diff --git a/data/syk/03_edges/nohup.out b/data/syk/03_edges/nohup.out new file mode 100644 index 000000000..f2e264e0e --- /dev/null +++ b/data/syk/03_edges/nohup.out @@ -0,0 +1,25 @@ +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. +lig_CHEMBL3265001_lig_CHEMBL3265035 exceeds 1 A pairwise distance +lig_CHEMBL3265022_lig_CHEMBL3264994 exceeds 1 A pairwise distance +lig_CHEMBL3265000_lig_CHEMBL3265036 exceeds 1 A pairwise distance +lig_CHEMBL3265004_lig_CHEMBL3265031 exceeds 1 A pairwise distance +lig_CHEMBL3265016_lig_CHEMBL3264994 exceeds 1 A pairwise distance +lig_CHEMBL3264996_lig_CHEMBL3265027 exceeds 1 A pairwise distance +lig_CHEMBL3265003_lig_CHEMBL3265031 exceeds 1 A pairwise distance +lig_CHEMBL3265019_lig_CHEMBL3264994 exceeds 1 A pairwise distance +lig_CHEMBL3265001_lig_CHEMBL3265029 exceeds 1 A pairwise distance +lig_CHEMBL3265021_lig_CHEMBL3265031 exceeds 1 A pairwise distance +lig_CHEMBL3265018_lig_CHEMBL3264994 exceeds 1 A pairwise distance +lig_CHEMBL3265017_lig_CHEMBL3264994 exceeds 1 A pairwise distance +lig_CHEMBL3265002_lig_CHEMBL3265031 exceeds 1 A pairwise distance +lig_CHEMBL3265001_lig_CHEMBL3265035 exceeds 1 A pairwise distance +lig_CHEMBL3265031_lig_CHEMBL3264994 exceeds 1 A pairwise distance +lig_CHEMBL3265031_lig_CHEMBL3264999 exceeds 1 A pairwise distance diff --git a/data/thrombin/00_data/edges.yml b/data/thrombin/00_data/edges.yml deleted file mode 100644 index de4bf1c41..000000000 --- a/data/thrombin/00_data/edges.yml +++ /dev/null @@ -1,64 +0,0 @@ -edge_1a_3b: - ligand_a: lig_1a - ligand_b: lig_3b - name: edge_1a_3b -edge_1a_5: - ligand_a: lig_1a - ligand_b: lig_5 - name: edge_1a_5 -edge_1b_1a: - ligand_a: lig_1b - ligand_b: lig_1a - name: edge_1b_1a -edge_1b_1c: - ligand_a: lig_1b - ligand_b: lig_1c - name: edge_1b_1c -edge_1b_3b: - ligand_a: lig_1b - ligand_b: lig_3b - name: edge_1b_3b -edge_1b_7a: - ligand_a: lig_1b - ligand_b: lig_7a - name: edge_1b_7a -edge_1d_1a: - ligand_a: lig_1d - ligand_b: lig_1a - name: edge_1d_1a -edge_1d_1c: - ligand_a: lig_1d - ligand_b: lig_1c - name: edge_1d_1c -edge_1d_5: - ligand_a: lig_1d - ligand_b: lig_5 - name: edge_1d_5 -edge_1d_6e: - ligand_a: lig_1d - ligand_b: lig_6e - name: edge_1d_6e -edge_1d_7a: - ligand_a: lig_1d - ligand_b: lig_7a - name: edge_1d_7a -edge_3a_1b: - ligand_a: lig_3a - ligand_b: lig_1b - name: edge_3a_1b -edge_3a_1d: - ligand_a: lig_3a - ligand_b: lig_1d - name: edge_3a_1d -edge_6a_1b: - ligand_a: lig_6a - ligand_b: lig_1b - name: edge_6a_1b -edge_6a_6b: - ligand_a: lig_6a - ligand_b: lig_6b - name: edge_6a_6b -edge_6e_6b: - ligand_a: lig_6e - ligand_b: lig_6b - name: edge_6e_6b diff --git a/data/thrombin/03_edges/01_perses_openfe.yaml b/data/thrombin/03_edges/01_perses_openfe.yaml new file mode 100644 index 000000000..95274ad61 --- /dev/null +++ b/data/thrombin/03_edges/01_perses_openfe.yaml @@ -0,0 +1,94 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_7a_lig_5: + ligand_a: lig_7a + ligand_b: lig_5 + atom mapping: (1, 21) (2, 22) (3, 23) (4, 24) (5, 19) (6, 20) (7, 18) (8, 17) + (9, 15) (10, 16) (11, 14) (12, 13) (13, 12) (14, 11) (15, 10) (16, 8) (17, 9) + (18, 7) (19, 6) (20, 3) (21, 2) (22, 1) (23, 0) (24, 5) (25, 4) (26, 25) (28, + 27) (29, 26) (30, 51) (31, 29) (35, 48) (36, 49) (37, 46) (38, 45) (39, 44) + (40, 43) (41, 42) (42, 41) (43, 39) (44, 40) (45, 37) (46, 38) (47, 35) (48, + 36) (49, 32) (50, 31) (51, 30) (52, 34) (53, 33) (57, 28) + score: '0.964' + edge_lig_1d_lig_1a: + ligand_a: lig_1d + ligand_b: lig_1a + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, + 18) (19, 19) (20, 24) (21, 23) (22, 22) (23, 21) (24, 20) (26, 26) (27, 27) + (28, 28) (29, 51) (30, 30) (31, 31) (32, 32) (33, 33) (34, 34) (35, 35) (36, + 37) (37, 36) (38, 39) (39, 38) (40, 41) (41, 40) (42, 42) (43, 43) (44, 44) + (45, 46) (46, 45) (47, 50) (49, 49) (50, 47) (51, 29) + score: '0.969' + edge_lig_6a_lig_3a: + ligand_a: lig_6a + ligand_b: lig_3a + atom mapping: (0, 23) (1, 24) (2, 25) (3, 20) (4, 21) (5, 22) (6, 19) (7, 18) + (8, 16) (9, 17) (10, 15) (11, 14) (12, 13) (13, 12) (14, 11) (15, 9) (16, 10) + (17, 8) (18, 7) (19, 5) (20, 4) (21, 3) (22, 2) (23, 1) (24, 6) (27, 26) (28, + 28) (29, 27) (30, 54) (31, 30) (32, 51) (33, 52) (34, 53) (35, 49) (36, 50) + (37, 48) (38, 47) (39, 46) (40, 45) (41, 44) (42, 43) (43, 41) (44, 42) (45, + 40) (46, 39) (47, 38) (48, 36) (49, 34) (51, 29) + score: '0.951' + edge_lig_1a_lig_5: + ligand_a: lig_1a + ligand_b: lig_5 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, + 18) (19, 19) (20, 24) (21, 23) (22, 22) (23, 21) (24, 20) (26, 25) (27, 26) + (28, 27) (29, 51) (30, 29) (31, 30) (32, 31) (33, 32) (34, 33) (35, 34) (36, + 36) (37, 35) (38, 38) (39, 37) (40, 40) (41, 39) (42, 41) (43, 42) (44, 43) + (45, 45) (46, 44) (47, 50) (48, 49) (49, 48) (50, 46) (51, 28) + score: '0.982' + edge_lig_1b_lig_1a: + ligand_a: lig_1b + ligand_b: lig_1a + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, + 18) (19, 19) (20, 24) (21, 23) (22, 22) (23, 21) (24, 20) (26, 26) (27, 27) + (28, 28) (29, 51) (30, 30) (31, 31) (32, 32) (33, 33) (34, 34) (35, 35) (36, + 37) (37, 36) (38, 39) (39, 38) (40, 41) (41, 40) (42, 42) (43, 43) (44, 44) + (45, 46) (46, 45) (47, 50) (49, 49) (50, 47) (51, 29) + score: '0.969' + edge_lig_6a_lig_5: + ligand_a: lig_6a + ligand_b: lig_5 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, + 18) (19, 19) (20, 24) (21, 23) (22, 22) (23, 21) (24, 20) (27, 25) (28, 26) + (29, 27) (30, 51) (31, 29) (32, 30) (33, 31) (34, 32) (35, 33) (36, 34) (37, + 36) (38, 35) (39, 38) (40, 37) (41, 40) (42, 39) (43, 41) (44, 42) (45, 43) + (46, 45) (47, 44) (48, 50) (49, 48) (50, 47) (51, 28) + score: '0.964' + edge_lig_1c_lig_1a: + ligand_a: lig_1c + ligand_b: lig_1a + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, + 18) (19, 19) (20, 24) (21, 23) (22, 22) (23, 21) (24, 20) (26, 26) (27, 27) + (28, 28) (29, 51) (30, 30) (31, 31) (32, 32) (33, 33) (34, 34) (35, 35) (36, + 37) (37, 36) (38, 39) (39, 38) (40, 41) (41, 40) (42, 42) (43, 43) (44, 44) + (45, 46) (46, 45) (47, 50) (49, 49) (50, 47) (51, 29) + score: '0.969' + edge_lig_6b_lig_3a: + ligand_a: lig_6b + ligand_b: lig_3a + atom mapping: (1, 4) (2, 3) (3, 2) (4, 1) (5, 6) (6, 5) (7, 7) (8, 8) (9, 9) (10, + 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, 18) + (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 24) (25, 25) (26, 26) (27, + 0) (28, 27) (29, 28) (30, 29) (31, 30) (35, 35) (36, 34) (37, 37) (38, 38) (39, + 39) (40, 40) (41, 41) (42, 42) (43, 44) (44, 43) (45, 46) (46, 45) (47, 48) + (48, 47) (49, 49) (50, 50) (51, 51) (52, 52) (53, 53) (54, 54) + score: '0.947' + edge_lig_6a_lig_6e: + ligand_a: lig_6a + ligand_b: lig_6e + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, + 18) (19, 19) (20, 24) (21, 23) (22, 22) (23, 21) (24, 20) (27, 27) (28, 28) + (29, 29) (30, 51) (31, 31) (32, 32) (33, 33) (34, 34) (35, 35) (36, 36) (37, + 38) (38, 37) (39, 40) (40, 39) (41, 42) (42, 41) (43, 43) (44, 44) (45, 45) + (46, 47) (47, 46) (49, 49) (51, 30) + score: '0.939' diff --git a/data/thrombin/03_edges/nohup.out b/data/thrombin/03_edges/nohup.out new file mode 100644 index 000000000..4a27c7426 --- /dev/null +++ b/data/thrombin/03_edges/nohup.out @@ -0,0 +1,18 @@ +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. +lig_7a_lig_5 exceeds 1 A pairwise distance +lig_1d_lig_1a exceeds 1 A pairwise distance +lig_6a_lig_3a exceeds 1 A pairwise distance +lig_1a_lig_5 exceeds 1 A pairwise distance +lig_1b_lig_1a exceeds 1 A pairwise distance +lig_6a_lig_5 exceeds 1 A pairwise distance +lig_1c_lig_1a exceeds 1 A pairwise distance +lig_6b_lig_3a exceeds 1 A pairwise distance +lig_6a_lig_6e exceeds 1 A pairwise distance diff --git a/data/tnks2/00_data/edges.yml b/data/tnks2/00_data/edges.yml deleted file mode 100644 index f9eeda3ab..000000000 --- a/data/tnks2/00_data/edges.yml +++ /dev/null @@ -1,240 +0,0 @@ -edge_1a_5d: - ligand_a: lig_1a - ligand_b: lig_5d - name: edge_1a_5d -edge_1b_1a: - ligand_a: lig_1b - ligand_b: lig_1a - name: edge_1b_1a -edge_1b_5c: - ligand_a: lig_1b - ligand_b: lig_5c - name: edge_1b_5c -edge_1b_5d: - ligand_a: lig_1b - ligand_b: lig_5d - name: edge_1b_5d -edge_1b_5h: - ligand_a: lig_1b - ligand_b: lig_5h - name: edge_1b_5h -edge_1b_5n: - ligand_a: lig_1b - ligand_b: lig_5n - name: edge_1b_5n -edge_3a_3b: - ligand_a: lig_3a - ligand_b: lig_3b - name: edge_3a_3b -edge_3a_5m: - ligand_a: lig_3a - ligand_b: lig_5m - name: edge_3a_5m -edge_3a_7: - ligand_a: lig_3a - ligand_b: lig_7 - name: edge_3a_7 -edge_5a_5c: - ligand_a: lig_5a - ligand_b: lig_5c - name: edge_5a_5c -edge_5a_5d: - ligand_a: lig_5a - ligand_b: lig_5d - name: edge_5a_5d -edge_5a_5j: - ligand_a: lig_5a - ligand_b: lig_5j - name: edge_5a_5j -edge_5a_5k: - ligand_a: lig_5a - ligand_b: lig_5k - name: edge_5a_5k -edge_5a_5n: - ligand_a: lig_5a - ligand_b: lig_5n - name: edge_5a_5n -edge_5b_5c: - ligand_a: lig_5b - ligand_b: lig_5c - name: edge_5b_5c -edge_5b_5j: - ligand_a: lig_5b - ligand_b: lig_5j - name: edge_5b_5j -edge_5b_5n: - ligand_a: lig_5b - ligand_b: lig_5n - name: edge_5b_5n -edge_5b_5o: - ligand_a: lig_5b - ligand_b: lig_5o - name: edge_5b_5o -edge_5d_5m: - ligand_a: lig_5d - ligand_b: lig_5m - name: edge_5d_5m -edge_5e_5a: - ligand_a: lig_5e - ligand_b: lig_5a - name: edge_5e_5a -edge_5e_5h: - ligand_a: lig_5e - ligand_b: lig_5h - name: edge_5e_5h -edge_5e_5i: - ligand_a: lig_5e - ligand_b: lig_5i - name: edge_5e_5i -edge_5e_5k: - ligand_a: lig_5e - ligand_b: lig_5k - name: edge_5e_5k -edge_5e_5n: - ligand_a: lig_5e - ligand_b: lig_5n - name: edge_5e_5n -edge_5e_5p: - ligand_a: lig_5e - ligand_b: lig_5p - name: edge_5e_5p -edge_5f_5a: - ligand_a: lig_5f - ligand_b: lig_5a - name: edge_5f_5a -edge_5f_5i: - ligand_a: lig_5f - ligand_b: lig_5i - name: edge_5f_5i -edge_5f_5l: - ligand_a: lig_5f - ligand_b: lig_5l - name: edge_5f_5l -edge_5g_5a: - ligand_a: lig_5g - ligand_b: lig_5a - name: edge_5g_5a -edge_5g_5b: - ligand_a: lig_5g - ligand_b: lig_5b - name: edge_5g_5b -edge_5g_5d: - ligand_a: lig_5g - ligand_b: lig_5d - name: edge_5g_5d -edge_5g_5h: - ligand_a: lig_5g - ligand_b: lig_5h - name: edge_5g_5h -edge_5h_5m: - ligand_a: lig_5h - ligand_b: lig_5m - name: edge_5h_5m -edge_5i_5a: - ligand_a: lig_5i - ligand_b: lig_5a - name: edge_5i_5a -edge_5i_5m: - ligand_a: lig_5i - ligand_b: lig_5m - name: edge_5i_5m -edge_5i_5o: - ligand_a: lig_5i - ligand_b: lig_5o - name: edge_5i_5o -edge_5k_5d: - ligand_a: lig_5k - ligand_b: lig_5d - name: edge_5k_5d -edge_5l_5e: - ligand_a: lig_5l - ligand_b: lig_5e - name: edge_5l_5e -edge_5l_5j: - ligand_a: lig_5l - ligand_b: lig_5j - name: edge_5l_5j -edge_5l_5p: - ligand_a: lig_5l - ligand_b: lig_5p - name: edge_5l_5p -edge_5o_5m: - ligand_a: lig_5o - ligand_b: lig_5m - name: edge_5o_5m -edge_5p_5n: - ligand_a: lig_5p - ligand_b: lig_5n - name: edge_5p_5n -edge_7_3b: - ligand_a: lig_7 - ligand_b: lig_3b - name: edge_7_3b -edge_7_5d: - ligand_a: lig_7 - ligand_b: lig_5d - name: edge_7_5d -edge_7_5j: - ligand_a: lig_7 - ligand_b: lig_5j - name: edge_7_5j -edge_7_8a: - ligand_a: lig_7 - ligand_b: lig_8a - name: edge_7_8a -edge_8a_5d: - ligand_a: lig_8a - ligand_b: lig_5d - name: edge_8a_5d -edge_8b_8a: - ligand_a: lig_8b - ligand_b: lig_8a - name: edge_8b_8a -edge_8b_8d: - ligand_a: lig_8b - ligand_b: lig_8d - name: edge_8b_8d -edge_8b_8f: - ligand_a: lig_8b - ligand_b: lig_8f - name: edge_8b_8f -edge_8c_5k: - ligand_a: lig_8c - ligand_b: lig_5k - name: edge_8c_5k -edge_8d_1a: - ligand_a: lig_8d - ligand_b: lig_1a - name: edge_8d_1a -edge_8d_8c: - ligand_a: lig_8d - ligand_b: lig_8c - name: edge_8d_8c -edge_8d_8f: - ligand_a: lig_8d - ligand_b: lig_8f - name: edge_8d_8f -edge_8e_5k: - ligand_a: lig_8e - ligand_b: lig_5k - name: edge_8e_5k -edge_8e_8a: - ligand_a: lig_8e - ligand_b: lig_8a - name: edge_8e_8a -edge_8e_8b: - ligand_a: lig_8e - ligand_b: lig_8b - name: edge_8e_8b -edge_8e_8c: - ligand_a: lig_8e - ligand_b: lig_8c - name: edge_8e_8c -edge_8f_5m: - ligand_a: lig_8f - ligand_b: lig_5m - name: edge_8f_5m -edge_8f_8a: - ligand_a: lig_8f - ligand_b: lig_8a - name: edge_8f_8a diff --git a/data/tnks2/03_edges/01_perses_openfe.yaml b/data/tnks2/03_edges/01_perses_openfe.yaml new file mode 100644 index 000000000..c55810359 --- /dev/null +++ b/data/tnks2/03_edges/01_perses_openfe.yaml @@ -0,0 +1,180 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_5i_lig_8a: + ligand_a: lig_5i + ligand_b: lig_8a + atom mapping: (3, 20) (4, 18) (5, 19) (6, 16) (7, 17) (8, 15) (9, 14) (10, 43) + (11, 4) (12, 5) (13, 6) (14, 7) (15, 8) (17, 1) (18, 0) (19, 2) (24, 10) (25, + 11) (26, 12) (27, 13) (28, 41) (29, 42) (30, 39) (31, 40) + score: '0.684' + edge_lig_1a_lig_8b: + ligand_a: lig_1a + ligand_b: lig_8b + atom mapping: (1, 4) (2, 23) (3, 24) (4, 25) (5, 26) (6, 27) (7, 28) (8, 29) (9, + 30) (10, 38) (12, 36) (13, 37) (14, 34) (16, 32) (17, 33) (18, 31) (19, 43) + (20, 44) (21, 45) (22, 46) (23, 1) (24, 0) (25, 2) (26, 3) + score: '0.830' + edge_lig_5p_lig_8f: + ligand_a: lig_5p + ligand_b: lig_8f + atom mapping: (0, 38) (1, 37) (2, 39) (4, 31) (5, 32) (6, 33) (7, 34) (8, 35) + (9, 36) (10, 44) (11, 45) (12, 46) (13, 47) (14, 29) (15, 28) (16, 1) (17, 0) + (18, 2) (19, 3) (20, 4) (42, 24) (43, 25) (44, 26) (45, 27) (46, 30) + score: '0.638' + edge_lig_5f_lig_8a: + ligand_a: lig_5f + ligand_b: lig_8a + atom mapping: (3, 20) (4, 18) (5, 19) (6, 16) (7, 17) (8, 15) (9, 14) (10, 43) + (11, 4) (12, 2) (14, 1) (15, 0) (16, 8) (18, 6) (19, 7) (20, 5) (21, 10) (22, + 11) (23, 12) (24, 13) (25, 41) (26, 42) (27, 39) (28, 40) + score: '0.714' + edge_lig_5o_lig_8a: + ligand_a: lig_5o + ligand_b: lig_8a + atom mapping: (10, 20) (11, 18) (12, 19) (13, 16) (14, 17) (15, 15) (16, 14) (17, + 43) (18, 4) (19, 5) (20, 6) (21, 7) (22, 8) (23, 9) (24, 1) (25, 0) (26, 2) + (31, 10) (32, 11) (33, 12) (34, 13) (35, 41) (36, 42) (37, 39) (38, 40) + score: '0.654' + edge_lig_5k_lig_8a: + ligand_a: lig_5k + ligand_b: lig_8a + atom mapping: (3, 20) (4, 18) (5, 19) (6, 16) (7, 17) (8, 15) (9, 14) (10, 43) + (11, 4) (12, 2) (14, 1) (15, 0) (16, 8) (17, 9) (18, 6) (19, 7) (20, 5) (21, + 10) (22, 11) (23, 12) (24, 13) (25, 41) (26, 42) (27, 39) (28, 40) + score: '0.736' + edge_lig_8d_lig_5p: + ligand_a: lig_8d + ligand_b: lig_5p + atom mapping: (0, 17) (1, 16) (2, 18) (3, 19) (4, 20) (21, 42) (22, 43) (23, 44) + (24, 45) (25, 15) (26, 14) (27, 46) (28, 4) (29, 5) (30, 6) (31, 7) (32, 8) + (33, 9) (34, 1) (35, 0) (36, 2) (41, 10) (42, 11) (43, 12) (44, 13) + score: '0.646' + edge_lig_5h_lig_8a: + ligand_a: lig_5h + ligand_b: lig_8a + atom mapping: (3, 20) (4, 18) (5, 19) (6, 16) (7, 17) (8, 15) (9, 14) (10, 43) + (11, 4) (12, 2) (18, 1) (19, 0) (20, 8) (22, 6) (23, 7) (24, 5) (25, 10) (26, + 11) (27, 12) (28, 13) (29, 41) (30, 42) (31, 39) (32, 40) + score: '0.675' + edge_lig_5d_lig_8e: + ligand_a: lig_5d + ligand_b: lig_8e + atom mapping: (3, 17) (4, 15) (5, 16) (6, 13) (7, 14) (8, 12) (9, 11) (10, 10) + (11, 7) (12, 8) (14, 1) (15, 0) (16, 2) (17, 3) (18, 4) (19, 5) (20, 6) (21, + 43) (22, 44) (23, 41) (24, 42) (25, 39) (26, 40) (27, 37) (28, 38) + score: '0.731' + edge_lig_8e_lig_7: + ligand_a: lig_8e + ligand_b: lig_7 + atom mapping: (0, 14) (1, 13) (2, 15) (3, 16) (4, 17) (5, 18) (6, 19) (7, 10) + (8, 11) (10, 9) (11, 8) (12, 7) (13, 6) (15, 4) (16, 5) (17, 3) (37, 25) (38, + 26) (39, 23) (40, 24) (41, 22) (43, 20) (44, 21) + score: '0.723' + edge_lig_5o_lig_8e: + ligand_a: lig_5o + ligand_b: lig_8e + atom mapping: (10, 17) (11, 15) (12, 16) (13, 13) (14, 14) (15, 12) (16, 11) (17, + 10) (18, 7) (19, 6) (20, 4) (21, 5) (22, 2) (23, 3) (24, 1) (25, 0) (26, 8) + (27, 9) (31, 43) (32, 44) (33, 41) (34, 42) (35, 39) (36, 40) (37, 37) (38, + 38) + score: '0.665' + edge_lig_5a_lig_8e: + ligand_a: lig_5a + ligand_b: lig_8e + atom mapping: (3, 17) (4, 15) (5, 16) (6, 13) (7, 14) (8, 12) (9, 11) (10, 10) + (11, 7) (12, 8) (14, 1) (15, 0) (16, 2) (18, 4) (19, 5) (20, 6) (21, 43) (22, + 44) (23, 41) (24, 42) (25, 39) (26, 40) (27, 37) (28, 38) + score: '0.709' + edge_lig_3a_lig_8e: + ligand_a: lig_3a + ligand_b: lig_8e + atom mapping: (0, 0) (1, 1) (2, 2) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (10, 10) + (11, 11) (12, 12) (13, 39) (14, 40) (15, 37) (16, 38) (17, 17) (31, 15) (32, + 16) (33, 13) (34, 14) (35, 41) (36, 42) (37, 43) (38, 44) + score: '0.689' + edge_lig_5n_lig_8e: + ligand_a: lig_5n + ligand_b: lig_8e + atom mapping: (10, 17) (11, 15) (12, 16) (13, 13) (14, 14) (15, 12) (16, 11) (17, + 10) (18, 7) (19, 8) (21, 1) (22, 0) (23, 2) (24, 3) (25, 4) (26, 5) (27, 6) + (28, 43) (29, 44) (30, 41) (31, 42) (32, 39) (33, 40) (34, 37) (35, 38) + score: '0.663' + edge_lig_5p_lig_8e: + ligand_a: lig_5p + ligand_b: lig_8e + atom mapping: (0, 0) (1, 1) (2, 8) (4, 7) (5, 6) (6, 4) (7, 5) (8, 2) (9, 3) (10, + 43) (11, 44) (12, 41) (13, 42) (14, 11) (15, 12) (16, 39) (17, 40) (18, 37) + (19, 38) (20, 17) (42, 15) (43, 16) (44, 13) (45, 14) (46, 10) + score: '0.646' + edge_lig_5c_lig_8e: + ligand_a: lig_5c + ligand_b: lig_8e + atom mapping: (3, 17) (4, 15) (5, 16) (6, 13) (7, 14) (8, 12) (9, 11) (10, 10) + (11, 7) (12, 8) (14, 1) (15, 0) (16, 2) (18, 4) (20, 6) (21, 43) (22, 44) (23, + 41) (24, 42) (25, 39) (26, 40) (27, 37) (28, 38) + score: '0.694' + edge_lig_8e_lig_1b: + ligand_a: lig_8e + ligand_b: lig_1b + atom mapping: (0, 0) (1, 1) (2, 2) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (10, 10) + (11, 11) (12, 12) (13, 25) (14, 26) (15, 23) (16, 24) (17, 17) (37, 15) (38, + 16) (39, 13) (40, 14) (41, 27) (42, 28) (43, 29) (44, 30) + score: '0.777' + edge_lig_5m_lig_8a: + ligand_a: lig_5m + ligand_b: lig_8a + atom mapping: (3, 20) (4, 18) (5, 19) (6, 16) (7, 17) (8, 15) (9, 14) (10, 43) + (11, 4) (12, 5) (13, 6) (14, 7) (15, 8) (16, 9) (17, 1) (18, 0) (19, 2) (24, + 10) (25, 11) (26, 12) (27, 13) (28, 41) (29, 42) (30, 39) (31, 40) + score: '0.705' + edge_lig_8c_lig_5p: + ligand_a: lig_8c + ligand_b: lig_5p + atom mapping: (0, 0) (1, 1) (2, 8) (3, 9) (4, 6) (5, 7) (6, 5) (7, 4) (8, 2) (10, + 46) (11, 14) (12, 15) (13, 44) (14, 45) (15, 42) (16, 43) (17, 20) (34, 18) + (35, 19) (36, 16) (37, 17) (38, 12) (39, 13) (40, 10) (41, 11) + score: '0.672' + edge_lig_5l_lig_8a: + ligand_a: lig_5l + ligand_b: lig_8a + atom mapping: (3, 20) (4, 18) (5, 19) (6, 16) (7, 17) (8, 15) (9, 14) (10, 43) + (11, 4) (12, 2) (14, 1) (15, 0) (16, 8) (18, 6) (20, 5) (21, 10) (22, 11) (23, + 12) (24, 13) (25, 41) (26, 42) (27, 39) (28, 40) + score: '0.700' + edge_lig_5j_lig_8e: + ligand_a: lig_5j + ligand_b: lig_8e + atom mapping: (3, 17) (4, 15) (5, 16) (6, 13) (7, 14) (8, 12) (9, 11) (10, 10) + (11, 7) (12, 8) (14, 1) (15, 0) (16, 2) (17, 3) (18, 4) (20, 6) (21, 43) (22, + 44) (23, 41) (24, 42) (25, 39) (26, 40) (27, 37) (28, 38) + score: '0.716' + edge_lig_5p_lig_8b: + ligand_a: lig_5p + ligand_b: lig_8b + atom mapping: (0, 37) (1, 36) (2, 38) (4, 30) (5, 31) (6, 32) (7, 33) (8, 34) + (9, 35) (10, 43) (11, 44) (12, 45) (13, 46) (14, 28) (15, 27) (16, 1) (17, 0) + (18, 2) (19, 3) (20, 4) (42, 23) (43, 24) (44, 25) (45, 26) (46, 29) + score: '0.638' + edge_lig_5g_lig_8a: + ligand_a: lig_5g + ligand_b: lig_8a + atom mapping: (3, 20) (4, 18) (5, 19) (6, 16) (7, 17) (8, 15) (9, 14) (10, 43) + (11, 4) (12, 2) (14, 1) (15, 0) (16, 8) (18, 6) (19, 7) (20, 5) (21, 10) (22, + 11) (23, 12) (24, 13) (25, 41) (26, 42) (27, 39) (28, 40) + score: '0.714' + edge_lig_5b_lig_8e: + ligand_a: lig_5b + ligand_b: lig_8e + atom mapping: (3, 17) (4, 15) (5, 16) (6, 13) (7, 14) (8, 12) (9, 11) (10, 10) + (11, 7) (12, 8) (14, 1) (15, 0) (16, 2) (18, 4) (20, 6) (21, 43) (22, 44) (23, + 41) (24, 42) (25, 39) (26, 40) (27, 37) (28, 38) + score: '0.694' + edge_lig_3b_lig_8e: + ligand_a: lig_3b + ligand_b: lig_8e + atom mapping: (0, 0) (1, 1) (2, 8) (4, 7) (5, 6) (6, 4) (7, 5) (8, 2) (9, 3) (10, + 43) (11, 44) (12, 41) (13, 42) (14, 11) (15, 12) (16, 39) (17, 40) (18, 37) + (19, 38) (20, 17) (34, 15) (35, 16) (36, 13) (37, 14) (38, 10) + score: '0.710' diff --git a/data/tnks2/03_edges/nohup.out b/data/tnks2/03_edges/nohup.out new file mode 100644 index 000000000..8d0a105fb --- /dev/null +++ b/data/tnks2/03_edges/nohup.out @@ -0,0 +1,22 @@ +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. +lig_5f_lig_8a exceeds 1 A pairwise distance +lig_5o_lig_8a exceeds 1 A pairwise distance +lig_5k_lig_8a exceeds 1 A pairwise distance +lig_8d_lig_5p exceeds 1 A pairwise distance +lig_5h_lig_8a exceeds 1 A pairwise distance +lig_5d_lig_8e exceeds 1 A pairwise distance +lig_8e_lig_7 exceeds 1 A pairwise distance +lig_5a_lig_8e exceeds 1 A pairwise distance +lig_3a_lig_8e exceeds 1 A pairwise distance +lig_5c_lig_8e exceeds 1 A pairwise distance +lig_5m_lig_8a exceeds 1 A pairwise distance +lig_8c_lig_5p exceeds 1 A pairwise distance +lig_5p_lig_8b exceeds 1 A pairwise distance diff --git a/data/tyk2/00_data/edges.yml b/data/tyk2/00_data/edges.yml deleted file mode 100644 index 5b77ac0d1..000000000 --- a/data/tyk2/00_data/edges.yml +++ /dev/null @@ -1,96 +0,0 @@ -edge_ejm_31_ejm_43: - ligand_a: lig_ejm_31 - ligand_b: lig_ejm_43 - name: edge_ejm_31_ejm_43 -edge_ejm_31_ejm_45: - ligand_a: lig_ejm_31 - ligand_b: lig_ejm_45 - name: edge_ejm_31_ejm_45 -edge_ejm_31_ejm_46: - ligand_a: lig_ejm_31 - ligand_b: lig_ejm_46 - name: edge_ejm_31_ejm_46 -edge_ejm_31_ejm_48: - ligand_a: lig_ejm_31 - ligand_b: lig_ejm_48 - name: edge_ejm_31_ejm_48 -edge_ejm_31_jmc_28: - ligand_a: lig_ejm_31 - ligand_b: lig_jmc_28 - name: edge_ejm_31_jmc_28 -edge_ejm_42_ejm_48: - ligand_a: lig_ejm_42 - ligand_b: lig_ejm_48 - name: edge_ejm_42_ejm_48 -edge_ejm_42_ejm_54: - ligand_a: lig_ejm_42 - ligand_b: lig_ejm_54 - name: edge_ejm_42_ejm_54 -edge_ejm_42_ejm_55: - ligand_a: lig_ejm_42 - ligand_b: lig_ejm_55 - name: edge_ejm_42_ejm_55 -edge_ejm_43_ejm_55: - ligand_a: lig_ejm_43 - ligand_b: lig_ejm_55 - name: edge_ejm_43_ejm_55 -edge_ejm_44_ejm_42: - ligand_a: lig_ejm_44 - ligand_b: lig_ejm_42 - name: edge_ejm_44_ejm_42 -edge_ejm_44_ejm_55: - ligand_a: lig_ejm_44 - ligand_b: lig_ejm_55 - name: edge_ejm_44_ejm_55 -edge_ejm_45_ejm_42: - ligand_a: lig_ejm_45 - ligand_b: lig_ejm_42 - name: edge_ejm_45_ejm_42 -edge_ejm_47_ejm_31: - ligand_a: lig_ejm_47 - ligand_b: lig_ejm_31 - name: edge_ejm_47_ejm_31 -edge_ejm_47_ejm_55: - ligand_a: lig_ejm_47 - ligand_b: lig_ejm_55 - name: edge_ejm_47_ejm_55 -edge_ejm_49_ejm_31: - ligand_a: lig_ejm_49 - ligand_b: lig_ejm_31 - name: edge_ejm_49_ejm_31 -edge_ejm_49_ejm_50: - ligand_a: lig_ejm_49 - ligand_b: lig_ejm_50 - name: edge_ejm_49_ejm_50 -edge_ejm_50_ejm_42: - ligand_a: lig_ejm_50 - ligand_b: lig_ejm_42 - name: edge_ejm_50_ejm_42 -edge_ejm_55_ejm_54: - ligand_a: lig_ejm_55 - ligand_b: lig_ejm_54 - name: edge_ejm_55_ejm_54 -edge_jmc_23_ejm_46: - ligand_a: lig_jmc_23 - ligand_b: lig_ejm_46 - name: edge_jmc_23_ejm_46 -edge_jmc_23_ejm_55: - ligand_a: lig_jmc_23 - ligand_b: lig_ejm_55 - name: edge_jmc_23_ejm_55 -edge_jmc_23_jmc_27: - ligand_a: lig_jmc_23 - ligand_b: lig_jmc_27 - name: edge_jmc_23_jmc_27 -edge_jmc_23_jmc_30: - ligand_a: lig_jmc_23 - ligand_b: lig_jmc_30 - name: edge_jmc_23_jmc_30 -edge_jmc_28_jmc_27: - ligand_a: lig_jmc_28 - ligand_b: lig_jmc_27 - name: edge_jmc_28_jmc_27 -edge_jmc_28_jmc_30: - ligand_a: lig_jmc_28 - ligand_b: lig_jmc_30 - name: edge_jmc_28_jmc_30 diff --git a/data/tyk2/03_edges/01_perses_openfe.yaml b/data/tyk2/03_edges/01_perses_openfe.yaml new file mode 100644 index 000000000..d0e0d70da --- /dev/null +++ b/data/tyk2/03_edges/01_perses_openfe.yaml @@ -0,0 +1,108 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_ejm_47_lig_ejm_48: + ligand_a: lig_ejm_47 + ligand_b: lig_ejm_48 + atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 41) (8, 40) + (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) + (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (35, 38) (36, 39) (37, + 8) (38, 7) + score: '0.772' + edge_lig_jmc_23_lig_ejm_48: + ligand_a: lig_jmc_23 + ligand_b: lig_ejm_48 + atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 41) (8, 40) + (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) + (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (32, 38) (33, 39) (34, + 8) (35, 7) + score: '0.807' + edge_lig_jmc_27_lig_ejm_48: + ligand_a: lig_jmc_27 + ligand_b: lig_ejm_48 + atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 41) (8, 40) + (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) + (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (32, 38) (33, 39) (34, + 8) (35, 7) + score: '0.807' + edge_lig_ejm_54_lig_ejm_48: + ligand_a: lig_ejm_54 + ligand_b: lig_ejm_48 + atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 41) (8, 40) + (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) + (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (33, 38) (34, 39) (35, + 8) (36, 7) + score: '0.795' + edge_lig_ejm_48_lig_ejm_43: + ligand_a: lig_ejm_48 + ligand_b: lig_ejm_43 + atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 37) (8, 36) + (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) + (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (38, 34) (39, 35) (40, + 8) (41, 7) + score: '0.783' + edge_lig_ejm_45_lig_ejm_48: + ligand_a: lig_ejm_45 + ligand_b: lig_ejm_48 + atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 41) (8, 40) + (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) + (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (35, 38) (36, 39) (37, + 8) (38, 7) + score: '0.772' + edge_lig_jmc_28_lig_ejm_48: + ligand_a: lig_jmc_28 + ligand_b: lig_ejm_48 + atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 41) (8, 40) + (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) + (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (35, 38) (36, 39) (37, + 8) (38, 7) + score: '0.772' + edge_lig_ejm_50_lig_ejm_48: + ligand_a: lig_ejm_50 + ligand_b: lig_ejm_48 + atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 41) (8, 40) + (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) + (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (29, 38) (30, 39) (31, + 8) (32, 7) + score: '0.847' + edge_lig_ejm_55_lig_ejm_48: + ligand_a: lig_ejm_55 + ligand_b: lig_ejm_48 + atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 41) (8, 40) + (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) + (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (29, 38) (30, 39) (31, + 8) (32, 7) + score: '0.847' + edge_lig_ejm_31_lig_ejm_48: + ligand_a: lig_ejm_31 + ligand_b: lig_ejm_48 + atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 41) (8, 40) + (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) + (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (28, 38) (29, 39) (30, + 8) (31, 7) + score: '0.860' + edge_lig_ejm_46_lig_ejm_48: + ligand_a: lig_ejm_46 + ligand_b: lig_ejm_48 + atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 41) (8, 40) + (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) + (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (32, 38) (33, 39) (34, + 8) (35, 7) + score: '0.807' + edge_lig_jmc_30_lig_ejm_48: + ligand_a: lig_jmc_30 + ligand_b: lig_ejm_48 + atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, + 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, + 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (33, 38) (34, 39) (35, 40) + (36, 41) + score: '0.795' + edge_lig_ejm_42_lig_ejm_48: + ligand_a: lig_ejm_42 + ligand_b: lig_ejm_48 + atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 41) (8, 40) + (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) + (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (31, 38) (32, 39) (33, + 8) (34, 7) + score: '0.820' diff --git a/data/tyk2/03_edges/nohup.out b/data/tyk2/03_edges/nohup.out new file mode 100644 index 000000000..b170ed64c --- /dev/null +++ b/data/tyk2/03_edges/nohup.out @@ -0,0 +1,21 @@ +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. + setattr(self, word, getattr(machar, word).flat[0]) +/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. + return self._float_to_str(self.smallest_subnormal) +WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. +lig_ejm_47_lig_ejm_48 exceeds 1 A pairwise distance +lig_jmc_23_lig_ejm_48 exceeds 1 A pairwise distance +lig_jmc_27_lig_ejm_48 exceeds 1 A pairwise distance +lig_ejm_54_lig_ejm_48 exceeds 1 A pairwise distance +lig_ejm_45_lig_ejm_48 exceeds 1 A pairwise distance +lig_jmc_28_lig_ejm_48 exceeds 1 A pairwise distance +lig_ejm_50_lig_ejm_48 exceeds 1 A pairwise distance +lig_ejm_55_lig_ejm_48 exceeds 1 A pairwise distance +lig_ejm_31_lig_ejm_48 exceeds 1 A pairwise distance +lig_ejm_46_lig_ejm_48 exceeds 1 A pairwise distance +lig_jmc_30_lig_ejm_48 exceeds 1 A pairwise distance +lig_ejm_42_lig_ejm_48 exceeds 1 A pairwise distance From d9147822322181400ed44e7b427efb93340ba9fb Mon Sep 17 00:00:00 2001 From: Irfan Date: Tue, 8 Nov 2022 20:47:49 +0000 Subject: [PATCH 3/6] Updated yaml files, should roundtrip properly --- data/cdk2/03_edges/01_perses_openfe.yaml | 76 ----- data/cdk2/03_edges/01_perses_openfe.yml | 76 +++++ data/cdk8/03_edges/01_perses_openfe.yaml | 210 ------------- data/cdk8/03_edges/01_perses_openfe.yml | 190 +++++++++++ data/cdk8/03_edges/nohup.out | 26 -- data/cmet/03_edges/01_perses_openfe.yaml | 28 -- data/cmet/03_edges/01_perses_openfe.yml | 28 ++ data/cmet/03_edges/nohup.out | 12 - data/eg5/03_edges/01_perses_openfe.yml | 203 ++++++++++++ data/eg5/03_edges/nohup.out | 9 - data/hif2a/03_edges/01_perses_openfe.yaml | 210 ------------- data/hif2a/03_edges/01_perses_openfe.yml | 210 +++++++++++++ data/hif2a/03_edges/nohup.out | 36 --- data/mcl1/03_edges/01_perses_openfe.yaml | 180 ----------- data/mcl1/03_edges/01_perses_openfe.yml | 172 ++++++++++ data/mcl1/03_edges/nohup.out | 31 -- data/p38/03_edges/01_perses_openfe.yaml | 225 ------------- data/p38/03_edges/01_perses_openfe.yml | 207 ++++++++++++ data/p38/03_edges/nohup.out | 39 --- data/pde2/03_edges/01_perses_openfe.yaml | 202 ------------ data/pde2/03_edges/01_perses_openfe.yml | 184 +++++++++++ data/pde2/03_edges/nohup.out | 29 -- data/pfkfb3/03_edges/01_perses_openfe.yaml | 279 ----------------- data/pfkfb3/03_edges/01_perses_openfe.yml | 273 ++++++++++++++++ data/pfkfb3/03_edges/nohup.out | 45 --- data/ptp1b/03_edges/01_perses_openfe.yaml | 172 ---------- data/ptp1b/03_edges/01_perses_openfe.yml | 151 +++++++++ data/ptp1b/03_edges/nohup.out | 24 -- data/shp2/03_edges/01_perses_openfe.yaml | 153 --------- data/shp2/03_edges/01_perses_openfe.yml | 151 +++++++++ data/shp2/03_edges/nohup.out | 29 -- data/syk/03_edges/01_perses_openfe.yaml | 312 ------------------- data/syk/03_edges/01_perses_openfe.yml | 305 ++++++++++++++++++ data/syk/03_edges/nohup.out | 25 -- data/thrombin/03_edges/01_perses_openfe.yaml | 94 ------ data/thrombin/03_edges/01_perses_openfe.yml | 85 +++++ data/thrombin/03_edges/nohup.out | 18 -- data/tnks2/03_edges/01_perses_openfe.yaml | 180 ----------- data/tnks2/03_edges/01_perses_openfe.yml | 179 +++++++++++ data/tnks2/03_edges/nohup.out | 22 -- data/tyk2/03_edges/01_perses_openfe.yaml | 108 ------- data/tyk2/03_edges/01_perses_openfe.yml | 95 ++++++ data/tyk2/03_edges/nohup.out | 21 -- preparation/mappers/perses-mapper.py | 11 +- 44 files changed, 2515 insertions(+), 2800 deletions(-) delete mode 100644 data/cdk2/03_edges/01_perses_openfe.yaml create mode 100644 data/cdk2/03_edges/01_perses_openfe.yml delete mode 100644 data/cdk8/03_edges/01_perses_openfe.yaml create mode 100644 data/cdk8/03_edges/01_perses_openfe.yml delete mode 100644 data/cdk8/03_edges/nohup.out delete mode 100644 data/cmet/03_edges/01_perses_openfe.yaml create mode 100644 data/cmet/03_edges/01_perses_openfe.yml delete mode 100644 data/cmet/03_edges/nohup.out create mode 100644 data/eg5/03_edges/01_perses_openfe.yml delete mode 100644 data/eg5/03_edges/nohup.out delete mode 100644 data/hif2a/03_edges/01_perses_openfe.yaml create mode 100644 data/hif2a/03_edges/01_perses_openfe.yml delete mode 100644 data/hif2a/03_edges/nohup.out delete mode 100644 data/mcl1/03_edges/01_perses_openfe.yaml create mode 100644 data/mcl1/03_edges/01_perses_openfe.yml delete mode 100644 data/mcl1/03_edges/nohup.out delete mode 100644 data/p38/03_edges/01_perses_openfe.yaml create mode 100644 data/p38/03_edges/01_perses_openfe.yml delete mode 100644 data/p38/03_edges/nohup.out delete mode 100644 data/pde2/03_edges/01_perses_openfe.yaml create mode 100644 data/pde2/03_edges/01_perses_openfe.yml delete mode 100644 data/pde2/03_edges/nohup.out delete mode 100644 data/pfkfb3/03_edges/01_perses_openfe.yaml create mode 100644 data/pfkfb3/03_edges/01_perses_openfe.yml delete mode 100644 data/pfkfb3/03_edges/nohup.out delete mode 100644 data/ptp1b/03_edges/01_perses_openfe.yaml create mode 100644 data/ptp1b/03_edges/01_perses_openfe.yml delete mode 100644 data/ptp1b/03_edges/nohup.out delete mode 100644 data/shp2/03_edges/01_perses_openfe.yaml create mode 100644 data/shp2/03_edges/01_perses_openfe.yml delete mode 100644 data/shp2/03_edges/nohup.out delete mode 100644 data/syk/03_edges/01_perses_openfe.yaml create mode 100644 data/syk/03_edges/01_perses_openfe.yml delete mode 100644 data/syk/03_edges/nohup.out delete mode 100644 data/thrombin/03_edges/01_perses_openfe.yaml create mode 100644 data/thrombin/03_edges/01_perses_openfe.yml delete mode 100644 data/thrombin/03_edges/nohup.out delete mode 100644 data/tnks2/03_edges/01_perses_openfe.yaml create mode 100644 data/tnks2/03_edges/01_perses_openfe.yml delete mode 100644 data/tnks2/03_edges/nohup.out delete mode 100644 data/tyk2/03_edges/01_perses_openfe.yaml create mode 100644 data/tyk2/03_edges/01_perses_openfe.yml delete mode 100644 data/tyk2/03_edges/nohup.out diff --git a/data/cdk2/03_edges/01_perses_openfe.yaml b/data/cdk2/03_edges/01_perses_openfe.yaml deleted file mode 100644 index 45004a6e9..000000000 --- a/data/cdk2/03_edges/01_perses_openfe.yaml +++ /dev/null @@ -1,76 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph -edges: - edge_lig_1oiu_lig_1h1q: - ligand_a: lig_1oiu - ligand_b: lig_1h1q - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 13) (13, 12) (14, 14) (15, 16) (16, 15) (17, 17) (18, - 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 25) (25, 24) (26, 26) - (27, 27) (28, 28) (29, 29) (30, 30) (31, 39) (32, 40) (33, 37) (40, 35) (41, - 36) (42, 33) (43, 34) (44, 31) (45, 32) (46, 41) (47, 42) (48, 43) (49, 44) - score: '0.961' - edge_lig_26_lig_1oiu: - ligand_a: lig_26 - ligand_b: lig_1oiu - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 13) (13, 12) (14, 14) (15, 16) (16, 15) (17, 17) (18, - 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 25) (25, 24) (26, 26) - (27, 27) (28, 28) (29, 29) (30, 30) (31, 44) (32, 45) (33, 42) (34, 43) (35, - 40) (41, 33) (43, 31) (44, 32) (45, 46) (46, 47) (47, 48) (48, 49) - score: '0.901' - edge_lig_22_lig_26: - ligand_a: lig_22 - ligand_b: lig_26 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 13) (13, 12) (14, 14) (15, 16) (16, 15) (17, 17) (18, - 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 25) (25, 24) (26, 26) - (27, 27) (28, 28) (29, 29) (30, 30) (31, 43) (32, 44) (33, 41) (34, 42) (35, - 35) (37, 33) (43, 31) (44, 32) (45, 45) (46, 46) (47, 47) (48, 48) - score: '0.912' - edge_lig_17_lig_26: - ligand_a: lig_17 - ligand_b: lig_26 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 13) (13, 12) (14, 14) (15, 16) (16, 15) (17, 17) (18, - 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 25) (25, 24) (26, 26) - (27, 27) (28, 28) (29, 29) (30, 30) (31, 43) (32, 44) (33, 41) (34, 42) (35, - 35) (37, 33) (39, 31) (40, 32) (41, 45) (42, 46) (43, 47) (44, 48) - score: '0.961' - edge_lig_21_lig_26: - ligand_a: lig_21 - ligand_b: lig_26 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 13) (13, 12) (14, 14) (15, 16) (16, 15) (17, 17) (18, - 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 25) (25, 24) (26, 26) - (27, 27) (28, 28) (29, 29) (30, 30) (31, 43) (32, 44) (33, 41) (34, 42) (35, - 35) (37, 33) (43, 31) (44, 32) (45, 45) (46, 46) (47, 47) (48, 48) - score: '0.912' - edge_lig_1h1r_lig_1oiu: - ligand_a: lig_1h1r - ligand_b: lig_1oiu - atom mapping: (1, 33) (2, 31) (3, 30) (4, 44) (5, 42) (6, 40) (7, 41) (9, 45) - (10, 28) (11, 29) (12, 27) (13, 46) (14, 47) (15, 3) (16, 4) (17, 26) (18, 5) - (19, 6) (20, 7) (21, 8) (22, 9) (23, 23) (24, 20) (25, 17) (26, 14) (27, 11) - (28, 13) (29, 12) (30, 16) (31, 15) (32, 18) (33, 19) (34, 21) (35, 22) (36, - 24) (37, 25) (38, 10) (39, 2) (40, 1) (41, 48) (42, 49) (43, 0) (44, 32) - score: '0.948' - edge_lig_20_lig_26: - ligand_a: lig_20 - ligand_b: lig_26 - atom mapping: (5, 33) (6, 35) (8, 41) (9, 42) (10, 43) (11, 44) (12, 30) (13, - 28) (14, 29) (15, 27) (16, 26) (17, 4) (18, 5) (19, 6) (20, 8) (21, 7) (22, - 9) (23, 10) (24, 23) (25, 24) (26, 25) (27, 20) (28, 21) (29, 22) (30, 17) (31, - 19) (32, 18) (33, 14) (34, 16) (35, 15) (36, 11) (37, 12) (38, 13) (39, 3) (40, - 2) (41, 1) (42, 0) (43, 47) (44, 48) (45, 46) (46, 45) (47, 31) (48, 32) - score: '0.912' - edge_lig_1oi9_lig_1oiu: - ligand_a: lig_1oi9 - ligand_b: lig_1oiu - atom mapping: (2, 40) (3, 33) (5, 31) (6, 32) (7, 30) (8, 28) (9, 29) (10, 27) - (11, 26) (12, 4) (13, 5) (14, 6) (15, 7) (16, 8) (17, 9) (18, 10) (19, 11) (20, - 12) (21, 13) (22, 14) (23, 16) (24, 15) (25, 17) (26, 18) (27, 19) (28, 20) - (29, 22) (30, 21) (31, 23) (32, 24) (33, 25) (34, 3) (35, 2) (36, 1) (37, 0) - (38, 48) (39, 49) (40, 47) (41, 46) (42, 44) (43, 45) (44, 42) (45, 43) - score: '0.936' diff --git a/data/cdk2/03_edges/01_perses_openfe.yml b/data/cdk2/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..4cff5e081 --- /dev/null +++ b/data/cdk2/03_edges/01_perses_openfe.yml @@ -0,0 +1,76 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_1oiu_lig_1h1q: + ligand_a: lig_1oiu + ligand_b: lig_1h1q + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, + 31: 39, 32: 40, 33: 37, 40: 35, 41: 36, 42: 33, 43: 34, 44: 31, 45: 32, 46: 41, + 47: 42, 48: 43, 49: 44} + score: '0.961' + edge_lig_21_lig_26: + ligand_a: lig_21 + ligand_b: lig_26 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, + 31: 43, 32: 44, 33: 41, 34: 42, 35: 35, 37: 33, 43: 31, 44: 32, 45: 45, 46: 46, + 47: 47, 48: 48} + score: '0.912' + edge_lig_26_lig_1oiu: + ligand_a: lig_26 + ligand_b: lig_1oiu + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, + 31: 44, 32: 45, 33: 42, 34: 43, 35: 40, 41: 33, 43: 31, 44: 32, 45: 46, 46: 47, + 47: 48, 48: 49} + score: '0.901' + edge_lig_21_lig_17: + ligand_a: lig_21 + ligand_b: lig_17 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, + 31: 39, 32: 40, 33: 37, 35: 35, 36: 36, 37: 33, 43: 31, 44: 32, 45: 41, 46: 42, + 47: 43, 48: 44} + score: '0.961' + edge_lig_22_lig_26: + ligand_a: lig_22 + ligand_b: lig_26 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, + 31: 43, 32: 44, 33: 41, 34: 42, 35: 35, 37: 33, 43: 31, 44: 32, 45: 45, 46: 46, + 47: 47, 48: 48} + score: '0.912' + edge_lig_1h1r_lig_1oiu: + ligand_a: lig_1h1r + ligand_b: lig_1oiu + atom mapping: {1: 33, 2: 31, 3: 30, 4: 44, 5: 42, 6: 40, 7: 41, 9: 45, 10: 28, + 11: 29, 12: 27, 13: 46, 14: 47, 15: 3, 16: 4, 17: 26, 18: 5, 19: 6, 20: 7, 21: 8, + 22: 9, 23: 23, 24: 20, 25: 17, 26: 14, 27: 11, 28: 13, 29: 12, 30: 16, 31: 15, + 32: 18, 33: 19, 34: 21, 35: 22, 36: 24, 37: 25, 38: 10, 39: 2, 40: 1, 41: 48, + 42: 49, 43: 0, 44: 32} + score: '0.948' + edge_lig_1oi9_lig_1oiu: + ligand_a: lig_1oi9 + ligand_b: lig_1oiu + atom mapping: {2: 40, 3: 33, 5: 31, 6: 32, 7: 30, 8: 28, 9: 29, 10: 27, 11: 26, + 12: 4, 13: 5, 14: 6, 15: 7, 16: 8, 17: 9, 18: 10, 19: 11, 20: 12, 21: 13, 22: 14, + 23: 16, 24: 15, 25: 17, 26: 18, 27: 19, 28: 20, 29: 22, 30: 21, 31: 23, 32: 24, + 33: 25, 34: 3, 35: 2, 36: 1, 37: 0, 38: 48, 39: 49, 40: 47, 41: 46, 42: 44, + 43: 45, 44: 42, 45: 43} + score: '0.936' + edge_lig_20_lig_26: + ligand_a: lig_20 + ligand_b: lig_26 + atom mapping: {5: 33, 6: 35, 8: 41, 9: 42, 10: 43, 11: 44, 12: 30, 13: 28, 14: 29, + 15: 27, 16: 26, 17: 4, 18: 5, 19: 6, 20: 8, 21: 7, 22: 9, 23: 10, 24: 23, 25: 24, + 26: 25, 27: 20, 28: 21, 29: 22, 30: 17, 31: 19, 32: 18, 33: 14, 34: 16, 35: 15, + 36: 11, 37: 12, 38: 13, 39: 3, 40: 2, 41: 1, 42: 0, 43: 47, 44: 48, 45: 46, + 46: 45, 47: 31, 48: 32} + score: '0.912' diff --git a/data/cdk8/03_edges/01_perses_openfe.yaml b/data/cdk8/03_edges/01_perses_openfe.yaml deleted file mode 100644 index 4b788d5f9..000000000 --- a/data/cdk8/03_edges/01_perses_openfe.yaml +++ /dev/null @@ -1,210 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph -edges: - edge_lig_28_lig_45: - ligand_a: lig_28 - ligand_b: lig_45 - atom mapping: (17, 13) (18, 15) (19, 14) (20, 16) (21, 17) (22, 18) (23, 19) (24, - 20) (25, 21) (26, 22) (27, 23) (28, 24) (43, 41) (44, 42) (45, 43) (46, 44) - score: '0.354' - edge_lig_30_lig_45: - ligand_a: lig_30 - ligand_b: lig_45 - atom mapping: (8, 25) (9, 26) (10, 24) (11, 22) (12, 23) (13, 21) (14, 20) (15, - 43) (16, 44) (17, 41) (18, 42) (19, 18) (20, 19) (21, 17) (22, 16) (23, 13) - (24, 15) (25, 14) - score: '0.388' - edge_lig_42_lig_23: - ligand_a: lig_42 - ligand_b: lig_23 - atom mapping: (10, 28) (11, 26) (12, 27) (13, 25) (14, 24) (15, 43) (16, 44) (17, - 41) (18, 42) (19, 22) (20, 23) (21, 21) (22, 20) (23, 17) (24, 19) (25, 18) - score: '0.333' - edge_lig_43_lig_24: - ligand_a: lig_43 - ligand_b: lig_24 - atom mapping: (13, 17) (14, 19) (15, 18) (16, 20) (17, 21) (18, 22) (19, 23) (20, - 24) (21, 25) (22, 26) (23, 27) (24, 28) (25, 29) (40, 37) (41, 38) (42, 39) - (43, 40) - score: '0.395' - edge_lig_18_lig_23: - ligand_a: lig_18 - ligand_b: lig_23 - atom mapping: (13, 17) (14, 18) (15, 19) (16, 20) (17, 21) (18, 22) (19, 23) (20, - 24) (21, 25) (22, 26) (23, 27) (24, 28) (33, 41) (34, 42) (35, 43) (36, 44) - score: '0.366' - edge_lig_43_lig_15: - ligand_a: lig_43 - ligand_b: lig_15 - atom mapping: (13, 5) (14, 6) (15, 7) (16, 8) (17, 9) (18, 10) (19, 11) (20, 12) - (21, 13) (22, 14) (23, 15) (24, 16) (25, 17) (26, 18) (40, 25) (41, 26) (42, - 27) (43, 28) - score: '0.425' - edge_lig_43_lig_19: - ligand_a: lig_43 - ligand_b: lig_19 - atom mapping: (13, 17) (14, 19) (15, 18) (16, 20) (17, 21) (18, 22) (19, 23) (20, - 24) (21, 25) (22, 26) (23, 27) (24, 28) (25, 29) (26, 30) (40, 37) (41, 38) - (42, 39) (43, 40) - score: '0.414' - edge_lig_42_lig_20: - ligand_a: lig_42 - ligand_b: lig_20 - atom mapping: (8, 37) (9, 38) (10, 36) (11, 34) (12, 35) (13, 33) (14, 32) (15, - 47) (16, 48) (17, 45) (18, 46) (19, 30) (20, 31) (21, 29) (22, 28) (23, 25) - (24, 27) (25, 26) - score: '0.391' - edge_lig_42_lig_36: - ligand_a: lig_42 - ligand_b: lig_36 - atom mapping: (8, 29) (9, 30) (10, 28) (11, 26) (12, 27) (13, 25) (14, 24) (15, - 47) (16, 48) (17, 45) (18, 46) (19, 22) (20, 23) (21, 21) (22, 20) (23, 17) - (24, 19) (25, 18) - score: '0.389' - edge_lig_44_lig_23: - ligand_a: lig_44 - ligand_b: lig_23 - atom mapping: (10, 28) (11, 26) (12, 27) (13, 25) (14, 24) (15, 43) (16, 44) (17, - 41) (18, 42) (19, 22) (20, 23) (21, 21) (22, 20) (23, 17) (24, 19) (25, 18) - score: '0.345' - edge_lig_43_lig_23: - ligand_a: lig_43 - ligand_b: lig_23 - atom mapping: (13, 17) (14, 19) (15, 18) (16, 20) (17, 21) (18, 22) (19, 23) (20, - 24) (21, 25) (22, 26) (23, 27) (24, 28) (40, 41) (41, 42) (42, 43) (43, 44) - score: '0.337' - edge_lig_29_lig_45: - ligand_a: lig_29 - ligand_b: lig_45 - atom mapping: (17, 13) (18, 14) (19, 15) (20, 16) (21, 17) (22, 18) (23, 19) (24, - 20) (25, 21) (26, 22) (27, 23) (28, 24) (29, 25) (30, 26) (42, 41) (43, 42) - (44, 43) (45, 44) - score: '0.394' - edge_lig_17_lig_23: - ligand_a: lig_17 - ligand_b: lig_23 - atom mapping: (15, 17) (16, 19) (17, 18) (18, 20) (19, 21) (20, 22) (21, 23) (22, - 24) (23, 25) (24, 26) (25, 27) (26, 28) (35, 41) (36, 42) (37, 43) (38, 44) - score: '0.366' - edge_lig_43_lig_32: - ligand_a: lig_43 - ligand_b: lig_32 - atom mapping: (13, 17) (14, 19) (15, 18) (16, 20) (17, 21) (18, 22) (19, 23) (20, - 24) (21, 25) (22, 26) (23, 27) (24, 28) (25, 29) (26, 30) (40, 34) (41, 35) - (42, 36) (43, 37) - score: '0.430' - edge_lig_13_lig_45: - ligand_a: lig_13 - ligand_b: lig_45 - atom mapping: (2, 41) (3, 24) (4, 25) (5, 26) (20, 22) (21, 23) (22, 21) (23, - 16) (24, 13) (25, 15) (26, 14) (41, 17) (42, 18) (43, 19) (44, 20) (45, 43) - (46, 44) - score: '0.395' - edge_lig_42_lig_35: - ligand_a: lig_42 - ligand_b: lig_35 - atom mapping: (8, 8) (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, - 15) (16, 16) (17, 17) (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) - (24, 25) (25, 24) - score: '0.392' - edge_lig_38_lig_45: - ligand_a: lig_38 - ligand_b: lig_45 - atom mapping: (17, 13) (18, 14) (19, 15) (20, 16) (21, 17) (22, 18) (23, 19) (24, - 20) (25, 21) (26, 22) (27, 23) (28, 24) (29, 25) (30, 26) (44, 41) (45, 42) - (46, 43) (47, 44) - score: '0.385' - edge_lig_14_lig_23: - ligand_a: lig_14 - ligand_b: lig_23 - atom mapping: (0, 42) (1, 41) (2, 43) (3, 44) (4, 24) (5, 25) (6, 20) (7, 17) - (9, 19) (20, 21) (21, 22) (22, 23) (23, 26) (24, 27) (25, 28) - score: '0.387' - edge_lig_22_lig_43: - ligand_a: lig_22 - ligand_b: lig_43 - atom mapping: (17, 13) (18, 14) (19, 15) (20, 16) (21, 17) (22, 18) (23, 19) (24, - 20) (25, 21) (26, 22) (27, 23) (28, 24) (40, 40) (41, 41) (42, 42) (43, 43) - score: '0.358' - edge_lig_39_lig_45: - ligand_a: lig_39 - ligand_b: lig_45 - atom mapping: (17, 13) (18, 15) (19, 14) (20, 16) (21, 17) (22, 18) (23, 19) (24, - 20) (25, 21) (26, 22) (27, 23) (28, 24) (29, 25) (30, 26) (45, 41) (46, 42) - (47, 43) (48, 44) - score: '0.386' - edge_lig_26_lig_45: - ligand_a: lig_26 - ligand_b: lig_45 - atom mapping: (17, 13) (18, 15) (19, 14) (20, 16) (21, 17) (22, 18) (23, 19) (24, - 20) (25, 21) (26, 22) (27, 23) (28, 24) (41, 41) (42, 42) (43, 43) (44, 44) - score: '0.356' - edge_lig_42_lig_27: - ligand_a: lig_42 - ligand_b: lig_27 - atom mapping: (8, 29) (10, 28) (11, 26) (12, 27) (13, 25) (14, 24) (15, 47) (16, - 48) (17, 45) (18, 46) (19, 22) (20, 23) (21, 21) (22, 20) (23, 17) (24, 19) - (25, 18) - score: '0.375' - edge_lig_45_lig_23: - ligand_a: lig_45 - ligand_b: lig_23 - atom mapping: (13, 17) (14, 18) (15, 19) (16, 20) (17, 21) (18, 22) (19, 23) (20, - 24) (21, 25) (22, 26) (23, 27) (24, 28) (41, 41) (42, 42) (43, 43) (44, 44) - score: '0.333' - edge_lig_43_lig_25: - ligand_a: lig_43 - ligand_b: lig_25 - atom mapping: (13, 17) (14, 19) (15, 18) (16, 20) (17, 21) (18, 22) (19, 23) (20, - 24) (21, 25) (22, 26) (23, 27) (24, 28) (25, 29) (40, 38) (41, 39) (42, 40) - (43, 41) - score: '0.390' - edge_lig_43_lig_16: - ligand_a: lig_43 - ligand_b: lig_16 - atom mapping: (13, 5) (14, 6) (15, 7) (16, 8) (17, 9) (18, 10) (19, 11) (20, 12) - (21, 13) (22, 14) (23, 15) (24, 16) (25, 17) (26, 18) (40, 25) (41, 26) (42, - 27) (43, 28) - score: '0.454' - edge_lig_33_lig_45: - ligand_a: lig_33 - ligand_b: lig_45 - atom mapping: (17, 13) (18, 15) (19, 14) (20, 16) (21, 17) (22, 18) (23, 19) (24, - 20) (25, 21) (26, 22) (27, 23) (28, 24) (29, 25) (30, 26) (41, 41) (42, 42) - (43, 43) (44, 44) - score: '0.396' - edge_lig_41_lig_45: - ligand_a: lig_41 - ligand_b: lig_45 - atom mapping: (17, 13) (18, 14) (19, 15) (20, 16) (21, 17) (22, 18) (23, 19) (24, - 20) (25, 21) (26, 22) (27, 23) (28, 24) (29, 25) (30, 26) (47, 41) (48, 42) - (49, 43) (50, 44) - score: '0.386' - edge_lig_21_lig_43: - ligand_a: lig_21 - ligand_b: lig_43 - atom mapping: (17, 13) (18, 14) (19, 15) (20, 16) (21, 17) (22, 18) (23, 19) (24, - 20) (25, 21) (26, 22) (27, 23) (28, 24) (40, 40) (41, 41) (42, 42) (43, 43) - score: '0.358' - edge_lig_40_lig_45: - ligand_a: lig_40 - ligand_b: lig_45 - atom mapping: (17, 13) (18, 14) (19, 15) (20, 16) (21, 17) (22, 18) (23, 19) (24, - 20) (25, 21) (26, 22) (27, 23) (28, 24) (29, 25) (30, 26) (46, 41) (47, 42) - (48, 43) (49, 44) - score: '0.386' - edge_lig_42_lig_34: - ligand_a: lig_42 - ligand_b: lig_34 - atom mapping: (8, 29) (9, 30) (10, 28) (11, 26) (12, 27) (13, 25) (14, 24) (15, - 43) (16, 44) (17, 41) (18, 42) (19, 22) (20, 23) (21, 21) (22, 20) (23, 17) - (24, 19) (25, 18) - score: '0.389' - edge_lig_37_lig_45: - ligand_a: lig_37 - ligand_b: lig_45 - atom mapping: (17, 13) (18, 15) (19, 14) (20, 16) (21, 17) (22, 18) (23, 19) (24, - 20) (25, 21) (26, 22) (27, 23) (28, 24) (29, 25) (30, 26) (44, 41) (45, 42) - (46, 43) (47, 44) - score: '0.390' diff --git a/data/cdk8/03_edges/01_perses_openfe.yml b/data/cdk8/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..76282c098 --- /dev/null +++ b/data/cdk8/03_edges/01_perses_openfe.yml @@ -0,0 +1,190 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_26_lig_45: + ligand_a: lig_26 + ligand_b: lig_45 + atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 41: 41, 42: 42, 43: 43, 44: 44} + score: '0.356' + edge_lig_14_lig_23: + ligand_a: lig_14 + ligand_b: lig_23 + atom mapping: {0: 42, 1: 41, 2: 43, 3: 44, 4: 24, 5: 25, 6: 20, 7: 17, 9: 19, + 20: 21, 21: 22, 22: 23, 23: 26, 24: 27, 25: 28} + score: '0.387' + edge_lig_42_lig_35: + ligand_a: lig_42 + ligand_b: lig_35 + atom mapping: {8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, + 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, 22: 22, 23: 23, 24: 25, 25: 24} + score: '0.392' + edge_lig_17_lig_23: + ligand_a: lig_17 + ligand_b: lig_23 + atom mapping: {15: 17, 16: 19, 17: 18, 18: 20, 19: 21, 20: 22, 21: 23, 22: 24, + 23: 25, 24: 26, 25: 27, 26: 28, 35: 41, 36: 42, 37: 43, 38: 44} + score: '0.366' + edge_lig_40_lig_45: + ligand_a: lig_40 + ligand_b: lig_45 + atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 46: 41, 47: 42, 48: 43, 49: 44} + score: '0.386' + edge_lig_22_lig_43: + ligand_a: lig_22 + ligand_b: lig_43 + atom mapping: {17: 13, 18: 14, 19: 15, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 40: 40, 41: 41, 42: 42, 43: 43} + score: '0.358' + edge_lig_42_lig_23: + ligand_a: lig_42 + ligand_b: lig_23 + atom mapping: {10: 28, 11: 26, 12: 27, 13: 25, 14: 24, 15: 43, 16: 44, 17: 41, + 18: 42, 19: 22, 20: 23, 21: 21, 22: 20, 23: 17, 24: 19, 25: 18} + score: '0.333' + edge_lig_42_lig_20: + ligand_a: lig_42 + ligand_b: lig_20 + atom mapping: {8: 37, 9: 38, 10: 36, 11: 34, 12: 35, 13: 33, 14: 32, 15: 47, 16: 48, + 17: 45, 18: 46, 19: 30, 20: 31, 21: 29, 22: 28, 23: 25, 24: 27, 25: 26} + score: '0.391' + edge_lig_43_lig_16: + ligand_a: lig_43 + ligand_b: lig_16 + atom mapping: {13: 5, 14: 6, 15: 7, 16: 8, 17: 9, 18: 10, 19: 11, 20: 12, 21: 13, + 22: 14, 23: 15, 24: 16, 25: 17, 26: 18, 40: 25, 41: 26, 42: 27, 43: 28} + score: '0.454' + edge_lig_42_lig_36: + ligand_a: lig_42 + ligand_b: lig_36 + atom mapping: {8: 29, 9: 30, 10: 28, 11: 26, 12: 27, 13: 25, 14: 24, 15: 47, 16: 48, + 17: 45, 18: 46, 19: 22, 20: 23, 21: 21, 22: 20, 23: 17, 24: 19, 25: 18} + score: '0.389' + edge_lig_39_lig_45: + ligand_a: lig_39 + ligand_b: lig_45 + atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 45: 41, 46: 42, 47: 43, 48: 44} + score: '0.386' + edge_lig_38_lig_45: + ligand_a: lig_38 + ligand_b: lig_45 + atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 44: 41, 45: 42, 46: 43, 47: 44} + score: '0.385' + edge_lig_21_lig_43: + ligand_a: lig_21 + ligand_b: lig_43 + atom mapping: {17: 13, 18: 14, 19: 15, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 40: 40, 41: 41, 42: 42, 43: 43} + score: '0.358' + edge_lig_45_lig_23: + ligand_a: lig_45 + ligand_b: lig_23 + atom mapping: {13: 17, 14: 18, 15: 19, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, + 21: 25, 22: 26, 23: 27, 24: 28, 41: 41, 42: 42, 43: 43, 44: 44} + score: '0.333' + edge_lig_42_lig_34: + ligand_a: lig_42 + ligand_b: lig_34 + atom mapping: {8: 29, 9: 30, 10: 28, 11: 26, 12: 27, 13: 25, 14: 24, 15: 43, 16: 44, + 17: 41, 18: 42, 19: 22, 20: 23, 21: 21, 22: 20, 23: 17, 24: 19, 25: 18} + score: '0.389' + edge_lig_43_lig_25: + ligand_a: lig_43 + ligand_b: lig_25 + atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, + 21: 25, 22: 26, 23: 27, 24: 28, 25: 29, 40: 38, 41: 39, 42: 40, 43: 41} + score: '0.390' + edge_lig_43_lig_15: + ligand_a: lig_43 + ligand_b: lig_15 + atom mapping: {13: 5, 14: 6, 15: 7, 16: 8, 17: 9, 18: 10, 19: 11, 20: 12, 21: 13, + 22: 14, 23: 15, 24: 16, 25: 17, 26: 18, 40: 25, 41: 26, 42: 27, 43: 28} + score: '0.425' + edge_lig_42_lig_27: + ligand_a: lig_42 + ligand_b: lig_27 + atom mapping: {8: 29, 10: 28, 11: 26, 12: 27, 13: 25, 14: 24, 15: 47, 16: 48, + 17: 45, 18: 46, 19: 22, 20: 23, 21: 21, 22: 20, 23: 17, 24: 19, 25: 18} + score: '0.375' + edge_lig_43_lig_23: + ligand_a: lig_43 + ligand_b: lig_23 + atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, + 21: 25, 22: 26, 23: 27, 24: 28, 40: 41, 41: 42, 42: 43, 43: 44} + score: '0.337' + edge_lig_28_lig_45: + ligand_a: lig_28 + ligand_b: lig_45 + atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 43: 41, 44: 42, 45: 43, 46: 44} + score: '0.354' + edge_lig_44_lig_23: + ligand_a: lig_44 + ligand_b: lig_23 + atom mapping: {10: 28, 11: 26, 12: 27, 13: 25, 14: 24, 15: 43, 16: 44, 17: 41, + 18: 42, 19: 22, 20: 23, 21: 21, 22: 20, 23: 17, 24: 19, 25: 18} + score: '0.345' + edge_lig_41_lig_45: + ligand_a: lig_41 + ligand_b: lig_45 + atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 47: 41, 48: 42, 49: 43, 50: 44} + score: '0.386' + edge_lig_37_lig_45: + ligand_a: lig_37 + ligand_b: lig_45 + atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 44: 41, 45: 42, 46: 43, 47: 44} + score: '0.390' + edge_lig_18_lig_23: + ligand_a: lig_18 + ligand_b: lig_23 + atom mapping: {13: 17, 14: 18, 15: 19, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, + 21: 25, 22: 26, 23: 27, 24: 28, 33: 41, 34: 42, 35: 43, 36: 44} + score: '0.366' + edge_lig_43_lig_19: + ligand_a: lig_43 + ligand_b: lig_19 + atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, + 21: 25, 22: 26, 23: 27, 24: 28, 25: 29, 26: 30, 40: 37, 41: 38, 42: 39, 43: 40} + score: '0.414' + edge_lig_33_lig_45: + ligand_a: lig_33 + ligand_b: lig_45 + atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 41: 41, 42: 42, 43: 43, 44: 44} + score: '0.396' + edge_lig_29_lig_45: + ligand_a: lig_29 + ligand_b: lig_45 + atom mapping: {17: 13, 18: 14, 19: 15, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 42: 41, 43: 42, 44: 43, 45: 44} + score: '0.394' + edge_lig_43_lig_24: + ligand_a: lig_43 + ligand_b: lig_24 + atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, + 21: 25, 22: 26, 23: 27, 24: 28, 25: 29, 40: 37, 41: 38, 42: 39, 43: 40} + score: '0.395' + edge_lig_43_lig_32: + ligand_a: lig_43 + ligand_b: lig_32 + atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, + 21: 25, 22: 26, 23: 27, 24: 28, 25: 29, 26: 30, 40: 34, 41: 35, 42: 36, 43: 37} + score: '0.430' + edge_lig_13_lig_45: + ligand_a: lig_13 + ligand_b: lig_45 + atom mapping: {2: 41, 3: 24, 4: 25, 5: 26, 20: 22, 21: 23, 22: 21, 23: 16, 24: 13, + 25: 15, 26: 14, 41: 17, 42: 18, 43: 19, 44: 20, 45: 43, 46: 44} + score: '0.395' + edge_lig_30_lig_45: + ligand_a: lig_30 + ligand_b: lig_45 + atom mapping: {8: 25, 9: 26, 10: 24, 11: 22, 12: 23, 13: 21, 14: 20, 15: 43, 16: 44, + 17: 41, 18: 42, 19: 18, 20: 19, 21: 17, 22: 16, 23: 13, 24: 14, 25: 15} + score: '0.388' diff --git a/data/cdk8/03_edges/nohup.out b/data/cdk8/03_edges/nohup.out deleted file mode 100644 index fdb137b26..000000000 --- a/data/cdk8/03_edges/nohup.out +++ /dev/null @@ -1,26 +0,0 @@ -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. -lig_30_lig_45 exceeds 1 A pairwise distance -lig_43_lig_24 exceeds 1 A pairwise distance -lig_18_lig_23 exceeds 1 A pairwise distance -lig_43_lig_19 exceeds 1 A pairwise distance -lig_42_lig_36 exceeds 1 A pairwise distance -lig_29_lig_45 exceeds 1 A pairwise distance -lig_43_lig_32 exceeds 1 A pairwise distance -lig_13_lig_45 exceeds 1 A pairwise distance -lig_42_lig_35 exceeds 1 A pairwise distance -lig_22_lig_43 exceeds 1 A pairwise distance -lig_39_lig_45 exceeds 1 A pairwise distance -lig_42_lig_27 exceeds 1 A pairwise distance -lig_45_lig_23 exceeds 1 A pairwise distance -lig_33_lig_45 exceeds 1 A pairwise distance -lig_21_lig_43 exceeds 1 A pairwise distance -lig_42_lig_34 exceeds 1 A pairwise distance -lig_37_lig_45 exceeds 1 A pairwise distance diff --git a/data/cmet/03_edges/01_perses_openfe.yaml b/data/cmet/03_edges/01_perses_openfe.yaml deleted file mode 100644 index ebcfead03..000000000 --- a/data/cmet/03_edges/01_perses_openfe.yaml +++ /dev/null @@ -1,28 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph -edges: - edge_lig_CHEMBL3402761_1_21_lig_CHEMBL3402749_500_9: - ligand_a: lig_CHEMBL3402761_1_21 - ligand_b: lig_CHEMBL3402749_500_9 - atom mapping: (0, 37) (1, 36) (2, 34) (3, 35) (4, 22) (5, 23) (6, 32) (7, 33) - (8, 30) (10, 28) (11, 29) (12, 26) (13, 27) (15, 24) (16, 25) (17, 21) (18, - 20) (19, 17) (20, 18) (21, 19) (22, 16) (23, 14) (24, 15) (25, 12) (26, 13) - (27, 10) (28, 11) (29, 9) (59, 40) (60, 41) (61, 38) (62, 39) - score: '0.675' - edge_lig_CHEMBL3402744_300_4_lig_CHEMBL3402761_1_21: - ligand_a: lig_CHEMBL3402744_300_4 - ligand_b: lig_CHEMBL3402761_1_21 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 15) (7, 16) (8, 12) - (9, 13) (10, 10) (11, 11) (12, 8) (14, 6) (15, 7) (16, 17) (17, 18) (18, 19) - (19, 20) (20, 21) (21, 22) (22, 59) (23, 60) (24, 29) (26, 27) (27, 28) (28, - 25) (38, 23) (39, 24) (40, 61) (41, 62) - score: '0.671' - edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402761_1_21: - ligand_a: lig_CHEMBL3402745_200_5 - ligand_b: lig_CHEMBL3402761_1_21 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 15) (7, 16) (8, 12) - (9, 13) (10, 10) (11, 11) (12, 8) (14, 6) (15, 7) (16, 17) (17, 18) (18, 19) - (19, 20) (20, 21) (21, 22) (22, 59) (23, 60) (24, 29) (26, 27) (27, 28) (28, - 25) (41, 23) (42, 24) (43, 61) (44, 62) - score: '0.648' diff --git a/data/cmet/03_edges/01_perses_openfe.yml b/data/cmet/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..323b566b8 --- /dev/null +++ b/data/cmet/03_edges/01_perses_openfe.yml @@ -0,0 +1,28 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402761_1_21: + ligand_a: lig_CHEMBL3402745_200_5 + ligand_b: lig_CHEMBL3402761_1_21 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 15, 7: 16, 8: 12, 9: 13, + 10: 10, 11: 11, 12: 8, 14: 6, 15: 7, 16: 17, 17: 18, 18: 19, 19: 20, 20: 21, + 21: 22, 22: 59, 23: 60, 24: 29, 26: 27, 27: 28, 28: 25, 41: 23, 42: 24, 43: 61, + 44: 62} + score: '0.648' + edge_lig_CHEMBL3402744_300_4_lig_CHEMBL3402761_1_21: + ligand_a: lig_CHEMBL3402744_300_4 + ligand_b: lig_CHEMBL3402761_1_21 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 15, 7: 16, 8: 12, 9: 13, + 10: 10, 11: 11, 12: 8, 14: 6, 15: 7, 16: 17, 17: 18, 18: 19, 19: 20, 20: 21, + 21: 22, 22: 59, 23: 60, 24: 29, 26: 27, 27: 28, 28: 25, 38: 23, 39: 24, 40: 61, + 41: 62} + score: '0.671' + edge_lig_CHEMBL3402761_1_21_lig_CHEMBL3402749_500_9: + ligand_a: lig_CHEMBL3402761_1_21 + ligand_b: lig_CHEMBL3402749_500_9 + atom mapping: {0: 37, 1: 36, 2: 34, 3: 35, 4: 22, 5: 23, 6: 32, 7: 33, 8: 30, + 10: 28, 11: 29, 12: 26, 13: 27, 15: 24, 16: 25, 17: 21, 18: 20, 19: 17, 20: 18, + 21: 19, 22: 16, 23: 14, 24: 15, 25: 12, 26: 13, 27: 10, 28: 11, 29: 9, 59: 40, + 60: 41, 61: 38, 62: 39} + score: '0.675' diff --git a/data/cmet/03_edges/nohup.out b/data/cmet/03_edges/nohup.out deleted file mode 100644 index 023250f71..000000000 --- a/data/cmet/03_edges/nohup.out +++ /dev/null @@ -1,12 +0,0 @@ -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. -lig_CHEMBL3402761_1_21_lig_CHEMBL3402749_500_9 exceeds 1 A pairwise distance -lig_CHEMBL3402744_300_4_lig_CHEMBL3402761_1_21 exceeds 1 A pairwise distance -lig_CHEMBL3402745_200_5_lig_CHEMBL3402761_1_21 exceeds 1 A pairwise distance diff --git a/data/eg5/03_edges/01_perses_openfe.yml b/data/eg5/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..98d166b4b --- /dev/null +++ b/data/eg5/03_edges/01_perses_openfe.yml @@ -0,0 +1,203 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_CHEMBL1083836_lig_CHEMBL1084115: + ligand_a: lig_CHEMBL1083836 + ligand_b: lig_CHEMBL1084115 + atom mapping: {7: 5, 8: 6, 9: 7, 10: 8, 11: 9, 12: 10, 13: 11, 14: 12, 15: 13, + 16: 14, 25: 28, 26: 29, 27: 30, 28: 31, 29: 32, 30: 33, 31: 34, 32: 36, 42: 37, + 43: 38, 44: 39, 45: 40, 46: 41, 47: 42, 48: 43, 49: 44} + score: '0.544' + edge_lig_CHEMBL1096003_lig_CHEMBL1084115: + ligand_a: lig_CHEMBL1096003 + ligand_b: lig_CHEMBL1084115 + atom mapping: {7: 5, 8: 6, 9: 7, 10: 8, 11: 9, 12: 10, 14: 12, 15: 13, 16: 14, + 17: 15, 18: 28, 19: 29, 20: 30, 21: 31, 22: 32, 23: 33, 24: 34, 25: 35, 49: 37, + 50: 39, 51: 38, 52: 40, 53: 42, 54: 41, 55: 43, 56: 44} + score: '0.538' + edge_lig_CHEMBL1084677_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1084677 + ligand_b: lig_CHEMBL1078998 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 17: 17, 18: 26, 19: 22, 20: 18, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, + 26: 35, 27: 36, 28: 37, 49: 39, 50: 41, 51: 40, 52: 42, 53: 44, 54: 43, 55: 45, + 56: 46} + score: '0.602' + edge_lig_CHEMBL1088740_lig_CHEMBL1077227: + ligand_a: lig_CHEMBL1088740 + ligand_b: lig_CHEMBL1077227 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 17: 17, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, 26: 35, 27: 36, 28: 37, + 30: 47, 31: 49, 32: 48, 33: 50, 34: 52, 35: 51, 36: 53, 37: 54} + score: '0.618' + edge_lig_CHEMBL1093087_lig_CHEMBL1084115: + ligand_a: lig_CHEMBL1093087 + ligand_b: lig_CHEMBL1084115 + atom mapping: {20: 34, 21: 36, 22: 33, 23: 31, 24: 32, 25: 30, 26: 28, 27: 29, + 28: 14, 29: 15, 30: 16, 31: 20, 32: 24, 33: 12, 34: 13, 35: 10, 36: 11, 37: 9, + 38: 7, 39: 8, 40: 5, 41: 6, 53: 43, 54: 44, 55: 40, 56: 41, 57: 42, 58: 37, + 59: 39, 60: 38} + score: '0.547' + edge_lig_CHEMBL1086409_lig_CHEMBL1084115: + ligand_a: lig_CHEMBL1086409 + ligand_b: lig_CHEMBL1084115 + atom mapping: {5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, + 15: 15, 16: 16, 17: 20, 18: 24, 19: 28, 20: 29, 21: 30, 22: 31, 23: 32, 24: 33, + 25: 34, 26: 36, 36: 37, 37: 39, 38: 38, 39: 40, 40: 42, 41: 41, 42: 43, 43: 44} + score: '0.621' + edge_lig_CHEMBL1089056_lig_CHEMBL1077227: + ligand_a: lig_CHEMBL1089056 + ligand_b: lig_CHEMBL1077227 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, + 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, 31: 31, 32: 32, 33: 33, 34: 34, 35: 35, + 36: 36, 38: 37, 39: 47, 40: 48, 41: 49, 42: 50, 43: 51, 44: 52, 45: 53, 46: 54} + score: '0.716' + edge_lig_CHEMBL1078691_lig_CHEMBL1077227: + ligand_a: lig_CHEMBL1078691 + ligand_b: lig_CHEMBL1077227 + atom mapping: {8: 7, 9: 8, 10: 9, 11: 10, 12: 11, 13: 12, 14: 13, 15: 14, 16: 15, + 17: 16, 18: 17, 19: 26, 20: 27, 21: 28, 22: 29, 23: 22, 24: 25, 25: 24, 26: 23, + 27: 18, 28: 19, 29: 20, 30: 21, 31: 30, 32: 31, 33: 32, 34: 33, 35: 34, 36: 35, + 37: 36, 38: 37, 40: 47, 41: 48, 42: 49, 43: 50, 44: 51, 45: 52, 46: 53, 47: 54} + score: '0.707' + edge_lig_CHEMBL1089393_lig_CHEMBL1077227: + ligand_a: lig_CHEMBL1089393 + ligand_b: lig_CHEMBL1077227 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 17: 17, 18: 30, 19: 31, 20: 32, 21: 33, 22: 34, 23: 35, 24: 36, 26: 37, + 27: 47, 28: 48, 29: 49, 30: 50, 31: 51, 32: 52, 33: 53, 34: 54} + score: '0.645' + edge_lig_CHEMBL1077204_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1077204 + ligand_b: lig_CHEMBL1078998 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 17: 17, 18: 26, 19: 22, 20: 18, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, + 26: 35, 27: 36, 28: 37, 53: 39, 54: 41, 55: 40, 56: 42, 57: 44, 58: 43, 59: 45, + 60: 46} + score: '0.598' + edge_lig_CHEMBL1093088_lig_CHEMBL1084115: + ligand_a: lig_CHEMBL1093088 + ligand_b: lig_CHEMBL1084115 + atom mapping: {7: 34, 8: 35, 9: 33, 10: 31, 11: 32, 12: 30, 13: 28, 14: 29, 15: 14, + 16: 15, 17: 24, 18: 20, 19: 16, 20: 12, 21: 13, 22: 10, 23: 11, 24: 9, 25: 7, + 26: 8, 27: 5, 28: 6, 40: 43, 41: 44, 42: 40, 43: 42, 44: 41, 45: 37, 46: 39, + 47: 38} + score: '0.598' + edge_lig_CHEMBL1084676_lig_CHEMBL1084115: + ligand_a: lig_CHEMBL1084676 + ligand_b: lig_CHEMBL1084115 + atom mapping: {7: 5, 8: 6, 9: 7, 10: 8, 11: 9, 12: 10, 13: 11, 14: 12, 15: 13, + 16: 14, 17: 15, 18: 16, 19: 20, 20: 24, 21: 28, 22: 29, 23: 30, 24: 31, 25: 32, + 26: 33, 27: 34, 28: 36, 52: 37, 53: 38, 54: 39, 55: 40, 56: 41, 57: 42, 58: 43, + 59: 44} + score: '0.598' + edge_lig_CHEMBL1096003_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1096003 + ligand_b: lig_CHEMBL1078998 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 14: 14, 15: 15, 16: 16, + 17: 17, 18: 30, 19: 31, 20: 32, 21: 33, 22: 34, 23: 35, 24: 36, 25: 37, 49: 39, + 50: 41, 51: 40, 52: 42, 53: 44, 54: 43, 55: 45, 56: 46} + score: '0.538' + edge_lig_CHEMBL1096002_lig_CHEMBL1084115: + ligand_a: lig_CHEMBL1096002 + ligand_b: lig_CHEMBL1084115 + atom mapping: {13: 34, 14: 36, 15: 33, 16: 31, 17: 32, 18: 30, 19: 28, 20: 29, + 21: 14, 22: 15, 23: 12, 24: 13, 25: 10, 27: 9, 28: 7, 29: 8, 30: 5, 31: 6, 43: 43, + 44: 44, 45: 40, 46: 41, 47: 42, 48: 37, 49: 39, 50: 38} + score: '0.555' + edge_lig_CHEMBL1084935_lig_CHEMBL1084115: + ligand_a: lig_CHEMBL1084935 + ligand_b: lig_CHEMBL1084115 + atom mapping: {19: 34, 20: 36, 21: 33, 22: 31, 23: 32, 24: 30, 25: 28, 26: 29, + 27: 14, 28: 15, 29: 16, 30: 17, 31: 18, 32: 19, 33: 20, 34: 23, 35: 22, 36: 21, + 37: 24, 38: 25, 39: 26, 40: 27, 41: 12, 42: 13, 43: 10, 44: 11, 45: 9, 46: 7, + 47: 8, 48: 5, 49: 6, 61: 43, 62: 44, 63: 40, 64: 42, 65: 41, 66: 37, 67: 39, + 68: 38} + score: '0.720' + edge_lig_CHEMBL1084115_lig_CHEMBL1082248: + ligand_a: lig_CHEMBL1084115 + ligand_b: lig_CHEMBL1082248 + atom mapping: {5: 7, 6: 8, 7: 9, 8: 10, 9: 11, 10: 12, 12: 14, 13: 15, 14: 16, + 15: 17, 28: 18, 29: 19, 30: 20, 31: 21, 32: 22, 33: 23, 34: 24, 36: 25, 37: 35, + 38: 37, 39: 36, 40: 38, 41: 39, 42: 40, 43: 41, 44: 42} + score: '0.562' + edge_lig_CHEMBL1086410_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1086410 + ligand_b: lig_CHEMBL1078998 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 17: 17, 18: 26, 19: 29, 20: 28, 21: 27, 22: 22, 23: 25, 24: 24, 25: 23, + 26: 18, 27: 21, 28: 20, 29: 19, 30: 30, 31: 31, 32: 32, 33: 33, 34: 34, 35: 35, + 36: 36, 37: 37, 47: 39, 48: 41, 49: 40, 50: 42, 51: 44, 52: 43, 53: 45, 54: 46} + score: '0.738' + edge_lig_CHEMBL1085895_lig_CHEMBL1084115: + ligand_a: lig_CHEMBL1085895 + ligand_b: lig_CHEMBL1084115 + atom mapping: {20: 34, 21: 36, 22: 33, 23: 31, 24: 32, 25: 30, 26: 28, 27: 29, + 28: 14, 29: 15, 30: 24, 31: 20, 32: 16, 33: 12, 34: 13, 35: 10, 36: 11, 37: 9, + 38: 7, 39: 8, 40: 5, 41: 6, 53: 43, 54: 44, 55: 40, 56: 42, 57: 41, 58: 37, + 59: 39, 60: 38} + score: '0.602' + edge_lig_CHEMBL1082249_lig_CHEMBL1084115: + ligand_a: lig_CHEMBL1082249 + ligand_b: lig_CHEMBL1084115 + atom mapping: {7: 5, 8: 6, 9: 7, 10: 8, 11: 9, 12: 10, 14: 12, 15: 13, 16: 14, + 17: 15, 18: 28, 19: 29, 20: 30, 21: 31, 22: 32, 23: 33, 24: 34, 25: 35, 45: 37, + 46: 39, 47: 38, 48: 40, 49: 42, 50: 41, 51: 43, 52: 44} + score: '0.545' + edge_lig_CHEMBL1085692_lig_CHEMBL1084115: + ligand_a: lig_CHEMBL1085692 + ligand_b: lig_CHEMBL1084115 + atom mapping: {7: 5, 8: 6, 9: 7, 10: 8, 11: 9, 12: 10, 14: 12, 15: 13, 16: 14, + 17: 15, 18: 28, 19: 29, 20: 30, 21: 31, 22: 32, 23: 33, 24: 34, 25: 35, 51: 37, + 52: 39, 53: 38, 54: 40, 55: 42, 56: 41, 57: 43, 58: 44} + score: '0.538' + edge_lig_CHEMBL1084143_lig_CHEMBL1084115: + ligand_a: lig_CHEMBL1084143 + ligand_b: lig_CHEMBL1084115 + atom mapping: {7: 5, 8: 6, 9: 7, 10: 8, 11: 9, 12: 10, 13: 11, 14: 12, 15: 13, + 16: 14, 17: 15, 19: 20, 20: 21, 21: 22, 22: 23, 23: 16, 24: 17, 25: 18, 26: 19, + 27: 28, 28: 29, 29: 30, 30: 31, 31: 32, 32: 33, 33: 34, 34: 35, 61: 37, 62: 39, + 63: 38, 64: 40, 65: 42, 66: 41, 67: 43, 68: 44} + score: '0.653' + edge_lig_CHEMBL1083517_lig_CHEMBL1084115: + ligand_a: lig_CHEMBL1083517 + ligand_b: lig_CHEMBL1084115 + atom mapping: {8: 5, 9: 6, 10: 7, 11: 8, 12: 9, 13: 10, 14: 11, 15: 12, 16: 13, + 17: 14, 18: 15, 19: 16, 20: 20, 21: 24, 22: 28, 23: 29, 24: 30, 25: 31, 26: 32, + 27: 33, 28: 34, 29: 35, 39: 37, 40: 38, 41: 39, 42: 40, 43: 41, 44: 42, 45: 43, + 46: 44} + score: '0.621' + edge_lig_CHEMBL1078774_lig_CHEMBL1077227: + ligand_a: lig_CHEMBL1078774 + ligand_b: lig_CHEMBL1077227 + atom mapping: {8: 7, 9: 8, 10: 9, 11: 10, 12: 11, 13: 12, 14: 13, 15: 14, 16: 15, + 17: 16, 18: 17, 19: 26, 20: 27, 21: 28, 22: 29, 23: 22, 24: 25, 25: 24, 26: 23, + 27: 18, 28: 19, 29: 20, 30: 21, 31: 30, 32: 31, 33: 32, 34: 33, 35: 34, 36: 35, + 37: 36, 38: 37, 40: 47, 41: 48, 42: 49, 43: 50, 44: 51, 45: 52, 46: 53, 47: 54} + score: '0.707' + edge_lig_CHEMBL1084678_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1084678 + ligand_b: lig_CHEMBL1078998 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 17: 17, 18: 18, 19: 22, 20: 26, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, + 26: 35, 27: 36, 28: 38, 52: 39, 53: 40, 54: 41, 55: 42, 56: 43, 57: 44, 58: 45, + 59: 46} + score: '0.598' + edge_lig_CHEMBL1096003_lig_CHEMBL1077227: + ligand_a: lig_CHEMBL1096003 + ligand_b: lig_CHEMBL1077227 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 14: 14, 15: 15, 16: 16, + 17: 17, 18: 30, 19: 31, 20: 32, 21: 33, 22: 34, 23: 35, 24: 36, 25: 37, 26: 38, + 27: 40, 28: 39, 29: 41, 30: 42, 31: 43, 49: 47, 50: 49, 51: 48, 52: 50, 53: 52, + 54: 51, 55: 53, 56: 54} + score: '0.567' + edge_lig_CHEMBL1085666_lig_CHEMBL1084115: + ligand_a: lig_CHEMBL1085666 + ligand_b: lig_CHEMBL1084115 + atom mapping: {7: 5, 8: 6, 9: 7, 10: 8, 11: 9, 12: 10, 13: 11, 14: 12, 15: 13, + 16: 14, 17: 15, 18: 24, 19: 20, 20: 16, 21: 28, 22: 29, 23: 30, 24: 31, 25: 32, + 26: 33, 27: 34, 28: 35, 35: 37, 36: 39, 37: 38, 38: 40, 39: 42, 40: 41, 41: 43, + 42: 44} + score: '0.628' diff --git a/data/eg5/03_edges/nohup.out b/data/eg5/03_edges/nohup.out deleted file mode 100644 index 386a103af..000000000 --- a/data/eg5/03_edges/nohup.out +++ /dev/null @@ -1,9 +0,0 @@ -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. diff --git a/data/hif2a/03_edges/01_perses_openfe.yaml b/data/hif2a/03_edges/01_perses_openfe.yaml deleted file mode 100644 index 666c808c4..000000000 --- a/data/hif2a/03_edges/01_perses_openfe.yaml +++ /dev/null @@ -1,210 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph -edges: - edge_lig_54_lig_235: - ligand_a: lig_54 - ligand_b: lig_235 - atom mapping: (12, 7) (13, 8) (14, 9) (15, 10) (16, 11) (18, 12) (19, 13) (20, - 14) (21, 15) (22, 17) (23, 18) - score: '0.338' - edge_lig_163_lig_54: - ligand_a: lig_163 - ligand_b: lig_54 - atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (12, 21) (13, 18) (14, - 19) (15, 16) (16, 17) (18, 14) (19, 15) - score: '0.367' - edge_lig_50_lig_224: - ligand_a: lig_50 - ligand_b: lig_224 - atom mapping: (14, 24) (15, 25) (16, 26) (17, 27) - score: '0.098' - edge_lig_67_lig_124: - ligand_a: lig_67 - ligand_b: lig_124 - atom mapping: (7, 7) (8, 8) (9, 9) (10, 10) (11, 11) (13, 13) (15, 21) (17, 23) - score: '0.311' - edge_lig_290_lig_54: - ligand_a: lig_290 - ligand_b: lig_54 - atom mapping: (0, 19) (1, 18) (2, 16) (3, 17) (4, 14) (5, 15) (6, 13) (7, 12) - (34, 22) (35, 23) (36, 20) (37, 21) - score: '0.359' - edge_lig_256_lig_43: - ligand_a: lig_256 - ligand_b: lig_43 - atom mapping: (7, 9) (8, 10) (9, 11) (10, 12) (11, 13) (13, 15) (14, 16) (15, - 17) (16, 18) (17, 20) (18, 21) - score: '0.357' - edge_lig_215_lig_54: - ligand_a: lig_215 - ligand_b: lig_54 - atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (12, 21) (13, 18) (14, - 19) (15, 16) (16, 17) (18, 14) (19, 15) - score: '0.364' - edge_lig_61_lig_31: - ligand_a: lig_61 - ligand_b: lig_31 - atom mapping: (7, 10) (8, 9) (9, 7) (10, 8) (11, 4) (12, 5) (13, 2) (14, 3) (15, - 1) (17, 32) (18, 33) - score: '0.360' - edge_lig_167_lig_54: - ligand_a: lig_167 - ligand_b: lig_54 - atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (12, 21) (13, 18) (14, - 19) (15, 16) (16, 17) (18, 14) (19, 15) - score: '0.364' - edge_lig_43_lig_224: - ligand_a: lig_43 - ligand_b: lig_224 - atom mapping: (27, 24) (28, 25) (29, 26) (30, 27) (32, 29) (33, 30) - score: '0.145' - edge_lig_35_lig_224: - ligand_a: lig_35 - ligand_b: lig_224 - atom mapping: (27, 24) (28, 25) (29, 26) (30, 27) (32, 29) (33, 30) - score: '0.145' - edge_lig_227_lig_54: - ligand_a: lig_227 - ligand_b: lig_54 - atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (12, 21) (13, 18) (14, - 19) (15, 16) (16, 17) (18, 14) (19, 15) - score: '0.361' - edge_lig_31_lig_224: - ligand_a: lig_31 - ligand_b: lig_224 - atom mapping: (17, 24) (18, 26) (19, 25) (20, 27) (22, 29) (23, 28) - score: '0.145' - edge_lig_31_lig_25: - ligand_a: lig_31 - ligand_b: lig_25 - atom mapping: (1, 11) (2, 13) (3, 14) (4, 15) (7, 16) (8, 17) (9, 8) (10, 7) (32, - 9) (33, 10) - score: '0.331' - edge_lig_1_lig_31: - ligand_a: lig_1 - ligand_b: lig_31 - atom mapping: (7, 10) (8, 9) (9, 7) (10, 8) (11, 4) (12, 5) (13, 2) (14, 3) (15, - 1) (17, 32) (18, 33) - score: '0.357' - edge_lig_41_lig_224: - ligand_a: lig_41 - ligand_b: lig_224 - atom mapping: (26, 24) (27, 25) (28, 26) (29, 27) (31, 29) (32, 30) - score: '0.147' - edge_lig_234_lig_54: - ligand_a: lig_234 - ligand_b: lig_54 - atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (12, 21) (13, 18) (14, - 19) (15, 16) (16, 17) (18, 14) (19, 15) - score: '0.367' - edge_lig_336_lig_54: - ligand_a: lig_336 - ligand_b: lig_54 - atom mapping: (7, 12) (8, 13) (9, 14) (10, 15) (11, 16) (12, 17) (13, 18) (14, - 19) (15, 20) (16, 21) (18, 22) (19, 23) - score: '0.367' - edge_lig_84_lig_31: - ligand_a: lig_84 - ligand_b: lig_31 - atom mapping: (0, 3) (1, 2) (2, 1) (4, 32) (5, 33) (6, 9) (7, 10) (29, 7) (30, - 8) (31, 4) (32, 5) - score: '0.363' - edge_lig_42_lig_224: - ligand_a: lig_42 - ligand_b: lig_224 - atom mapping: (27, 24) (28, 26) (29, 25) (30, 27) (32, 29) (33, 30) - score: '0.145' - edge_lig_124_lig_224: - ligand_a: lig_124 - ligand_b: lig_224 - atom mapping: (14, 24) (15, 26) (16, 25) (17, 27) (18, 28) (19, 29) (20, 30) - score: '0.174' - edge_lig_231_lig_54: - ligand_a: lig_231 - ligand_b: lig_54 - atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (12, 21) (13, 18) (14, - 19) (15, 16) (16, 17) (18, 14) (19, 15) - score: '0.370' - edge_lig_206_lig_54: - ligand_a: lig_206 - ligand_b: lig_54 - atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (12, 21) (13, 18) (14, - 19) (15, 16) (16, 17) (18, 14) (19, 15) - score: '0.364' - edge_lig_30_lig_224: - ligand_a: lig_30 - ligand_b: lig_224 - atom mapping: (14, 24) (15, 26) (16, 25) (17, 27) (19, 29) (20, 28) - score: '0.152' - edge_lig_23_lig_31: - ligand_a: lig_23 - ligand_b: lig_31 - atom mapping: (7, 10) (8, 9) (9, 7) (10, 8) (11, 4) (12, 5) (13, 2) (14, 3) (15, - 1) (17, 32) (18, 33) - score: '0.355' - edge_lig_252_lig_54: - ligand_a: lig_252 - ligand_b: lig_54 - atom mapping: (7, 12) (8, 13) (9, 14) (10, 15) (11, 16) (12, 17) (13, 18) (14, - 19) (15, 20) (16, 21) (18, 22) (19, 23) - score: '0.367' - edge_lig_155_lig_54: - ligand_a: lig_155 - ligand_b: lig_54 - atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (12, 21) (13, 18) (14, - 19) (15, 16) (16, 17) (18, 14) (19, 15) - score: '0.367' - edge_lig_57_lig_54: - ligand_a: lig_57 - ligand_b: lig_54 - atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (12, 21) (13, 18) (14, - 19) (15, 16) (16, 17) (18, 14) (19, 15) - score: '0.364' - edge_lig_289_lig_54: - ligand_a: lig_289 - ligand_b: lig_54 - atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (12, 21) (13, 18) (14, - 19) (15, 16) (16, 17) (18, 14) (19, 15) - score: '0.367' - edge_lig_254_lig_54: - ligand_a: lig_254 - ligand_b: lig_54 - atom mapping: (7, 12) (8, 13) (9, 14) (10, 15) (11, 16) (12, 17) (13, 18) (14, - 19) (15, 20) (16, 21) (18, 22) (19, 23) - score: '0.364' - edge_lig_338_lig_54: - ligand_a: lig_338 - ligand_b: lig_54 - atom mapping: (7, 12) (8, 13) (9, 14) (10, 15) (11, 16) (12, 17) (13, 18) (14, - 19) (15, 20) (16, 21) (18, 22) (19, 23) - score: '0.364' - edge_lig_251_lig_43: - ligand_a: lig_251 - ligand_b: lig_43 - atom mapping: (7, 9) (8, 10) (9, 11) (10, 12) (11, 13) (13, 15) (14, 16) (15, - 17) (16, 18) (17, 20) (18, 21) - score: '0.355' - edge_lig_156_lig_54: - ligand_a: lig_156 - ligand_b: lig_54 - atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (13, 18) (14, 19) (15, - 16) (16, 17) (18, 14) (19, 15) - score: '0.346' - edge_lig_15_lig_54: - ligand_a: lig_15 - ligand_b: lig_54 - atom mapping: (7, 12) (8, 13) (9, 22) (10, 23) (11, 20) (12, 21) (13, 18) (14, - 19) (15, 16) (16, 17) (18, 14) (19, 15) - score: '0.361' - edge_lig_165_lig_54: - ligand_a: lig_165 - ligand_b: lig_54 - atom mapping: (0, 19) (1, 18) (2, 16) (3, 17) (4, 14) (5, 15) (6, 13) (7, 12) - (34, 22) (35, 23) (36, 20) (37, 21) - score: '0.367' - edge_lig_54_lig_224: - ligand_a: lig_54 - ligand_b: lig_224 - atom mapping: (29, 24) (30, 25) (31, 26) (32, 27) - score: '0.093' diff --git a/data/hif2a/03_edges/01_perses_openfe.yml b/data/hif2a/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..e5a43a353 --- /dev/null +++ b/data/hif2a/03_edges/01_perses_openfe.yml @@ -0,0 +1,210 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_67_lig_124: + ligand_a: lig_67 + ligand_b: lig_124 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 13: 13, 15: 21, 17: 23} + score: '0.311' + edge_lig_42_lig_224: + ligand_a: lig_42 + ligand_b: lig_224 + atom mapping: {27: 24, 28: 25, 29: 26, 30: 27, 32: 29, 33: 30} + score: '0.145' + edge_lig_231_lig_54: + ligand_a: lig_231 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.370' + edge_lig_54_lig_235: + ligand_a: lig_54 + ligand_b: lig_235 + atom mapping: {12: 7, 13: 8, 14: 17, 15: 18, 16: 14, 17: 15, 18: 12, 19: 13, 20: 11, + 22: 9, 23: 10} + score: '0.338' + edge_lig_1_lig_43: + ligand_a: lig_1 + ligand_b: lig_43 + atom mapping: {7: 9, 8: 10, 9: 20, 10: 21, 11: 17, 12: 18, 13: 15, 14: 16, 15: 13, + 17: 11, 18: 12} + score: '0.357' + edge_lig_23_lig_43: + ligand_a: lig_23 + ligand_b: lig_43 + atom mapping: {7: 9, 8: 10, 9: 20, 10: 21, 11: 17, 12: 18, 13: 15, 14: 16, 15: 13, + 17: 11, 18: 12} + score: '0.355' + edge_lig_61_lig_43: + ligand_a: lig_61 + ligand_b: lig_43 + atom mapping: {7: 9, 8: 10, 9: 20, 10: 21, 11: 17, 12: 18, 13: 15, 14: 16, 15: 13, + 17: 11, 18: 12} + score: '0.360' + edge_lig_215_lig_54: + ligand_a: lig_215 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.364' + edge_lig_252_lig_54: + ligand_a: lig_252 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 14, 10: 15, 11: 16, 12: 17, 13: 18, 14: 19, 15: 20, + 16: 21, 18: 22, 19: 23} + score: '0.367' + edge_lig_290_lig_54: + ligand_a: lig_290 + ligand_b: lig_54 + atom mapping: {0: 19, 1: 18, 2: 16, 3: 17, 4: 14, 5: 15, 6: 13, 7: 12, 34: 22, + 35: 23, 36: 20, 37: 21} + score: '0.359' + edge_lig_163_lig_54: + ligand_a: lig_163 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.367' + edge_lig_155_lig_54: + ligand_a: lig_155 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.367' + edge_lig_54_lig_224: + ligand_a: lig_54 + ligand_b: lig_224 + atom mapping: {29: 24, 30: 25, 31: 26, 32: 27} + score: '0.093' + edge_lig_15_lig_54: + ligand_a: lig_15 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.361' + edge_lig_165_lig_54: + ligand_a: lig_165 + ligand_b: lig_54 + atom mapping: {0: 19, 1: 18, 2: 16, 3: 17, 4: 14, 5: 15, 6: 13, 7: 12, 34: 22, + 35: 23, 36: 20, 37: 21} + score: '0.367' + edge_lig_41_lig_224: + ligand_a: lig_41 + ligand_b: lig_224 + atom mapping: {26: 24, 27: 25, 28: 26, 29: 27, 31: 29, 32: 28} + score: '0.147' + edge_lig_167_lig_54: + ligand_a: lig_167 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.364' + edge_lig_254_lig_54: + ligand_a: lig_254 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 14, 10: 15, 11: 16, 12: 17, 13: 18, 14: 19, 15: 20, + 16: 21, 18: 22, 19: 23} + score: '0.364' + edge_lig_35_lig_224: + ligand_a: lig_35 + ligand_b: lig_224 + atom mapping: {27: 24, 28: 25, 29: 26, 30: 27, 32: 29, 33: 30} + score: '0.145' + edge_lig_124_lig_224: + ligand_a: lig_124 + ligand_b: lig_224 + atom mapping: {14: 24, 15: 26, 16: 25, 17: 27, 18: 28, 19: 29, 20: 30} + score: '0.174' + edge_lig_31_lig_224: + ligand_a: lig_31 + ligand_b: lig_224 + atom mapping: {17: 24, 18: 26, 19: 25, 20: 27, 22: 29, 23: 28} + score: '0.145' + edge_lig_234_lig_54: + ligand_a: lig_234 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.367' + edge_lig_336_lig_54: + ligand_a: lig_336 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 14, 10: 15, 11: 16, 12: 17, 13: 18, 14: 19, 15: 20, + 16: 21, 18: 22, 19: 23} + score: '0.367' + edge_lig_156_lig_54: + ligand_a: lig_156 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 13: 18, 14: 19, 15: 16, 16: 17, + 18: 14, 19: 15} + score: '0.346' + edge_lig_289_lig_54: + ligand_a: lig_289 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.367' + edge_lig_227_lig_54: + ligand_a: lig_227 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.361' + edge_lig_256_lig_43: + ligand_a: lig_256 + ligand_b: lig_43 + atom mapping: {7: 9, 8: 10, 9: 11, 10: 12, 11: 13, 13: 15, 14: 16, 15: 17, 16: 18, + 17: 20, 18: 21} + score: '0.357' + edge_lig_43_lig_84: + ligand_a: lig_43 + ligand_b: lig_84 + atom mapping: {9: 7, 10: 6, 11: 4, 12: 5, 13: 2, 15: 1, 16: 0, 17: 31, 18: 32, + 20: 29, 21: 30} + score: '0.363' + edge_lig_30_lig_224: + ligand_a: lig_30 + ligand_b: lig_224 + atom mapping: {14: 24, 15: 26, 16: 25, 17: 27, 19: 29, 20: 28} + score: '0.152' + edge_lig_338_lig_54: + ligand_a: lig_338 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 14, 10: 15, 11: 16, 12: 17, 13: 18, 14: 19, 15: 20, + 16: 21, 18: 22, 19: 23} + score: '0.364' + edge_lig_50_lig_224: + ligand_a: lig_50 + ligand_b: lig_224 + atom mapping: {14: 24, 15: 25, 16: 26, 17: 27} + score: '0.098' + edge_lig_43_lig_25: + ligand_a: lig_43 + ligand_b: lig_25 + atom mapping: {9: 7, 10: 8, 11: 9, 12: 10, 13: 11, 15: 13, 16: 14, 17: 15, 20: 16, + 21: 17} + score: '0.331' + edge_lig_57_lig_54: + ligand_a: lig_57 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.364' + edge_lig_251_lig_43: + ligand_a: lig_251 + ligand_b: lig_43 + atom mapping: {7: 9, 8: 10, 9: 11, 10: 12, 11: 13, 13: 15, 14: 16, 15: 17, 16: 18, + 17: 20, 18: 21} + score: '0.355' + edge_lig_206_lig_54: + ligand_a: lig_206 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.364' + edge_lig_43_lig_224: + ligand_a: lig_43 + ligand_b: lig_224 + atom mapping: {27: 24, 28: 26, 29: 25, 30: 27, 32: 29, 33: 30} + score: '0.145' diff --git a/data/hif2a/03_edges/nohup.out b/data/hif2a/03_edges/nohup.out deleted file mode 100644 index b21d476c5..000000000 --- a/data/hif2a/03_edges/nohup.out +++ /dev/null @@ -1,36 +0,0 @@ -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. -lig_163_lig_54 exceeds 1 A pairwise distance -lig_50_lig_224 exceeds 1 A pairwise distance -lig_67_lig_124 exceeds 1 A pairwise distance -lig_215_lig_54 exceeds 1 A pairwise distance -lig_61_lig_31 exceeds 1 A pairwise distance -lig_167_lig_54 exceeds 1 A pairwise distance -lig_43_lig_224 exceeds 1 A pairwise distance -lig_35_lig_224 exceeds 1 A pairwise distance -lig_227_lig_54 exceeds 1 A pairwise distance -lig_31_lig_224 exceeds 1 A pairwise distance -lig_31_lig_25 exceeds 1 A pairwise distance -lig_1_lig_31 exceeds 1 A pairwise distance -lig_41_lig_224 exceeds 1 A pairwise distance -lig_234_lig_54 exceeds 1 A pairwise distance -lig_42_lig_224 exceeds 1 A pairwise distance -lig_124_lig_224 exceeds 1 A pairwise distance -lig_231_lig_54 exceeds 1 A pairwise distance -lig_206_lig_54 exceeds 1 A pairwise distance -lig_30_lig_224 exceeds 1 A pairwise distance -lig_23_lig_31 exceeds 1 A pairwise distance -lig_155_lig_54 exceeds 1 A pairwise distance -lig_57_lig_54 exceeds 1 A pairwise distance -lig_289_lig_54 exceeds 1 A pairwise distance -lig_251_lig_43 exceeds 1 A pairwise distance -lig_156_lig_54 exceeds 1 A pairwise distance -lig_15_lig_54 exceeds 1 A pairwise distance -lig_54_lig_224 exceeds 1 A pairwise distance diff --git a/data/mcl1/03_edges/01_perses_openfe.yaml b/data/mcl1/03_edges/01_perses_openfe.yaml deleted file mode 100644 index 21b464bf5..000000000 --- a/data/mcl1/03_edges/01_perses_openfe.yaml +++ /dev/null @@ -1,180 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph -edges: - edge_lig_53_lig_43: - ligand_a: lig_53 - ligand_b: lig_43 - atom mapping: (0, 36) (1, 29) (2, 30) (3, 31) (4, 32) (5, 27) (6, 28) (7, 24) - (8, 25) (9, 26) (10, 37) (11, 38) (12, 39) (13, 40) (14, 21) (15, 23) (16, 22) - (17, 18) (18, 20) (19, 19) (20, 15) (21, 17) (22, 16) (23, 14) (41, 33) (43, - 35) - score: '0.548' - edge_lig_34_lig_47: - ligand_a: lig_34 - ligand_b: lig_47 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 17) (17, 16) (18, - 18) (19, 19) (20, 20) (21, 21) (22, 23) (23, 22) (24, 24) (39, 41) (40, 42) - score: '0.583' - edge_lig_28_lig_43: - ligand_a: lig_28 - ligand_b: lig_43 - atom mapping: (0, 35) (1, 30) (2, 31) (3, 32) (4, 27) (5, 28) (6, 29) (7, 36) - (8, 24) (9, 25) (10, 26) (11, 37) (12, 38) (13, 39) (14, 40) (15, 21) (16, 23) - (17, 22) (18, 18) (19, 19) (20, 20) (21, 15) (22, 17) (23, 16) (24, 14) (39, - 33) (40, 34) - score: '0.583' - edge_lig_56_lig_43: - ligand_a: lig_56 - ligand_b: lig_43 - atom mapping: (0, 35) (1, 30) (2, 31) (3, 32) (4, 27) (5, 28) (6, 29) (7, 36) - (8, 24) (9, 25) (10, 26) (15, 38) (16, 39) (17, 40) (18, 21) (19, 23) (20, 22) - (21, 18) (22, 19) (23, 20) (24, 15) (25, 16) (26, 17) (27, 14) (45, 33) (46, - 34) - score: '0.548' - edge_lig_37_lig_43: - ligand_a: lig_37 - ligand_b: lig_43 - atom mapping: (0, 35) (1, 30) (2, 31) (3, 32) (4, 27) (5, 28) (6, 29) (7, 36) - (8, 24) (9, 25) (10, 26) (11, 37) (12, 38) (13, 39) (14, 40) (15, 21) (16, 23) - (17, 22) (18, 18) (19, 19) (20, 20) (21, 15) (22, 17) (23, 16) (24, 14) (42, - 33) (43, 34) - score: '0.561' - edge_lig_58_lig_47: - ligand_a: lig_58 - ligand_b: lig_47 - atom mapping: (0, 7) (1, 6) (2, 1) (3, 2) (4, 3) (5, 4) (6, 5) (7, 8) (8, 9) (9, - 10) (14, 12) (15, 13) (16, 14) (17, 15) (18, 17) (19, 16) (20, 18) (21, 20) - (22, 19) (23, 21) (24, 23) (25, 22) (26, 24) (44, 41) (46, 0) - score: '0.538' - edge_lig_52_lig_47: - ligand_a: lig_52 - ligand_b: lig_47 - atom mapping: (0, 7) (1, 6) (2, 1) (3, 2) (4, 3) (5, 4) (6, 5) (7, 8) (8, 9) (9, - 10) (10, 11) (11, 12) (12, 13) (13, 14) (14, 15) (15, 17) (16, 16) (17, 18) - (18, 20) (19, 19) (20, 21) (21, 23) (22, 22) (23, 24) (38, 41) (40, 0) - score: '0.570' - edge_lig_63_lig_47: - ligand_a: lig_63 - ligand_b: lig_47 - atom mapping: (0, 7) (1, 6) (2, 1) (3, 2) (4, 3) (5, 4) (6, 5) (7, 8) (8, 9) (9, - 10) (10, 12) (11, 13) (12, 14) (13, 15) (14, 17) (15, 16) (16, 18) (17, 20) - (18, 19) (19, 21) (20, 22) (21, 23) (22, 24) (40, 41) (42, 0) - score: '0.542' - edge_lig_58_lig_46: - ligand_a: lig_58 - ligand_b: lig_46 - atom mapping: (0, 7) (1, 6) (2, 1) (3, 2) (4, 3) (5, 4) (6, 5) (7, 8) (8, 9) (9, - 10) (14, 12) (15, 13) (16, 14) (17, 15) (18, 17) (19, 16) (20, 18) (21, 20) - (22, 19) (23, 21) (24, 23) (25, 22) (26, 24) (44, 43) (46, 0) - score: '0.550' - edge_lig_58_lig_43: - ligand_a: lig_58 - ligand_b: lig_43 - atom mapping: (0, 36) (1, 29) (2, 30) (3, 31) (4, 32) (5, 27) (6, 28) (7, 24) - (8, 25) (9, 26) (14, 38) (15, 39) (16, 40) (17, 21) (18, 23) (19, 22) (20, 18) - (21, 20) (22, 19) (23, 15) (24, 17) (25, 16) (26, 14) (44, 33) (46, 35) - score: '0.531' - edge_lig_50_lig_43: - ligand_a: lig_50 - ligand_b: lig_43 - atom mapping: (0, 34) (1, 31) (2, 32) (3, 27) (4, 28) (5, 29) (6, 30) (7, 35) - (9, 24) (10, 25) (11, 26) (12, 37) (13, 38) (14, 39) (15, 40) (16, 21) (17, - 23) (18, 22) (19, 18) (20, 19) (21, 20) (22, 15) (23, 17) (24, 16) (25, 14) - (43, 33) - score: '0.548' - edge_lig_67_lig_47: - ligand_a: lig_67 - ligand_b: lig_47 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 12) (12, 13) (13, 14) (14, 15) (15, 17) (16, 16) (17, 18) (18, - 20) (19, 19) (20, 21) (21, 22) (22, 23) (23, 24) (41, 41) (42, 42) - score: '0.555' - edge_lig_58_lig_48: - ligand_a: lig_58 - ligand_b: lig_48 - atom mapping: (0, 7) (1, 6) (2, 1) (3, 2) (4, 3) (5, 4) (6, 5) (7, 8) (8, 9) (9, - 10) (14, 12) (15, 13) (16, 14) (17, 15) (18, 17) (19, 16) (20, 18) (21, 20) - (22, 19) (23, 21) (24, 23) (25, 22) (26, 24) (44, 40) (46, 0) - score: '0.573' - edge_lig_30_lig_47: - ligand_a: lig_30 - ligand_b: lig_47 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 17) (17, 16) (18, - 18) (19, 19) (20, 20) (21, 21) (22, 23) (23, 22) (24, 24) (39, 41) (40, 42) - score: '0.583' - edge_lig_31_lig_47: - ligand_a: lig_31 - ligand_b: lig_47 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 17) (17, 16) (18, - 18) (19, 19) (20, 20) (21, 21) (22, 23) (23, 22) (24, 24) (39, 41) (40, 42) - score: '0.583' - edge_lig_49_lig_47: - ligand_a: lig_49 - ligand_b: lig_47 - atom mapping: (0, 42) (1, 2) (2, 3) (3, 4) (4, 5) (5, 6) (6, 1) (7, 0) (9, 8) - (10, 9) (11, 10) (12, 11) (13, 12) (14, 13) (15, 14) (16, 15) (17, 17) (18, - 16) (19, 18) (20, 19) (21, 20) (22, 21) (23, 23) (24, 22) (25, 24) (40, 41) - score: '0.570' - edge_lig_27_lig_47: - ligand_a: lig_27 - ligand_b: lig_47 - atom mapping: (9, 24) (10, 21) (11, 22) (12, 23) (13, 18) (14, 19) (15, 20) (16, - 15) (17, 16) (18, 17) (19, 8) (20, 9) (21, 10) (22, 4) (23, 5) (24, 6) (25, - 1) (26, 2) (27, 3) (28, 41) (29, 42) (30, 0) (31, 7) (32, 11) (33, 12) (34, - 13) (35, 14) - score: '0.608' - edge_lig_32_lig_47: - ligand_a: lig_32 - ligand_b: lig_47 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 17) (17, 16) (18, - 18) (19, 19) (20, 20) (21, 21) (22, 23) (23, 22) (24, 24) (39, 41) (40, 42) - score: '0.583' - edge_lig_65_lig_47: - ligand_a: lig_65 - ligand_b: lig_47 - atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 42) (9, 10) - (10, 9) (11, 8) (12, 15) (13, 16) (14, 17) (15, 18) (16, 20) (17, 19) (18, 21) - (19, 22) (20, 23) (21, 24) (39, 12) (40, 13) (41, 14) (42, 7) - score: '0.542' - edge_lig_35_lig_47: - ligand_a: lig_35 - ligand_b: lig_47 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 17) (17, 16) (18, - 18) (19, 19) (20, 20) (21, 21) (22, 23) (23, 22) (24, 24) (39, 41) (40, 42) - score: '0.583' - edge_lig_61_lig_47: - ligand_a: lig_61 - ligand_b: lig_47 - atom mapping: (0, 42) (1, 2) (2, 3) (3, 4) (4, 5) (5, 6) (6, 1) (7, 0) (9, 8) - (10, 9) (11, 10) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, - 18) (19, 20) (20, 19) (21, 21) (22, 22) (23, 23) (24, 24) (42, 41) - score: '0.542' - edge_lig_33_lig_43: - ligand_a: lig_33 - ligand_b: lig_43 - atom mapping: (0, 35) (1, 30) (2, 31) (3, 32) (4, 27) (5, 28) (6, 29) (7, 36) - (8, 24) (9, 25) (10, 26) (11, 37) (12, 38) (13, 39) (14, 40) (15, 21) (16, 23) - (17, 22) (18, 18) (19, 19) (20, 20) (21, 15) (22, 17) (23, 16) (24, 14) (36, - 33) (37, 34) - score: '0.608' - edge_lig_60_lig_47: - ligand_a: lig_60 - ligand_b: lig_47 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 12) (12, 13) (13, 14) (14, 15) (15, 17) (16, 16) (17, 18) (18, - 20) (19, 19) (20, 21) (21, 22) (22, 23) (23, 24) (41, 41) (42, 42) - score: '0.555' - edge_lig_36_lig_43: - ligand_a: lig_36 - ligand_b: lig_43 - atom mapping: (0, 35) (1, 30) (2, 31) (3, 32) (4, 27) (5, 28) (6, 29) (7, 36) - (8, 24) (9, 25) (10, 26) (11, 37) (12, 38) (13, 39) (14, 40) (15, 21) (16, 23) - (17, 22) (18, 18) (19, 19) (20, 20) (21, 15) (22, 17) (23, 16) (24, 14) (42, - 33) (43, 34) - score: '0.561' diff --git a/data/mcl1/03_edges/01_perses_openfe.yml b/data/mcl1/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..d64e38ac2 --- /dev/null +++ b/data/mcl1/03_edges/01_perses_openfe.yml @@ -0,0 +1,172 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_67_lig_43: + ligand_a: lig_67 + ligand_b: lig_43 + atom mapping: {0: 35, 1: 30, 2: 31, 3: 32, 4: 27, 5: 28, 6: 29, 7: 36, 8: 24, + 9: 25, 10: 26, 11: 38, 12: 39, 13: 40, 14: 21, 15: 23, 16: 22, 17: 18, 18: 20, + 19: 19, 20: 15, 21: 16, 22: 17, 23: 14, 41: 33, 42: 34} + score: '0.555' + edge_lig_31_lig_43: + ligand_a: lig_31 + ligand_b: lig_43 + atom mapping: {0: 35, 1: 30, 2: 31, 3: 32, 4: 27, 5: 28, 6: 29, 7: 36, 8: 24, + 9: 25, 10: 26, 11: 37, 12: 38, 13: 39, 14: 40, 15: 21, 16: 23, 17: 22, 18: 18, + 19: 19, 20: 20, 21: 15, 22: 17, 23: 16, 24: 14, 39: 33, 40: 34} + score: '0.583' + edge_lig_63_lig_43: + ligand_a: lig_63 + ligand_b: lig_43 + atom mapping: {0: 36, 1: 29, 2: 30, 3: 31, 4: 32, 5: 27, 6: 28, 7: 24, 8: 25, + 9: 26, 10: 38, 11: 39, 12: 40, 13: 21, 14: 23, 15: 22, 16: 18, 17: 20, 18: 19, + 19: 15, 20: 16, 21: 17, 22: 14, 40: 33, 42: 35} + score: '0.542' + edge_lig_43_lig_27: + ligand_a: lig_43 + ligand_b: lig_27 + atom mapping: {14: 9, 15: 10, 16: 11, 17: 12, 18: 13, 19: 15, 20: 14, 21: 16, + 22: 18, 23: 17, 24: 19, 25: 20, 26: 21, 27: 22, 28: 23, 29: 24, 30: 25, 31: 26, + 32: 27, 33: 28, 34: 29, 35: 30, 36: 31, 37: 32, 38: 33, 39: 34, 40: 35} + score: '0.608' + edge_lig_58_lig_43: + ligand_a: lig_58 + ligand_b: lig_43 + atom mapping: {0: 36, 1: 29, 2: 30, 3: 31, 4: 32, 5: 27, 6: 28, 7: 24, 8: 25, + 9: 26, 14: 38, 15: 39, 16: 40, 17: 21, 18: 23, 19: 22, 20: 18, 21: 20, 22: 19, + 23: 15, 24: 17, 25: 16, 26: 14, 44: 33, 46: 35} + score: '0.531' + edge_lig_35_lig_43: + ligand_a: lig_35 + ligand_b: lig_43 + atom mapping: {0: 35, 1: 30, 2: 31, 3: 32, 4: 27, 5: 28, 6: 29, 7: 36, 8: 24, + 9: 25, 10: 26, 11: 37, 12: 38, 13: 39, 14: 40, 15: 21, 16: 23, 17: 22, 18: 18, + 19: 19, 20: 20, 21: 15, 22: 17, 23: 16, 24: 14, 39: 33, 40: 34} + score: '0.583' + edge_lig_36_lig_43: + ligand_a: lig_36 + ligand_b: lig_43 + atom mapping: {0: 35, 1: 30, 2: 31, 3: 32, 4: 27, 5: 28, 6: 29, 7: 36, 8: 24, + 9: 25, 10: 26, 11: 37, 12: 38, 13: 39, 14: 40, 15: 21, 16: 23, 17: 22, 18: 18, + 19: 19, 20: 20, 21: 15, 22: 17, 23: 16, 24: 14, 42: 33, 43: 34} + score: '0.561' + edge_lig_32_lig_43: + ligand_a: lig_32 + ligand_b: lig_43 + atom mapping: {0: 35, 1: 30, 2: 31, 3: 32, 4: 27, 5: 28, 6: 29, 7: 36, 8: 24, + 9: 25, 10: 26, 11: 37, 12: 38, 13: 39, 14: 40, 15: 21, 16: 23, 17: 22, 18: 18, + 19: 19, 20: 20, 21: 15, 22: 17, 23: 16, 24: 14, 39: 33, 40: 34} + score: '0.583' + edge_lig_50_lig_43: + ligand_a: lig_50 + ligand_b: lig_43 + atom mapping: {0: 34, 1: 31, 2: 32, 3: 27, 4: 28, 5: 29, 6: 30, 7: 35, 9: 24, + 10: 25, 11: 26, 12: 37, 13: 38, 14: 39, 15: 40, 16: 21, 17: 23, 18: 22, 19: 18, + 20: 19, 21: 20, 22: 15, 23: 17, 24: 16, 25: 14, 43: 33} + score: '0.548' + edge_lig_56_lig_43: + ligand_a: lig_56 + ligand_b: lig_43 + atom mapping: {0: 35, 1: 30, 2: 31, 3: 32, 4: 27, 5: 28, 6: 29, 7: 36, 8: 24, + 9: 25, 10: 26, 15: 38, 16: 39, 17: 40, 18: 21, 19: 23, 20: 22, 21: 18, 22: 19, + 23: 20, 24: 15, 25: 16, 26: 17, 27: 14, 45: 33, 46: 34} + score: '0.548' + edge_lig_58_lig_48: + ligand_a: lig_58 + ligand_b: lig_48 + atom mapping: {0: 7, 1: 6, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 7: 8, 8: 9, 9: 10, 14: 12, + 15: 13, 16: 14, 17: 15, 18: 17, 19: 16, 20: 18, 21: 20, 22: 19, 23: 21, 24: 23, + 25: 22, 26: 24, 44: 40, 46: 0} + score: '0.573' + edge_lig_28_lig_43: + ligand_a: lig_28 + ligand_b: lig_43 + atom mapping: {0: 35, 1: 30, 2: 31, 3: 32, 4: 27, 5: 28, 6: 29, 7: 36, 8: 24, + 9: 25, 10: 26, 11: 37, 12: 38, 13: 39, 14: 40, 15: 21, 16: 23, 17: 22, 18: 18, + 19: 19, 20: 20, 21: 15, 22: 17, 23: 16, 24: 14, 39: 33, 40: 34} + score: '0.583' + edge_lig_37_lig_43: + ligand_a: lig_37 + ligand_b: lig_43 + atom mapping: {0: 35, 1: 30, 2: 31, 3: 32, 4: 27, 5: 28, 6: 29, 7: 36, 8: 24, + 9: 25, 10: 26, 11: 37, 12: 38, 13: 39, 14: 40, 15: 21, 16: 23, 17: 22, 18: 18, + 19: 19, 20: 20, 21: 15, 22: 17, 23: 16, 24: 14, 42: 33, 43: 34} + score: '0.561' + edge_lig_58_lig_47: + ligand_a: lig_58 + ligand_b: lig_47 + atom mapping: {0: 7, 1: 6, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 7: 8, 8: 9, 9: 10, 14: 12, + 15: 13, 16: 14, 17: 15, 18: 17, 19: 16, 20: 18, 21: 20, 22: 19, 23: 21, 24: 23, + 25: 22, 26: 24, 44: 41, 46: 0} + score: '0.538' + edge_lig_52_lig_47: + ligand_a: lig_52 + ligand_b: lig_47 + atom mapping: {0: 7, 1: 6, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 7: 8, 8: 9, 9: 10, 10: 11, + 11: 12, 12: 13, 13: 14, 14: 15, 15: 17, 16: 16, 17: 18, 18: 20, 19: 19, 20: 21, + 21: 23, 22: 22, 23: 24, 38: 41, 40: 0} + score: '0.570' + edge_lig_33_lig_43: + ligand_a: lig_33 + ligand_b: lig_43 + atom mapping: {0: 35, 1: 30, 2: 31, 3: 32, 4: 27, 5: 28, 6: 29, 7: 36, 8: 24, + 9: 25, 10: 26, 11: 37, 12: 38, 13: 39, 14: 40, 15: 21, 16: 23, 17: 22, 18: 18, + 19: 19, 20: 20, 21: 15, 22: 17, 23: 16, 24: 14, 36: 33, 37: 34} + score: '0.608' + edge_lig_53_lig_43: + ligand_a: lig_53 + ligand_b: lig_43 + atom mapping: {0: 36, 1: 29, 2: 30, 3: 31, 4: 32, 5: 27, 6: 28, 7: 24, 8: 25, + 9: 26, 10: 37, 11: 38, 12: 39, 13: 40, 14: 21, 15: 23, 16: 22, 17: 18, 18: 20, + 19: 19, 20: 15, 21: 17, 22: 16, 23: 14, 41: 33, 43: 35} + score: '0.548' + edge_lig_34_lig_43: + ligand_a: lig_34 + ligand_b: lig_43 + atom mapping: {0: 35, 1: 30, 2: 31, 3: 32, 4: 27, 5: 28, 6: 29, 7: 36, 8: 24, + 9: 25, 10: 26, 11: 37, 12: 38, 13: 39, 14: 40, 15: 21, 16: 23, 17: 22, 18: 18, + 19: 19, 20: 20, 21: 15, 22: 17, 23: 16, 24: 14, 39: 33, 40: 34} + score: '0.583' + edge_lig_65_lig_43: + ligand_a: lig_65 + ligand_b: lig_43 + atom mapping: {0: 35, 1: 30, 2: 29, 3: 28, 4: 27, 5: 32, 6: 31, 7: 34, 9: 26, + 10: 25, 11: 24, 12: 21, 13: 22, 14: 23, 15: 18, 16: 20, 17: 19, 18: 15, 19: 16, + 20: 17, 21: 14, 39: 38, 40: 39, 41: 40, 42: 36} + score: '0.542' + edge_lig_49_lig_43: + ligand_a: lig_49 + ligand_b: lig_43 + atom mapping: {0: 34, 1: 31, 2: 32, 3: 27, 4: 28, 5: 29, 6: 30, 7: 35, 9: 24, + 10: 25, 11: 26, 12: 37, 13: 38, 14: 39, 15: 40, 16: 21, 17: 23, 18: 22, 19: 18, + 20: 19, 21: 20, 22: 15, 23: 17, 24: 16, 25: 14, 40: 33} + score: '0.570' + edge_lig_58_lig_46: + ligand_a: lig_58 + ligand_b: lig_46 + atom mapping: {0: 7, 1: 6, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 7: 8, 8: 9, 9: 10, 14: 12, + 15: 13, 16: 14, 17: 15, 18: 17, 19: 16, 20: 18, 21: 20, 22: 19, 23: 21, 24: 23, + 25: 22, 26: 24, 44: 43, 46: 0} + score: '0.550' + edge_lig_60_lig_43: + ligand_a: lig_60 + ligand_b: lig_43 + atom mapping: {0: 35, 1: 30, 2: 31, 3: 32, 4: 27, 5: 28, 6: 29, 7: 36, 8: 24, + 9: 25, 10: 26, 11: 38, 12: 39, 13: 40, 14: 21, 15: 23, 16: 22, 17: 18, 18: 20, + 19: 19, 20: 15, 21: 16, 22: 17, 23: 14, 41: 33, 42: 34} + score: '0.555' + edge_lig_61_lig_43: + ligand_a: lig_61 + ligand_b: lig_43 + atom mapping: {0: 34, 1: 31, 2: 32, 3: 27, 4: 28, 5: 29, 6: 30, 7: 35, 9: 24, + 10: 25, 11: 26, 12: 38, 13: 39, 14: 40, 15: 21, 16: 22, 17: 23, 18: 18, 19: 20, + 20: 19, 21: 15, 22: 16, 23: 17, 24: 14, 42: 33} + score: '0.542' + edge_lig_43_lig_30: + ligand_a: lig_43 + ligand_b: lig_30 + atom mapping: {14: 24, 15: 21, 16: 22, 17: 23, 18: 18, 19: 20, 20: 19, 21: 15, + 22: 17, 23: 16, 24: 8, 25: 9, 26: 10, 27: 4, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, + 33: 39, 34: 40, 35: 0, 36: 7, 37: 11, 38: 12, 39: 13, 40: 14} + score: '0.583' diff --git a/data/mcl1/03_edges/nohup.out b/data/mcl1/03_edges/nohup.out deleted file mode 100644 index 6ab1627ad..000000000 --- a/data/mcl1/03_edges/nohup.out +++ /dev/null @@ -1,31 +0,0 @@ -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. -lig_34_lig_47 exceeds 1 A pairwise distance -lig_28_lig_43 exceeds 1 A pairwise distance -lig_56_lig_43 exceeds 1 A pairwise distance -lig_37_lig_43 exceeds 1 A pairwise distance -lig_58_lig_47 exceeds 1 A pairwise distance -lig_52_lig_47 exceeds 1 A pairwise distance -lig_63_lig_47 exceeds 1 A pairwise distance -lig_58_lig_46 exceeds 1 A pairwise distance -lig_50_lig_43 exceeds 1 A pairwise distance -lig_67_lig_47 exceeds 1 A pairwise distance -lig_58_lig_48 exceeds 1 A pairwise distance -lig_30_lig_47 exceeds 1 A pairwise distance -lig_31_lig_47 exceeds 1 A pairwise distance -lig_49_lig_47 exceeds 1 A pairwise distance -lig_27_lig_47 exceeds 1 A pairwise distance -lig_32_lig_47 exceeds 1 A pairwise distance -lig_65_lig_47 exceeds 1 A pairwise distance -lig_35_lig_47 exceeds 1 A pairwise distance -lig_61_lig_47 exceeds 1 A pairwise distance -lig_33_lig_43 exceeds 1 A pairwise distance -lig_60_lig_47 exceeds 1 A pairwise distance -lig_36_lig_43 exceeds 1 A pairwise distance diff --git a/data/p38/03_edges/01_perses_openfe.yaml b/data/p38/03_edges/01_perses_openfe.yaml deleted file mode 100644 index 06e33b1e2..000000000 --- a/data/p38/03_edges/01_perses_openfe.yaml +++ /dev/null @@ -1,225 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph -edges: - edge_lig_p38a_3flw_lig_p38a_2gg: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2gg - atom mapping: (10, 4) (12, 3) (13, 2) (14, 1) (15, 0) (16, 25) (17, 24) (18, 23) - (19, 43) (20, 44) (21, 47) (22, 46) (23, 45) (24, 41) (25, 42) (26, 28) (27, - 29) (28, 30) (29, 39) (31, 37) (32, 38) (33, 35) (34, 36) (35, 33) (36, 34) - (37, 31) (39, 26) (40, 27) - score: '0.670' - edge_lig_p38a_3flw_lig_p38a_2j: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2j - atom mapping: (10, 4) (11, 5) (12, 3) (13, 2) (14, 1) (15, 0) (16, 23) (17, 22) - (18, 21) (19, 43) (20, 44) (21, 45) (22, 46) (23, 47) (24, 41) (25, 42) (26, - 26) (27, 27) (28, 30) (29, 31) (31, 33) (32, 34) (33, 35) (34, 36) (35, 37) - (36, 38) (37, 39) (39, 24) (40, 25) - score: '0.686' - edge_lig_p38a_3flw_lig_p38a_2m: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2m - atom mapping: (10, 4) (12, 3) (13, 2) (14, 1) (15, 0) (16, 23) (17, 22) (18, 21) - (19, 41) (24, 39) (25, 40) (26, 26) (27, 27) (28, 28) (29, 37) (31, 35) (32, - 36) (33, 33) (34, 34) (35, 31) (36, 32) (37, 29) (39, 24) (40, 25) - score: '0.598' - edge_lig_p38a_3fmh_lig_p38a_2g: - ligand_a: lig_p38a_3fmh - ligand_b: lig_p38a_2g - atom mapping: (9, 4) (11, 3) (12, 2) (13, 1) (14, 0) (15, 23) (16, 22) (17, 21) - (18, 41) (19, 42) (20, 43) (21, 44) (22, 45) (23, 39) (24, 40) (25, 26) (26, - 27) (27, 28) (28, 37) (30, 35) (31, 36) (32, 33) (34, 31) (35, 32) (36, 29) - (38, 24) (39, 25) - score: '0.668' - edge_lig_p38a_3flw_lig_p38a_2i: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2i - atom mapping: (10, 4) (11, 5) (12, 3) (13, 2) (14, 1) (15, 0) (16, 23) (17, 22) - (18, 21) (19, 43) (20, 44) (21, 45) (22, 46) (23, 47) (24, 41) (25, 42) (26, - 26) (27, 27) (28, 30) (29, 31) (31, 33) (32, 34) (33, 35) (35, 37) (36, 38) - (37, 39) (39, 24) (40, 25) - score: '0.667' - edge_lig_p38a_2z_lig_p38a_2m: - ligand_a: lig_p38a_2z - ligand_b: lig_p38a_2m - atom mapping: (6, 4) (7, 5) (8, 3) (9, 21) (10, 22) (11, 23) (12, 1) (13, 0) (14, - 2) (15, 24) (16, 25) (17, 26) (18, 27) (19, 28) (20, 37) (22, 35) (23, 36) (24, - 33) (25, 34) (26, 31) (27, 32) (28, 29) (30, 39) (31, 40) (32, 41) - score: '0.641' - edge_lig_p38a_3flw_lig_p38a_2p: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2p - atom mapping: (10, 4) (12, 3) (13, 2) (14, 1) (15, 0) (16, 23) (17, 22) (18, 21) - (19, 41) (20, 42) (22, 44) (23, 43) (24, 39) (25, 40) (26, 26) (27, 27) (28, - 28) (29, 37) (31, 35) (32, 36) (33, 33) (34, 34) (35, 31) (36, 32) (37, 29) - (39, 24) (40, 25) - score: '0.634' - edge_lig_p38a_3flw_lig_p38a_2ff: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2ff - atom mapping: (10, 12) (12, 14) (13, 20) (14, 18) (15, 19) (16, 17) (17, 16) (18, - 15) (19, 38) (20, 39) (21, 42) (22, 41) (23, 40) (24, 36) (25, 37) (26, 23) - (27, 24) (28, 25) (29, 34) (31, 32) (32, 33) (33, 30) (34, 31) (35, 28) (36, - 29) (37, 26) (39, 21) (40, 22) - score: '0.665' - edge_lig_p38a_2v_lig_p38a_2m: - ligand_a: lig_p38a_2v - ligand_b: lig_p38a_2m - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (10, 21) (11, 22) (12, 23) (13, - 24) (14, 25) (15, 26) (16, 27) (17, 28) (18, 37) (20, 35) (21, 36) (22, 33) - (23, 34) (24, 31) (25, 32) (26, 29) (28, 39) (29, 40) (30, 41) - score: '0.718' - edge_lig_p38a_3fmk_lig_p38a_2m: - ligand_a: lig_p38a_3fmk - ligand_b: lig_p38a_2m - atom mapping: (9, 4) (11, 3) (12, 2) (13, 1) (14, 0) (15, 23) (16, 22) (17, 21) - (18, 41) (23, 39) (24, 40) (25, 26) (26, 27) (27, 28) (28, 37) (30, 35) (31, - 36) (32, 33) (33, 34) (34, 31) (35, 32) (36, 29) (38, 24) (39, 25) - score: '0.620' - edge_lig_p38a_3flw_lig_p38a_2t: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2t - atom mapping: (10, 4) (12, 3) (13, 2) (14, 1) (15, 0) (16, 23) (17, 22) (18, 21) - (19, 41) (20, 42) (22, 44) (23, 43) (24, 39) (25, 40) (26, 26) (27, 27) (28, - 28) (29, 37) (31, 35) (32, 36) (33, 33) (34, 34) (35, 31) (36, 32) (37, 29) - (39, 24) (40, 25) - score: '0.665' - edge_lig_p38a_3fmh_lig_p38a_2k: - ligand_a: lig_p38a_3fmh - ligand_b: lig_p38a_2k - atom mapping: (9, 4) (11, 3) (12, 2) (13, 1) (14, 0) (15, 23) (16, 22) (17, 21) - (18, 41) (23, 39) (24, 40) (25, 26) (26, 27) (27, 28) (28, 37) (30, 35) (31, - 36) (32, 33) (33, 34) (34, 31) (35, 32) (36, 29) (38, 24) (39, 25) - score: '0.654' - edge_lig_p38a_3fmh_lig_p38a_3fln: - ligand_a: lig_p38a_3fmh - ligand_b: lig_p38a_3fln - atom mapping: (9, 4) (11, 3) (12, 2) (13, 1) (14, 0) (15, 23) (16, 22) (17, 21) - (18, 41) (19, 42) (20, 43) (21, 44) (22, 45) (23, 39) (24, 40) (25, 26) (26, - 27) (27, 28) (28, 37) (30, 35) (31, 36) (32, 33) (33, 34) (34, 31) (35, 32) - (36, 29) (38, 24) (39, 25) - score: '0.686' - edge_lig_p38a_3fmh_lig_p38a_2e: - ligand_a: lig_p38a_3fmh - ligand_b: lig_p38a_2e - atom mapping: (9, 4) (11, 3) (12, 2) (13, 1) (14, 0) (15, 23) (16, 22) (17, 21) - (18, 41) (19, 42) (20, 43) (21, 44) (22, 45) (23, 39) (24, 40) (25, 26) (26, - 27) (27, 28) (28, 37) (30, 35) (31, 36) (32, 33) (33, 34) (34, 31) (35, 32) - (36, 29) (37, 30) (38, 24) (39, 25) - score: '0.699' - edge_lig_p38a_3flw_lig_p38a_2n: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2n - atom mapping: (10, 33) (11, 34) (12, 32) (13, 50) (14, 51) (15, 52) (16, 29) (17, - 30) (18, 31) (19, 11) (20, 8) (22, 9) (23, 10) (24, 12) (25, 13) (26, 14) (27, - 15) (28, 16) (29, 17) (31, 19) (32, 20) (33, 21) (34, 22) (35, 23) (36, 24) - (37, 25) (39, 27) (40, 28) - score: '0.657' - edge_lig_p38a_2s_lig_p38a_3flw: - ligand_a: lig_p38a_2s - ligand_b: lig_p38a_3flw - atom mapping: (9, 20) (10, 23) (11, 22) (12, 19) (13, 24) (14, 25) (15, 26) (16, - 27) (17, 28) (18, 29) (20, 31) (21, 32) (22, 33) (23, 34) (24, 35) (25, 36) - (26, 37) (28, 39) (29, 40) (30, 16) (31, 17) (32, 18) (33, 12) (34, 10) (51, - 13) (52, 14) (53, 15) - score: '0.641' - edge_lig_p38a_2x_lig_p38a_2m: - ligand_a: lig_p38a_2x - ligand_b: lig_p38a_2m - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (18, 21) (19, 22) (20, - 23) (21, 24) (22, 25) (23, 26) (24, 27) (25, 28) (26, 37) (28, 35) (29, 36) - (30, 33) (31, 34) (32, 31) (33, 32) (34, 29) (36, 39) (37, 40) (38, 41) - score: '0.657' - edge_lig_p38a_2y_lig_p38a_2m: - ligand_a: lig_p38a_2y - ligand_b: lig_p38a_2m - atom mapping: (14, 4) (15, 5) (16, 3) (17, 21) (18, 22) (19, 23) (20, 1) (21, - 0) (22, 2) (23, 24) (24, 25) (25, 26) (26, 27) (27, 28) (28, 37) (30, 35) (31, - 36) (32, 33) (33, 34) (34, 31) (35, 32) (36, 29) (38, 39) (39, 40) (40, 41) - score: '0.641' - edge_lig_p38a_3fly_lig_p38a_2m: - ligand_a: lig_p38a_3fly - ligand_b: lig_p38a_2m - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (16, 21) (17, 22) (18, 23) (19, - 24) (20, 25) (21, 26) (22, 27) (23, 28) (24, 37) (26, 35) (27, 36) (28, 33) - (29, 34) (30, 31) (31, 32) (32, 29) (34, 39) (35, 40) (36, 41) - score: '0.661' - edge_lig_p38a_3flw_lig_p38a_2r: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2r - atom mapping: (10, 36) (12, 35) (13, 53) (14, 54) (15, 55) (16, 32) (17, 33) (18, - 34) (19, 14) (20, 11) (21, 13) (22, 12) (24, 15) (25, 16) (26, 17) (27, 18) - (28, 19) (29, 28) (31, 26) (32, 27) (33, 24) (34, 25) (35, 22) (36, 23) (37, - 20) (39, 30) (40, 31) - score: '0.641' - edge_lig_p38a_3fmh_lig_p38a_2f: - ligand_a: lig_p38a_3fmh - ligand_b: lig_p38a_2f - atom mapping: (9, 4) (11, 3) (12, 2) (13, 1) (14, 0) (15, 23) (16, 22) (17, 21) - (18, 41) (19, 42) (20, 43) (21, 44) (22, 45) (23, 39) (24, 40) (25, 26) (26, - 27) (27, 28) (28, 37) (30, 35) (32, 33) (34, 31) (35, 32) (36, 29) (37, 30) - (38, 24) (39, 25) - score: '0.668' - edge_lig_p38a_3flw_lig_p38a_2o: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2o - atom mapping: (10, 4) (12, 3) (13, 2) (14, 1) (15, 0) (16, 23) (17, 22) (18, 21) - (19, 41) (20, 42) (22, 44) (23, 43) (24, 39) (25, 40) (26, 26) (27, 27) (28, - 28) (29, 37) (31, 35) (32, 36) (33, 33) (34, 34) (35, 31) (36, 32) (37, 29) - (39, 24) (40, 25) - score: '0.638' - edge_lig_p38a_3flw_lig_p38a_2ee: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2ee - atom mapping: (10, 4) (12, 3) (13, 2) (14, 1) (15, 0) (16, 29) (17, 28) (18, 27) - (19, 47) (20, 48) (21, 51) (22, 50) (23, 49) (24, 45) (25, 46) (26, 32) (27, - 33) (28, 34) (29, 43) (31, 41) (32, 42) (33, 39) (34, 40) (35, 37) (36, 38) - (37, 35) (39, 30) (40, 31) - score: '0.657' - edge_lig_p38a_3flw_lig_p38a_2l: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2l - atom mapping: (10, 4) (12, 3) (13, 2) (14, 1) (15, 0) (16, 23) (17, 22) (18, 21) - (19, 41) (20, 42) (22, 44) (23, 43) (24, 39) (25, 40) (26, 26) (27, 27) (28, - 28) (29, 37) (31, 35) (32, 36) (33, 33) (34, 34) (35, 31) (36, 32) (37, 29) - (39, 24) (40, 25) - score: '0.653' - edge_lig_p38a_3fmh_lig_p38a_2h: - ligand_a: lig_p38a_3fmh - ligand_b: lig_p38a_2h - atom mapping: (9, 4) (10, 5) (11, 3) (12, 2) (13, 1) (14, 0) (15, 23) (16, 22) - (17, 21) (18, 41) (19, 42) (20, 43) (21, 44) (22, 45) (23, 39) (24, 40) (25, - 26) (26, 27) (27, 28) (28, 29) (30, 31) (31, 32) (32, 33) (34, 35) (35, 36) - (36, 37) (38, 24) (39, 25) - score: '0.680' - edge_lig_p38a_2bb_lig_p38a_2m: - ligand_a: lig_p38a_2bb - ligand_b: lig_p38a_2m - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (19, 21) (20, 22) (21, 23) (22, - 24) (23, 25) (24, 26) (25, 27) (26, 28) (27, 37) (29, 35) (30, 36) (31, 33) - (32, 34) (33, 31) (34, 32) (35, 29) (37, 39) (38, 40) (39, 41) - score: '0.636' - edge_lig_p38a_2aa_lig_p38a_2m: - ligand_a: lig_p38a_2aa - ligand_b: lig_p38a_2m - atom mapping: (7, 4) (9, 3) (10, 21) (11, 22) (12, 23) (13, 1) (14, 0) (15, 2) - (16, 24) (17, 25) (18, 26) (19, 27) (20, 28) (21, 37) (23, 35) (24, 36) (25, - 33) (26, 34) (27, 31) (28, 32) (29, 29) (31, 39) (32, 40) (33, 41) - score: '0.644' - edge_lig_p38a_3fmh_lig_p38a_3flz: - ligand_a: lig_p38a_3fmh - ligand_b: lig_p38a_3flz - atom mapping: (9, 4) (11, 3) (12, 2) (13, 1) (14, 0) (15, 23) (16, 22) (17, 21) - (18, 41) (19, 42) (20, 43) (21, 44) (22, 45) (23, 39) (24, 40) (25, 26) (26, - 27) (27, 28) (28, 37) (30, 35) (31, 36) (32, 33) (34, 31) (35, 32) (36, 29) - (37, 30) (38, 24) (39, 25) - score: '0.680' - edge_lig_p38a_3fmh_lig_p38a_2m: - ligand_a: lig_p38a_3fmh - ligand_b: lig_p38a_2m - atom mapping: (9, 4) (11, 3) (12, 2) (13, 1) (14, 0) (15, 23) (16, 22) (17, 21) - (18, 41) (23, 39) (24, 40) (25, 26) (26, 27) (27, 28) (28, 37) (30, 35) (31, - 36) (32, 33) (33, 34) (34, 31) (35, 32) (36, 29) (38, 24) (39, 25) - score: '0.620' diff --git a/data/p38/03_edges/01_perses_openfe.yml b/data/p38/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..5202799ef --- /dev/null +++ b/data/p38/03_edges/01_perses_openfe.yml @@ -0,0 +1,207 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_p38a_3flw_lig_p38a_2t: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2t + atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, 19: 41, + 20: 42, 22: 44, 23: 43, 24: 39, 25: 40, 26: 26, 27: 27, 28: 28, 29: 37, 31: 35, + 32: 36, 33: 33, 34: 34, 35: 31, 36: 32, 37: 29, 39: 24, 40: 25} + score: '0.665' + edge_lig_p38a_3fmh_lig_p38a_2f: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_2f + atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, + 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, + 30: 35, 32: 33, 34: 31, 35: 32, 36: 29, 37: 30, 38: 24, 39: 25} + score: '0.668' + edge_lig_p38a_3fmh_lig_p38a_2k: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_2k + atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, + 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, 30: 35, 31: 36, 32: 33, 33: 34, + 34: 31, 35: 32, 36: 29, 38: 24, 39: 25} + score: '0.654' + edge_lig_p38a_3fmh_lig_p38a_2e: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_2e + atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, + 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, + 30: 35, 31: 36, 32: 33, 33: 34, 34: 31, 35: 32, 36: 29, 37: 30, 38: 24, 39: 25} + score: '0.699' + edge_lig_p38a_3flw_lig_p38a_2ff: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2ff + atom mapping: {10: 12, 12: 14, 13: 20, 14: 18, 15: 19, 16: 17, 17: 16, 18: 15, + 19: 38, 20: 39, 21: 42, 22: 41, 23: 40, 24: 36, 25: 37, 26: 23, 27: 24, 28: 25, + 29: 34, 31: 32, 32: 33, 33: 30, 34: 31, 35: 28, 36: 29, 37: 26, 39: 21, 40: 22} + score: '0.665' + edge_lig_p38a_3flw_lig_p38a_2j: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2j + atom mapping: {10: 4, 11: 5, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, + 19: 43, 20: 44, 21: 45, 22: 46, 23: 47, 24: 41, 25: 42, 26: 26, 27: 27, 28: 30, + 29: 31, 31: 33, 32: 34, 33: 35, 34: 36, 35: 37, 36: 38, 37: 39, 39: 24, 40: 25} + score: '0.686' + edge_lig_p38a_3fmh_lig_p38a_2h: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_2h + atom mapping: {9: 4, 10: 5, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, + 18: 41, 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, + 28: 29, 30: 31, 31: 32, 32: 33, 34: 35, 35: 36, 36: 37, 38: 24, 39: 25} + score: '0.680' + edge_lig_p38a_2aa_lig_p38a_2m: + ligand_a: lig_p38a_2aa + ligand_b: lig_p38a_2m + atom mapping: {7: 4, 9: 3, 10: 21, 11: 22, 12: 23, 13: 1, 14: 0, 15: 2, 16: 24, + 17: 25, 18: 26, 19: 27, 20: 28, 21: 37, 23: 35, 24: 36, 25: 33, 26: 34, 27: 31, + 28: 32, 29: 29, 31: 39, 32: 40, 33: 41} + score: '0.644' + edge_lig_p38a_3flw_lig_p38a_2o: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2o + atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, 19: 41, + 20: 42, 22: 44, 23: 43, 24: 39, 25: 40, 26: 26, 27: 27, 28: 28, 29: 37, 31: 35, + 32: 36, 33: 33, 34: 34, 35: 31, 36: 32, 37: 29, 39: 24, 40: 25} + score: '0.638' + edge_lig_p38a_3fmh_lig_p38a_2m: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_2m + atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, + 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, 30: 35, 31: 36, 32: 33, 33: 34, + 34: 31, 35: 32, 36: 29, 38: 24, 39: 25} + score: '0.620' + edge_lig_p38a_2bb_lig_p38a_2m: + ligand_a: lig_p38a_2bb + ligand_b: lig_p38a_2m + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 19: 21, 20: 22, 21: 23, 22: 24, 23: 25, + 24: 26, 25: 27, 26: 28, 27: 37, 29: 35, 30: 36, 31: 33, 32: 34, 33: 31, 34: 32, + 35: 29, 37: 39, 38: 40, 39: 41} + score: '0.636' + edge_lig_p38a_3flw_lig_p38a_2ee: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2ee + atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 29, 17: 28, 18: 27, 19: 47, + 20: 48, 21: 51, 22: 50, 23: 49, 24: 45, 25: 46, 26: 32, 27: 33, 28: 34, 29: 43, + 31: 41, 32: 42, 33: 39, 34: 40, 35: 37, 36: 38, 37: 35, 39: 30, 40: 31} + score: '0.657' + edge_lig_p38a_3flw_lig_p38a_2r: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2r + atom mapping: {10: 36, 12: 35, 13: 53, 14: 54, 15: 55, 16: 32, 17: 33, 18: 34, + 19: 14, 20: 11, 21: 13, 22: 12, 24: 15, 25: 16, 26: 17, 27: 18, 28: 19, 29: 28, + 31: 26, 32: 27, 33: 24, 34: 25, 35: 22, 36: 23, 37: 20, 39: 30, 40: 31} + score: '0.641' + edge_lig_p38a_3flw_lig_p38a_2p: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2p + atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, 19: 41, + 20: 42, 22: 44, 23: 43, 24: 39, 25: 40, 26: 26, 27: 27, 28: 28, 29: 37, 31: 35, + 32: 36, 33: 33, 34: 34, 35: 31, 36: 32, 37: 29, 39: 24, 40: 25} + score: '0.634' + edge_lig_p38a_3flw_lig_p38a_2l: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2l + atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, 19: 41, + 20: 42, 22: 44, 23: 43, 24: 39, 25: 40, 26: 26, 27: 27, 28: 28, 29: 37, 31: 35, + 32: 36, 33: 33, 34: 34, 35: 31, 36: 32, 37: 29, 39: 24, 40: 25} + score: '0.653' + edge_lig_p38a_3fmh_lig_p38a_2g: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_2g + atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, + 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, + 30: 35, 31: 36, 32: 33, 34: 31, 35: 32, 36: 29, 38: 24, 39: 25} + score: '0.668' + edge_lig_p38a_2z_lig_p38a_2m: + ligand_a: lig_p38a_2z + ligand_b: lig_p38a_2m + atom mapping: {6: 4, 7: 5, 8: 3, 9: 21, 10: 22, 11: 23, 12: 1, 13: 0, 14: 2, 15: 24, + 16: 25, 17: 26, 18: 27, 19: 28, 20: 37, 22: 35, 23: 36, 24: 33, 25: 34, 26: 31, + 27: 32, 28: 29, 30: 39, 31: 40, 32: 41} + score: '0.641' + edge_lig_p38a_2v_lig_p38a_2m: + ligand_a: lig_p38a_2v + ligand_b: lig_p38a_2m + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 10: 21, 11: 22, 12: 23, 13: 24, 14: 25, + 15: 26, 16: 27, 17: 28, 18: 37, 20: 35, 21: 36, 22: 33, 23: 34, 24: 31, 25: 32, + 26: 29, 28: 39, 29: 40, 30: 41} + score: '0.718' + edge_lig_p38a_2y_lig_p38a_2m: + ligand_a: lig_p38a_2y + ligand_b: lig_p38a_2m + atom mapping: {14: 4, 15: 5, 16: 3, 17: 21, 18: 22, 19: 23, 20: 1, 21: 0, 22: 2, + 23: 24, 24: 25, 25: 26, 26: 27, 27: 28, 28: 37, 30: 35, 31: 36, 32: 33, 33: 34, + 34: 31, 35: 32, 36: 29, 38: 39, 39: 40, 40: 41} + score: '0.641' + edge_lig_p38a_3fmh_lig_p38a_3flz: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_3flz + atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, + 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, + 30: 35, 31: 36, 32: 33, 34: 31, 35: 32, 36: 29, 37: 30, 38: 24, 39: 25} + score: '0.680' + edge_lig_p38a_3fly_lig_p38a_2m: + ligand_a: lig_p38a_3fly + ligand_b: lig_p38a_2m + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 16: 21, 17: 22, 18: 23, 19: 24, 20: 25, + 21: 26, 22: 27, 23: 28, 24: 37, 26: 35, 27: 36, 28: 33, 29: 34, 30: 31, 31: 32, + 32: 29, 34: 39, 35: 40, 36: 41} + score: '0.661' + edge_lig_p38a_3flw_lig_p38a_2i: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2i + atom mapping: {10: 4, 11: 5, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, + 19: 43, 20: 44, 21: 45, 22: 46, 23: 47, 24: 41, 25: 42, 26: 26, 27: 27, 28: 30, + 29: 31, 31: 33, 32: 34, 33: 35, 35: 37, 36: 38, 37: 39, 39: 24, 40: 25} + score: '0.667' + edge_lig_p38a_3flw_lig_p38a_2m: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2m + atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, 19: 41, + 24: 39, 25: 40, 26: 26, 27: 27, 28: 28, 29: 37, 31: 35, 32: 36, 33: 33, 34: 34, + 35: 31, 36: 32, 37: 29, 39: 24, 40: 25} + score: '0.598' + edge_lig_p38a_3flw_lig_p38a_2n: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2n + atom mapping: {10: 33, 11: 34, 12: 32, 13: 50, 14: 51, 15: 52, 16: 29, 17: 30, + 18: 31, 19: 11, 20: 8, 22: 9, 23: 10, 24: 12, 25: 13, 26: 14, 27: 15, 28: 16, + 29: 17, 31: 19, 32: 20, 33: 21, 34: 22, 35: 23, 36: 24, 37: 25, 39: 27, 40: 28} + score: '0.657' + edge_lig_p38a_3flw_lig_p38a_2gg: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2gg + atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 25, 17: 24, 18: 23, 19: 43, + 20: 44, 21: 47, 22: 46, 23: 45, 24: 41, 25: 42, 26: 28, 27: 29, 28: 30, 29: 39, + 31: 37, 32: 38, 33: 35, 34: 36, 35: 33, 36: 34, 37: 31, 39: 26, 40: 27} + score: '0.670' + edge_lig_p38a_2x_lig_p38a_2m: + ligand_a: lig_p38a_2x + ligand_b: lig_p38a_2m + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 18: 21, 19: 22, 20: 23, 21: 24, + 22: 25, 23: 26, 24: 27, 25: 28, 26: 37, 28: 35, 29: 36, 30: 33, 31: 34, 32: 31, + 33: 32, 34: 29, 36: 39, 37: 40, 38: 41} + score: '0.657' + edge_lig_p38a_2s_lig_p38a_3flw: + ligand_a: lig_p38a_2s + ligand_b: lig_p38a_3flw + atom mapping: {9: 20, 10: 23, 11: 22, 12: 19, 13: 24, 14: 25, 15: 26, 16: 27, + 17: 28, 18: 29, 20: 31, 21: 32, 22: 33, 23: 34, 24: 35, 25: 36, 26: 37, 28: 39, + 29: 40, 30: 16, 31: 17, 32: 18, 33: 12, 34: 10, 51: 13, 52: 14, 53: 15} + score: '0.641' + edge_lig_p38a_3fmk_lig_p38a_2m: + ligand_a: lig_p38a_3fmk + ligand_b: lig_p38a_2m + atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, + 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, 30: 35, 31: 36, 32: 33, 33: 34, + 34: 31, 35: 32, 36: 29, 38: 24, 39: 25} + score: '0.620' + edge_lig_p38a_3fmh_lig_p38a_3fln: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_3fln + atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, + 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, + 30: 35, 31: 36, 32: 33, 33: 34, 34: 31, 35: 32, 36: 29, 38: 24, 39: 25} + score: '0.686' diff --git a/data/p38/03_edges/nohup.out b/data/p38/03_edges/nohup.out deleted file mode 100644 index b0a937e5b..000000000 --- a/data/p38/03_edges/nohup.out +++ /dev/null @@ -1,39 +0,0 @@ -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. -lig_p38a_3flw_lig_p38a_2gg exceeds 1 A pairwise distance -lig_p38a_3flw_lig_p38a_2j exceeds 1 A pairwise distance -lig_p38a_3flw_lig_p38a_2m exceeds 1 A pairwise distance -lig_p38a_3fmh_lig_p38a_2g exceeds 1 A pairwise distance -lig_p38a_3flw_lig_p38a_2i exceeds 1 A pairwise distance -lig_p38a_2z_lig_p38a_2m exceeds 1 A pairwise distance -lig_p38a_3flw_lig_p38a_2p exceeds 1 A pairwise distance -lig_p38a_3flw_lig_p38a_2ff exceeds 1 A pairwise distance -lig_p38a_3flw_lig_p38a_2ff exceeds 1 A pairwise distance -lig_p38a_2v_lig_p38a_2m exceeds 1 A pairwise distance -lig_p38a_3fmk_lig_p38a_2m exceeds 1 A pairwise distance -lig_p38a_3flw_lig_p38a_2t exceeds 1 A pairwise distance -lig_p38a_3fmh_lig_p38a_2k exceeds 1 A pairwise distance -lig_p38a_3fmh_lig_p38a_3fln exceeds 1 A pairwise distance -lig_p38a_3fmh_lig_p38a_2e exceeds 1 A pairwise distance -lig_p38a_3flw_lig_p38a_2n exceeds 1 A pairwise distance -lig_p38a_2s_lig_p38a_3flw exceeds 1 A pairwise distance -lig_p38a_2x_lig_p38a_2m exceeds 1 A pairwise distance -lig_p38a_2y_lig_p38a_2m exceeds 1 A pairwise distance -lig_p38a_3fly_lig_p38a_2m exceeds 1 A pairwise distance -lig_p38a_3flw_lig_p38a_2r exceeds 1 A pairwise distance -lig_p38a_3fmh_lig_p38a_2f exceeds 1 A pairwise distance -lig_p38a_3flw_lig_p38a_2o exceeds 1 A pairwise distance -lig_p38a_3flw_lig_p38a_2ee exceeds 1 A pairwise distance -lig_p38a_3flw_lig_p38a_2l exceeds 1 A pairwise distance -lig_p38a_3fmh_lig_p38a_2h exceeds 1 A pairwise distance -lig_p38a_2bb_lig_p38a_2m exceeds 1 A pairwise distance -lig_p38a_2aa_lig_p38a_2m exceeds 1 A pairwise distance -lig_p38a_3fmh_lig_p38a_3flz exceeds 1 A pairwise distance -lig_p38a_3fmh_lig_p38a_2m exceeds 1 A pairwise distance diff --git a/data/pde2/03_edges/01_perses_openfe.yaml b/data/pde2/03_edges/01_perses_openfe.yaml deleted file mode 100644 index 43e7cfdbd..000000000 --- a/data/pde2/03_edges/01_perses_openfe.yaml +++ /dev/null @@ -1,202 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph -edges: - edge_lig_48271249_lig_48168913: - ligand_a: lig_48271249 - ligand_b: lig_48168913 - atom mapping: (0, 20) (1, 19) (2, 10) (3, 9) (4, 8) (5, 7) (6, 11) (7, 12) (8, - 13) (9, 14) (10, 15) (11, 16) (12, 17) (13, 18) (14, 21) (15, 22) (16, 23) (17, - 24) (18, 25) (19, 26) (20, 27) (21, 2) (22, 3) (23, 4) (24, 5) (25, 6) (26, - 1) (29, 37) (30, 38) (31, 39) (32, 34) (33, 35) (34, 36) (35, 41) (36, 40) (37, - 42) (38, 43) (39, 45) (40, 44) (41, 46) (42, 47) (43, 49) (44, 48) (45, 31) - (46, 33) - score: '0.929' - edge_lig_49582390_lig_49175789: - ligand_a: lig_49582390 - ligand_b: lig_49175789 - atom mapping: (0, 24) (1, 23) (2, 14) (3, 13) (4, 12) (5, 11) (6, 15) (7, 16) - (8, 17) (9, 18) (10, 19) (11, 20) (12, 21) (13, 22) (14, 25) (15, 26) (16, 27) - (17, 28) (18, 29) (19, 30) (20, 31) (21, 9) (22, 10) (23, 5) (24, 6) (25, 7) - (26, 8) (27, 4) (28, 3) (32, 48) (33, 49) (34, 50) (35, 45) (36, 46) (37, 47) - (38, 52) (39, 51) (40, 53) (41, 54) (42, 56) (43, 55) (44, 57) (45, 58) (46, - 60) (47, 59) (48, 44) (49, 42) (52, 41) - score: '0.861' - edge_lig_49582390_lig_49220392: - ligand_a: lig_49582390 - ligand_b: lig_49220392 - atom mapping: (0, 22) (1, 21) (2, 12) (3, 11) (4, 10) (5, 9) (6, 13) (7, 14) (8, - 15) (9, 16) (10, 17) (11, 18) (12, 19) (13, 20) (14, 23) (15, 24) (16, 25) (17, - 26) (18, 27) (19, 28) (20, 29) (21, 7) (22, 8) (23, 3) (24, 4) (25, 5) (26, - 6) (27, 2) (28, 1) (32, 42) (33, 43) (34, 44) (35, 39) (36, 40) (37, 41) (38, - 46) (39, 45) (40, 47) (41, 48) (42, 50) (43, 49) (44, 51) (45, 52) (46, 54) - (47, 53) (48, 38) (49, 36) (52, 35) - score: '0.894' - edge_lig_49582390_lig_49585367: - ligand_a: lig_49582390 - ligand_b: lig_49585367 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, - 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 24) (25, 25) (26, 26) - (27, 27) (28, 28) (32, 32) (33, 33) (34, 34) (35, 35) (36, 36) (37, 37) (38, - 39) (39, 38) (40, 40) (41, 41) (42, 43) (43, 42) (44, 44) (45, 45) (46, 47) - (47, 46) (48, 48) (49, 49) (50, 50) (52, 52) - score: '0.877' - edge_lig_49582390_lig_49396360: - ligand_a: lig_49582390 - ligand_b: lig_49396360 - atom mapping: (0, 23) (1, 22) (2, 13) (3, 12) (4, 11) (5, 10) (6, 14) (7, 15) - (8, 16) (9, 17) (10, 18) (11, 19) (12, 20) (13, 21) (14, 24) (15, 25) (16, 26) - (17, 27) (18, 28) (19, 29) (20, 30) (21, 6) (22, 5) (23, 4) (24, 9) (25, 8) - (26, 7) (27, 3) (28, 2) (32, 44) (33, 45) (34, 46) (35, 41) (36, 42) (37, 43) - (38, 48) (39, 47) (40, 49) (41, 50) (42, 52) (43, 51) (44, 53) (45, 54) (46, - 56) (47, 55) (48, 38) (49, 40) (50, 39) (52, 36) - score: '0.886' - edge_lig_50181001_lig_48168913: - ligand_a: lig_50181001 - ligand_b: lig_48168913 - atom mapping: (5, 4) (6, 3) (7, 2) (8, 1) (9, 6) (10, 5) (12, 7) (13, 8) (14, - 9) (15, 10) (16, 11) (17, 12) (18, 13) (19, 14) (20, 15) (21, 16) (22, 17) (23, - 18) (24, 19) (25, 20) (26, 21) (27, 22) (28, 27) (29, 26) (30, 25) (31, 24) - (32, 23) (42, 31) (44, 34) (45, 35) (46, 36) (47, 37) (48, 38) (49, 39) (50, - 40) (51, 41) (52, 49) (53, 48) (54, 47) (55, 46) (56, 44) (57, 45) (58, 42) - (59, 43) - score: '0.895' - edge_lig_49582390_lig_49932129: - ligand_a: lig_49582390 - ligand_b: lig_49932129 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, - 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 24) (25, 25) (26, 26) - (27, 27) (28, 28) (32, 31) (33, 32) (34, 33) (35, 34) (36, 35) (37, 36) (38, - 38) (39, 37) (40, 39) (41, 40) (42, 42) (43, 41) (44, 43) (45, 44) (46, 46) - (47, 45) (48, 47) (49, 48) (50, 49) (52, 52) - score: '0.886' - edge_lig_49582390_lig_49932714: - ligand_a: lig_49582390 - ligand_b: lig_49932714 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, - 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 24) (25, 25) (26, 26) - (27, 27) (28, 28) (32, 32) (33, 33) (34, 34) (35, 35) (36, 36) (37, 37) (38, - 39) (39, 38) (40, 40) (41, 41) (42, 43) (43, 42) (44, 44) (45, 45) (46, 47) - (47, 46) (48, 48) (49, 49) (50, 50) (52, 51) - score: '0.886' - edge_lig_50181001_lig_43249674: - ligand_a: lig_50181001 - ligand_b: lig_43249674 - atom mapping: (5, 23) (6, 22) (7, 21) (8, 26) (9, 25) (10, 24) (12, 5) (13, 4) - (14, 3) (15, 2) (16, 6) (17, 7) (18, 8) (19, 9) (20, 10) (21, 11) (22, 12) (23, - 13) (24, 1) (25, 0) (26, 14) (27, 15) (28, 20) (29, 19) (30, 18) (31, 17) (32, - 16) (42, 44) (44, 31) (45, 32) (46, 33) (47, 28) (48, 29) (49, 30) (50, 34) - (51, 35) (52, 43) (53, 42) (54, 41) (55, 40) (56, 38) (57, 39) (58, 36) (59, - 37) - score: '0.917' - edge_lig_49582390_lig_50107616: - ligand_a: lig_49582390 - ligand_b: lig_50107616 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, - 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 24) (25, 25) (26, 26) - (27, 27) (28, 28) (32, 32) (33, 33) (34, 34) (35, 35) (36, 36) (37, 37) (38, - 39) (39, 38) (40, 40) (41, 41) (42, 43) (43, 42) (44, 44) (45, 45) (46, 47) - (47, 46) (48, 48) (49, 49) (50, 50) (52, 54) - score: '0.877' - edge_lig_49582390_lig_49580115: - ligand_a: lig_49582390 - ligand_b: lig_49580115 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, - 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 24) (25, 25) (26, 26) - (27, 27) (28, 28) (32, 31) (33, 32) (34, 33) (35, 34) (36, 35) (37, 36) (38, - 38) (39, 37) (40, 39) (41, 40) (42, 42) (43, 41) (44, 43) (45, 44) (46, 46) - (47, 45) (48, 47) (49, 48) (50, 49) (52, 51) - score: '0.915' - edge_lig_50181001_lig_48022468: - ligand_a: lig_50181001 - ligand_b: lig_48022468 - atom mapping: (5, 23) (6, 22) (7, 21) (8, 26) (9, 25) (10, 24) (12, 5) (13, 4) - (14, 3) (15, 2) (16, 6) (17, 7) (18, 8) (19, 9) (20, 10) (21, 11) (22, 12) (23, - 13) (24, 1) (25, 0) (26, 14) (27, 15) (28, 20) (29, 19) (30, 18) (31, 17) (32, - 16) (44, 32) (45, 33) (46, 34) (47, 29) (48, 30) (49, 31) (50, 35) (51, 36) - (52, 44) (53, 43) (54, 42) (55, 41) (56, 39) (57, 40) (58, 37) (59, 38) - score: '0.905' - edge_lig_49137374_lig_48168913: - ligand_a: lig_49137374 - ligand_b: lig_48168913 - atom mapping: (0, 20) (1, 19) (2, 10) (3, 9) (4, 8) (5, 7) (6, 11) (7, 12) (8, - 13) (9, 14) (10, 15) (11, 16) (12, 17) (13, 18) (14, 21) (15, 22) (16, 27) (17, - 26) (18, 25) (19, 24) (20, 23) (21, 2) (22, 1) (23, 6) (24, 5) (25, 4) (26, - 3) (30, 37) (31, 38) (32, 39) (33, 34) (34, 35) (35, 36) (36, 41) (37, 40) (38, - 48) (39, 49) (40, 47) (41, 46) (42, 44) (43, 45) (44, 43) (45, 42) (47, 33) - (48, 32) - score: '0.923' - edge_lig_49582390_lig_49137530: - ligand_a: lig_49582390 - ligand_b: lig_49137530 - atom mapping: (0, 24) (1, 23) (2, 14) (3, 13) (4, 12) (5, 11) (6, 15) (7, 16) - (8, 17) (9, 18) (10, 19) (11, 20) (12, 21) (13, 22) (14, 25) (15, 26) (16, 27) - (17, 28) (18, 29) (19, 30) (20, 31) (21, 7) (22, 6) (23, 5) (24, 10) (25, 9) - (26, 8) (27, 4) (28, 3) (32, 47) (33, 48) (34, 49) (35, 44) (36, 45) (37, 46) - (38, 51) (39, 50) (40, 52) (41, 53) (42, 55) (43, 54) (44, 56) (45, 57) (46, - 59) (47, 58) (48, 41) (49, 43) (50, 42) (52, 39) - score: '0.877' - edge_lig_49582390_lig_49220548: - ligand_a: lig_49582390 - ligand_b: lig_49220548 - atom mapping: (0, 23) (1, 22) (2, 13) (3, 12) (4, 11) (5, 10) (6, 14) (7, 15) - (8, 16) (9, 17) (10, 18) (11, 19) (12, 20) (13, 21) (14, 24) (15, 25) (16, 26) - (17, 27) (18, 28) (19, 29) (20, 30) (21, 8) (22, 9) (23, 4) (24, 5) (25, 6) - (26, 7) (27, 3) (28, 2) (32, 45) (33, 46) (34, 47) (35, 42) (36, 43) (37, 44) - (38, 49) (39, 48) (40, 50) (41, 51) (42, 53) (43, 52) (44, 54) (45, 55) (46, - 57) (47, 56) (48, 41) (49, 39) (52, 37) - score: '0.866' - edge_lig_49582390_lig_50181001: - ligand_a: lig_49582390 - ligand_b: lig_50181001 - atom mapping: (0, 25) (1, 24) (2, 15) (3, 14) (4, 13) (5, 12) (6, 16) (7, 17) - (8, 18) (9, 19) (10, 20) (11, 21) (12, 22) (13, 23) (14, 26) (15, 27) (16, 28) - (17, 29) (18, 30) (19, 31) (20, 32) (21, 7) (22, 6) (23, 5) (24, 10) (25, 9) - (26, 8) (27, 4) (28, 3) (32, 47) (33, 48) (34, 49) (35, 44) (36, 45) (37, 46) - (38, 51) (39, 50) (40, 52) (41, 53) (42, 55) (43, 54) (44, 56) (45, 57) (46, - 59) (47, 58) (48, 42) (50, 43) (52, 40) - score: '0.861' - edge_lig_49582390_lig_49582468: - ligand_a: lig_49582390 - ligand_b: lig_49582468 - atom mapping: (0, 23) (1, 22) (2, 13) (3, 12) (4, 11) (5, 10) (6, 14) (7, 15) - (8, 16) (9, 17) (10, 18) (11, 19) (12, 20) (13, 21) (14, 24) (15, 25) (16, 26) - (17, 27) (18, 28) (19, 29) (20, 30) (21, 6) (22, 5) (23, 4) (24, 9) (25, 8) - (26, 7) (27, 3) (28, 2) (32, 46) (33, 45) (34, 44) (35, 41) (36, 42) (37, 43) - (38, 47) (39, 48) (40, 49) (41, 50) (42, 52) (43, 51) (44, 53) (45, 54) (46, - 56) (47, 55) (48, 38) (49, 40) (50, 39) - score: '0.875' - edge_lig_49582390_lig_49072088: - ligand_a: lig_49582390 - ligand_b: lig_49072088 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, - 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 24) (25, 25) (26, 26) - (27, 27) (28, 28) (32, 31) (33, 32) (34, 33) (35, 34) (36, 35) (37, 36) (38, - 38) (39, 37) (40, 39) (41, 40) (42, 42) (43, 41) (44, 43) (45, 44) (46, 46) - (47, 45) (48, 47) (49, 48) (50, 49) - score: '0.875' - edge_lig_49582390_lig_49175828: - ligand_a: lig_49582390 - ligand_b: lig_49175828 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, - 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 24) (25, 25) (26, 26) - (27, 28) (28, 29) (32, 32) (33, 33) (34, 34) (35, 35) (36, 36) (37, 37) (38, - 39) (39, 38) (40, 40) (41, 41) (42, 43) (43, 42) (44, 44) (45, 45) (46, 47) - (47, 46) (48, 48) (49, 49) - score: '0.855' - edge_lig_49582390_lig_48009208: - ligand_a: lig_49582390 - ligand_b: lig_48009208 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, - 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 24) (25, 25) (26, 26) - (32, 29) (33, 30) (34, 31) (35, 32) (36, 33) (37, 34) (38, 36) (39, 35) (40, - 37) (41, 38) (42, 40) (43, 39) (44, 41) (45, 42) (46, 44) (47, 43) (48, 45) - score: '0.909' diff --git a/data/pde2/03_edges/01_perses_openfe.yml b/data/pde2/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..db2317202 --- /dev/null +++ b/data/pde2/03_edges/01_perses_openfe.yml @@ -0,0 +1,184 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_49137374_lig_48168913: + ligand_a: lig_49137374 + ligand_b: lig_48168913 + atom mapping: {0: 20, 1: 19, 2: 10, 3: 9, 4: 8, 5: 7, 6: 11, 7: 12, 8: 13, 9: 14, + 10: 15, 11: 16, 12: 17, 13: 18, 14: 21, 15: 22, 16: 27, 17: 26, 18: 25, 19: 24, + 20: 23, 21: 2, 22: 1, 23: 6, 24: 5, 25: 4, 26: 3, 30: 37, 31: 38, 32: 39, 33: 34, + 34: 35, 35: 36, 36: 41, 37: 40, 38: 48, 39: 49, 40: 47, 41: 46, 42: 44, 43: 45, + 44: 43, 45: 42, 47: 33, 48: 32} + score: '0.923' + edge_lig_48271249_lig_48168913: + ligand_a: lig_48271249 + ligand_b: lig_48168913 + atom mapping: {0: 20, 1: 19, 2: 10, 3: 9, 4: 8, 5: 7, 6: 11, 7: 12, 8: 13, 9: 14, + 10: 15, 11: 16, 12: 17, 13: 18, 14: 21, 15: 22, 16: 23, 17: 24, 18: 25, 19: 26, + 20: 27, 21: 2, 22: 3, 23: 4, 24: 5, 25: 6, 26: 1, 29: 37, 30: 38, 31: 39, 32: 34, + 33: 35, 34: 36, 35: 41, 36: 40, 37: 42, 38: 43, 39: 45, 40: 44, 41: 46, 42: 47, + 43: 49, 44: 48, 45: 31, 46: 33} + score: '0.929' + edge_lig_49582390_lig_50107616: + ligand_a: lig_49582390 + ligand_b: lig_50107616 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 32, 33: 33, + 34: 34, 35: 35, 36: 36, 37: 37, 38: 39, 39: 38, 40: 40, 41: 41, 42: 43, 43: 42, + 44: 44, 45: 45, 46: 47, 47: 46, 48: 48, 49: 49, 50: 50, 52: 53} + score: '0.877' + edge_lig_49582390_lig_50181001: + ligand_a: lig_49582390 + ligand_b: lig_50181001 + atom mapping: {0: 25, 1: 24, 2: 15, 3: 14, 4: 13, 5: 12, 6: 16, 7: 17, 8: 18, + 9: 19, 10: 20, 11: 21, 12: 22, 13: 23, 14: 26, 15: 27, 16: 28, 17: 29, 18: 30, + 19: 31, 20: 32, 21: 7, 22: 6, 23: 5, 24: 10, 25: 9, 26: 8, 27: 4, 28: 3, 32: 47, + 33: 48, 34: 49, 35: 44, 36: 45, 37: 46, 38: 51, 39: 50, 40: 52, 41: 53, 42: 55, + 43: 54, 44: 56, 45: 57, 46: 59, 47: 58, 48: 42, 50: 43, 52: 40} + score: '0.861' + edge_lig_49582390_lig_49396360: + ligand_a: lig_49582390 + ligand_b: lig_49396360 + atom mapping: {0: 23, 1: 22, 2: 13, 3: 12, 4: 11, 5: 10, 6: 14, 7: 15, 8: 16, + 9: 17, 10: 18, 11: 19, 12: 20, 13: 21, 14: 24, 15: 25, 16: 26, 17: 27, 18: 28, + 19: 29, 20: 30, 21: 6, 22: 5, 23: 4, 24: 9, 25: 8, 26: 7, 27: 3, 28: 2, 32: 44, + 33: 45, 34: 46, 35: 41, 36: 42, 37: 43, 38: 48, 39: 47, 40: 49, 41: 50, 42: 52, + 43: 51, 44: 53, 45: 54, 46: 56, 47: 55, 48: 38, 49: 40, 50: 39, 52: 37} + score: '0.886' + edge_lig_49582390_lig_48009208: + ligand_a: lig_49582390 + ligand_b: lig_48009208 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 26, 23: 25, 24: 24, 25: 23, 26: 22, 32: 29, 33: 30, 34: 31, 35: 32, + 36: 33, 37: 34, 38: 36, 39: 35, 40: 37, 41: 38, 42: 40, 43: 39, 44: 41, 45: 42, + 46: 44, 47: 43, 50: 45} + score: '0.909' + edge_lig_50181001_lig_43249674: + ligand_a: lig_50181001 + ligand_b: lig_43249674 + atom mapping: {5: 23, 6: 22, 7: 21, 8: 26, 9: 25, 10: 24, 12: 5, 13: 4, 14: 3, + 15: 2, 16: 6, 17: 7, 18: 8, 19: 9, 20: 10, 21: 11, 22: 12, 23: 13, 24: 1, 25: 0, + 26: 14, 27: 15, 28: 20, 29: 19, 30: 18, 31: 17, 32: 16, 42: 44, 44: 31, 45: 32, + 46: 33, 47: 28, 48: 29, 49: 30, 50: 34, 51: 35, 52: 43, 53: 42, 54: 41, 55: 40, + 56: 38, 57: 39, 58: 36, 59: 37} + score: '0.917' + edge_lig_50181001_lig_48022468: + ligand_a: lig_50181001 + ligand_b: lig_48022468 + atom mapping: {5: 23, 6: 22, 7: 21, 8: 26, 9: 25, 10: 24, 12: 5, 13: 4, 14: 3, + 15: 2, 16: 6, 17: 7, 18: 8, 19: 9, 20: 10, 21: 11, 22: 12, 23: 13, 24: 1, 25: 0, + 26: 14, 27: 15, 28: 20, 29: 19, 30: 18, 31: 17, 32: 16, 44: 32, 45: 33, 46: 34, + 47: 29, 48: 30, 49: 31, 50: 35, 51: 36, 52: 44, 53: 43, 54: 42, 55: 41, 56: 39, + 57: 40, 58: 37, 59: 38} + score: '0.905' + edge_lig_49582390_lig_49220392: + ligand_a: lig_49582390 + ligand_b: lig_49220392 + atom mapping: {0: 22, 1: 21, 2: 12, 3: 11, 4: 10, 5: 9, 6: 13, 7: 14, 8: 15, 9: 16, + 10: 17, 11: 18, 12: 19, 13: 20, 14: 23, 15: 24, 16: 25, 17: 26, 18: 27, 19: 28, + 20: 29, 21: 7, 22: 8, 23: 3, 24: 4, 25: 5, 26: 6, 27: 2, 28: 1, 32: 42, 33: 43, + 34: 44, 35: 39, 36: 40, 37: 41, 38: 46, 39: 45, 40: 47, 41: 48, 42: 50, 43: 49, + 44: 51, 45: 52, 46: 54, 47: 53, 48: 38, 49: 36, 52: 35} + score: '0.894' + edge_lig_49582390_lig_49137530: + ligand_a: lig_49582390 + ligand_b: lig_49137530 + atom mapping: {0: 24, 1: 23, 2: 14, 3: 13, 4: 12, 5: 11, 6: 15, 7: 16, 8: 17, + 9: 18, 10: 19, 11: 20, 12: 21, 13: 22, 14: 25, 15: 26, 16: 27, 17: 28, 18: 29, + 19: 30, 20: 31, 21: 7, 22: 6, 23: 5, 24: 10, 25: 9, 26: 8, 27: 4, 28: 3, 32: 47, + 33: 48, 34: 49, 35: 44, 36: 45, 37: 46, 38: 51, 39: 50, 40: 52, 41: 53, 42: 55, + 43: 54, 44: 56, 45: 57, 46: 59, 47: 58, 48: 41, 49: 43, 50: 42, 52: 39} + score: '0.877' + edge_lig_49582390_lig_49582468: + ligand_a: lig_49582390 + ligand_b: lig_49582468 + atom mapping: {0: 23, 1: 22, 2: 13, 3: 12, 4: 11, 5: 10, 6: 14, 7: 15, 8: 16, + 9: 17, 10: 18, 11: 19, 12: 20, 13: 21, 14: 24, 15: 25, 16: 26, 17: 27, 18: 28, + 19: 29, 20: 30, 21: 6, 22: 5, 23: 4, 24: 9, 25: 8, 26: 7, 27: 3, 28: 2, 32: 46, + 33: 45, 34: 44, 35: 41, 36: 42, 37: 43, 38: 47, 39: 48, 40: 49, 41: 50, 42: 52, + 43: 51, 44: 53, 45: 54, 46: 56, 47: 55, 48: 38, 49: 40, 50: 39} + score: '0.875' + edge_lig_49582390_lig_49220548: + ligand_a: lig_49582390 + ligand_b: lig_49220548 + atom mapping: {0: 23, 1: 22, 2: 13, 3: 12, 4: 11, 5: 10, 6: 14, 7: 15, 8: 16, + 9: 17, 10: 18, 11: 19, 12: 20, 13: 21, 14: 24, 15: 25, 16: 26, 17: 27, 18: 28, + 19: 29, 20: 30, 21: 8, 22: 9, 23: 4, 24: 5, 25: 6, 26: 7, 27: 3, 28: 2, 32: 45, + 33: 46, 34: 47, 35: 42, 36: 43, 37: 44, 38: 49, 39: 48, 40: 50, 41: 51, 42: 53, + 43: 52, 44: 54, 45: 55, 46: 57, 47: 56, 48: 41, 49: 39, 52: 37} + score: '0.866' + edge_lig_50181001_lig_48168913: + ligand_a: lig_50181001 + ligand_b: lig_48168913 + atom mapping: {5: 4, 6: 3, 7: 2, 8: 1, 9: 6, 10: 5, 12: 7, 13: 8, 14: 9, 15: 10, + 16: 11, 17: 12, 18: 13, 19: 14, 20: 15, 21: 16, 22: 17, 23: 18, 24: 19, 25: 20, + 26: 21, 27: 22, 28: 27, 29: 26, 30: 25, 31: 24, 32: 23, 42: 31, 44: 34, 45: 35, + 46: 36, 47: 37, 48: 38, 49: 39, 50: 40, 51: 41, 52: 49, 53: 48, 54: 47, 55: 46, + 56: 44, 57: 45, 58: 42, 59: 43} + score: '0.895' + edge_lig_49582390_lig_49932714: + ligand_a: lig_49582390 + ligand_b: lig_49932714 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 32, 33: 33, + 34: 34, 35: 35, 36: 36, 37: 37, 38: 39, 39: 38, 40: 40, 41: 41, 42: 43, 43: 42, + 44: 44, 45: 45, 46: 47, 47: 46, 48: 48, 49: 49, 50: 50, 52: 51} + score: '0.886' + edge_lig_49582390_lig_49932129: + ligand_a: lig_49582390 + ligand_b: lig_49932129 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 31, 33: 32, + 34: 33, 35: 34, 36: 35, 37: 36, 38: 38, 39: 37, 40: 39, 41: 40, 42: 42, 43: 41, + 44: 43, 45: 44, 46: 46, 47: 45, 48: 47, 49: 48, 50: 49, 52: 53} + score: '0.886' + edge_lig_49582390_lig_49072088: + ligand_a: lig_49582390 + ligand_b: lig_49072088 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 31, 33: 32, + 34: 33, 35: 34, 36: 35, 37: 36, 38: 38, 39: 37, 40: 39, 41: 40, 42: 42, 43: 41, + 44: 43, 45: 44, 46: 46, 47: 45, 48: 47, 49: 48, 50: 49} + score: '0.875' + edge_lig_49582390_lig_49580115: + ligand_a: lig_49582390 + ligand_b: lig_49580115 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 31, 33: 32, + 34: 33, 35: 34, 36: 35, 37: 36, 38: 38, 39: 37, 40: 39, 41: 40, 42: 42, 43: 41, + 44: 43, 45: 44, 46: 46, 47: 45, 48: 47, 49: 48, 50: 49, 52: 50} + score: '0.915' + edge_lig_49582390_lig_49585367: + ligand_a: lig_49582390 + ligand_b: lig_49585367 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 32, 33: 33, + 34: 34, 35: 35, 36: 36, 37: 37, 38: 39, 39: 38, 40: 40, 41: 41, 42: 43, 43: 42, + 44: 44, 45: 45, 46: 47, 47: 46, 48: 48, 49: 49, 50: 50, 52: 52} + score: '0.877' + edge_lig_49582390_lig_49175789: + ligand_a: lig_49582390 + ligand_b: lig_49175789 + atom mapping: {0: 24, 1: 23, 2: 14, 3: 13, 4: 12, 5: 11, 6: 15, 7: 16, 8: 17, + 9: 18, 10: 19, 11: 20, 12: 21, 13: 22, 14: 25, 15: 26, 16: 27, 17: 28, 18: 29, + 19: 30, 20: 31, 21: 9, 22: 10, 23: 5, 24: 6, 25: 7, 26: 8, 27: 4, 28: 3, 32: 48, + 33: 49, 34: 50, 35: 45, 36: 46, 37: 47, 38: 52, 39: 51, 40: 53, 41: 54, 42: 56, + 43: 55, 44: 57, 45: 58, 46: 60, 47: 59, 48: 44, 49: 42, 52: 40} + score: '0.861' + edge_lig_49582390_lig_49175828: + ligand_a: lig_49582390 + ligand_b: lig_49175828 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 28, 28: 29, 32: 32, 33: 33, + 34: 34, 35: 35, 36: 36, 37: 37, 38: 39, 39: 38, 40: 40, 41: 41, 42: 43, 43: 42, + 44: 44, 45: 45, 46: 47, 47: 46, 48: 48, 49: 49} + score: '0.855' diff --git a/data/pde2/03_edges/nohup.out b/data/pde2/03_edges/nohup.out deleted file mode 100644 index 7f1311d96..000000000 --- a/data/pde2/03_edges/nohup.out +++ /dev/null @@ -1,29 +0,0 @@ -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. -lig_48271249_lig_48168913 exceeds 1 A pairwise distance -lig_49582390_lig_49175789 exceeds 1 A pairwise distance -lig_49582390_lig_49220392 exceeds 1 A pairwise distance -lig_49582390_lig_49585367 exceeds 1 A pairwise distance -lig_49582390_lig_49396360 exceeds 1 A pairwise distance -lig_50181001_lig_48168913 exceeds 1 A pairwise distance -lig_49582390_lig_49932129 exceeds 1 A pairwise distance -lig_49582390_lig_49932714 exceeds 1 A pairwise distance -lig_50181001_lig_43249674 exceeds 1 A pairwise distance -lig_49582390_lig_50107616 exceeds 1 A pairwise distance -lig_49582390_lig_49580115 exceeds 1 A pairwise distance -lig_50181001_lig_48022468 exceeds 1 A pairwise distance -lig_49137374_lig_48168913 exceeds 1 A pairwise distance -lig_49582390_lig_49137530 exceeds 1 A pairwise distance -lig_49582390_lig_49220548 exceeds 1 A pairwise distance -lig_49582390_lig_50181001 exceeds 1 A pairwise distance -lig_49582390_lig_49582468 exceeds 1 A pairwise distance -lig_49582390_lig_49072088 exceeds 1 A pairwise distance -lig_49582390_lig_49175828 exceeds 1 A pairwise distance -lig_49582390_lig_48009208 exceeds 1 A pairwise distance diff --git a/data/pfkfb3/03_edges/01_perses_openfe.yaml b/data/pfkfb3/03_edges/01_perses_openfe.yaml deleted file mode 100644 index 2527ce342..000000000 --- a/data/pfkfb3/03_edges/01_perses_openfe.yaml +++ /dev/null @@ -1,279 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph -edges: - edge_lig_29_lig_38: - ligand_a: lig_29 - ligand_b: lig_38 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 49) (5, 50) (6, 30) (7, 31) (8, - 32) (9, 33) (10, 41) (11, 42) (12, 44) (13, 43) (14, 45) (15, 46) (16, 47) (17, - 48) (18, 39) (19, 40) (20, 37) (21, 38) (22, 36) (24, 34) (25, 35) (26, 28) - (27, 29) (28, 8) (47, 4) (48, 5) (49, 6) (50, 7) - score: '0.656' - edge_lig_19_lig_41: - ligand_a: lig_19 - ligand_b: lig_41 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 45) (5, 46) (6, 26) (7, 27) (8, - 28) (9, 29) (10, 30) (11, 31) (12, 32) (14, 33) (15, 34) (16, 35) (17, 36) (18, - 37) (20, 24) (21, 25) (22, 8) (41, 4) (42, 5) (43, 6) (44, 7) - score: '0.595' - edge_lig_58_lig_59: - ligand_a: lig_58 - ligand_b: lig_59 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (25, - 26) (26, 27) (27, 28) (28, 29) (29, 30) (30, 31) (31, 32) (32, 33) (33, 34) - (34, 35) (35, 36) (36, 37) (37, 38) (38, 39) (39, 40) (40, 42) (41, 41) (42, - 43) (43, 44) (44, 45) (45, 46) (46, 47) (47, 48) - score: '0.674' - edge_lig_24_lig_38: - ligand_a: lig_24 - ligand_b: lig_38 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, - 28) (28, 29) (29, 30) (30, 31) (31, 32) (32, 33) (33, 41) (35, 39) (36, 40) - (37, 37) (38, 38) (39, 36) (41, 34) (44, 49) (45, 50) - score: '0.584' - edge_lig_46_lig_24: - ligand_a: lig_46 - ligand_b: lig_24 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (23, - 27) (24, 28) (25, 29) (26, 30) (27, 31) (28, 32) (29, 41) (31, 39) (32, 37) - (33, 38) (34, 35) (35, 36) (36, 33) (44, 44) (45, 45) - score: '0.580' - edge_lig_24_lig_42: - ligand_a: lig_24 - ligand_b: lig_42 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, - 24) (28, 25) (29, 26) (30, 27) (31, 28) (32, 29) (33, 37) (35, 35) (36, 36) - (37, 33) (38, 34) (39, 32) (41, 30) (44, 45) (45, 46) - score: '0.587' - edge_lig_56_lig_38: - ligand_a: lig_56 - ligand_b: lig_38 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (30, - 28) (31, 29) (32, 30) (33, 31) (34, 32) (35, 33) (36, 34) (37, 35) (38, 36) - (39, 37) (40, 38) (41, 39) (42, 40) (43, 41) (44, 42) (45, 43) (46, 44) (47, - 45) (48, 46) (49, 47) (50, 48) (51, 49) (52, 50) - score: '0.652' - edge_lig_38_lig_36: - ligand_a: lig_38 - ligand_b: lig_36 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (28, - 27) (29, 28) (30, 29) (31, 30) (33, 31) (34, 45) (35, 46) (36, 44) (37, 42) - (38, 43) (39, 40) (40, 41) (41, 32) (42, 33) (43, 35) (44, 34) (45, 36) (46, - 39) (47, 38) (48, 37) (49, 51) (50, 52) - score: '0.642' - edge_lig_69_lig_24: - ligand_a: lig_69 - ligand_b: lig_24 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (26, - 27) (27, 28) (28, 29) (29, 30) (30, 31) (31, 32) (32, 33) (40, 35) (41, 36) - (42, 37) (43, 38) (44, 39) (45, 41) (47, 44) (48, 45) - score: '0.580' - edge_lig_24_lig_43: - ligand_a: lig_24 - ligand_b: lig_43 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, - 20) (28, 21) (29, 22) (30, 23) (31, 24) (32, 25) (33, 33) (35, 31) (36, 32) - (37, 29) (38, 30) (39, 28) (41, 26) (44, 41) (45, 42) - score: '0.608' - edge_lig_26_lig_59: - ligand_a: lig_26 - ligand_b: lig_59 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, - 26) (28, 27) (29, 28) (30, 29) (31, 30) (32, 31) (33, 39) (34, 40) (35, 41) - (36, 43) (39, 37) (40, 38) (41, 35) (42, 36) (43, 34) (45, 32) (46, 33) (47, - 47) (48, 48) - score: '0.618' - edge_lig_41_lig_64: - ligand_a: lig_41 - ligand_b: lig_64 - atom mapping: (0, 39) (1, 38) (2, 40) (3, 33) (4, 34) (5, 35) (6, 36) (7, 37) - (8, 9) (24, 10) (25, 11) (26, 12) (27, 13) (28, 14) (29, 15) (30, 29) (31, 30) - (32, 28) (33, 26) (34, 27) (35, 24) (36, 25) (37, 16) (38, 17) (39, 19) (40, - 18) (41, 20) (42, 23) (43, 22) (44, 21) (45, 31) (46, 32) - score: '0.696' - edge_lig_38_lig_37: - ligand_a: lig_38 - ligand_b: lig_37 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (28, - 27) (29, 28) (30, 29) (31, 30) (32, 31) (33, 32) (34, 33) (35, 34) (36, 35) - (37, 36) (38, 37) (39, 38) (40, 39) (41, 40) (42, 41) (44, 42) (45, 43) (49, - 60) (50, 61) - score: '0.578' - edge_lig_24_lig_49: - ligand_a: lig_24 - ligand_b: lig_49 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, - 22) (28, 23) (29, 24) (30, 25) (31, 26) (32, 27) (33, 35) (35, 33) (36, 34) - (37, 31) (38, 32) (39, 30) (41, 28) (44, 43) (45, 44) - score: '0.594' - edge_lig_59_lig_31: - ligand_a: lig_59 - ligand_b: lig_31 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 44) (5, 45) (6, 46) (7, 47) (8, - 25) (26, 23) (27, 24) (28, 6) (29, 7) (30, 8) (31, 9) (32, 10) (33, 11) (34, - 12) (35, 13) (36, 14) (37, 15) (38, 16) (39, 17) (40, 18) (43, 19) (44, 22) - (45, 21) (46, 20) (47, 4) (48, 5) - score: '0.642' - edge_lig_24_lig_41: - ligand_a: lig_24 - ligand_b: lig_41 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, - 24) (28, 25) (29, 26) (30, 27) (31, 28) (32, 29) (33, 37) (35, 35) (36, 36) - (37, 33) (38, 34) (39, 32) (41, 30) (44, 45) (45, 46) - score: '0.577' - edge_lig_34_lig_59: - ligand_a: lig_34 - ligand_b: lig_59 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, - 26) (28, 27) (29, 28) (30, 29) (31, 30) (32, 31) (33, 39) (34, 40) (35, 41) - (36, 43) (39, 37) (40, 38) (41, 35) (42, 36) (43, 34) (44, 32) (45, 33) (46, - 47) (47, 48) - score: '0.625' - edge_lig_54_lig_38: - ligand_a: lig_54 - ligand_b: lig_38 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 49) (5, 50) (6, 30) (7, 31) (8, - 32) (9, 33) (10, 34) (11, 35) (12, 36) (13, 37) (14, 38) (15, 39) (16, 40) (17, - 41) (18, 42) (19, 44) (20, 43) (21, 45) (22, 48) (23, 47) (24, 46) (25, 28) - (26, 29) (27, 8) (52, 4) (53, 5) (54, 6) (55, 7) - score: '0.649' - edge_lig_24_lig_59: - ligand_a: lig_24 - ligand_b: lig_59 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, - 26) (28, 27) (29, 28) (30, 29) (31, 30) (32, 31) (33, 39) (35, 37) (36, 38) - (37, 35) (38, 36) (39, 34) (41, 32) (44, 47) (45, 48) - score: '0.578' - edge_lig_24_lig_39: - ligand_a: lig_24 - ligand_b: lig_39 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, - 22) (28, 23) (29, 24) (30, 25) (31, 26) (32, 27) (33, 35) (35, 33) (36, 34) - (37, 31) (38, 32) (39, 30) (41, 28) (44, 43) (45, 44) - score: '0.594' - edge_lig_24_lig_65: - ligand_a: lig_24 - ligand_b: lig_65 - atom mapping: (0, 37) (1, 36) (2, 38) (3, 31) (4, 32) (5, 33) (6, 34) (7, 35) - (8, 7) (27, 8) (28, 9) (29, 10) (30, 11) (31, 12) (32, 13) (33, 21) (35, 19) - (36, 20) (37, 17) (38, 18) (39, 16) (41, 14) (44, 29) (45, 30) - score: '0.590' - edge_lig_67_lig_24: - ligand_a: lig_67 - ligand_b: lig_24 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (24, - 27) (25, 28) (26, 29) (27, 30) (28, 31) (29, 32) (30, 41) (32, 39) (33, 37) - (34, 38) (35, 35) (36, 36) (37, 33) (45, 44) (46, 45) - score: '0.580' - edge_lig_24_lig_20: - ligand_a: lig_24 - ligand_b: lig_20 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, - 24) (28, 25) (29, 26) (30, 27) (31, 28) (32, 29) (33, 37) (35, 35) (36, 36) - (37, 33) (38, 34) (39, 32) (41, 30) (44, 45) (45, 46) - score: '0.587' - edge_lig_55_lig_38: - ligand_a: lig_55 - ligand_b: lig_38 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 49) (5, 50) (6, 30) (7, 31) (8, - 32) (9, 33) (10, 34) (11, 35) (12, 36) (13, 37) (14, 38) (15, 39) (16, 40) (17, - 41) (18, 42) (19, 44) (20, 43) (21, 45) (22, 48) (23, 47) (24, 46) (25, 28) - (26, 29) (27, 8) (46, 4) (47, 5) (48, 6) (49, 7) - score: '0.659' - edge_lig_35_lig_38: - ligand_a: lig_35 - ligand_b: lig_38 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 49) (5, 50) (6, 30) (7, 31) (8, - 32) (9, 33) (10, 41) (11, 42) (12, 44) (13, 43) (14, 45) (15, 46) (16, 47) (17, - 48) (18, 39) (19, 40) (20, 37) (21, 38) (22, 36) (23, 34) (24, 35) (25, 28) - (26, 29) (27, 8) (46, 4) (47, 5) (48, 6) (49, 7) - score: '0.663' - edge_lig_24_lig_47: - ligand_a: lig_24 - ligand_b: lig_47 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 45) (5, 46) (6, 47) (7, 48) (8, - 27) (27, 25) (28, 26) (29, 6) (30, 7) (31, 8) (32, 9) (33, 17) (35, 15) (36, - 16) (37, 13) (38, 14) (39, 12) (41, 10) (44, 4) (45, 5) - score: '0.587' - edge_lig_33_lig_41: - ligand_a: lig_33 - ligand_b: lig_41 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 45) (5, 46) (6, 26) (7, 27) (8, - 28) (9, 29) (10, 37) (11, 38) (13, 35) (14, 36) (15, 33) (16, 34) (17, 32) (18, - 30) (19, 31) (20, 24) (21, 25) (22, 8) (41, 4) (42, 5) (43, 6) (44, 7) - score: '0.612' - edge_lig_24_lig_63: - ligand_a: lig_24 - ligand_b: lig_63 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, - 21) (28, 22) (29, 23) (30, 24) (31, 25) (32, 26) (33, 27) (35, 35) (36, 36) - (37, 37) (38, 38) (39, 39) (41, 40) (44, 42) (45, 43) - score: '0.597' - edge_lig_57_lig_38: - ligand_a: lig_57 - ligand_b: lig_38 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, - 28) (28, 29) (29, 30) (30, 31) (31, 32) (32, 33) (33, 34) (34, 35) (35, 36) - (36, 37) (37, 38) (38, 39) (39, 40) (40, 41) (41, 42) (42, 44) (43, 43) (44, - 45) (45, 48) (46, 47) (47, 46) (48, 49) (49, 50) - score: '0.656' - edge_lig_70_lig_24: - ligand_a: lig_70 - ligand_b: lig_24 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (26, - 27) (27, 28) (28, 29) (29, 30) (30, 31) (31, 32) (32, 33) (40, 35) (41, 36) - (42, 37) (43, 38) (44, 39) (45, 41) (47, 44) (48, 45) - score: '0.580' - edge_lig_24_lig_44: - ligand_a: lig_24 - ligand_b: lig_44 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, - 20) (28, 21) (29, 22) (30, 23) (31, 24) (32, 25) (33, 33) (35, 31) (36, 32) - (37, 29) (38, 30) (39, 28) (41, 26) (44, 41) (45, 42) - score: '0.608' - edge_lig_53_lig_38: - ligand_a: lig_53 - ligand_b: lig_38 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (33, - 28) (34, 29) (35, 30) (36, 31) (37, 32) (38, 33) (39, 34) (40, 35) (41, 36) - (42, 37) (43, 38) (44, 39) (45, 40) (46, 41) (47, 42) (48, 44) (49, 43) (50, - 45) (51, 48) (52, 47) (53, 46) (54, 49) (55, 50) - score: '0.649' - edge_lig_24_lig_48: - ligand_a: lig_24 - ligand_b: lig_48 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, - 24) (28, 25) (29, 26) (30, 27) (31, 28) (32, 29) (33, 37) (35, 35) (36, 36) - (37, 33) (38, 34) (39, 32) (41, 30) (44, 45) (45, 46) - score: '0.587' - edge_lig_59_lig_30: - ligand_a: lig_59 - ligand_b: lig_30 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 44) (5, 45) (6, 46) (7, 47) (8, - 25) (26, 23) (27, 24) (28, 6) (29, 7) (30, 8) (31, 9) (32, 21) (33, 22) (34, - 19) (35, 17) (36, 18) (37, 16) (39, 10) (40, 11) (43, 12) (44, 15) (45, 14) - (46, 13) (47, 4) (48, 5) - score: '0.631' - edge_lig_41_lig_23: - ligand_a: lig_41 - ligand_b: lig_23 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 40) (5, 41) (6, 42) (7, 43) (8, - 21) (24, 19) (25, 20) (26, 6) (27, 7) (28, 8) (29, 9) (30, 10) (31, 11) (32, - 12) (33, 13) (34, 14) (35, 15) (36, 16) (37, 17) (45, 4) (46, 5) - score: '0.602' - edge_lig_52_lig_38: - ligand_a: lig_52 - ligand_b: lig_38 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (30, - 28) (31, 29) (32, 30) (33, 31) (34, 32) (35, 33) (36, 34) (37, 35) (38, 36) - (39, 37) (40, 38) (41, 39) (42, 40) (43, 41) (44, 42) (45, 44) (46, 43) (47, - 45) (48, 48) (49, 47) (50, 46) (51, 49) (52, 50) - score: '0.652' - edge_lig_24_lig_62: - ligand_a: lig_24 - ligand_b: lig_62 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, - 21) (28, 22) (29, 23) (30, 24) (31, 25) (32, 26) (33, 27) (35, 35) (36, 36) - (37, 37) (38, 38) (39, 39) (41, 40) (44, 42) (45, 43) - score: '0.597' diff --git a/data/pfkfb3/03_edges/01_perses_openfe.yml b/data/pfkfb3/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..0e07df5f6 --- /dev/null +++ b/data/pfkfb3/03_edges/01_perses_openfe.yml @@ -0,0 +1,273 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_24_lig_44: + ligand_a: lig_24 + ligand_b: lig_44 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 20, 28: 21, + 29: 22, 30: 23, 31: 24, 32: 25, 33: 33, 35: 31, 36: 32, 37: 29, 38: 30, 39: 28, + 41: 26, 44: 41, 45: 42} + score: '0.608' + edge_lig_19_lig_41: + ligand_a: lig_19 + ligand_b: lig_41 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 45, 5: 46, 6: 26, 7: 27, 8: 28, 9: 29, + 10: 30, 11: 31, 12: 32, 14: 33, 15: 34, 16: 35, 17: 36, 18: 37, 20: 24, 21: 25, + 22: 8, 41: 4, 42: 5, 43: 6, 44: 7} + score: '0.595' + edge_lig_59_lig_31: + ligand_a: lig_59 + ligand_b: lig_31 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 44, 5: 45, 6: 46, 7: 47, 8: 25, 26: 23, + 27: 24, 28: 6, 29: 7, 30: 8, 31: 9, 32: 10, 33: 11, 34: 12, 35: 13, 36: 14, + 37: 15, 38: 16, 39: 17, 40: 18, 43: 19, 44: 22, 45: 21, 46: 20, 47: 4, 48: 5} + score: '0.642' + edge_lig_24_lig_41: + ligand_a: lig_24 + ligand_b: lig_41 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, + 29: 26, 30: 27, 31: 28, 32: 29, 33: 37, 35: 35, 36: 36, 37: 33, 38: 34, 39: 32, + 41: 30, 44: 45, 45: 46} + score: '0.577' + edge_lig_24_lig_20: + ligand_a: lig_24 + ligand_b: lig_20 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, + 29: 26, 30: 27, 31: 28, 32: 29, 33: 37, 35: 35, 36: 36, 37: 33, 38: 34, 39: 32, + 41: 30, 44: 45, 45: 46} + score: '0.587' + edge_lig_24_lig_59: + ligand_a: lig_24 + ligand_b: lig_59 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 26, 28: 27, + 29: 28, 30: 29, 31: 30, 32: 31, 33: 39, 35: 37, 36: 38, 37: 35, 38: 36, 39: 34, + 41: 32, 44: 47, 45: 48} + score: '0.578' + edge_lig_24_lig_62: + ligand_a: lig_24 + ligand_b: lig_62 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 21, 28: 22, + 29: 23, 30: 24, 31: 25, 32: 26, 33: 27, 35: 35, 36: 36, 37: 37, 38: 38, 39: 39, + 41: 40, 44: 42, 45: 43} + score: '0.597' + edge_lig_26_lig_59: + ligand_a: lig_26 + ligand_b: lig_59 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 26, 28: 27, + 29: 28, 30: 29, 31: 30, 32: 31, 33: 39, 34: 40, 35: 42, 36: 43, 39: 37, 40: 38, + 41: 35, 42: 36, 43: 34, 45: 32, 46: 33, 47: 47, 48: 48} + score: '0.618' + edge_lig_57_lig_38: + ligand_a: lig_57 + ligand_b: lig_38 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 28, 28: 29, + 29: 30, 30: 31, 31: 32, 32: 33, 33: 34, 34: 35, 35: 36, 36: 37, 37: 38, 38: 39, + 39: 40, 40: 41, 41: 42, 42: 44, 43: 43, 44: 45, 45: 48, 46: 47, 47: 46, 48: 49, + 49: 50} + score: '0.656' + edge_lig_24_lig_43: + ligand_a: lig_24 + ligand_b: lig_43 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 20, 28: 21, + 29: 22, 30: 23, 31: 24, 32: 25, 33: 33, 35: 31, 36: 32, 37: 29, 38: 30, 39: 28, + 41: 26, 44: 41, 45: 42} + score: '0.608' + edge_lig_56_lig_38: + ligand_a: lig_56 + ligand_b: lig_38 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 30: 28, 31: 29, + 32: 30, 33: 31, 34: 32, 35: 33, 36: 34, 37: 35, 38: 36, 39: 37, 40: 38, 41: 39, + 42: 40, 43: 41, 44: 42, 45: 43, 46: 44, 47: 45, 48: 46, 49: 47, 50: 48, 51: 49, + 52: 50} + score: '0.652' + edge_lig_41_lig_23: + ligand_a: lig_41 + ligand_b: lig_23 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 40, 5: 41, 6: 42, 7: 43, 8: 21, 24: 19, + 25: 20, 26: 6, 27: 7, 28: 8, 29: 9, 30: 10, 31: 11, 32: 12, 33: 13, 34: 14, + 35: 15, 36: 16, 37: 17, 45: 4, 46: 5} + score: '0.602' + edge_lig_38_lig_36: + ligand_a: lig_38 + ligand_b: lig_36 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 28: 27, 29: 28, + 30: 29, 31: 30, 33: 31, 34: 45, 35: 46, 36: 44, 37: 42, 38: 43, 39: 40, 40: 41, + 41: 32, 42: 33, 43: 35, 44: 34, 45: 36, 46: 39, 47: 38, 48: 37, 49: 51, 50: 52} + score: '0.642' + edge_lig_35_lig_38: + ligand_a: lig_35 + ligand_b: lig_38 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 49, 5: 50, 6: 30, 7: 31, 8: 32, 9: 33, + 10: 41, 11: 42, 12: 44, 13: 43, 14: 45, 15: 46, 16: 47, 17: 48, 18: 39, 19: 40, + 20: 37, 21: 38, 22: 36, 23: 34, 24: 35, 25: 28, 26: 29, 27: 8, 46: 4, 47: 5, + 48: 6, 49: 7} + score: '0.663' + edge_lig_33_lig_41: + ligand_a: lig_33 + ligand_b: lig_41 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 45, 5: 46, 6: 26, 7: 27, 8: 28, 9: 29, + 10: 37, 11: 38, 13: 35, 14: 36, 15: 33, 16: 34, 17: 32, 18: 30, 19: 31, 20: 24, + 21: 25, 22: 8, 41: 4, 42: 5, 43: 6, 44: 7} + score: '0.612' + edge_lig_55_lig_38: + ligand_a: lig_55 + ligand_b: lig_38 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 49, 5: 50, 6: 30, 7: 31, 8: 32, 9: 33, + 10: 34, 11: 35, 12: 36, 13: 37, 14: 38, 15: 39, 16: 40, 17: 41, 18: 42, 19: 44, + 20: 43, 21: 45, 22: 48, 23: 47, 24: 46, 25: 28, 26: 29, 27: 8, 46: 4, 47: 5, + 48: 6, 49: 7} + score: '0.659' + edge_lig_54_lig_38: + ligand_a: lig_54 + ligand_b: lig_38 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 49, 5: 50, 6: 30, 7: 31, 8: 32, 9: 33, + 10: 34, 11: 35, 12: 36, 13: 37, 14: 38, 15: 39, 16: 40, 17: 41, 18: 42, 19: 44, + 20: 43, 21: 45, 22: 48, 23: 47, 24: 46, 25: 28, 26: 29, 27: 8, 52: 4, 53: 5, + 54: 6, 55: 7} + score: '0.649' + edge_lig_34_lig_59: + ligand_a: lig_34 + ligand_b: lig_59 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 26, 28: 27, + 29: 28, 30: 29, 31: 30, 32: 31, 33: 39, 34: 40, 35: 41, 36: 43, 39: 37, 40: 38, + 41: 35, 42: 36, 43: 34, 44: 32, 45: 33, 46: 47, 47: 48} + score: '0.625' + edge_lig_46_lig_24: + ligand_a: lig_46 + ligand_b: lig_24 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 23: 27, 24: 28, + 25: 29, 26: 30, 27: 31, 28: 32, 29: 41, 31: 39, 32: 37, 33: 38, 34: 35, 35: 36, + 36: 33, 44: 44, 45: 45} + score: '0.580' + edge_lig_59_lig_30: + ligand_a: lig_59 + ligand_b: lig_30 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 44, 5: 45, 6: 46, 7: 47, 8: 25, 26: 23, + 27: 24, 28: 6, 29: 7, 30: 8, 31: 9, 32: 21, 33: 22, 34: 19, 35: 17, 36: 18, + 37: 16, 39: 10, 40: 11, 43: 12, 44: 15, 45: 14, 46: 13, 47: 4, 48: 5} + score: '0.631' + edge_lig_24_lig_63: + ligand_a: lig_24 + ligand_b: lig_63 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 21, 28: 22, + 29: 23, 30: 24, 31: 25, 32: 26, 33: 27, 35: 35, 36: 36, 37: 37, 38: 38, 39: 39, + 41: 40, 44: 42, 45: 43} + score: '0.597' + edge_lig_24_lig_65: + ligand_a: lig_24 + ligand_b: lig_65 + atom mapping: {0: 37, 1: 36, 2: 38, 3: 31, 4: 32, 5: 33, 6: 34, 7: 35, 8: 7, 27: 8, + 28: 9, 29: 10, 30: 11, 31: 12, 32: 13, 33: 21, 35: 19, 36: 20, 37: 17, 38: 18, + 39: 16, 41: 14, 44: 29, 45: 30} + score: '0.590' + edge_lig_24_lig_39: + ligand_a: lig_24 + ligand_b: lig_39 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 22, 28: 23, + 29: 24, 30: 25, 31: 26, 32: 27, 33: 35, 35: 33, 36: 34, 37: 31, 38: 32, 39: 30, + 41: 28, 44: 43, 45: 44} + score: '0.594' + edge_lig_53_lig_38: + ligand_a: lig_53 + ligand_b: lig_38 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 33: 28, 34: 29, + 35: 30, 36: 31, 37: 32, 38: 33, 39: 34, 40: 35, 41: 36, 42: 37, 43: 38, 44: 39, + 45: 40, 46: 41, 47: 42, 48: 44, 49: 43, 50: 45, 51: 48, 52: 47, 53: 46, 54: 49, + 55: 50} + score: '0.649' + edge_lig_24_lig_38: + ligand_a: lig_24 + ligand_b: lig_38 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 28, 28: 29, + 29: 30, 30: 31, 31: 32, 32: 33, 33: 41, 35: 39, 36: 40, 37: 37, 38: 38, 39: 36, + 41: 34, 44: 49, 45: 50} + score: '0.584' + edge_lig_24_lig_48: + ligand_a: lig_24 + ligand_b: lig_48 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, + 29: 26, 30: 27, 31: 28, 32: 29, 33: 37, 35: 35, 36: 36, 37: 33, 38: 34, 39: 32, + 41: 30, 44: 45, 45: 46} + score: '0.587' + edge_lig_52_lig_38: + ligand_a: lig_52 + ligand_b: lig_38 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 30: 28, 31: 29, + 32: 30, 33: 31, 34: 32, 35: 33, 36: 34, 37: 35, 38: 36, 39: 37, 40: 38, 41: 39, + 42: 40, 43: 41, 44: 42, 45: 44, 46: 43, 47: 45, 48: 48, 49: 47, 50: 46, 51: 49, + 52: 50} + score: '0.652' + edge_lig_70_lig_24: + ligand_a: lig_70 + ligand_b: lig_24 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 26: 27, 27: 28, + 28: 29, 29: 30, 30: 31, 31: 32, 32: 33, 40: 35, 41: 36, 42: 37, 43: 38, 44: 39, + 45: 41, 47: 44, 48: 45} + score: '0.580' + edge_lig_58_lig_59: + ligand_a: lig_58 + ligand_b: lig_59 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 25: 26, 26: 27, + 27: 28, 28: 29, 29: 30, 30: 31, 31: 32, 32: 33, 33: 34, 34: 35, 35: 36, 36: 37, + 37: 38, 38: 39, 39: 40, 40: 42, 41: 41, 42: 43, 43: 44, 44: 45, 45: 46, 46: 47, + 47: 48} + score: '0.674' + edge_lig_69_lig_24: + ligand_a: lig_69 + ligand_b: lig_24 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 26: 27, 27: 28, + 28: 29, 29: 30, 30: 31, 31: 32, 32: 33, 40: 35, 41: 36, 42: 37, 43: 38, 44: 39, + 45: 41, 47: 44, 48: 45} + score: '0.580' + edge_lig_24_lig_49: + ligand_a: lig_24 + ligand_b: lig_49 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 22, 28: 23, + 29: 24, 30: 25, 31: 26, 32: 27, 33: 35, 35: 33, 36: 34, 37: 31, 38: 32, 39: 30, + 41: 28, 44: 43, 45: 44} + score: '0.594' + edge_lig_24_lig_42: + ligand_a: lig_24 + ligand_b: lig_42 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, + 29: 26, 30: 27, 31: 28, 32: 29, 33: 37, 35: 35, 36: 36, 37: 33, 38: 34, 39: 32, + 41: 30, 44: 45, 45: 46} + score: '0.587' + edge_lig_29_lig_38: + ligand_a: lig_29 + ligand_b: lig_38 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 49, 5: 50, 6: 30, 7: 31, 8: 32, 9: 33, + 10: 41, 11: 42, 12: 44, 13: 43, 14: 45, 15: 46, 16: 47, 17: 48, 18: 39, 19: 40, + 20: 37, 21: 38, 22: 36, 24: 34, 25: 35, 26: 28, 27: 29, 28: 8, 47: 4, 48: 5, + 49: 6, 50: 7} + score: '0.656' + edge_lig_41_lig_64: + ligand_a: lig_41 + ligand_b: lig_64 + atom mapping: {0: 39, 1: 38, 2: 40, 3: 33, 4: 34, 5: 35, 6: 36, 7: 37, 8: 9, 24: 10, + 25: 11, 26: 12, 27: 13, 28: 14, 29: 15, 30: 29, 31: 30, 32: 28, 33: 26, 34: 27, + 35: 24, 36: 25, 37: 16, 38: 17, 39: 19, 40: 18, 41: 20, 42: 23, 43: 22, 44: 21, + 45: 31, 46: 32} + score: '0.696' + edge_lig_38_lig_37: + ligand_a: lig_38 + ligand_b: lig_37 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 28: 27, 29: 28, + 30: 29, 31: 30, 32: 31, 33: 32, 34: 33, 35: 34, 36: 35, 37: 36, 38: 37, 39: 38, + 40: 39, 41: 40, 42: 41, 43: 42, 45: 43, 49: 60, 50: 61} + score: '0.578' + edge_lig_24_lig_47: + ligand_a: lig_24 + ligand_b: lig_47 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 45, 5: 46, 6: 47, 7: 48, 8: 27, 27: 25, + 28: 26, 29: 6, 30: 7, 31: 8, 32: 9, 33: 17, 35: 15, 36: 16, 37: 13, 38: 14, + 39: 12, 41: 10, 44: 4, 45: 5} + score: '0.587' + edge_lig_67_lig_24: + ligand_a: lig_67 + ligand_b: lig_24 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 24: 27, 25: 28, + 26: 29, 27: 30, 28: 31, 29: 32, 30: 41, 32: 39, 33: 37, 34: 38, 35: 35, 36: 36, + 37: 33, 45: 44, 46: 45} + score: '0.580' diff --git a/data/pfkfb3/03_edges/nohup.out b/data/pfkfb3/03_edges/nohup.out deleted file mode 100644 index 99d2f26e2..000000000 --- a/data/pfkfb3/03_edges/nohup.out +++ /dev/null @@ -1,45 +0,0 @@ -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. -lig_29_lig_38 exceeds 1 A pairwise distance -lig_19_lig_41 exceeds 1 A pairwise distance -lig_58_lig_59 exceeds 1 A pairwise distance -lig_24_lig_38 exceeds 1 A pairwise distance -lig_46_lig_24 exceeds 1 A pairwise distance -lig_24_lig_42 exceeds 1 A pairwise distance -lig_56_lig_38 exceeds 1 A pairwise distance -lig_38_lig_36 exceeds 1 A pairwise distance -lig_69_lig_24 exceeds 1 A pairwise distance -lig_24_lig_43 exceeds 1 A pairwise distance -lig_26_lig_59 exceeds 1 A pairwise distance -lig_41_lig_64 exceeds 1 A pairwise distance -lig_38_lig_37 exceeds 1 A pairwise distance -lig_24_lig_49 exceeds 1 A pairwise distance -lig_59_lig_31 exceeds 1 A pairwise distance -lig_24_lig_41 exceeds 1 A pairwise distance -lig_34_lig_59 exceeds 1 A pairwise distance -lig_54_lig_38 exceeds 1 A pairwise distance -lig_24_lig_59 exceeds 1 A pairwise distance -lig_24_lig_39 exceeds 1 A pairwise distance -lig_24_lig_65 exceeds 1 A pairwise distance -lig_67_lig_24 exceeds 1 A pairwise distance -lig_24_lig_20 exceeds 1 A pairwise distance -lig_55_lig_38 exceeds 1 A pairwise distance -lig_35_lig_38 exceeds 1 A pairwise distance -lig_24_lig_47 exceeds 1 A pairwise distance -lig_24_lig_63 exceeds 1 A pairwise distance -lig_57_lig_38 exceeds 1 A pairwise distance -lig_70_lig_24 exceeds 1 A pairwise distance -lig_24_lig_44 exceeds 1 A pairwise distance -lig_53_lig_38 exceeds 1 A pairwise distance -lig_24_lig_48 exceeds 1 A pairwise distance -lig_59_lig_30 exceeds 1 A pairwise distance -lig_41_lig_23 exceeds 1 A pairwise distance -lig_52_lig_38 exceeds 1 A pairwise distance -lig_24_lig_62 exceeds 1 A pairwise distance diff --git a/data/ptp1b/03_edges/01_perses_openfe.yaml b/data/ptp1b/03_edges/01_perses_openfe.yaml deleted file mode 100644 index 10697030b..000000000 --- a/data/ptp1b/03_edges/01_perses_openfe.yaml +++ /dev/null @@ -1,172 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph -edges: - edge_lig_23480_lig_23485: - ligand_a: lig_23480 - ligand_b: lig_23485 - atom mapping: (0, 62) (1, 2) (2, 1) (3, 6) (4, 5) (5, 4) (6, 3) (7, 61) (8, 9) - (10, 12) (13, 15) (14, 20) (15, 19) (16, 18) (17, 17) (18, 16) (19, 59) (20, - 60) (21, 58) (22, 57) (23, 26) (30, 23) (31, 24) (32, 22) (33, 21) (35, 8) (52, - 0) - score: '0.488' - edge_lig_23484_lig_23475: - ligand_a: lig_23484 - ligand_b: lig_23475 - atom mapping: (26, 8) (27, 9) (28, 5) (29, 6) (30, 1) (31, 2) (32, 3) (33, 4) - (34, 24) (35, 25) (36, 26) (37, 27) (38, 28) (39, 29) (40, 30) (41, 31) (42, - 32) (43, 33) (44, 34) (45, 36) (46, 35) (47, 37) (48, 38) (49, 39) (51, 41) - (52, 0) (53, 7) - score: '0.586' - edge_lig_23466_lig_23483: - ligand_a: lig_23466 - ligand_b: lig_23483 - atom mapping: (0, 49) (1, 27) (2, 28) (3, 29) (4, 30) (5, 25) (6, 26) (7, 50) - (8, 23) (10, 24) (11, 31) (12, 32) (13, 33) (14, 34) (15, 35) (16, 36) (17, - 37) (18, 38) (19, 39) (20, 40) (21, 41) (22, 42) (23, 43) (24, 44) (25, 45) - (26, 46) (27, 47) (28, 48) - score: '0.725' - edge_lig_23484_lig_23472: - ligand_a: lig_23484 - ligand_b: lig_23472 - atom mapping: (26, 8) (28, 5) (29, 6) (30, 1) (31, 2) (32, 3) (33, 4) (34, 24) - (35, 25) (36, 26) (37, 27) (38, 28) (39, 29) (40, 30) (41, 31) (42, 32) (43, - 33) (44, 34) (45, 36) (46, 35) (47, 37) (48, 38) (49, 39) (51, 41) (52, 0) (53, - 7) - score: '0.574' - edge_lig_20667_2qbp_lig_23480: - ligand_a: lig_20667_2qbp - ligand_b: lig_23480 - atom mapping: (0, 52) (1, 2) (2, 1) (3, 6) (4, 5) (5, 4) (6, 3) (8, 35) (9, 8) - (12, 10) (15, 13) (16, 18) (17, 17) (18, 16) (19, 15) (20, 14) (21, 33) (22, - 32) (23, 30) (24, 31) (26, 23) (54, 22) (55, 21) (56, 19) (57, 20) (58, 7) (59, - 0) - score: '0.488' - edge_lig_23484_lig_23468: - ligand_a: lig_23484 - ligand_b: lig_23468 - atom mapping: (26, 8) (28, 5) (29, 6) (30, 1) (31, 2) (32, 3) (33, 4) (34, 19) - (35, 20) (36, 21) (37, 22) (38, 23) (39, 24) (40, 25) (41, 26) (42, 27) (43, - 28) (44, 29) (45, 31) (46, 30) (47, 32) (48, 33) (49, 34) (51, 36) (52, 0) (53, - 7) - score: '0.612' - edge_lig_23477_lig_23472: - ligand_a: lig_23477 - ligand_b: lig_23472 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (25, - 24) (26, 25) (27, 26) (28, 27) (29, 28) (30, 29) (31, 30) (32, 31) (33, 32) - (34, 33) (35, 34) (36, 35) (37, 36) (38, 37) (39, 38) (40, 39) (41, 40) (42, - 41) - score: '0.632' - edge_lig_20670_2qbs_lig_23472: - ligand_a: lig_20670_2qbs - ligand_b: lig_23472 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (27, - 24) (28, 25) (29, 26) (30, 27) (31, 28) (32, 29) (33, 30) (34, 31) (35, 32) - (36, 33) (37, 34) (38, 35) (39, 36) (40, 37) (41, 38) (42, 39) (43, 40) (44, - 41) - score: '0.632' - edge_lig_23484_lig_23469: - ligand_a: lig_23484 - ligand_b: lig_23469 - atom mapping: (26, 11) (28, 13) (29, 14) (30, 15) (31, 16) (32, 17) (33, 18) (34, - 19) (35, 20) (36, 21) (37, 22) (38, 23) (39, 24) (40, 25) (41, 26) (42, 27) - (43, 28) (44, 29) (45, 31) (46, 30) (47, 32) (48, 33) (49, 34) (51, 36) (52, - 37) (53, 38) - score: '0.581' - edge_lig_23484_lig_23476: - ligand_a: lig_23484 - ligand_b: lig_23476 - atom mapping: (26, 8) (27, 9) (28, 5) (29, 6) (30, 1) (31, 2) (32, 3) (33, 4) - (34, 30) (35, 31) (36, 32) (37, 33) (38, 34) (39, 35) (40, 36) (41, 37) (42, - 38) (43, 39) (44, 40) (45, 41) (46, 42) (47, 43) (48, 44) (49, 45) (51, 47) - (52, 0) (53, 7) - score: '0.545' - edge_lig_23482_lig_23480: - ligand_a: lig_23482 - ligand_b: lig_23480 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (32, - 35) (33, 36) (34, 37) (35, 38) (36, 39) (37, 40) (38, 41) (39, 42) (40, 43) - (41, 44) (42, 45) (43, 46) (44, 47) (45, 48) (46, 49) (47, 50) (48, 51) (49, - 52) - score: '0.602' - edge_lig_23471_lig_23483: - ligand_a: lig_23471 - ligand_b: lig_23483 - atom mapping: (0, 49) (1, 27) (2, 28) (3, 29) (4, 30) (5, 25) (6, 26) (7, 50) - (8, 23) (17, 31) (18, 32) (19, 33) (20, 34) (21, 35) (22, 36) (23, 37) (24, - 38) (25, 39) (26, 40) (27, 41) (28, 43) (29, 42) (30, 44) (31, 45) (32, 46) - (33, 47) (34, 48) - score: '0.650' - edge_lig_23484_lig_20669_2qbr: - ligand_a: lig_23484 - ligand_b: lig_20669_2qbr - atom mapping: (26, 12) (28, 14) (29, 15) (30, 16) (31, 17) (32, 18) (33, 19) (34, - 20) (35, 21) (36, 22) (37, 23) (38, 24) (39, 25) (40, 26) (41, 27) (42, 28) - (43, 29) (44, 30) (45, 32) (46, 31) (47, 33) (48, 34) (49, 35) (51, 37) (52, - 38) (53, 39) - score: '0.574' - edge_lig_23480_lig_23483: - ligand_a: lig_23480 - ligand_b: lig_23483 - atom mapping: (0, 49) (1, 27) (2, 28) (3, 29) (4, 30) (5, 25) (6, 26) (7, 50) - (8, 23) (35, 31) (36, 32) (37, 33) (38, 34) (39, 35) (40, 36) (41, 37) (42, - 38) (43, 39) (44, 40) (45, 41) (46, 43) (47, 42) (48, 44) (49, 45) (50, 46) - (51, 47) (52, 48) - score: '0.520' - edge_lig_23484_lig_23470: - ligand_a: lig_23484 - ligand_b: lig_23470 - atom mapping: (26, 8) (28, 5) (29, 6) (30, 1) (31, 2) (32, 3) (33, 4) (34, 24) - (35, 25) (36, 26) (37, 27) (38, 28) (39, 29) (40, 30) (41, 31) (42, 32) (43, - 33) (44, 34) (45, 36) (46, 35) (47, 37) (48, 38) (49, 39) (51, 41) (52, 0) (53, - 7) - score: '0.574' - edge_lig_23484_lig_23480: - ligand_a: lig_23484 - ligand_b: lig_23480 - atom mapping: (0, 52) (1, 2) (2, 1) (3, 6) (4, 5) (5, 4) (6, 3) (8, 35) (9, 8) - (12, 10) (15, 13) (16, 14) (17, 15) (18, 16) (19, 17) (20, 18) (21, 20) (22, - 19) (23, 22) (24, 21) (26, 23) (54, 30) (55, 31) (56, 32) (57, 33) (58, 7) (59, - 0) - score: '0.491' - edge_lig_23474_lig_23486: - ligand_a: lig_23474 - ligand_b: lig_23486 - atom mapping: (0, 7) (1, 6) (2, 1) (3, 2) (4, 3) (5, 4) (6, 5) (7, 8) (8, 9) (10, - 12) (13, 15) (14, 20) (15, 19) (16, 18) (17, 17) (18, 16) (19, 56) (20, 57) - (21, 55) (22, 54) (24, 25) (25, 23) (26, 24) (27, 22) (28, 21) (30, 58) (47, - 0) - score: '0.511' - edge_lig_23473_lig_23484: - ligand_a: lig_23473 - ligand_b: lig_23484 - atom mapping: (12, 26) (13, 28) (14, 29) (15, 30) (16, 31) (17, 32) (18, 33) (19, - 34) (20, 35) (21, 36) (22, 37) (23, 38) (24, 39) (25, 40) (26, 41) (27, 42) - (28, 43) (29, 44) (30, 46) (31, 45) (32, 47) (33, 48) (34, 49) (36, 51) (37, - 52) (38, 53) - score: '0.581' - edge_lig_23479_lig_23480: - ligand_a: lig_23479 - ligand_b: lig_23480 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (31, - 35) (32, 36) (33, 37) (34, 38) (35, 39) (36, 40) (37, 41) (38, 42) (39, 43) - (40, 44) (41, 45) (42, 46) (43, 47) (44, 48) (45, 49) (46, 50) (47, 51) (48, - 52) - score: '0.610' - edge_lig_23467_lig_23486: - ligand_a: lig_23467 - ligand_b: lig_23486 - atom mapping: (0, 52) (1, 30) (2, 31) (3, 32) (4, 33) (5, 28) (6, 29) (7, 53) - (8, 26) (13, 34) (14, 35) (15, 36) (16, 37) (17, 38) (18, 39) (19, 40) (20, - 41) (21, 42) (22, 43) (23, 44) (24, 46) (25, 45) (26, 47) (27, 48) (28, 49) - (29, 50) (30, 51) - score: '0.684' - edge_lig_23480_lig_23486: - ligand_a: lig_23480 - ligand_b: lig_23486 - atom mapping: (0, 7) (1, 6) (2, 1) (3, 2) (4, 3) (5, 4) (6, 5) (7, 8) (8, 9) (10, - 12) (13, 15) (14, 20) (15, 19) (16, 18) (17, 17) (18, 16) (19, 56) (20, 57) - (21, 55) (22, 54) (23, 26) (30, 23) (31, 24) (32, 22) (33, 21) (35, 58) (52, - 0) - score: '0.488' diff --git a/data/ptp1b/03_edges/01_perses_openfe.yml b/data/ptp1b/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..03f8e8105 --- /dev/null +++ b/data/ptp1b/03_edges/01_perses_openfe.yml @@ -0,0 +1,151 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_23480_lig_23485: + ligand_a: lig_23480 + ligand_b: lig_23485 + atom mapping: {0: 62, 1: 2, 2: 1, 3: 6, 4: 5, 5: 4, 6: 3, 7: 61, 8: 9, 10: 12, + 13: 15, 14: 20, 15: 19, 16: 18, 17: 17, 18: 16, 19: 59, 20: 60, 21: 58, 22: 57, + 23: 26, 30: 23, 31: 24, 32: 22, 33: 21, 35: 8, 52: 0} + score: '0.488' + edge_lig_20667_2qbp_lig_23474: + ligand_a: lig_20667_2qbp + ligand_b: lig_23474 + atom mapping: {0: 47, 1: 2, 2: 1, 3: 6, 4: 5, 5: 4, 6: 3, 8: 30, 9: 8, 12: 10, + 15: 13, 16: 18, 17: 17, 18: 16, 19: 15, 20: 14, 21: 28, 22: 27, 23: 26, 24: 25, + 25: 23, 54: 21, 55: 22, 56: 19, 57: 20, 58: 7, 59: 0} + score: '0.511' + edge_lig_23484_lig_23469: + ligand_a: lig_23484 + ligand_b: lig_23469 + atom mapping: {26: 11, 28: 13, 29: 14, 30: 15, 31: 16, 32: 17, 33: 18, 34: 19, + 35: 20, 36: 21, 37: 22, 38: 23, 39: 24, 40: 25, 41: 26, 42: 27, 43: 28, 44: 29, + 45: 31, 46: 30, 47: 32, 48: 33, 49: 34, 51: 36, 52: 37, 53: 38} + score: '0.581' + edge_lig_23473_lig_23484: + ligand_a: lig_23473 + ligand_b: lig_23484 + atom mapping: {12: 26, 13: 28, 14: 29, 15: 30, 16: 31, 17: 32, 18: 33, 19: 34, + 20: 35, 21: 36, 22: 37, 23: 38, 24: 39, 25: 40, 26: 41, 27: 42, 28: 43, 29: 44, + 30: 46, 31: 45, 32: 47, 33: 48, 34: 49, 36: 51, 37: 52, 38: 53} + score: '0.581' + edge_lig_23466_lig_23483: + ligand_a: lig_23466 + ligand_b: lig_23483 + atom mapping: {0: 49, 1: 27, 2: 28, 3: 29, 4: 30, 5: 25, 6: 26, 7: 50, 8: 23, + 10: 24, 11: 31, 12: 32, 13: 33, 14: 34, 15: 35, 16: 36, 17: 37, 18: 38, 19: 39, + 20: 40, 21: 41, 22: 42, 23: 43, 24: 44, 25: 45, 26: 46, 27: 47, 28: 48} + score: '0.725' + edge_lig_23484_lig_20669_2qbr: + ligand_a: lig_23484 + ligand_b: lig_20669_2qbr + atom mapping: {26: 12, 28: 14, 29: 15, 30: 16, 31: 17, 32: 18, 33: 19, 34: 20, + 35: 21, 36: 22, 37: 23, 38: 24, 39: 25, 40: 26, 41: 27, 42: 28, 43: 29, 44: 30, + 45: 32, 46: 31, 47: 33, 48: 34, 49: 35, 51: 37, 52: 38, 53: 39} + score: '0.574' + edge_lig_23482_lig_23480: + ligand_a: lig_23482 + ligand_b: lig_23480 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 32: 35, 33: 36, + 34: 37, 35: 38, 36: 39, 37: 40, 38: 41, 39: 42, 40: 43, 41: 44, 42: 45, 43: 46, + 44: 47, 45: 48, 46: 49, 47: 50, 48: 51, 49: 52} + score: '0.602' + edge_lig_23484_lig_23468: + ligand_a: lig_23484 + ligand_b: lig_23468 + atom mapping: {26: 8, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, 33: 4, 34: 19, 35: 20, + 36: 21, 37: 22, 38: 23, 39: 24, 40: 25, 41: 26, 42: 27, 43: 28, 44: 29, 45: 31, + 46: 30, 47: 32, 48: 33, 49: 34, 51: 36, 52: 0, 53: 7} + score: '0.612' + edge_lig_23479_lig_23480: + ligand_a: lig_23479 + ligand_b: lig_23480 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 31: 35, 32: 36, + 33: 37, 34: 38, 35: 39, 36: 40, 37: 41, 38: 42, 39: 43, 40: 44, 41: 45, 42: 46, + 43: 47, 44: 48, 45: 49, 46: 50, 47: 51, 48: 52} + score: '0.610' + edge_lig_20667_2qbp_lig_23480: + ligand_a: lig_20667_2qbp + ligand_b: lig_23480 + atom mapping: {0: 52, 1: 2, 2: 3, 3: 4, 4: 5, 5: 6, 6: 1, 7: 0, 8: 7, 9: 8, 12: 10, + 15: 13, 16: 18, 17: 17, 18: 16, 19: 15, 20: 14, 21: 33, 22: 32, 23: 30, 24: 31, + 26: 23, 54: 22, 55: 21, 56: 19, 57: 20, 58: 35} + score: '0.488' + edge_lig_20670_2qbs_lig_23472: + ligand_a: lig_20670_2qbs + ligand_b: lig_23472 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, + 29: 26, 30: 27, 31: 28, 32: 29, 33: 30, 34: 31, 35: 32, 36: 33, 37: 34, 38: 35, + 39: 36, 40: 37, 41: 38, 42: 39, 43: 40, 44: 41} + score: '0.632' + edge_lig_23471_lig_23483: + ligand_a: lig_23471 + ligand_b: lig_23483 + atom mapping: {0: 49, 1: 27, 2: 28, 3: 29, 4: 30, 5: 25, 6: 26, 7: 50, 8: 23, + 17: 31, 18: 32, 19: 33, 20: 34, 21: 35, 22: 36, 23: 37, 24: 38, 25: 39, 26: 40, + 27: 41, 28: 43, 29: 42, 30: 44, 31: 45, 32: 46, 33: 47, 34: 48} + score: '0.650' + edge_lig_23477_lig_23472: + ligand_a: lig_23477 + ligand_b: lig_23472 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 25: 24, 26: 25, + 27: 26, 28: 27, 29: 28, 30: 29, 31: 30, 32: 31, 33: 32, 34: 33, 35: 34, 36: 35, + 37: 36, 38: 37, 39: 38, 40: 39, 41: 40, 42: 41} + score: '0.632' + edge_lig_23480_lig_23483: + ligand_a: lig_23480 + ligand_b: lig_23483 + atom mapping: {0: 49, 1: 27, 2: 28, 3: 29, 4: 30, 5: 25, 6: 26, 7: 50, 8: 23, + 35: 31, 36: 32, 37: 33, 38: 34, 39: 35, 40: 36, 41: 37, 42: 38, 43: 39, 44: 40, + 45: 41, 46: 43, 47: 42, 48: 44, 49: 45, 50: 46, 51: 47, 52: 48} + score: '0.520' + edge_lig_23480_lig_23486: + ligand_a: lig_23480 + ligand_b: lig_23486 + atom mapping: {0: 7, 1: 6, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 7: 8, 8: 9, 10: 12, 13: 15, + 14: 20, 15: 19, 16: 18, 17: 17, 18: 16, 19: 56, 20: 57, 21: 55, 22: 54, 23: 26, + 30: 23, 31: 24, 32: 22, 33: 21, 35: 58, 52: 0} + score: '0.488' + edge_lig_23484_lig_23480: + ligand_a: lig_23484 + ligand_b: lig_23480 + atom mapping: {0: 52, 1: 2, 2: 3, 3: 4, 4: 5, 5: 6, 6: 1, 7: 0, 8: 7, 9: 8, 12: 10, + 15: 13, 16: 18, 17: 17, 18: 16, 19: 15, 20: 14, 21: 33, 22: 32, 23: 30, 24: 31, + 26: 23, 54: 22, 55: 21, 56: 19, 57: 20, 58: 35} + score: '0.491' + edge_lig_23484_lig_23475: + ligand_a: lig_23484 + ligand_b: lig_23475 + atom mapping: {26: 8, 27: 9, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, 33: 4, 34: 24, + 35: 25, 36: 26, 37: 27, 38: 28, 39: 29, 40: 30, 41: 31, 42: 32, 43: 33, 44: 34, + 45: 36, 46: 35, 47: 37, 48: 38, 49: 39, 51: 41, 52: 0, 53: 7} + score: '0.586' + edge_lig_23484_lig_23470: + ligand_a: lig_23484 + ligand_b: lig_23470 + atom mapping: {26: 8, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, 33: 4, 34: 24, 35: 25, + 36: 26, 37: 27, 38: 28, 39: 29, 40: 30, 41: 31, 42: 32, 43: 33, 44: 34, 45: 36, + 46: 35, 47: 37, 48: 38, 49: 39, 51: 41, 52: 0, 53: 7} + score: '0.574' + edge_lig_23484_lig_23476: + ligand_a: lig_23484 + ligand_b: lig_23476 + atom mapping: {26: 8, 27: 9, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, 33: 4, 34: 30, + 35: 31, 36: 32, 37: 33, 38: 34, 39: 35, 40: 36, 41: 37, 42: 38, 43: 39, 44: 40, + 45: 41, 46: 42, 47: 43, 48: 44, 49: 45, 51: 47, 52: 0, 53: 7} + score: '0.545' + edge_lig_23484_lig_23472: + ligand_a: lig_23484 + ligand_b: lig_23472 + atom mapping: {26: 8, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, 33: 4, 34: 24, 35: 25, + 36: 26, 37: 27, 38: 28, 39: 29, 40: 30, 41: 31, 42: 32, 43: 33, 44: 34, 45: 36, + 46: 35, 47: 37, 48: 38, 49: 39, 51: 41, 52: 0, 53: 7} + score: '0.574' + edge_lig_23467_lig_23485: + ligand_a: lig_23467 + ligand_b: lig_23485 + atom mapping: {0: 55, 1: 30, 2: 31, 3: 32, 4: 33, 5: 28, 6: 29, 7: 56, 8: 26, + 13: 34, 14: 35, 15: 36, 16: 37, 17: 38, 18: 39, 19: 40, 20: 41, 21: 42, 22: 43, + 23: 44, 24: 46, 25: 45, 26: 47, 27: 48, 28: 49, 29: 50, 30: 54} + score: '0.684' diff --git a/data/ptp1b/03_edges/nohup.out b/data/ptp1b/03_edges/nohup.out deleted file mode 100644 index 8bf8e8274..000000000 --- a/data/ptp1b/03_edges/nohup.out +++ /dev/null @@ -1,24 +0,0 @@ -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. -lig_23480_lig_23485 exceeds 1 A pairwise distance -lig_23484_lig_23475 exceeds 1 A pairwise distance -lig_23484_lig_23472 exceeds 1 A pairwise distance -lig_20667_2qbp_lig_23480 exceeds 1 A pairwise distance -lig_23484_lig_23469 exceeds 1 A pairwise distance -lig_23471_lig_23483 exceeds 1 A pairwise distance -lig_23484_lig_20669_2qbr exceeds 1 A pairwise distance -lig_23480_lig_23483 exceeds 1 A pairwise distance -lig_23484_lig_23470 exceeds 1 A pairwise distance -lig_23484_lig_23480 exceeds 1 A pairwise distance -lig_23474_lig_23486 exceeds 1 A pairwise distance -lig_23473_lig_23484 exceeds 1 A pairwise distance -lig_23479_lig_23480 exceeds 1 A pairwise distance -lig_23467_lig_23486 exceeds 1 A pairwise distance -lig_23480_lig_23486 exceeds 1 A pairwise distance diff --git a/data/shp2/03_edges/01_perses_openfe.yaml b/data/shp2/03_edges/01_perses_openfe.yaml deleted file mode 100644 index c67260f39..000000000 --- a/data/shp2/03_edges/01_perses_openfe.yaml +++ /dev/null @@ -1,153 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph -edges: - edge_lig_7_lig_E28: - ligand_a: lig_7 - ligand_b: lig_E28 - atom mapping: (1, 16) (2, 17) (3, 19) (4, 20) (5, 21) (6, 23) (7, 22) (8, 24) - (9, 26) (10, 25) (11, 27) (13, 28) (22, 35) (23, 37) (24, 36) (25, 38) (26, - 40) (27, 39) (28, 41) (29, 42) (30, 43) (31, 44) (32, 45) (33, 15) - score: '0.534' - edge_lig_SHP836-2_lig_E28: - ligand_a: lig_SHP836-2 - ligand_b: lig_E28 - atom mapping: (1, 16) (2, 17) (3, 19) (4, 20) (5, 38) (6, 40) (7, 39) (8, 35) - (9, 36) (14, 27) (16, 24) (17, 25) (22, 21) (23, 23) (24, 22) (25, 41) (26, - 42) (27, 43) (28, 45) (29, 44) (30, 15) - score: '0.508' - edge_lig_E14_lig_E3: - ligand_a: lig_E14 - ligand_b: lig_E3 - atom mapping: (1, 9) (2, 7) (3, 6) (15, 33) (16, 34) (17, 35) (18, 36) (19, 32) - (20, 10) - score: '0.292' - edge_lig_E14_lig_E26: - ligand_a: lig_E14 - ligand_b: lig_E26 - atom mapping: (1, 11) (2, 10) (3, 9) (4, 8) (5, 6) (7, 4) (9, 2) (10, 3) (11, - 1) (13, 44) (15, 40) (16, 41) (17, 43) (18, 42) (19, 39) (20, 17) - score: '0.529' - edge_lig_E14_lig_E28: - ligand_a: lig_E14 - ligand_b: lig_E28 - atom mapping: (0, 18) (1, 17) (2, 16) (3, 15) (15, 42) (16, 43) (17, 44) (18, - 45) (19, 41) (20, 19) - score: '0.296' - edge_lig_E14_lig_E4: - ligand_a: lig_E14 - ligand_b: lig_E4 - atom mapping: (1, 6) (2, 4) (3, 3) (15, 30) (16, 31) (17, 32) (18, 33) (19, 29) - (20, 7) - score: '0.292' - edge_lig_E14_lig_E23: - ligand_a: lig_E14 - ligand_b: lig_E23 - atom mapping: (1, 11) (2, 10) (3, 9) (4, 8) (5, 6) (7, 4) (9, 2) (10, 3) (11, - 1) (13, 40) (15, 36) (16, 37) (17, 39) (18, 38) (19, 35) (20, 13) - score: '0.536' - edge_lig_E14_lig_E24: - ligand_a: lig_E14 - ligand_b: lig_E24 - atom mapping: (1, 11) (2, 10) (3, 9) (4, 8) (5, 6) (7, 4) (9, 2) (10, 3) (11, - 1) (13, 43) (15, 39) (16, 40) (17, 42) (18, 41) (19, 38) (20, 16) - score: '0.536' - edge_lig_E14_lig_SHP099-1: - ligand_a: lig_E14 - ligand_b: lig_SHP099-1 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 13) (7, 11) (9, 9) (10, 10) - (11, 7) (13, 5) (15, 15) (16, 16) (17, 18) (18, 17) (19, 19) (20, 20) - score: '0.555' - edge_lig_E28_lig_E5: - ligand_a: lig_E28 - ligand_b: lig_E5 - atom mapping: (15, 30) (16, 1) (17, 2) (19, 3) (20, 4) (21, 5) (22, 6) (23, 7) - (24, 8) (25, 9) (26, 10) (27, 11) (28, 16) (32, 12) (35, 19) (36, 21) (37, 20) - (38, 22) (39, 24) (40, 23) (41, 25) (42, 26) (43, 27) (44, 29) (45, 28) - score: '0.543' - edge_lig_E14_lig_E30: - ligand_a: lig_E14 - ligand_b: lig_E30 - atom mapping: (1, 11) (2, 10) (3, 9) (4, 8) (5, 6) (7, 4) (9, 2) (10, 3) (11, - 1) (13, 39) (15, 35) (16, 36) (17, 38) (18, 37) (19, 34) (20, 12) - score: '0.540' - edge_lig_E14_lig_E1: - ligand_a: lig_E14 - ligand_b: lig_E1 - atom mapping: (1, 2) (2, 1) (3, 30) (4, 31) (5, 40) (7, 38) (9, 36) (10, 37) (11, - 34) (13, 32) (15, 26) (16, 27) (17, 29) (18, 28) (19, 25) (20, 3) - score: '0.540' - edge_lig_E14_lig_E25: - ligand_a: lig_E14 - ligand_b: lig_E25 - atom mapping: (1, 11) (2, 10) (3, 9) (4, 8) (5, 6) (7, 4) (9, 2) (10, 3) (11, - 1) (13, 41) (15, 37) (16, 38) (17, 40) (18, 39) (19, 36) (20, 14) - score: '0.532' - edge_lig_E14_lig_11: - ligand_a: lig_E14 - ligand_b: lig_11 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 13) (7, 11) (9, 9) (10, 10) - (11, 7) (13, 5) (15, 15) (16, 16) (18, 17) (19, 22) (20, 23) - score: '0.536' - edge_lig_E4_lig_E27: - ligand_a: lig_E4 - ligand_b: lig_E27 - atom mapping: (3, 3) (4, 2) (6, 1) (7, 20) (8, 21) (9, 39) (10, 41) (11, 40) (12, - 33) (14, 34) (15, 31) (23, 25) (25, 26) (26, 22) (27, 24) (28, 23) (29, 19) - (30, 15) (31, 16) (32, 18) (33, 17) - score: '0.520' - edge_lig_3_lig_E28: - ligand_a: lig_3 - ligand_b: lig_E28 - atom mapping: (1, 16) (2, 17) (3, 19) (4, 20) (5, 38) (6, 40) (7, 39) (8, 35) - (9, 36) (14, 27) (16, 24) (17, 25) (22, 21) (23, 23) (24, 22) (25, 41) (26, - 42) (27, 43) (28, 45) (29, 44) (30, 15) - score: '0.508' - edge_lig_E14_lig_E2: - ligand_a: lig_E14 - ligand_b: lig_E2 - atom mapping: (1, 2) (2, 1) (3, 30) (4, 31) (5, 43) (7, 38) (9, 36) (10, 37) (11, - 34) (13, 32) (15, 26) (16, 27) (17, 29) (18, 28) (19, 25) (20, 3) - score: '0.540' - edge_lig_E14_lig_10: - ligand_a: lig_E14 - ligand_b: lig_10 - atom mapping: (0, 26) (1, 25) (2, 27) (3, 28) (4, 29) (5, 38) (7, 36) (9, 34) - (10, 35) (11, 32) (13, 30) (15, 1) (19, 2) (20, 3) - score: '0.507' - edge_lig_E8_lig_E14: - ligand_a: lig_E8 - ligand_b: lig_E14 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 13) (7, 11) (9, 9) (10, 10) - (11, 7) (13, 5) (15, 15) (16, 16) (17, 17) (18, 18) (19, 19) (20, 20) - score: '0.551' - edge_lig_E14_lig_E22: - ligand_a: lig_E14 - ligand_b: lig_E22 - atom mapping: (1, 11) (2, 10) (3, 9) (4, 8) (5, 6) (7, 4) (9, 2) (10, 3) (11, - 1) (13, 40) (15, 36) (16, 37) (17, 39) (18, 38) (19, 35) (20, 13) - score: '0.536' - edge_lig_6_lig_E14: - ligand_a: lig_6 - ligand_b: lig_E14 - atom mapping: (1, 2) (2, 1) (3, 20) (22, 19) (23, 15) (24, 16) (25, 18) (26, 17) - (27, 3) (28, 4) (29, 13) (31, 11) (33, 9) (34, 10) (35, 7) (37, 5) - score: '0.544' - edge_lig_E14_lig_E29: - ligand_a: lig_E14 - ligand_b: lig_E29 - atom mapping: (0, 6) (1, 5) (2, 4) (3, 3) (15, 30) (16, 31) (17, 32) (18, 33) - (19, 29) (20, 7) - score: '0.305' - edge_lig_E9_lig_E14: - ligand_a: lig_E9 - ligand_b: lig_E14 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 13) (7, 11) (9, 9) (10, 10) - (11, 7) (13, 5) (15, 15) (16, 16) (17, 18) (18, 17) (19, 19) (20, 20) - score: '0.555' - edge_lig_E14_lig_E6: - ligand_a: lig_E14 - ligand_b: lig_E6 - atom mapping: (1, 13) (2, 11) (3, 10) (4, 9) (5, 7) (7, 5) (9, 3) (10, 4) (11, - 2) (12, 1) (13, 41) (15, 37) (16, 38) (17, 40) (18, 39) (19, 36) (20, 14) - score: '0.558' diff --git a/data/shp2/03_edges/01_perses_openfe.yml b/data/shp2/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..559c2a728 --- /dev/null +++ b/data/shp2/03_edges/01_perses_openfe.yml @@ -0,0 +1,151 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_E14_lig_E29: + ligand_a: lig_E14 + ligand_b: lig_E29 + atom mapping: {0: 6, 1: 5, 2: 4, 3: 3, 15: 30, 16: 31, 17: 32, 18: 33, 19: 29, + 20: 7} + score: '0.305' + edge_lig_E14_lig_E6: + ligand_a: lig_E14 + ligand_b: lig_E6 + atom mapping: {1: 13, 2: 11, 3: 10, 4: 9, 5: 7, 7: 5, 9: 3, 10: 4, 11: 2, 12: 1, + 13: 41, 15: 37, 16: 38, 17: 40, 18: 39, 19: 36, 20: 14} + score: '0.558' + edge_lig_E14_lig_10: + ligand_a: lig_E14 + ligand_b: lig_10 + atom mapping: {0: 26, 1: 25, 2: 27, 3: 28, 4: 29, 5: 38, 7: 36, 9: 34, 10: 35, + 11: 32, 13: 30, 15: 1, 19: 2, 20: 3} + score: '0.507' + edge_lig_E14_lig_E2: + ligand_a: lig_E14 + ligand_b: lig_E2 + atom mapping: {1: 2, 2: 1, 3: 30, 4: 31, 5: 43, 7: 38, 9: 36, 10: 37, 11: 34, + 13: 32, 15: 26, 16: 27, 17: 29, 18: 28, 19: 25, 20: 3} + score: '0.540' + edge_lig_E14_lig_E1: + ligand_a: lig_E14 + ligand_b: lig_E1 + atom mapping: {1: 2, 2: 1, 3: 30, 4: 31, 5: 40, 7: 38, 9: 36, 10: 37, 11: 34, + 13: 32, 15: 26, 16: 27, 17: 29, 18: 28, 19: 25, 20: 3} + score: '0.540' + edge_lig_E4_lig_E27: + ligand_a: lig_E4 + ligand_b: lig_E27 + atom mapping: {3: 3, 4: 2, 6: 1, 7: 20, 8: 21, 9: 39, 10: 41, 11: 40, 12: 33, + 14: 34, 15: 31, 23: 25, 25: 26, 26: 22, 27: 24, 28: 23, 29: 19, 30: 15, 31: 16, + 32: 18, 33: 17} + score: '0.520' + edge_lig_E14_lig_E3: + ligand_a: lig_E14 + ligand_b: lig_E3 + atom mapping: {1: 9, 2: 7, 3: 6, 15: 33, 16: 34, 17: 35, 18: 36, 19: 32, 20: 10} + score: '0.292' + edge_lig_E14_lig_E26: + ligand_a: lig_E14 + ligand_b: lig_E26 + atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 44, + 15: 40, 16: 41, 17: 43, 18: 42, 19: 39, 20: 17} + score: '0.529' + edge_lig_E14_lig_E28: + ligand_a: lig_E14 + ligand_b: lig_E28 + atom mapping: {0: 18, 1: 17, 2: 16, 3: 15, 15: 42, 16: 43, 17: 44, 18: 45, 19: 41, + 20: 19} + score: '0.296' + edge_lig_E8_lig_E14: + ligand_a: lig_E8 + ligand_b: lig_E14 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 13, 7: 11, 9: 9, 10: 10, 11: 7, + 13: 5, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20} + score: '0.551' + edge_lig_7_lig_E28: + ligand_a: lig_7 + ligand_b: lig_E28 + atom mapping: {1: 16, 2: 17, 3: 19, 4: 20, 5: 21, 6: 23, 7: 22, 8: 24, 9: 26, + 10: 25, 11: 27, 13: 28, 22: 35, 23: 37, 24: 36, 25: 38, 26: 40, 27: 39, 28: 41, + 29: 42, 30: 43, 31: 44, 32: 45, 33: 15} + score: '0.534' + edge_lig_E9_lig_E14: + ligand_a: lig_E9 + ligand_b: lig_E14 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 13, 7: 11, 9: 9, 10: 10, 11: 7, + 13: 5, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20} + score: '0.555' + edge_lig_3_lig_E28: + ligand_a: lig_3 + ligand_b: lig_E28 + atom mapping: {1: 16, 2: 17, 3: 19, 4: 20, 5: 38, 6: 40, 7: 39, 8: 35, 9: 36, + 14: 27, 16: 24, 17: 25, 22: 21, 23: 23, 24: 22, 25: 41, 26: 42, 27: 43, 28: 45, + 29: 44, 30: 15} + score: '0.508' + edge_lig_E14_lig_E24: + ligand_a: lig_E14 + ligand_b: lig_E24 + atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 43, + 15: 39, 16: 40, 17: 42, 18: 41, 19: 38, 20: 16} + score: '0.536' + edge_lig_E28_lig_E5: + ligand_a: lig_E28 + ligand_b: lig_E5 + atom mapping: {15: 30, 16: 1, 17: 2, 19: 3, 20: 4, 21: 5, 22: 6, 23: 7, 24: 8, + 25: 9, 26: 10, 27: 11, 28: 16, 32: 12, 35: 19, 36: 21, 37: 20, 38: 22, 39: 24, + 40: 23, 41: 25, 42: 26, 43: 27, 44: 29, 45: 28} + score: '0.543' + edge_lig_SHP836-2_lig_E28: + ligand_a: lig_SHP836-2 + ligand_b: lig_E28 + atom mapping: {1: 16, 2: 17, 3: 19, 4: 20, 5: 38, 6: 40, 7: 39, 8: 35, 9: 36, + 14: 27, 16: 24, 17: 25, 22: 21, 23: 23, 24: 22, 25: 41, 26: 42, 27: 43, 28: 45, + 29: 44, 30: 15} + score: '0.508' + edge_lig_E14_lig_11: + ligand_a: lig_E14 + ligand_b: lig_11 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 13, 7: 11, 9: 9, 10: 10, 11: 7, + 13: 5, 15: 15, 16: 16, 18: 17, 19: 22, 20: 23} + score: '0.536' + edge_lig_E14_lig_E23: + ligand_a: lig_E14 + ligand_b: lig_E23 + atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 40, + 15: 36, 16: 37, 17: 39, 18: 38, 19: 35, 20: 13} + score: '0.536' + edge_lig_E14_lig_SHP099-1: + ligand_a: lig_E14 + ligand_b: lig_SHP099-1 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 13, 7: 11, 9: 9, 10: 10, 11: 7, + 13: 5, 15: 15, 16: 16, 17: 18, 18: 17, 19: 19, 20: 20} + score: '0.555' + edge_lig_E14_lig_E30: + ligand_a: lig_E14 + ligand_b: lig_E30 + atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 39, + 15: 35, 16: 36, 17: 38, 18: 37, 19: 34, 20: 12} + score: '0.540' + edge_lig_E14_lig_E25: + ligand_a: lig_E14 + ligand_b: lig_E25 + atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 41, + 15: 37, 16: 38, 17: 40, 18: 39, 19: 36, 20: 14} + score: '0.532' + edge_lig_E14_lig_E4: + ligand_a: lig_E14 + ligand_b: lig_E4 + atom mapping: {1: 6, 2: 4, 3: 3, 15: 30, 16: 31, 17: 33, 18: 32, 19: 29, 20: 7} + score: '0.292' + edge_lig_E14_lig_E22: + ligand_a: lig_E14 + ligand_b: lig_E22 + atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 40, + 15: 36, 16: 37, 17: 39, 18: 38, 19: 35, 20: 13} + score: '0.536' + edge_lig_6_lig_E14: + ligand_a: lig_6 + ligand_b: lig_E14 + atom mapping: {1: 2, 2: 1, 3: 20, 22: 19, 23: 15, 24: 16, 25: 18, 26: 17, 27: 3, + 28: 4, 29: 13, 31: 11, 33: 9, 34: 10, 35: 7, 37: 5} + score: '0.544' diff --git a/data/shp2/03_edges/nohup.out b/data/shp2/03_edges/nohup.out deleted file mode 100644 index e8a050dde..000000000 --- a/data/shp2/03_edges/nohup.out +++ /dev/null @@ -1,29 +0,0 @@ -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. -lig_7_lig_E28 exceeds 1 A pairwise distance -lig_SHP836-2_lig_E28 exceeds 1 A pairwise distance -lig_E14_lig_E26 exceeds 1 A pairwise distance -lig_E14_lig_E23 exceeds 1 A pairwise distance -lig_E14_lig_E24 exceeds 1 A pairwise distance -lig_E14_lig_SHP099-1 exceeds 1 A pairwise distance -lig_E28_lig_E5 exceeds 1 A pairwise distance -lig_E14_lig_E30 exceeds 1 A pairwise distance -lig_E14_lig_E1 exceeds 1 A pairwise distance -lig_E14_lig_E25 exceeds 1 A pairwise distance -lig_E14_lig_11 exceeds 1 A pairwise distance -lig_E4_lig_E27 exceeds 1 A pairwise distance -lig_3_lig_E28 exceeds 1 A pairwise distance -lig_E14_lig_E2 exceeds 1 A pairwise distance -lig_E14_lig_10 exceeds 1 A pairwise distance -lig_E8_lig_E14 exceeds 1 A pairwise distance -lig_E14_lig_E22 exceeds 1 A pairwise distance -lig_6_lig_E14 exceeds 1 A pairwise distance -lig_E9_lig_E14 exceeds 1 A pairwise distance -lig_E14_lig_E6 exceeds 1 A pairwise distance diff --git a/data/syk/03_edges/01_perses_openfe.yaml b/data/syk/03_edges/01_perses_openfe.yaml deleted file mode 100644 index 43ed4f820..000000000 --- a/data/syk/03_edges/01_perses_openfe.yaml +++ /dev/null @@ -1,312 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph -edges: - edge_lig_CHEMBL3265001_lig_CHEMBL3265035: - ligand_a: lig_CHEMBL3265001 - ligand_b: lig_CHEMBL3265035 - atom mapping: (0, 40) (1, 39) (2, 41) (3, 42) (4, 36) (5, 37) (6, 38) (7, 17) - (8, 15) (9, 16) (10, 14) (11, 43) (12, 44) (13, 45) (14, 46) (15, 9) (16, 8) - (17, 5) (18, 7) (19, 6) (21, 10) (27, 12) (28, 13) (29, 18) (30, 19) (60, 34) - (61, 35) - score: '0.472' - edge_lig_CHEMBL3265014_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265014 - ligand_b: lig_CHEMBL3265031 - atom mapping: (0, 45) (1, 44) (2, 46) (3, 47) (4, 41) (5, 42) (6, 43) (7, 22) - (8, 20) (9, 21) (10, 19) (11, 48) (12, 49) (13, 50) (14, 51) (15, 14) (21, 15) - (27, 17) (28, 18) (29, 23) (30, 24) (50, 39) (51, 40) - score: '0.464' - edge_lig_CHEMBL3265022_lig_CHEMBL3264994: - ligand_a: lig_CHEMBL3265022 - ligand_b: lig_CHEMBL3264994 - atom mapping: (12, 34) (13, 62) (14, 63) (15, 4) (16, 5) (17, 6) (18, 1) (19, - 0) (20, 2) (21, 3) (22, 7) (23, 8) (24, 9) (25, 10) (26, 31) (27, 32) (28, 29) - (29, 30) (30, 15) (31, 16) (32, 17) (33, 20) (34, 19) (35, 18) (36, 13) (42, - 11) (43, 12) (44, 33) - score: '0.507' - edge_lig_CHEMBL3265000_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3265000 - ligand_b: lig_CHEMBL3265033 - atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) - (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) - (27, 46) (28, 47) (29, 48) (30, 9) (65, 10) (66, 11) - score: '0.412' - edge_lig_CHEMBL3265001_lig_CHEMBL3265030_n: - ligand_a: lig_CHEMBL3265001 - ligand_b: lig_CHEMBL3265030_n - atom mapping: (0, 42) (1, 41) (2, 43) (3, 44) (4, 38) (5, 39) (6, 40) (7, 19) - (8, 17) (9, 18) (10, 16) (11, 45) (12, 46) (13, 47) (14, 48) (15, 11) (21, 12) - (27, 14) (28, 15) (29, 20) (30, 21) (60, 36) (61, 37) - score: '0.417' - edge_lig_CHEMBL3264995_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3264995 - ligand_b: lig_CHEMBL3265031 - atom mapping: (0, 45) (1, 44) (2, 46) (3, 47) (4, 41) (5, 42) (6, 43) (7, 22) - (8, 20) (9, 21) (10, 19) (11, 48) (12, 49) (13, 50) (14, 51) (15, 14) (21, 15) - (27, 17) (28, 18) (29, 23) (30, 24) (58, 39) (59, 40) - score: '0.404' - edge_lig_CHEMBL3265000_lig_CHEMBL3265036: - ligand_a: lig_CHEMBL3265000 - ligand_b: lig_CHEMBL3265036 - atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) - (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 45) - (27, 47) (28, 48) (29, 49) (30, 9) (65, 10) (66, 11) - score: '0.407' - edge_lig_CHEMBL3265004_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265004 - ligand_b: lig_CHEMBL3265031 - atom mapping: (26, 24) (27, 39) (28, 40) (29, 41) (30, 42) (31, 43) (32, 44) (33, - 45) (34, 46) (35, 47) (36, 22) (37, 20) (38, 21) (39, 19) (40, 17) (41, 18) - (42, 15) (43, 16) (44, 14) (50, 50) (56, 48) (57, 49) (58, 23) - score: '0.397' - edge_lig_CHEMBL3265005_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3265005 - ligand_b: lig_CHEMBL3265033 - atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) - (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) - (27, 46) (28, 47) (29, 48) (30, 9) (46, 10) (47, 11) - score: '0.485' - edge_lig_CHEMBL3265016_lig_CHEMBL3264994: - ligand_a: lig_CHEMBL3265016 - ligand_b: lig_CHEMBL3264994 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, - 20) (19, 19) (20, 18) (21, 29) (27, 31) (28, 32) (29, 33) (30, 34) (46, 62) - (47, 63) - score: '0.518' - edge_lig_CHEMBL3265009_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3265009 - ligand_b: lig_CHEMBL3265033 - atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) - (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) - (27, 46) (28, 47) (29, 48) (30, 9) (49, 10) (50, 11) - score: '0.469' - edge_lig_CHEMBL3264996_lig_CHEMBL3265027: - ligand_a: lig_CHEMBL3264996 - ligand_b: lig_CHEMBL3265027 - atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) - (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 29) - (27, 31) (28, 32) (29, 33) (30, 9) (62, 10) (63, 11) - score: '0.499' - edge_lig_CHEMBL3265003_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265003 - ligand_b: lig_CHEMBL3265031 - atom mapping: (24, 24) (25, 39) (26, 40) (27, 41) (28, 42) (29, 43) (30, 44) (31, - 45) (32, 46) (33, 47) (34, 22) (35, 20) (36, 21) (37, 19) (38, 17) (39, 18) - (40, 15) (41, 16) (42, 14) (48, 50) (54, 48) (55, 49) (56, 23) - score: '0.397' - edge_lig_CHEMBL3265019_lig_CHEMBL3264994: - ligand_a: lig_CHEMBL3265019 - ligand_b: lig_CHEMBL3264994 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 21) (18, - 24) (19, 23) (20, 22) (21, 29) (27, 31) (28, 32) (29, 33) (30, 34) (44, 62) - (45, 63) - score: '0.530' - edge_lig_CHEMBL3264997_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3264997 - ligand_b: lig_CHEMBL3265031 - atom mapping: (0, 45) (1, 44) (2, 46) (3, 47) (4, 41) (5, 42) (6, 43) (7, 22) - (8, 20) (9, 21) (10, 19) (11, 48) (12, 49) (13, 50) (14, 51) (15, 14) (21, 15) - (27, 17) (28, 18) (29, 23) (30, 24) (58, 39) (59, 40) - score: '0.404' - edge_lig_CHEMBL3265000_lig_CHEMBL3265034: - ligand_a: lig_CHEMBL3265000 - ligand_b: lig_CHEMBL3265034 - atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) - (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 43) - (27, 45) (28, 46) (29, 47) (30, 9) (65, 10) (66, 11) - score: '0.416' - edge_lig_CHEMBL3265001_lig_CHEMBL3265029: - ligand_a: lig_CHEMBL3265001 - ligand_b: lig_CHEMBL3265029 - atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) - (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (16, 28) - (17, 29) (18, 32) (19, 31) (20, 30) (21, 33) (27, 35) (28, 36) (29, 37) (30, - 9) (60, 10) (61, 11) - score: '0.530' - edge_lig_CHEMBL3265024_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3265024 - ligand_b: lig_CHEMBL3265033 - atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) - (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) - (27, 46) (28, 47) (29, 48) (30, 9) (48, 10) (49, 11) - score: '0.474' - edge_lig_CHEMBL3265021_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265021 - ligand_b: lig_CHEMBL3265031 - atom mapping: (11, 24) (12, 39) (13, 40) (14, 41) (15, 42) (16, 43) (17, 44) (18, - 45) (19, 46) (20, 47) (21, 22) (22, 20) (23, 21) (24, 19) (25, 17) (26, 18) - (27, 15) (28, 16) (29, 14) (35, 50) (41, 48) (42, 49) (43, 23) - score: '0.491' - edge_lig_CHEMBL3265018_lig_CHEMBL3264994: - ligand_a: lig_CHEMBL3265018 - ligand_b: lig_CHEMBL3264994 - atom mapping: (9, 34) (10, 62) (11, 63) (12, 4) (13, 5) (14, 6) (15, 1) (16, 0) - (17, 2) (18, 3) (19, 7) (20, 8) (21, 9) (22, 10) (23, 11) (24, 12) (25, 13) - (26, 14) (27, 15) (28, 16) (29, 25) (30, 26) (31, 27) (32, 28) (33, 29) (39, - 31) (40, 32) (41, 33) - score: '0.524' - edge_lig_CHEMBL3265000_lig_CHEMBL3265032: - ligand_a: lig_CHEMBL3265000 - ligand_b: lig_CHEMBL3265032 - atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) - (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 42) - (27, 44) (28, 45) (29, 46) (30, 9) (65, 10) (66, 11) - score: '0.421' - edge_lig_CHEMBL3265023_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3265023 - ligand_b: lig_CHEMBL3265033 - atom mapping: (14, 9) (15, 10) (16, 11) (17, 12) (18, 13) (19, 14) (20, 15) (21, - 16) (22, 17) (23, 18) (24, 19) (25, 20) (26, 21) (27, 22) (28, 23) (29, 24) - (30, 25) (31, 26) (32, 27) (38, 44) (44, 46) (45, 47) (46, 48) - score: '0.474' - edge_lig_CHEMBL3265017_lig_CHEMBL3264994: - ligand_a: lig_CHEMBL3265017 - ligand_b: lig_CHEMBL3264994 - atom mapping: (9, 34) (10, 62) (11, 63) (12, 4) (13, 5) (14, 6) (15, 1) (16, 0) - (17, 2) (18, 3) (19, 7) (20, 8) (21, 9) (22, 10) (23, 11) (24, 12) (25, 13) - (26, 14) (27, 15) (28, 16) (29, 21) (30, 24) (31, 23) (32, 22) (33, 29) (39, - 31) (40, 32) (41, 33) - score: '0.524' - edge_lig_CHEMBL3265025_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3265025 - ligand_b: lig_CHEMBL3265033 - atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) - (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) - (27, 46) (28, 47) (29, 48) (30, 9) (48, 10) (49, 11) - score: '0.474' - edge_lig_CHEMBL3265028_lig_CHEMBL3264994: - ligand_a: lig_CHEMBL3265028 - ligand_b: lig_CHEMBL3264994 - atom mapping: (9, 34) (10, 62) (11, 63) (12, 4) (13, 5) (14, 6) (15, 1) (16, 0) - (17, 2) (18, 3) (19, 7) (20, 8) (21, 9) (22, 10) (23, 11) (24, 12) (25, 13) - (26, 14) (27, 15) (29, 29) (35, 31) (36, 32) (37, 33) - score: '0.479' - edge_lig_CHEMBL3265006_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3265006 - ligand_b: lig_CHEMBL3265033 - atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) - (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) - (27, 46) (28, 47) (29, 48) (30, 9) (49, 10) (50, 11) - score: '0.469' - edge_lig_CHEMBL3265011_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265011 - ligand_b: lig_CHEMBL3265031 - atom mapping: (0, 45) (1, 44) (2, 46) (3, 47) (4, 41) (5, 42) (6, 43) (7, 22) - (8, 20) (9, 21) (10, 19) (11, 48) (12, 49) (13, 50) (14, 51) (15, 14) (21, 15) - (27, 17) (28, 18) (29, 23) (30, 24) (49, 39) (50, 40) - score: '0.469' - edge_lig_CHEMBL3265001_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265001 - ligand_b: lig_CHEMBL3265031 - atom mapping: (0, 45) (1, 44) (2, 46) (3, 47) (4, 41) (5, 42) (6, 43) (7, 22) - (8, 20) (9, 21) (10, 19) (11, 48) (12, 49) (13, 50) (14, 51) (15, 14) (21, 15) - (27, 17) (28, 18) (29, 23) (30, 24) (60, 39) (61, 40) - score: '0.397' - edge_lig_CHEMBL3265012_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3265012 - ligand_b: lig_CHEMBL3265033 - atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) - (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) - (27, 46) (28, 47) (29, 48) (30, 9) (46, 10) (47, 11) - score: '0.485' - edge_lig_CHEMBL3265002_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265002 - ligand_b: lig_CHEMBL3265031 - atom mapping: (25, 24) (26, 39) (27, 40) (28, 41) (29, 42) (30, 43) (31, 44) (32, - 45) (33, 46) (34, 47) (35, 22) (36, 20) (37, 21) (38, 19) (39, 17) (40, 18) - (41, 15) (42, 16) (43, 14) (49, 50) (55, 48) (56, 49) (57, 23) - score: '0.397' - edge_lig_CHEMBL3265013_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3265013 - ligand_b: lig_CHEMBL3265033 - atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) - (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) - (27, 46) (28, 47) (29, 48) (30, 9) (49, 10) (50, 11) - score: '0.469' - edge_lig_CHEMBL3265015_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3265015 - ligand_b: lig_CHEMBL3265033 - atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) - (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) - (27, 46) (28, 47) (29, 48) (30, 9) (49, 10) (50, 11) - score: '0.469' - edge_lig_CHEMBL3265008_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3265008 - ligand_b: lig_CHEMBL3265033 - atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) - (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) - (27, 46) (28, 47) (29, 48) (30, 9) (46, 10) (47, 11) - score: '0.485' - edge_lig_CHEMBL3265020_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3265020 - ligand_b: lig_CHEMBL3265033 - atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) - (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) - (27, 46) (28, 47) (29, 48) (30, 9) (46, 10) (47, 11) - score: '0.485' - edge_lig_CHEMBL3265000_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265000 - ligand_b: lig_CHEMBL3265031 - atom mapping: (0, 45) (1, 44) (2, 46) (3, 47) (4, 41) (5, 42) (6, 43) (7, 22) - (8, 20) (9, 21) (10, 19) (11, 48) (12, 49) (13, 50) (14, 51) (15, 14) (21, 15) - (27, 17) (28, 18) (29, 23) (30, 24) (65, 39) (66, 40) - score: '0.397' - edge_lig_CHEMBL3264998_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3264998 - ligand_b: lig_CHEMBL3265031 - atom mapping: (0, 45) (1, 44) (2, 46) (3, 47) (4, 41) (5, 42) (6, 43) (7, 22) - (8, 20) (9, 21) (10, 19) (11, 48) (12, 49) (13, 50) (14, 51) (15, 14) (21, 15) - (27, 17) (28, 18) (29, 23) (30, 24) (61, 39) (62, 40) - score: '0.402' - edge_lig_CHEMBL3265031_lig_CHEMBL3264994: - ligand_a: lig_CHEMBL3265031 - ligand_b: lig_CHEMBL3264994 - atom mapping: (14, 15) (15, 13) (16, 14) (17, 11) (18, 12) (19, 10) (20, 8) (21, - 9) (22, 7) (23, 33) (24, 34) (39, 62) (40, 63) (41, 4) (42, 5) (43, 6) (44, - 1) (45, 0) (46, 2) (47, 3) (48, 31) (49, 32) (50, 29) (51, 30) - score: '0.414' - edge_lig_CHEMBL3265010_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3265010 - ligand_b: lig_CHEMBL3265033 - atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) - (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) - (27, 46) (28, 47) (29, 48) (30, 9) (50, 10) (51, 11) - score: '0.464' - edge_lig_CHEMBL3265026_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3265026 - ligand_b: lig_CHEMBL3265033 - atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) - (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) - (27, 46) (28, 47) (29, 48) (30, 9) (49, 10) (50, 11) - score: '0.469' - edge_lig_CHEMBL3259820_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3259820 - ligand_b: lig_CHEMBL3265033 - atom mapping: (0, 16) (1, 15) (2, 17) (3, 18) (4, 12) (5, 13) (6, 14) (7, 19) - (8, 20) (9, 21) (10, 22) (11, 23) (12, 24) (13, 25) (14, 26) (15, 27) (21, 44) - (27, 46) (28, 47) (29, 48) (30, 9) (46, 10) (47, 11) - score: '0.485' - edge_lig_CHEMBL3264996_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3264996 - ligand_b: lig_CHEMBL3265031 - atom mapping: (0, 45) (1, 44) (2, 46) (3, 47) (4, 41) (5, 42) (6, 43) (7, 22) - (8, 20) (9, 21) (10, 19) (11, 48) (12, 49) (13, 50) (14, 51) (15, 14) (21, 15) - (27, 17) (28, 18) (29, 23) (30, 24) (62, 39) (63, 40) - score: '0.402' - edge_lig_CHEMBL3265031_lig_CHEMBL3264999: - ligand_a: lig_CHEMBL3265031 - ligand_b: lig_CHEMBL3264999 - atom mapping: (14, 15) (15, 13) (16, 14) (17, 11) (18, 12) (19, 10) (20, 8) (21, - 9) (22, 7) (23, 29) (24, 30) (39, 60) (40, 61) (41, 4) (42, 5) (43, 6) (44, - 1) (45, 0) (46, 2) (47, 3) (48, 27) (49, 28) (50, 21) - score: '0.404' - edge_lig_CHEMBL3265037_lig_CHEMBL3264994: - ligand_a: lig_CHEMBL3265037 - ligand_b: lig_CHEMBL3264994 - atom mapping: (9, 34) (10, 62) (11, 63) (12, 4) (13, 5) (14, 6) (15, 1) (16, 0) - (17, 2) (18, 3) (19, 7) (20, 8) (21, 9) (22, 10) (23, 11) (24, 12) (25, 13) - (26, 14) (27, 15) (42, 29) (48, 31) (49, 32) (50, 33) - score: '0.412' diff --git a/data/syk/03_edges/01_perses_openfe.yml b/data/syk/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..0ae6d65aa --- /dev/null +++ b/data/syk/03_edges/01_perses_openfe.yml @@ -0,0 +1,305 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_CHEMBL3265014_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265014 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 50: 39, 51: 40} + score: '0.464' + edge_lig_CHEMBL3265018_lig_CHEMBL3264994: + ligand_a: lig_CHEMBL3265018 + ligand_b: lig_CHEMBL3264994 + atom mapping: {9: 34, 10: 62, 11: 63, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, + 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, + 28: 16, 29: 17, 30: 18, 31: 19, 32: 20, 33: 29, 39: 31, 40: 32, 41: 33} + score: '0.524' + edge_lig_CHEMBL3264998_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3264998 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 61: 39, 62: 40} + score: '0.402' + edge_lig_CHEMBL3265021_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265021 + ligand_b: lig_CHEMBL3265031 + atom mapping: {11: 24, 12: 39, 13: 40, 14: 41, 15: 42, 16: 43, 17: 44, 18: 45, + 19: 46, 20: 47, 21: 22, 22: 20, 23: 21, 24: 19, 25: 17, 26: 18, 27: 15, 28: 16, + 29: 14, 35: 50, 41: 48, 42: 49, 43: 23} + score: '0.491' + edge_lig_CHEMBL3265005_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265005 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 46: 39, 47: 40} + score: '0.485' + edge_lig_CHEMBL3265031_lig_CHEMBL3264999: + ligand_a: lig_CHEMBL3265031 + ligand_b: lig_CHEMBL3264999 + atom mapping: {14: 15, 15: 13, 16: 14, 17: 11, 18: 12, 19: 10, 20: 8, 21: 9, 22: 7, + 23: 29, 24: 30, 39: 60, 40: 61, 41: 4, 42: 5, 43: 6, 44: 1, 45: 0, 46: 2, 47: 3, + 48: 27, 49: 28, 50: 21} + score: '0.404' + edge_lig_CHEMBL3265015_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265015 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 49: 39, 50: 40} + score: '0.469' + edge_lig_CHEMBL3265024_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265024 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 48: 39, 49: 40} + score: '0.474' + edge_lig_CHEMBL3264996_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3264996 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 62: 39, 63: 40} + score: '0.402' + edge_lig_CHEMBL3265000_lig_CHEMBL3265032: + ligand_a: lig_CHEMBL3265000 + ligand_b: lig_CHEMBL3265032 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 42, 27: 44, 28: 45, + 29: 46, 30: 9, 65: 10, 66: 11} + score: '0.421' + edge_lig_CHEMBL3265002_lig_CHEMBL3265035: + ligand_a: lig_CHEMBL3265002 + ligand_b: lig_CHEMBL3265035 + atom mapping: {25: 19, 26: 34, 27: 35, 28: 36, 29: 37, 30: 38, 31: 39, 32: 40, + 33: 41, 34: 42, 35: 17, 36: 15, 37: 16, 38: 14, 39: 12, 40: 13, 41: 10, 42: 11, + 43: 9, 44: 8, 45: 5, 46: 7, 47: 6, 49: 45, 55: 43, 56: 44, 57: 18} + score: '0.472' + edge_lig_CHEMBL3265011_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265011 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 49: 39, 50: 40} + score: '0.469' + edge_lig_CHEMBL3265000_lig_CHEMBL3265034: + ligand_a: lig_CHEMBL3265000 + ligand_b: lig_CHEMBL3265034 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 43, 27: 45, 28: 46, + 29: 47, 30: 9, 65: 10, 66: 11} + score: '0.416' + edge_lig_CHEMBL3265028_lig_CHEMBL3264994: + ligand_a: lig_CHEMBL3265028 + ligand_b: lig_CHEMBL3264994 + atom mapping: {9: 34, 10: 62, 11: 63, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, + 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, + 29: 29, 35: 31, 36: 32, 37: 33} + score: '0.479' + edge_lig_CHEMBL3259820_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3259820 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 46: 39, 47: 40} + score: '0.485' + edge_lig_CHEMBL3265025_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265025 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 48: 39, 49: 40} + score: '0.474' + edge_lig_CHEMBL3265004_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265004 + ligand_b: lig_CHEMBL3265031 + atom mapping: {26: 24, 27: 39, 28: 40, 29: 41, 30: 42, 31: 43, 32: 44, 33: 45, + 34: 46, 35: 47, 36: 22, 37: 20, 38: 21, 39: 19, 40: 48, 41: 49, 42: 50, 43: 51, + 44: 14, 50: 15, 56: 17, 57: 18, 58: 23} + score: '0.397' + edge_lig_CHEMBL3265000_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265000 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 65: 39, 66: 40} + score: '0.397' + edge_lig_CHEMBL3265016_lig_CHEMBL3264994: + ligand_a: lig_CHEMBL3265016 + ligand_b: lig_CHEMBL3264994 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 20, 19: 19, 20: 18, + 21: 29, 27: 31, 28: 32, 29: 33, 30: 34, 46: 62, 47: 63} + score: '0.518' + edge_lig_CHEMBL3265020_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265020 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 46: 39, 47: 40} + score: '0.485' + edge_lig_CHEMBL3265008_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265008 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 46: 39, 47: 40} + score: '0.485' + edge_lig_CHEMBL3265023_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265023 + ligand_b: lig_CHEMBL3265033 + atom mapping: {14: 9, 15: 10, 16: 11, 17: 12, 18: 13, 19: 14, 20: 15, 21: 16, + 22: 17, 23: 18, 24: 19, 25: 20, 26: 21, 27: 22, 28: 23, 29: 24, 30: 25, 31: 26, + 32: 27, 38: 44, 44: 46, 45: 47, 46: 48} + score: '0.474' + edge_lig_CHEMBL3265000_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265000 + ligand_b: lig_CHEMBL3265033 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 44, 27: 46, 28: 47, + 29: 48, 30: 9, 65: 10, 66: 11} + score: '0.412' + edge_lig_CHEMBL3265013_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265013 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 49: 39, 50: 40} + score: '0.469' + edge_lig_CHEMBL3265037_lig_CHEMBL3264994: + ligand_a: lig_CHEMBL3265037 + ligand_b: lig_CHEMBL3264994 + atom mapping: {9: 34, 10: 62, 11: 63, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, + 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, + 42: 29, 48: 31, 49: 32, 50: 33} + score: '0.412' + edge_lig_CHEMBL3265002_lig_CHEMBL3265030_n: + ligand_a: lig_CHEMBL3265002 + ligand_b: lig_CHEMBL3265030_n + atom mapping: {25: 21, 26: 36, 27: 37, 28: 38, 29: 39, 30: 40, 31: 41, 32: 42, + 33: 43, 34: 44, 35: 19, 36: 17, 37: 18, 38: 16, 39: 45, 40: 46, 41: 47, 42: 48, + 43: 11, 49: 12, 55: 14, 56: 15, 57: 20} + score: '0.417' + edge_lig_CHEMBL3265001_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265001 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 60: 39, 61: 40} + score: '0.397' + edge_lig_CHEMBL3265002_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265002 + ligand_b: lig_CHEMBL3265031 + atom mapping: {25: 24, 26: 39, 27: 40, 28: 41, 29: 42, 30: 43, 31: 44, 32: 45, + 33: 46, 34: 47, 35: 22, 36: 20, 37: 21, 38: 19, 39: 17, 40: 18, 41: 15, 42: 16, + 43: 14, 49: 50, 55: 48, 56: 49, 57: 23} + score: '0.397' + edge_lig_CHEMBL3265012_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265012 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 46: 39, 47: 40} + score: '0.485' + edge_lig_CHEMBL3265009_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265009 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 49: 39, 50: 40} + score: '0.469' + edge_lig_CHEMBL3265017_lig_CHEMBL3264994: + ligand_a: lig_CHEMBL3265017 + ligand_b: lig_CHEMBL3264994 + atom mapping: {9: 34, 10: 62, 11: 63, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, + 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, + 28: 16, 29: 21, 30: 24, 31: 23, 32: 22, 33: 29, 39: 31, 40: 32, 41: 33} + score: '0.524' + edge_lig_CHEMBL3265019_lig_CHEMBL3264994: + ligand_a: lig_CHEMBL3265019 + ligand_b: lig_CHEMBL3264994 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 21, 18: 24, 19: 23, 20: 22, + 21: 29, 27: 31, 28: 32, 29: 33, 30: 34, 44: 62, 45: 63} + score: '0.530' + edge_lig_CHEMBL3265022_lig_CHEMBL3264994: + ligand_a: lig_CHEMBL3265022 + ligand_b: lig_CHEMBL3264994 + atom mapping: {12: 34, 13: 62, 14: 63, 15: 4, 16: 5, 17: 6, 18: 1, 19: 0, 20: 2, + 21: 3, 22: 7, 23: 8, 24: 9, 25: 10, 26: 31, 27: 32, 28: 29, 29: 30, 30: 15, + 31: 16, 32: 25, 33: 28, 34: 27, 35: 26, 36: 13, 42: 11, 43: 12, 44: 33} + score: '0.507' + edge_lig_CHEMBL3264997_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3264997 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 58: 39, 59: 40} + score: '0.404' + edge_lig_CHEMBL3265000_lig_CHEMBL3265036: + ligand_a: lig_CHEMBL3265000 + ligand_b: lig_CHEMBL3265036 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 45, 27: 47, 28: 48, + 29: 49, 30: 9, 65: 10, 66: 11} + score: '0.407' + edge_lig_CHEMBL3265026_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265026 + ligand_b: lig_CHEMBL3265033 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 44, 27: 46, 28: 47, + 29: 48, 30: 9, 49: 10, 50: 11} + score: '0.469' + edge_lig_CHEMBL3265002_lig_CHEMBL3265029: + ligand_a: lig_CHEMBL3265002 + ligand_b: lig_CHEMBL3265029 + atom mapping: {25: 9, 26: 10, 27: 11, 28: 12, 29: 13, 30: 14, 31: 15, 32: 16, + 33: 17, 34: 18, 35: 19, 36: 20, 37: 21, 38: 22, 39: 23, 40: 24, 41: 25, 42: 26, + 43: 27, 44: 28, 45: 29, 46: 32, 47: 31, 48: 30, 49: 33, 55: 35, 56: 36, 57: 37} + score: '0.530' + edge_lig_CHEMBL3265031_lig_CHEMBL3264994: + ligand_a: lig_CHEMBL3265031 + ligand_b: lig_CHEMBL3264994 + atom mapping: {14: 15, 15: 13, 16: 14, 17: 11, 18: 12, 19: 10, 20: 8, 21: 9, 22: 7, + 23: 33, 24: 34, 39: 62, 40: 63, 41: 4, 42: 5, 43: 6, 44: 1, 45: 0, 46: 2, 47: 3, + 48: 31, 49: 32, 50: 29, 51: 30} + score: '0.414' + edge_lig_CHEMBL3265010_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265010 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 50: 39, 51: 40} + score: '0.464' + edge_lig_CHEMBL3264995_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3264995 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 58: 39, 59: 40} + score: '0.404' + edge_lig_CHEMBL3265006_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265006 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 49: 39, 50: 40} + score: '0.469' + edge_lig_CHEMBL3264996_lig_CHEMBL3265027: + ligand_a: lig_CHEMBL3264996 + ligand_b: lig_CHEMBL3265027 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 29, 27: 31, 28: 32, + 29: 33, 30: 9, 62: 10, 63: 11} + score: '0.499' + edge_lig_CHEMBL3265003_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265003 + ligand_b: lig_CHEMBL3265031 + atom mapping: {24: 24, 25: 39, 26: 40, 27: 41, 28: 42, 29: 43, 30: 44, 31: 45, + 32: 46, 33: 47, 34: 22, 35: 20, 36: 21, 37: 19, 38: 17, 39: 18, 40: 15, 41: 16, + 42: 14, 48: 50, 54: 48, 55: 49, 56: 23} + score: '0.397' diff --git a/data/syk/03_edges/nohup.out b/data/syk/03_edges/nohup.out deleted file mode 100644 index f2e264e0e..000000000 --- a/data/syk/03_edges/nohup.out +++ /dev/null @@ -1,25 +0,0 @@ -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. -lig_CHEMBL3265001_lig_CHEMBL3265035 exceeds 1 A pairwise distance -lig_CHEMBL3265022_lig_CHEMBL3264994 exceeds 1 A pairwise distance -lig_CHEMBL3265000_lig_CHEMBL3265036 exceeds 1 A pairwise distance -lig_CHEMBL3265004_lig_CHEMBL3265031 exceeds 1 A pairwise distance -lig_CHEMBL3265016_lig_CHEMBL3264994 exceeds 1 A pairwise distance -lig_CHEMBL3264996_lig_CHEMBL3265027 exceeds 1 A pairwise distance -lig_CHEMBL3265003_lig_CHEMBL3265031 exceeds 1 A pairwise distance -lig_CHEMBL3265019_lig_CHEMBL3264994 exceeds 1 A pairwise distance -lig_CHEMBL3265001_lig_CHEMBL3265029 exceeds 1 A pairwise distance -lig_CHEMBL3265021_lig_CHEMBL3265031 exceeds 1 A pairwise distance -lig_CHEMBL3265018_lig_CHEMBL3264994 exceeds 1 A pairwise distance -lig_CHEMBL3265017_lig_CHEMBL3264994 exceeds 1 A pairwise distance -lig_CHEMBL3265002_lig_CHEMBL3265031 exceeds 1 A pairwise distance -lig_CHEMBL3265001_lig_CHEMBL3265035 exceeds 1 A pairwise distance -lig_CHEMBL3265031_lig_CHEMBL3264994 exceeds 1 A pairwise distance -lig_CHEMBL3265031_lig_CHEMBL3264999 exceeds 1 A pairwise distance diff --git a/data/thrombin/03_edges/01_perses_openfe.yaml b/data/thrombin/03_edges/01_perses_openfe.yaml deleted file mode 100644 index 95274ad61..000000000 --- a/data/thrombin/03_edges/01_perses_openfe.yaml +++ /dev/null @@ -1,94 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph -edges: - edge_lig_7a_lig_5: - ligand_a: lig_7a - ligand_b: lig_5 - atom mapping: (1, 21) (2, 22) (3, 23) (4, 24) (5, 19) (6, 20) (7, 18) (8, 17) - (9, 15) (10, 16) (11, 14) (12, 13) (13, 12) (14, 11) (15, 10) (16, 8) (17, 9) - (18, 7) (19, 6) (20, 3) (21, 2) (22, 1) (23, 0) (24, 5) (25, 4) (26, 25) (28, - 27) (29, 26) (30, 51) (31, 29) (35, 48) (36, 49) (37, 46) (38, 45) (39, 44) - (40, 43) (41, 42) (42, 41) (43, 39) (44, 40) (45, 37) (46, 38) (47, 35) (48, - 36) (49, 32) (50, 31) (51, 30) (52, 34) (53, 33) (57, 28) - score: '0.964' - edge_lig_1d_lig_1a: - ligand_a: lig_1d - ligand_b: lig_1a - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, - 18) (19, 19) (20, 24) (21, 23) (22, 22) (23, 21) (24, 20) (26, 26) (27, 27) - (28, 28) (29, 51) (30, 30) (31, 31) (32, 32) (33, 33) (34, 34) (35, 35) (36, - 37) (37, 36) (38, 39) (39, 38) (40, 41) (41, 40) (42, 42) (43, 43) (44, 44) - (45, 46) (46, 45) (47, 50) (49, 49) (50, 47) (51, 29) - score: '0.969' - edge_lig_6a_lig_3a: - ligand_a: lig_6a - ligand_b: lig_3a - atom mapping: (0, 23) (1, 24) (2, 25) (3, 20) (4, 21) (5, 22) (6, 19) (7, 18) - (8, 16) (9, 17) (10, 15) (11, 14) (12, 13) (13, 12) (14, 11) (15, 9) (16, 10) - (17, 8) (18, 7) (19, 5) (20, 4) (21, 3) (22, 2) (23, 1) (24, 6) (27, 26) (28, - 28) (29, 27) (30, 54) (31, 30) (32, 51) (33, 52) (34, 53) (35, 49) (36, 50) - (37, 48) (38, 47) (39, 46) (40, 45) (41, 44) (42, 43) (43, 41) (44, 42) (45, - 40) (46, 39) (47, 38) (48, 36) (49, 34) (51, 29) - score: '0.951' - edge_lig_1a_lig_5: - ligand_a: lig_1a - ligand_b: lig_5 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, - 18) (19, 19) (20, 24) (21, 23) (22, 22) (23, 21) (24, 20) (26, 25) (27, 26) - (28, 27) (29, 51) (30, 29) (31, 30) (32, 31) (33, 32) (34, 33) (35, 34) (36, - 36) (37, 35) (38, 38) (39, 37) (40, 40) (41, 39) (42, 41) (43, 42) (44, 43) - (45, 45) (46, 44) (47, 50) (48, 49) (49, 48) (50, 46) (51, 28) - score: '0.982' - edge_lig_1b_lig_1a: - ligand_a: lig_1b - ligand_b: lig_1a - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, - 18) (19, 19) (20, 24) (21, 23) (22, 22) (23, 21) (24, 20) (26, 26) (27, 27) - (28, 28) (29, 51) (30, 30) (31, 31) (32, 32) (33, 33) (34, 34) (35, 35) (36, - 37) (37, 36) (38, 39) (39, 38) (40, 41) (41, 40) (42, 42) (43, 43) (44, 44) - (45, 46) (46, 45) (47, 50) (49, 49) (50, 47) (51, 29) - score: '0.969' - edge_lig_6a_lig_5: - ligand_a: lig_6a - ligand_b: lig_5 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, - 18) (19, 19) (20, 24) (21, 23) (22, 22) (23, 21) (24, 20) (27, 25) (28, 26) - (29, 27) (30, 51) (31, 29) (32, 30) (33, 31) (34, 32) (35, 33) (36, 34) (37, - 36) (38, 35) (39, 38) (40, 37) (41, 40) (42, 39) (43, 41) (44, 42) (45, 43) - (46, 45) (47, 44) (48, 50) (49, 48) (50, 47) (51, 28) - score: '0.964' - edge_lig_1c_lig_1a: - ligand_a: lig_1c - ligand_b: lig_1a - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, - 18) (19, 19) (20, 24) (21, 23) (22, 22) (23, 21) (24, 20) (26, 26) (27, 27) - (28, 28) (29, 51) (30, 30) (31, 31) (32, 32) (33, 33) (34, 34) (35, 35) (36, - 37) (37, 36) (38, 39) (39, 38) (40, 41) (41, 40) (42, 42) (43, 43) (44, 44) - (45, 46) (46, 45) (47, 50) (49, 49) (50, 47) (51, 29) - score: '0.969' - edge_lig_6b_lig_3a: - ligand_a: lig_6b - ligand_b: lig_3a - atom mapping: (1, 4) (2, 3) (3, 2) (4, 1) (5, 6) (6, 5) (7, 7) (8, 8) (9, 9) (10, - 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, 18) - (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (24, 24) (25, 25) (26, 26) (27, - 0) (28, 27) (29, 28) (30, 29) (31, 30) (35, 35) (36, 34) (37, 37) (38, 38) (39, - 39) (40, 40) (41, 41) (42, 42) (43, 44) (44, 43) (45, 46) (46, 45) (47, 48) - (48, 47) (49, 49) (50, 50) (51, 51) (52, 52) (53, 53) (54, 54) - score: '0.947' - edge_lig_6a_lig_6e: - ligand_a: lig_6a - ligand_b: lig_6e - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, - 18) (19, 19) (20, 24) (21, 23) (22, 22) (23, 21) (24, 20) (27, 27) (28, 28) - (29, 29) (30, 51) (31, 31) (32, 32) (33, 33) (34, 34) (35, 35) (36, 36) (37, - 38) (38, 37) (39, 40) (40, 39) (41, 42) (42, 41) (43, 43) (44, 44) (45, 45) - (46, 47) (47, 46) (49, 49) (51, 30) - score: '0.939' diff --git a/data/thrombin/03_edges/01_perses_openfe.yml b/data/thrombin/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..26e40c135 --- /dev/null +++ b/data/thrombin/03_edges/01_perses_openfe.yml @@ -0,0 +1,85 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_1d_lig_5: + ligand_a: lig_1d + ligand_b: lig_5 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 24, + 21: 23, 22: 22, 23: 21, 24: 20, 26: 25, 27: 26, 28: 27, 29: 51, 30: 29, 31: 30, + 32: 31, 33: 32, 34: 33, 35: 34, 36: 36, 37: 35, 38: 38, 39: 37, 40: 40, 41: 39, + 42: 41, 43: 42, 44: 43, 45: 45, 46: 44, 47: 50, 48: 49, 49: 48, 50: 46, 51: 28} + score: '0.982' + edge_lig_7a_lig_5: + ligand_a: lig_7a + ligand_b: lig_5 + atom mapping: {1: 21, 2: 22, 3: 23, 4: 24, 5: 19, 6: 20, 7: 18, 8: 17, 9: 15, + 10: 16, 11: 14, 12: 13, 13: 12, 14: 11, 15: 10, 16: 8, 17: 9, 18: 7, 19: 6, + 20: 3, 21: 2, 22: 1, 23: 0, 24: 5, 25: 4, 26: 25, 28: 27, 29: 26, 30: 51, 31: 29, + 35: 48, 36: 49, 37: 46, 38: 45, 39: 44, 40: 43, 41: 42, 42: 41, 43: 39, 44: 40, + 45: 37, 46: 38, 47: 35, 48: 36, 49: 32, 50: 31, 51: 30, 52: 34, 53: 33, 57: 28} + score: '0.964' + edge_lig_6b_lig_5: + ligand_a: lig_6b + ligand_b: lig_5 + atom mapping: {1: 20, 2: 21, 3: 22, 4: 23, 5: 24, 6: 19, 7: 18, 8: 17, 9: 15, + 10: 16, 11: 14, 12: 13, 13: 12, 14: 11, 15: 10, 16: 8, 17: 9, 18: 7, 19: 6, + 20: 3, 21: 4, 22: 5, 23: 0, 24: 1, 25: 2, 26: 25, 28: 27, 29: 26, 30: 28, 31: 29, + 35: 47, 36: 48, 37: 50, 38: 44, 39: 45, 40: 43, 41: 41, 42: 42, 43: 40, 44: 39, + 45: 38, 46: 37, 47: 36, 48: 35, 49: 33, 50: 34, 51: 30, 52: 31, 53: 32, 54: 51} + score: '0.964' + edge_lig_6a_lig_6e: + ligand_a: lig_6a + ligand_b: lig_6e + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 24, + 21: 23, 22: 22, 23: 21, 24: 20, 27: 27, 28: 28, 29: 29, 30: 51, 31: 31, 32: 32, + 33: 33, 34: 34, 35: 35, 36: 36, 37: 38, 38: 37, 39: 40, 40: 39, 41: 42, 42: 41, + 43: 43, 44: 44, 45: 45, 46: 47, 47: 46, 49: 49, 51: 30} + score: '0.939' + edge_lig_6a_lig_3a: + ligand_a: lig_6a + ligand_b: lig_3a + atom mapping: {0: 23, 1: 24, 2: 25, 3: 20, 4: 21, 5: 22, 6: 19, 7: 18, 8: 16, + 9: 17, 10: 15, 11: 14, 12: 13, 13: 12, 14: 11, 15: 9, 16: 10, 17: 8, 18: 7, + 19: 5, 20: 4, 21: 3, 22: 2, 23: 1, 24: 6, 27: 26, 28: 28, 29: 27, 30: 54, 31: 30, + 32: 51, 33: 52, 34: 53, 35: 49, 36: 50, 37: 48, 38: 47, 39: 46, 40: 45, 41: 44, + 42: 43, 43: 41, 44: 42, 45: 40, 46: 39, 47: 38, 48: 36, 49: 34, 51: 29} + score: '0.951' + edge_lig_1d_lig_1b: + ligand_a: lig_1d + ligand_b: lig_1b + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 24, + 21: 23, 22: 22, 23: 21, 24: 20, 26: 26, 27: 27, 28: 28, 29: 51, 30: 30, 31: 31, + 32: 32, 33: 33, 34: 34, 35: 35, 36: 37, 37: 36, 38: 39, 39: 38, 40: 41, 41: 40, + 42: 42, 43: 43, 44: 44, 45: 46, 46: 45, 47: 50, 49: 49, 50: 47, 51: 29} + score: '0.969' + edge_lig_1d_lig_1a: + ligand_a: lig_1d + ligand_b: lig_1a + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 24, + 21: 23, 22: 22, 23: 21, 24: 20, 26: 26, 27: 27, 28: 28, 29: 51, 30: 30, 31: 31, + 32: 32, 33: 33, 34: 34, 35: 35, 36: 37, 37: 36, 38: 39, 39: 38, 40: 41, 41: 40, + 42: 42, 43: 43, 44: 44, 45: 46, 46: 45, 47: 50, 49: 49, 50: 47, 51: 29} + score: '0.969' + edge_lig_1c_lig_1d: + ligand_a: lig_1c + ligand_b: lig_1d + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 24, + 21: 23, 22: 22, 23: 21, 24: 20, 26: 26, 27: 27, 28: 28, 29: 51, 30: 30, 31: 31, + 32: 32, 33: 33, 34: 34, 35: 35, 36: 37, 37: 36, 38: 39, 39: 38, 40: 41, 41: 40, + 42: 42, 43: 43, 44: 44, 45: 46, 46: 45, 47: 50, 49: 49, 50: 47, 51: 29} + score: '0.969' + edge_lig_6b_lig_3a: + ligand_a: lig_6b + ligand_b: lig_3a + atom mapping: {1: 4, 2: 3, 3: 2, 4: 1, 5: 6, 6: 5, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, + 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, + 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 0, 28: 27, 29: 28, 30: 29, 31: 30, + 35: 35, 36: 34, 37: 37, 38: 38, 39: 39, 40: 40, 41: 41, 42: 42, 43: 44, 44: 43, + 45: 46, 46: 45, 47: 48, 48: 47, 49: 49, 50: 50, 51: 51, 52: 52, 53: 53, 54: 54} + score: '0.947' diff --git a/data/thrombin/03_edges/nohup.out b/data/thrombin/03_edges/nohup.out deleted file mode 100644 index 4a27c7426..000000000 --- a/data/thrombin/03_edges/nohup.out +++ /dev/null @@ -1,18 +0,0 @@ -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. -lig_7a_lig_5 exceeds 1 A pairwise distance -lig_1d_lig_1a exceeds 1 A pairwise distance -lig_6a_lig_3a exceeds 1 A pairwise distance -lig_1a_lig_5 exceeds 1 A pairwise distance -lig_1b_lig_1a exceeds 1 A pairwise distance -lig_6a_lig_5 exceeds 1 A pairwise distance -lig_1c_lig_1a exceeds 1 A pairwise distance -lig_6b_lig_3a exceeds 1 A pairwise distance -lig_6a_lig_6e exceeds 1 A pairwise distance diff --git a/data/tnks2/03_edges/01_perses_openfe.yaml b/data/tnks2/03_edges/01_perses_openfe.yaml deleted file mode 100644 index c55810359..000000000 --- a/data/tnks2/03_edges/01_perses_openfe.yaml +++ /dev/null @@ -1,180 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph -edges: - edge_lig_5i_lig_8a: - ligand_a: lig_5i - ligand_b: lig_8a - atom mapping: (3, 20) (4, 18) (5, 19) (6, 16) (7, 17) (8, 15) (9, 14) (10, 43) - (11, 4) (12, 5) (13, 6) (14, 7) (15, 8) (17, 1) (18, 0) (19, 2) (24, 10) (25, - 11) (26, 12) (27, 13) (28, 41) (29, 42) (30, 39) (31, 40) - score: '0.684' - edge_lig_1a_lig_8b: - ligand_a: lig_1a - ligand_b: lig_8b - atom mapping: (1, 4) (2, 23) (3, 24) (4, 25) (5, 26) (6, 27) (7, 28) (8, 29) (9, - 30) (10, 38) (12, 36) (13, 37) (14, 34) (16, 32) (17, 33) (18, 31) (19, 43) - (20, 44) (21, 45) (22, 46) (23, 1) (24, 0) (25, 2) (26, 3) - score: '0.830' - edge_lig_5p_lig_8f: - ligand_a: lig_5p - ligand_b: lig_8f - atom mapping: (0, 38) (1, 37) (2, 39) (4, 31) (5, 32) (6, 33) (7, 34) (8, 35) - (9, 36) (10, 44) (11, 45) (12, 46) (13, 47) (14, 29) (15, 28) (16, 1) (17, 0) - (18, 2) (19, 3) (20, 4) (42, 24) (43, 25) (44, 26) (45, 27) (46, 30) - score: '0.638' - edge_lig_5f_lig_8a: - ligand_a: lig_5f - ligand_b: lig_8a - atom mapping: (3, 20) (4, 18) (5, 19) (6, 16) (7, 17) (8, 15) (9, 14) (10, 43) - (11, 4) (12, 2) (14, 1) (15, 0) (16, 8) (18, 6) (19, 7) (20, 5) (21, 10) (22, - 11) (23, 12) (24, 13) (25, 41) (26, 42) (27, 39) (28, 40) - score: '0.714' - edge_lig_5o_lig_8a: - ligand_a: lig_5o - ligand_b: lig_8a - atom mapping: (10, 20) (11, 18) (12, 19) (13, 16) (14, 17) (15, 15) (16, 14) (17, - 43) (18, 4) (19, 5) (20, 6) (21, 7) (22, 8) (23, 9) (24, 1) (25, 0) (26, 2) - (31, 10) (32, 11) (33, 12) (34, 13) (35, 41) (36, 42) (37, 39) (38, 40) - score: '0.654' - edge_lig_5k_lig_8a: - ligand_a: lig_5k - ligand_b: lig_8a - atom mapping: (3, 20) (4, 18) (5, 19) (6, 16) (7, 17) (8, 15) (9, 14) (10, 43) - (11, 4) (12, 2) (14, 1) (15, 0) (16, 8) (17, 9) (18, 6) (19, 7) (20, 5) (21, - 10) (22, 11) (23, 12) (24, 13) (25, 41) (26, 42) (27, 39) (28, 40) - score: '0.736' - edge_lig_8d_lig_5p: - ligand_a: lig_8d - ligand_b: lig_5p - atom mapping: (0, 17) (1, 16) (2, 18) (3, 19) (4, 20) (21, 42) (22, 43) (23, 44) - (24, 45) (25, 15) (26, 14) (27, 46) (28, 4) (29, 5) (30, 6) (31, 7) (32, 8) - (33, 9) (34, 1) (35, 0) (36, 2) (41, 10) (42, 11) (43, 12) (44, 13) - score: '0.646' - edge_lig_5h_lig_8a: - ligand_a: lig_5h - ligand_b: lig_8a - atom mapping: (3, 20) (4, 18) (5, 19) (6, 16) (7, 17) (8, 15) (9, 14) (10, 43) - (11, 4) (12, 2) (18, 1) (19, 0) (20, 8) (22, 6) (23, 7) (24, 5) (25, 10) (26, - 11) (27, 12) (28, 13) (29, 41) (30, 42) (31, 39) (32, 40) - score: '0.675' - edge_lig_5d_lig_8e: - ligand_a: lig_5d - ligand_b: lig_8e - atom mapping: (3, 17) (4, 15) (5, 16) (6, 13) (7, 14) (8, 12) (9, 11) (10, 10) - (11, 7) (12, 8) (14, 1) (15, 0) (16, 2) (17, 3) (18, 4) (19, 5) (20, 6) (21, - 43) (22, 44) (23, 41) (24, 42) (25, 39) (26, 40) (27, 37) (28, 38) - score: '0.731' - edge_lig_8e_lig_7: - ligand_a: lig_8e - ligand_b: lig_7 - atom mapping: (0, 14) (1, 13) (2, 15) (3, 16) (4, 17) (5, 18) (6, 19) (7, 10) - (8, 11) (10, 9) (11, 8) (12, 7) (13, 6) (15, 4) (16, 5) (17, 3) (37, 25) (38, - 26) (39, 23) (40, 24) (41, 22) (43, 20) (44, 21) - score: '0.723' - edge_lig_5o_lig_8e: - ligand_a: lig_5o - ligand_b: lig_8e - atom mapping: (10, 17) (11, 15) (12, 16) (13, 13) (14, 14) (15, 12) (16, 11) (17, - 10) (18, 7) (19, 6) (20, 4) (21, 5) (22, 2) (23, 3) (24, 1) (25, 0) (26, 8) - (27, 9) (31, 43) (32, 44) (33, 41) (34, 42) (35, 39) (36, 40) (37, 37) (38, - 38) - score: '0.665' - edge_lig_5a_lig_8e: - ligand_a: lig_5a - ligand_b: lig_8e - atom mapping: (3, 17) (4, 15) (5, 16) (6, 13) (7, 14) (8, 12) (9, 11) (10, 10) - (11, 7) (12, 8) (14, 1) (15, 0) (16, 2) (18, 4) (19, 5) (20, 6) (21, 43) (22, - 44) (23, 41) (24, 42) (25, 39) (26, 40) (27, 37) (28, 38) - score: '0.709' - edge_lig_3a_lig_8e: - ligand_a: lig_3a - ligand_b: lig_8e - atom mapping: (0, 0) (1, 1) (2, 2) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (10, 10) - (11, 11) (12, 12) (13, 39) (14, 40) (15, 37) (16, 38) (17, 17) (31, 15) (32, - 16) (33, 13) (34, 14) (35, 41) (36, 42) (37, 43) (38, 44) - score: '0.689' - edge_lig_5n_lig_8e: - ligand_a: lig_5n - ligand_b: lig_8e - atom mapping: (10, 17) (11, 15) (12, 16) (13, 13) (14, 14) (15, 12) (16, 11) (17, - 10) (18, 7) (19, 8) (21, 1) (22, 0) (23, 2) (24, 3) (25, 4) (26, 5) (27, 6) - (28, 43) (29, 44) (30, 41) (31, 42) (32, 39) (33, 40) (34, 37) (35, 38) - score: '0.663' - edge_lig_5p_lig_8e: - ligand_a: lig_5p - ligand_b: lig_8e - atom mapping: (0, 0) (1, 1) (2, 8) (4, 7) (5, 6) (6, 4) (7, 5) (8, 2) (9, 3) (10, - 43) (11, 44) (12, 41) (13, 42) (14, 11) (15, 12) (16, 39) (17, 40) (18, 37) - (19, 38) (20, 17) (42, 15) (43, 16) (44, 13) (45, 14) (46, 10) - score: '0.646' - edge_lig_5c_lig_8e: - ligand_a: lig_5c - ligand_b: lig_8e - atom mapping: (3, 17) (4, 15) (5, 16) (6, 13) (7, 14) (8, 12) (9, 11) (10, 10) - (11, 7) (12, 8) (14, 1) (15, 0) (16, 2) (18, 4) (20, 6) (21, 43) (22, 44) (23, - 41) (24, 42) (25, 39) (26, 40) (27, 37) (28, 38) - score: '0.694' - edge_lig_8e_lig_1b: - ligand_a: lig_8e - ligand_b: lig_1b - atom mapping: (0, 0) (1, 1) (2, 2) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (10, 10) - (11, 11) (12, 12) (13, 25) (14, 26) (15, 23) (16, 24) (17, 17) (37, 15) (38, - 16) (39, 13) (40, 14) (41, 27) (42, 28) (43, 29) (44, 30) - score: '0.777' - edge_lig_5m_lig_8a: - ligand_a: lig_5m - ligand_b: lig_8a - atom mapping: (3, 20) (4, 18) (5, 19) (6, 16) (7, 17) (8, 15) (9, 14) (10, 43) - (11, 4) (12, 5) (13, 6) (14, 7) (15, 8) (16, 9) (17, 1) (18, 0) (19, 2) (24, - 10) (25, 11) (26, 12) (27, 13) (28, 41) (29, 42) (30, 39) (31, 40) - score: '0.705' - edge_lig_8c_lig_5p: - ligand_a: lig_8c - ligand_b: lig_5p - atom mapping: (0, 0) (1, 1) (2, 8) (3, 9) (4, 6) (5, 7) (6, 5) (7, 4) (8, 2) (10, - 46) (11, 14) (12, 15) (13, 44) (14, 45) (15, 42) (16, 43) (17, 20) (34, 18) - (35, 19) (36, 16) (37, 17) (38, 12) (39, 13) (40, 10) (41, 11) - score: '0.672' - edge_lig_5l_lig_8a: - ligand_a: lig_5l - ligand_b: lig_8a - atom mapping: (3, 20) (4, 18) (5, 19) (6, 16) (7, 17) (8, 15) (9, 14) (10, 43) - (11, 4) (12, 2) (14, 1) (15, 0) (16, 8) (18, 6) (20, 5) (21, 10) (22, 11) (23, - 12) (24, 13) (25, 41) (26, 42) (27, 39) (28, 40) - score: '0.700' - edge_lig_5j_lig_8e: - ligand_a: lig_5j - ligand_b: lig_8e - atom mapping: (3, 17) (4, 15) (5, 16) (6, 13) (7, 14) (8, 12) (9, 11) (10, 10) - (11, 7) (12, 8) (14, 1) (15, 0) (16, 2) (17, 3) (18, 4) (20, 6) (21, 43) (22, - 44) (23, 41) (24, 42) (25, 39) (26, 40) (27, 37) (28, 38) - score: '0.716' - edge_lig_5p_lig_8b: - ligand_a: lig_5p - ligand_b: lig_8b - atom mapping: (0, 37) (1, 36) (2, 38) (4, 30) (5, 31) (6, 32) (7, 33) (8, 34) - (9, 35) (10, 43) (11, 44) (12, 45) (13, 46) (14, 28) (15, 27) (16, 1) (17, 0) - (18, 2) (19, 3) (20, 4) (42, 23) (43, 24) (44, 25) (45, 26) (46, 29) - score: '0.638' - edge_lig_5g_lig_8a: - ligand_a: lig_5g - ligand_b: lig_8a - atom mapping: (3, 20) (4, 18) (5, 19) (6, 16) (7, 17) (8, 15) (9, 14) (10, 43) - (11, 4) (12, 2) (14, 1) (15, 0) (16, 8) (18, 6) (19, 7) (20, 5) (21, 10) (22, - 11) (23, 12) (24, 13) (25, 41) (26, 42) (27, 39) (28, 40) - score: '0.714' - edge_lig_5b_lig_8e: - ligand_a: lig_5b - ligand_b: lig_8e - atom mapping: (3, 17) (4, 15) (5, 16) (6, 13) (7, 14) (8, 12) (9, 11) (10, 10) - (11, 7) (12, 8) (14, 1) (15, 0) (16, 2) (18, 4) (20, 6) (21, 43) (22, 44) (23, - 41) (24, 42) (25, 39) (26, 40) (27, 37) (28, 38) - score: '0.694' - edge_lig_3b_lig_8e: - ligand_a: lig_3b - ligand_b: lig_8e - atom mapping: (0, 0) (1, 1) (2, 8) (4, 7) (5, 6) (6, 4) (7, 5) (8, 2) (9, 3) (10, - 43) (11, 44) (12, 41) (13, 42) (14, 11) (15, 12) (16, 39) (17, 40) (18, 37) - (19, 38) (20, 17) (34, 15) (35, 16) (36, 13) (37, 14) (38, 10) - score: '0.710' diff --git a/data/tnks2/03_edges/01_perses_openfe.yml b/data/tnks2/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..beaece8aa --- /dev/null +++ b/data/tnks2/03_edges/01_perses_openfe.yml @@ -0,0 +1,179 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_8e_lig_7: + ligand_a: lig_8e + ligand_b: lig_7 + atom mapping: {0: 14, 1: 13, 2: 15, 3: 16, 4: 17, 5: 18, 6: 19, 7: 10, 8: 11, + 10: 9, 11: 8, 12: 7, 13: 6, 15: 4, 16: 5, 17: 3, 37: 25, 38: 26, 39: 23, 40: 24, + 41: 22, 43: 20, 44: 21} + score: '0.723' + edge_lig_5m_lig_8a: + ligand_a: lig_5m + ligand_b: lig_8a + atom mapping: {3: 20, 4: 18, 5: 19, 6: 16, 7: 17, 8: 15, 9: 14, 10: 43, 11: 4, + 12: 5, 13: 6, 14: 7, 15: 8, 16: 9, 17: 1, 18: 0, 19: 2, 24: 10, 25: 11, 26: 12, + 27: 13, 28: 41, 29: 42, 30: 39, 31: 40} + score: '0.705' + edge_lig_5l_lig_8a: + ligand_a: lig_5l + ligand_b: lig_8a + atom mapping: {3: 20, 4: 18, 5: 19, 6: 16, 7: 17, 8: 15, 9: 14, 10: 43, 11: 4, + 12: 2, 14: 1, 15: 0, 16: 8, 18: 6, 20: 5, 21: 10, 22: 11, 23: 12, 24: 13, 25: 41, + 26: 42, 27: 39, 28: 40} + score: '0.700' + edge_lig_5c_lig_8e: + ligand_a: lig_5c + ligand_b: lig_8e + atom mapping: {3: 17, 4: 15, 5: 16, 6: 13, 7: 14, 8: 12, 9: 11, 10: 10, 11: 7, + 12: 8, 14: 1, 15: 0, 16: 2, 18: 4, 20: 6, 21: 43, 22: 44, 23: 41, 24: 42, 25: 39, + 26: 40, 27: 37, 28: 38} + score: '0.694' + edge_lig_8e_lig_1b: + ligand_a: lig_8e + ligand_b: lig_1b + atom mapping: {0: 0, 1: 1, 2: 2, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 10: 10, 11: 11, + 12: 12, 13: 25, 14: 26, 15: 23, 16: 24, 17: 17, 37: 15, 38: 16, 39: 13, 40: 14, + 41: 27, 42: 28, 43: 29, 44: 30} + score: '0.777' + edge_lig_5j_lig_8e: + ligand_a: lig_5j + ligand_b: lig_8e + atom mapping: {3: 17, 4: 15, 5: 16, 6: 13, 7: 14, 8: 12, 9: 11, 10: 10, 11: 7, + 12: 8, 14: 1, 15: 0, 16: 2, 17: 3, 18: 4, 20: 6, 21: 43, 22: 44, 23: 41, 24: 42, + 25: 39, 26: 40, 27: 37, 28: 38} + score: '0.716' + edge_lig_5n_lig_8e: + ligand_a: lig_5n + ligand_b: lig_8e + atom mapping: {10: 17, 11: 15, 12: 16, 13: 13, 14: 14, 15: 12, 16: 11, 17: 10, + 18: 7, 19: 8, 21: 1, 22: 0, 23: 2, 24: 3, 25: 4, 26: 5, 27: 6, 28: 43, 29: 44, + 30: 41, 31: 42, 32: 39, 33: 40, 34: 37, 35: 38} + score: '0.663' + edge_lig_5f_lig_8a: + ligand_a: lig_5f + ligand_b: lig_8a + atom mapping: {3: 20, 4: 18, 5: 19, 6: 16, 7: 17, 8: 15, 9: 14, 10: 43, 11: 4, + 12: 2, 14: 1, 15: 0, 16: 8, 18: 6, 19: 7, 20: 5, 21: 10, 22: 11, 23: 12, 24: 13, + 25: 41, 26: 42, 27: 39, 28: 40} + score: '0.714' + edge_lig_3a_lig_8e: + ligand_a: lig_3a + ligand_b: lig_8e + atom mapping: {0: 0, 1: 1, 2: 2, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 10: 10, 11: 11, + 12: 12, 13: 39, 14: 40, 15: 37, 16: 38, 17: 17, 31: 15, 32: 16, 33: 13, 34: 14, + 35: 41, 36: 42, 37: 43, 38: 44} + score: '0.689' + edge_lig_3b_lig_8e: + ligand_a: lig_3b + ligand_b: lig_8e + atom mapping: {0: 0, 1: 1, 2: 8, 4: 7, 5: 6, 6: 4, 7: 5, 8: 2, 9: 3, 10: 43, 11: 44, + 12: 41, 13: 42, 14: 11, 15: 12, 16: 39, 17: 40, 18: 37, 19: 38, 20: 17, 34: 15, + 35: 16, 36: 13, 37: 14, 38: 10} + score: '0.710' + edge_lig_5p_lig_8e: + ligand_a: lig_5p + ligand_b: lig_8e + atom mapping: {0: 0, 1: 1, 2: 8, 4: 7, 5: 6, 6: 4, 7: 5, 8: 2, 9: 3, 10: 43, 11: 44, + 12: 41, 13: 42, 14: 11, 15: 12, 16: 39, 17: 40, 18: 37, 19: 38, 20: 17, 42: 15, + 43: 16, 44: 13, 45: 14, 46: 10} + score: '0.646' + edge_lig_8e_lig_1a: + ligand_a: lig_8e + ligand_b: lig_1a + atom mapping: {0: 13, 1: 12, 2: 14, 4: 16, 5: 17, 6: 18, 7: 9, 8: 10, 10: 8, 11: 7, + 12: 6, 13: 4, 14: 5, 15: 2, 16: 3, 17: 1, 37: 25, 38: 26, 39: 23, 40: 24, 41: 21, + 42: 22, 43: 19, 44: 20} + score: '0.830' + edge_lig_5p_lig_8f: + ligand_a: lig_5p + ligand_b: lig_8f + atom mapping: {0: 38, 1: 37, 2: 39, 4: 31, 5: 32, 6: 33, 7: 34, 8: 35, 9: 36, + 10: 44, 11: 45, 12: 46, 13: 47, 14: 29, 15: 28, 16: 1, 17: 0, 18: 2, 19: 3, + 20: 4, 42: 24, 43: 25, 44: 26, 45: 27, 46: 30} + score: '0.638' + edge_lig_5d_lig_8e: + ligand_a: lig_5d + ligand_b: lig_8e + atom mapping: {3: 17, 4: 15, 5: 16, 6: 13, 7: 14, 8: 12, 9: 11, 10: 10, 11: 7, + 12: 8, 14: 1, 15: 0, 16: 2, 17: 3, 18: 4, 19: 5, 20: 6, 21: 43, 22: 44, 23: 41, + 24: 42, 25: 39, 26: 40, 27: 37, 28: 38} + score: '0.731' + edge_lig_5b_lig_8e: + ligand_a: lig_5b + ligand_b: lig_8e + atom mapping: {3: 17, 4: 15, 5: 16, 6: 13, 7: 14, 8: 12, 9: 11, 10: 10, 11: 7, + 12: 8, 14: 1, 15: 0, 16: 2, 18: 4, 20: 6, 21: 43, 22: 44, 23: 41, 24: 42, 25: 39, + 26: 40, 27: 37, 28: 38} + score: '0.694' + edge_lig_5h_lig_8a: + ligand_a: lig_5h + ligand_b: lig_8a + atom mapping: {3: 20, 4: 18, 5: 19, 6: 16, 7: 17, 8: 15, 9: 14, 10: 43, 11: 4, + 12: 2, 18: 1, 19: 0, 20: 8, 22: 6, 23: 7, 24: 5, 25: 10, 26: 11, 27: 12, 28: 13, + 29: 41, 30: 42, 31: 39, 32: 40} + score: '0.675' + edge_lig_8c_lig_5p: + ligand_a: lig_8c + ligand_b: lig_5p + atom mapping: {0: 0, 1: 1, 2: 8, 3: 9, 4: 6, 5: 7, 6: 5, 7: 4, 8: 2, 10: 46, 11: 14, + 12: 15, 13: 44, 14: 45, 15: 42, 16: 43, 17: 20, 34: 18, 35: 19, 36: 16, 37: 17, + 38: 12, 39: 13, 40: 10, 41: 11} + score: '0.672' + edge_lig_5i_lig_8a: + ligand_a: lig_5i + ligand_b: lig_8a + atom mapping: {3: 20, 4: 18, 5: 19, 6: 16, 7: 17, 8: 15, 9: 14, 10: 43, 11: 4, + 12: 5, 13: 6, 14: 7, 15: 8, 17: 1, 18: 0, 19: 2, 24: 10, 25: 11, 26: 12, 27: 13, + 28: 41, 29: 42, 30: 39, 31: 40} + score: '0.684' + edge_lig_5o_lig_8a: + ligand_a: lig_5o + ligand_b: lig_8a + atom mapping: {10: 20, 11: 18, 12: 19, 13: 16, 14: 17, 15: 15, 16: 14, 17: 43, + 18: 4, 19: 5, 20: 6, 21: 7, 22: 8, 23: 9, 24: 1, 25: 0, 26: 2, 31: 10, 32: 11, + 33: 12, 34: 13, 35: 41, 36: 42, 37: 39, 38: 40} + score: '0.654' + edge_lig_5p_lig_8b: + ligand_a: lig_5p + ligand_b: lig_8b + atom mapping: {0: 37, 1: 36, 2: 38, 4: 30, 5: 31, 6: 32, 7: 33, 8: 34, 9: 35, + 10: 43, 11: 44, 12: 45, 13: 46, 14: 28, 15: 27, 16: 1, 17: 0, 18: 2, 19: 3, + 20: 4, 42: 23, 43: 24, 44: 25, 45: 26, 46: 29} + score: '0.638' + edge_lig_5k_lig_8a: + ligand_a: lig_5k + ligand_b: lig_8a + atom mapping: {3: 20, 4: 18, 5: 19, 6: 16, 7: 17, 8: 15, 9: 14, 10: 43, 11: 4, + 12: 2, 14: 1, 15: 0, 16: 8, 17: 9, 18: 6, 19: 7, 20: 5, 21: 10, 22: 11, 23: 12, + 24: 13, 25: 41, 26: 42, 27: 39, 28: 40} + score: '0.736' + edge_lig_5a_lig_8e: + ligand_a: lig_5a + ligand_b: lig_8e + atom mapping: {3: 17, 4: 15, 5: 16, 6: 13, 7: 14, 8: 12, 9: 11, 10: 10, 11: 7, + 12: 8, 14: 1, 15: 0, 16: 2, 18: 4, 19: 5, 20: 6, 21: 43, 22: 44, 23: 41, 24: 42, + 25: 39, 26: 40, 27: 37, 28: 38} + score: '0.709' + edge_lig_5g_lig_8a: + ligand_a: lig_5g + ligand_b: lig_8a + atom mapping: {3: 20, 4: 18, 5: 19, 6: 16, 7: 17, 8: 15, 9: 14, 10: 43, 11: 4, + 12: 2, 14: 1, 15: 0, 16: 8, 18: 6, 19: 7, 20: 5, 21: 10, 22: 11, 23: 12, 24: 13, + 25: 41, 26: 42, 27: 39, 28: 40} + score: '0.714' + edge_lig_8d_lig_5p: + ligand_a: lig_8d + ligand_b: lig_5p + atom mapping: {0: 17, 1: 16, 2: 18, 3: 19, 4: 20, 21: 42, 22: 43, 23: 44, 24: 45, + 25: 15, 26: 14, 27: 46, 28: 4, 29: 5, 30: 6, 31: 7, 32: 8, 33: 9, 34: 1, 35: 0, + 36: 2, 41: 10, 42: 11, 43: 12, 44: 13} + score: '0.646' + edge_lig_5o_lig_8e: + ligand_a: lig_5o + ligand_b: lig_8e + atom mapping: {10: 17, 11: 15, 12: 16, 13: 13, 14: 14, 15: 12, 16: 11, 17: 10, + 18: 7, 19: 6, 20: 4, 21: 5, 22: 2, 23: 3, 24: 1, 25: 0, 26: 8, 27: 9, 31: 43, + 32: 44, 33: 41, 34: 42, 35: 39, 36: 40, 37: 37, 38: 38} + score: '0.665' diff --git a/data/tnks2/03_edges/nohup.out b/data/tnks2/03_edges/nohup.out deleted file mode 100644 index 8d0a105fb..000000000 --- a/data/tnks2/03_edges/nohup.out +++ /dev/null @@ -1,22 +0,0 @@ -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. -lig_5f_lig_8a exceeds 1 A pairwise distance -lig_5o_lig_8a exceeds 1 A pairwise distance -lig_5k_lig_8a exceeds 1 A pairwise distance -lig_8d_lig_5p exceeds 1 A pairwise distance -lig_5h_lig_8a exceeds 1 A pairwise distance -lig_5d_lig_8e exceeds 1 A pairwise distance -lig_8e_lig_7 exceeds 1 A pairwise distance -lig_5a_lig_8e exceeds 1 A pairwise distance -lig_3a_lig_8e exceeds 1 A pairwise distance -lig_5c_lig_8e exceeds 1 A pairwise distance -lig_5m_lig_8a exceeds 1 A pairwise distance -lig_8c_lig_5p exceeds 1 A pairwise distance -lig_5p_lig_8b exceeds 1 A pairwise distance diff --git a/data/tyk2/03_edges/01_perses_openfe.yaml b/data/tyk2/03_edges/01_perses_openfe.yaml deleted file mode 100644 index d0e0d70da..000000000 --- a/data/tyk2/03_edges/01_perses_openfe.yaml +++ /dev/null @@ -1,108 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph -edges: - edge_lig_ejm_47_lig_ejm_48: - ligand_a: lig_ejm_47 - ligand_b: lig_ejm_48 - atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 41) (8, 40) - (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) - (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (35, 38) (36, 39) (37, - 8) (38, 7) - score: '0.772' - edge_lig_jmc_23_lig_ejm_48: - ligand_a: lig_jmc_23 - ligand_b: lig_ejm_48 - atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 41) (8, 40) - (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) - (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (32, 38) (33, 39) (34, - 8) (35, 7) - score: '0.807' - edge_lig_jmc_27_lig_ejm_48: - ligand_a: lig_jmc_27 - ligand_b: lig_ejm_48 - atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 41) (8, 40) - (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) - (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (32, 38) (33, 39) (34, - 8) (35, 7) - score: '0.807' - edge_lig_ejm_54_lig_ejm_48: - ligand_a: lig_ejm_54 - ligand_b: lig_ejm_48 - atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 41) (8, 40) - (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) - (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (33, 38) (34, 39) (35, - 8) (36, 7) - score: '0.795' - edge_lig_ejm_48_lig_ejm_43: - ligand_a: lig_ejm_48 - ligand_b: lig_ejm_43 - atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 37) (8, 36) - (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) - (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (38, 34) (39, 35) (40, - 8) (41, 7) - score: '0.783' - edge_lig_ejm_45_lig_ejm_48: - ligand_a: lig_ejm_45 - ligand_b: lig_ejm_48 - atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 41) (8, 40) - (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) - (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (35, 38) (36, 39) (37, - 8) (38, 7) - score: '0.772' - edge_lig_jmc_28_lig_ejm_48: - ligand_a: lig_jmc_28 - ligand_b: lig_ejm_48 - atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 41) (8, 40) - (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) - (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (35, 38) (36, 39) (37, - 8) (38, 7) - score: '0.772' - edge_lig_ejm_50_lig_ejm_48: - ligand_a: lig_ejm_50 - ligand_b: lig_ejm_48 - atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 41) (8, 40) - (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) - (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (29, 38) (30, 39) (31, - 8) (32, 7) - score: '0.847' - edge_lig_ejm_55_lig_ejm_48: - ligand_a: lig_ejm_55 - ligand_b: lig_ejm_48 - atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 41) (8, 40) - (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) - (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (29, 38) (30, 39) (31, - 8) (32, 7) - score: '0.847' - edge_lig_ejm_31_lig_ejm_48: - ligand_a: lig_ejm_31 - ligand_b: lig_ejm_48 - atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 41) (8, 40) - (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) - (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (28, 38) (29, 39) (30, - 8) (31, 7) - score: '0.860' - edge_lig_ejm_46_lig_ejm_48: - ligand_a: lig_ejm_46 - ligand_b: lig_ejm_48 - atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 41) (8, 40) - (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) - (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (32, 38) (33, 39) (34, - 8) (35, 7) - score: '0.807' - edge_lig_jmc_30_lig_ejm_48: - ligand_a: lig_jmc_30 - ligand_b: lig_ejm_48 - atom mapping: (0, 0) (1, 1) (2, 2) (3, 3) (4, 4) (5, 5) (6, 6) (7, 7) (8, 8) (9, - 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) (18, - 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (33, 38) (34, 39) (35, 40) - (36, 41) - score: '0.795' - edge_lig_ejm_42_lig_ejm_48: - ligand_a: lig_ejm_42 - ligand_b: lig_ejm_48 - atom mapping: (0, 0) (1, 1) (2, 6) (3, 5) (4, 4) (5, 3) (6, 2) (7, 41) (8, 40) - (9, 9) (10, 10) (11, 11) (12, 12) (13, 13) (14, 14) (15, 15) (16, 16) (17, 17) - (18, 18) (19, 19) (20, 20) (21, 21) (22, 22) (23, 23) (31, 38) (32, 39) (33, - 8) (34, 7) - score: '0.820' diff --git a/data/tyk2/03_edges/01_perses_openfe.yml b/data/tyk2/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..9f32ac7e5 --- /dev/null +++ b/data/tyk2/03_edges/01_perses_openfe.yml @@ -0,0 +1,95 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.4 minimal_spanning_graph +edges: + edge_lig_ejm_45_lig_ejm_48: + ligand_a: lig_ejm_45 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 35: 38, 36: 39, 37: 8, 38: 7} + score: '0.772' + edge_lig_ejm_48_lig_ejm_43: + ligand_a: lig_ejm_48 + ligand_b: lig_ejm_43 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 37, 8: 36, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 38: 34, 39: 35, 40: 8, 41: 7} + score: '0.783' + edge_lig_jmc_30_lig_ejm_48: + ligand_a: lig_jmc_30 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 33: 38, 34: 39, 35: 40, 36: 41} + score: '0.795' + edge_lig_ejm_46_lig_ejm_48: + ligand_a: lig_ejm_46 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 32: 38, 33: 39, 34: 8, 35: 7} + score: '0.807' + edge_lig_ejm_31_lig_ejm_48: + ligand_a: lig_ejm_31 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 28: 38, 29: 39, 30: 8, 31: 7} + score: '0.860' + edge_lig_ejm_50_lig_ejm_48: + ligand_a: lig_ejm_50 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 29: 38, 30: 39, 31: 8, 32: 7} + score: '0.847' + edge_lig_ejm_54_lig_ejm_48: + ligand_a: lig_ejm_54 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 33: 38, 34: 39, 35: 8, 36: 7} + score: '0.795' + edge_lig_jmc_27_lig_ejm_48: + ligand_a: lig_jmc_27 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 32: 38, 33: 39, 34: 8, 35: 7} + score: '0.807' + edge_lig_jmc_23_lig_ejm_48: + ligand_a: lig_jmc_23 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 32: 38, 33: 39, 34: 8, 35: 7} + score: '0.807' + edge_lig_ejm_55_lig_ejm_48: + ligand_a: lig_ejm_55 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 29: 38, 30: 39, 31: 8, 32: 7} + score: '0.847' + edge_lig_ejm_47_lig_ejm_48: + ligand_a: lig_ejm_47 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 35: 38, 36: 39, 37: 8, 38: 7} + score: '0.772' + edge_lig_ejm_42_lig_ejm_48: + ligand_a: lig_ejm_42 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 31: 38, 32: 39, 33: 8, 34: 7} + score: '0.820' + edge_lig_jmc_28_lig_ejm_48: + ligand_a: lig_jmc_28 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 35: 38, 36: 39, 37: 8, 38: 7} + score: '0.772' diff --git a/data/tyk2/03_edges/nohup.out b/data/tyk2/03_edges/nohup.out deleted file mode 100644 index b170ed64c..000000000 --- a/data/tyk2/03_edges/nohup.out +++ /dev/null @@ -1,21 +0,0 @@ -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:500: UserWarning: The value of the smallest subnormal for type is zero. - setattr(self, word, getattr(machar, word).flat[0]) -/biggin/b131/bioc1523/software/anaconda/python3.6/2019.7/envs/openfe-new/lib/python3.9/site-packages/numpy/core/getlimits.py:89: UserWarning: The value of the smallest subnormal for type is zero. - return self._float_to_str(self.smallest_subnormal) -WARNING:root:Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead. -lig_ejm_47_lig_ejm_48 exceeds 1 A pairwise distance -lig_jmc_23_lig_ejm_48 exceeds 1 A pairwise distance -lig_jmc_27_lig_ejm_48 exceeds 1 A pairwise distance -lig_ejm_54_lig_ejm_48 exceeds 1 A pairwise distance -lig_ejm_45_lig_ejm_48 exceeds 1 A pairwise distance -lig_jmc_28_lig_ejm_48 exceeds 1 A pairwise distance -lig_ejm_50_lig_ejm_48 exceeds 1 A pairwise distance -lig_ejm_55_lig_ejm_48 exceeds 1 A pairwise distance -lig_ejm_31_lig_ejm_48 exceeds 1 A pairwise distance -lig_ejm_46_lig_ejm_48 exceeds 1 A pairwise distance -lig_jmc_30_lig_ejm_48 exceeds 1 A pairwise distance -lig_ejm_42_lig_ejm_48 exceeds 1 A pairwise distance diff --git a/preparation/mappers/perses-mapper.py b/preparation/mappers/perses-mapper.py index 845845765..6d0513476 100644 --- a/preparation/mappers/perses-mapper.py +++ b/preparation/mappers/perses-mapper.py @@ -6,6 +6,7 @@ from openfe.setup.atom_mapping.perses_mapper import PersesAtomMapper from openfe.setup.atom_mapping.perses_scorers import default_perses_scorer from openmm import unit +from collections import OrderedDict # load ligands ligands_supp = Chem.SDMolSupplier('../02_ligands/ligands.sdf', removeHs=False) @@ -30,18 +31,18 @@ output['mapper'] = "Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, coordinate_tolerance=0.2), default non geometric scorer" output['planner'] = "openfe v0.4 minimal_spanning_graph" -edges_dict = {} +edges_dict = dict() for edge in network.edges: edge_name = f'edge_{edge.componentA.name}_{edge.componentB.name}' - mapping = list(edge.componentA_to_componentB.items()) + mapping = [list(i) for i in edge.componentA_to_componentB.items()] edges_dict[edge_name] = { 'ligand_a': edge.componentA.name, 'ligand_b': edge.componentB.name, - 'atom mapping': ' '.join(str(i) for i in mapping), + 'atom mapping': edge.componentA_to_componentB, 'score': f"{edge.annotations['score']:.3f}",} output['edges'] = edges_dict -with open('01_perses_openfe.yaml', 'w') as yaml_file: - yaml.dump(output, yaml_file, default_flow_style=False, sort_keys=False) +with open('01_perses_openfe.yml', 'w') as yaml_file: + yaml.dump(output, yaml_file, default_flow_style=None, sort_keys=False) From 23ca3e8257b82aad8af2974072050aa24ea8471c Mon Sep 17 00:00:00 2001 From: Irfan Date: Tue, 10 Jan 2023 14:22:31 +0000 Subject: [PATCH 4/6] Updated edges files based on new sdf files --- data/cdk2/03_edges/01_perses_openfe.yml | 103 +++-- data/cdk8/03_edges/01_perses_openfe.yml | 252 +++++------ data/cmet/03_edges/01_perses_openfe.yml | 40 +- data/eg5/03_edges/01_perses_openfe.yml | 311 ++++++------- data/hif2a/03_edges/01_perses_openfe.yml | 282 ++++++------ data/mcl1/03_edges/01_perses_openfe.yml | 298 ++++++------ data/p38/03_edges/01_perses_openfe.yml | 250 +++++----- data/pde2/03_edges/01_perses_openfe.yml | 264 +++++------ data/pfkfb3/03_edges/01_perses_openfe.yml | 350 +++++++------- data/ptp1b/03_edges/01_perses_openfe.yml | 200 ++++---- data/shp2/03_edges/01_perses_openfe.yml | 200 ++++---- data/syk/03_edges/01_perses_openfe.yml | 476 ++++++++++---------- data/thrombin/03_edges/01_perses_openfe.yml | 253 +++++++---- data/tnks2/03_edges/01_perses_openfe.yml | 285 ++++++------ data/tyk2/03_edges/01_perses_openfe.yml | 71 ++- preparation/mappers/perses-mapper.py | 2 +- 16 files changed, 1844 insertions(+), 1793 deletions(-) diff --git a/data/cdk2/03_edges/01_perses_openfe.yml b/data/cdk2/03_edges/01_perses_openfe.yml index 4cff5e081..e4edf0035 100644 --- a/data/cdk2/03_edges/01_perses_openfe.yml +++ b/data/cdk2/03_edges/01_perses_openfe.yml @@ -1,61 +1,70 @@ mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph +planner: openfe v0.5 minimal_spanning_graph edges: - edge_lig_1oiu_lig_1h1q: - ligand_a: lig_1oiu - ligand_b: lig_1h1q + edge_lig_22_lig_1oiy: + ligand_a: lig_22 + ligand_b: lig_1oiy atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, - 31: 39, 32: 40, 33: 37, 40: 35, 41: 36, 42: 33, 43: 34, 44: 31, 45: 32, 46: 41, - 47: 42, 48: 43, 49: 44} - score: '0.961' - edge_lig_21_lig_26: + 31: 43, 32: 44, 33: 41, 34: 42, 35: 35, 37: 33, 43: 31, 44: 32, 45: 45, 46: 46, + 47: 47, 48: 48} + score: '0.907' + edge_lig_20_lig_1oiy: + ligand_a: lig_20 + ligand_b: lig_1oiy + atom mapping: {5: 33, 6: 35, 8: 41, 9: 42, 10: 43, 11: 44, 12: 30, 13: 28, 14: 29, + 15: 27, 16: 26, 17: 4, 18: 5, 19: 6, 20: 8, 21: 7, 22: 9, 23: 10, 24: 23, 25: 24, + 26: 25, 27: 20, 28: 21, 29: 22, 30: 17, 31: 19, 32: 18, 33: 14, 34: 16, 35: 15, + 36: 11, 37: 12, 38: 13, 39: 3, 40: 2, 41: 1, 42: 0, 43: 47, 44: 48, 45: 46, + 46: 45, 47: 31, 48: 32} + score: '0.907' + edge_lig_17_lig_1oiy: + ligand_a: lig_17 + ligand_b: lig_1oiy + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, + 31: 43, 32: 44, 33: 41, 34: 42, 35: 35, 37: 33, 39: 31, 40: 32, 41: 45, 42: 46, + 43: 47, 44: 48} + score: '0.954' + edge_lig_21_lig_1oiy: ligand_a: lig_21 - ligand_b: lig_26 + ligand_b: lig_1oiy atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, 31: 43, 32: 44, 33: 41, 34: 42, 35: 35, 37: 33, 43: 31, 44: 32, 45: 45, 46: 46, 47: 47, 48: 48} - score: '0.912' - edge_lig_26_lig_1oiu: - ligand_a: lig_26 - ligand_b: lig_1oiu + score: '0.907' + edge_lig_1oiu_lig_1h1r: + ligand_a: lig_1oiu + ligand_b: lig_1h1r + atom mapping: {0: 43, 1: 40, 2: 39, 3: 15, 4: 16, 5: 18, 6: 19, 7: 20, 8: 21, + 9: 22, 10: 38, 11: 23, 12: 37, 13: 36, 14: 24, 15: 35, 16: 34, 17: 25, 18: 32, + 19: 33, 20: 26, 21: 30, 22: 31, 23: 27, 24: 29, 25: 28, 26: 17, 27: 12, 28: 10, + 29: 11, 30: 3, 31: 2, 32: 44, 33: 1, 40: 6, 41: 7, 42: 5, 44: 4, 45: 9, 46: 13, + 47: 14, 48: 41, 49: 42} + score: '0.948' + edge_lig_1oiu_lig_1oiy: + ligand_a: lig_1oiu + ligand_b: lig_1oiy atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, - 31: 44, 32: 45, 33: 42, 34: 43, 35: 40, 41: 33, 43: 31, 44: 32, 45: 46, 46: 47, - 47: 48, 48: 49} + 31: 43, 32: 44, 33: 41, 40: 35, 42: 33, 43: 34, 44: 31, 45: 32, 46: 45, 47: 46, + 48: 47, 49: 48} score: '0.901' - edge_lig_21_lig_17: - ligand_a: lig_21 - ligand_b: lig_17 + edge_lig_1oiu_lig_1h1q: + ligand_a: lig_1oiu + ligand_b: lig_1h1q atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, - 31: 39, 32: 40, 33: 37, 35: 35, 36: 36, 37: 33, 43: 31, 44: 32, 45: 41, 46: 42, - 47: 43, 48: 44} + 31: 39, 32: 40, 33: 37, 40: 35, 41: 36, 42: 33, 43: 34, 44: 31, 45: 32, 46: 41, + 47: 42, 48: 43, 49: 44} score: '0.961' - edge_lig_22_lig_26: - ligand_a: lig_22 - ligand_b: lig_26 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, - 31: 43, 32: 44, 33: 41, 34: 42, 35: 35, 37: 33, 43: 31, 44: 32, 45: 45, 46: 46, - 47: 47, 48: 48} - score: '0.912' - edge_lig_1h1r_lig_1oiu: - ligand_a: lig_1h1r - ligand_b: lig_1oiu - atom mapping: {1: 33, 2: 31, 3: 30, 4: 44, 5: 42, 6: 40, 7: 41, 9: 45, 10: 28, - 11: 29, 12: 27, 13: 46, 14: 47, 15: 3, 16: 4, 17: 26, 18: 5, 19: 6, 20: 7, 21: 8, - 22: 9, 23: 23, 24: 20, 25: 17, 26: 14, 27: 11, 28: 13, 29: 12, 30: 16, 31: 15, - 32: 18, 33: 19, 34: 21, 35: 22, 36: 24, 37: 25, 38: 10, 39: 2, 40: 1, 41: 48, - 42: 49, 43: 0, 44: 32} - score: '0.948' edge_lig_1oi9_lig_1oiu: ligand_a: lig_1oi9 ligand_b: lig_1oiu @@ -65,12 +74,12 @@ edges: 33: 25, 34: 3, 35: 2, 36: 1, 37: 0, 38: 48, 39: 49, 40: 47, 41: 46, 42: 44, 43: 45, 44: 42, 45: 43} score: '0.936' - edge_lig_20_lig_26: - ligand_a: lig_20 - ligand_b: lig_26 - atom mapping: {5: 33, 6: 35, 8: 41, 9: 42, 10: 43, 11: 44, 12: 30, 13: 28, 14: 29, - 15: 27, 16: 26, 17: 4, 18: 5, 19: 6, 20: 8, 21: 7, 22: 9, 23: 10, 24: 23, 25: 24, - 26: 25, 27: 20, 28: 21, 29: 22, 30: 17, 31: 19, 32: 18, 33: 14, 34: 16, 35: 15, - 36: 11, 37: 12, 38: 13, 39: 3, 40: 2, 41: 1, 42: 0, 43: 47, 44: 48, 45: 46, - 46: 45, 47: 31, 48: 32} - score: '0.912' + edge_lig_26_lig_1oiu: + ligand_a: lig_26 + ligand_b: lig_1oiu + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, + 31: 44, 32: 45, 33: 42, 34: 43, 35: 40, 41: 33, 43: 31, 44: 32, 45: 46, 46: 47, + 47: 48, 48: 49} + score: '0.901' diff --git a/data/cdk8/03_edges/01_perses_openfe.yml b/data/cdk8/03_edges/01_perses_openfe.yml index 76282c098..2ee334fc2 100644 --- a/data/cdk8/03_edges/01_perses_openfe.yml +++ b/data/cdk8/03_edges/01_perses_openfe.yml @@ -1,67 +1,37 @@ mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph +planner: openfe v0.5 minimal_spanning_graph edges: - edge_lig_26_lig_45: - ligand_a: lig_26 + edge_lig_22_lig_43: + ligand_a: lig_22 + ligand_b: lig_43 + atom mapping: {17: 13, 18: 14, 19: 15, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 40: 40, 41: 41, 42: 42, 43: 43} + score: '0.358' + edge_lig_33_lig_45: + ligand_a: lig_33 ligand_b: lig_45 atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, - 25: 21, 26: 22, 27: 23, 28: 24, 41: 41, 42: 42, 43: 43, 44: 44} - score: '0.356' - edge_lig_14_lig_23: - ligand_a: lig_14 - ligand_b: lig_23 - atom mapping: {0: 42, 1: 41, 2: 43, 3: 44, 4: 24, 5: 25, 6: 20, 7: 17, 9: 19, - 20: 21, 21: 22, 22: 23, 23: 26, 24: 27, 25: 28} - score: '0.387' - edge_lig_42_lig_35: - ligand_a: lig_42 - ligand_b: lig_35 - atom mapping: {8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, - 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, 22: 22, 23: 23, 24: 25, 25: 24} - score: '0.392' - edge_lig_17_lig_23: - ligand_a: lig_17 - ligand_b: lig_23 - atom mapping: {15: 17, 16: 19, 17: 18, 18: 20, 19: 21, 20: 22, 21: 23, 22: 24, - 23: 25, 24: 26, 25: 27, 26: 28, 35: 41, 36: 42, 37: 43, 38: 44} - score: '0.366' + 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 41: 41, 42: 42, 43: 43, 44: 44} + score: '0.396' edge_lig_40_lig_45: ligand_a: lig_40 ligand_b: lig_45 - atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + atom mapping: {17: 13, 18: 14, 19: 15, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 46: 41, 47: 42, 48: 43, 49: 44} score: '0.386' - edge_lig_22_lig_43: - ligand_a: lig_22 - ligand_b: lig_43 - atom mapping: {17: 13, 18: 14, 19: 15, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, - 25: 21, 26: 22, 27: 23, 28: 24, 40: 40, 41: 41, 42: 42, 43: 43} - score: '0.358' - edge_lig_42_lig_23: - ligand_a: lig_42 - ligand_b: lig_23 - atom mapping: {10: 28, 11: 26, 12: 27, 13: 25, 14: 24, 15: 43, 16: 44, 17: 41, - 18: 42, 19: 22, 20: 23, 21: 21, 22: 20, 23: 17, 24: 19, 25: 18} - score: '0.333' edge_lig_42_lig_20: ligand_a: lig_42 ligand_b: lig_20 atom mapping: {8: 37, 9: 38, 10: 36, 11: 34, 12: 35, 13: 33, 14: 32, 15: 47, 16: 48, 17: 45, 18: 46, 19: 30, 20: 31, 21: 29, 22: 28, 23: 25, 24: 27, 25: 26} score: '0.391' - edge_lig_43_lig_16: + edge_lig_43_lig_32: ligand_a: lig_43 - ligand_b: lig_16 - atom mapping: {13: 5, 14: 6, 15: 7, 16: 8, 17: 9, 18: 10, 19: 11, 20: 12, 21: 13, - 22: 14, 23: 15, 24: 16, 25: 17, 26: 18, 40: 25, 41: 26, 42: 27, 43: 28} - score: '0.454' - edge_lig_42_lig_36: - ligand_a: lig_42 - ligand_b: lig_36 - atom mapping: {8: 29, 9: 30, 10: 28, 11: 26, 12: 27, 13: 25, 14: 24, 15: 47, 16: 48, - 17: 45, 18: 46, 19: 22, 20: 23, 21: 21, 22: 20, 23: 17, 24: 19, 25: 18} - score: '0.389' + ligand_b: lig_32 + atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, + 21: 25, 22: 26, 23: 27, 24: 28, 25: 29, 26: 30, 40: 34, 41: 35, 42: 36, 43: 37} + score: '0.430' edge_lig_39_lig_45: ligand_a: lig_39 ligand_b: lig_45 @@ -74,117 +44,141 @@ edges: atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 44: 41, 45: 42, 46: 43, 47: 44} score: '0.385' + edge_lig_28_lig_17: + ligand_a: lig_28 + ligand_b: lig_17 + atom mapping: {17: 15, 18: 17, 19: 16, 20: 18, 21: 19, 22: 20, 23: 21, 24: 22, + 25: 23, 26: 24, 27: 25, 28: 26, 43: 35, 44: 36, 45: 37, 46: 38} + score: '0.392' edge_lig_21_lig_43: ligand_a: lig_21 ligand_b: lig_43 atom mapping: {17: 13, 18: 14, 19: 15, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, 25: 21, 26: 22, 27: 23, 28: 24, 40: 40, 41: 41, 42: 42, 43: 43} score: '0.358' - edge_lig_45_lig_23: - ligand_a: lig_45 - ligand_b: lig_23 - atom mapping: {13: 17, 14: 18, 15: 19, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, - 21: 25, 22: 26, 23: 27, 24: 28, 41: 41, 42: 42, 43: 43, 44: 44} - score: '0.333' - edge_lig_42_lig_34: - ligand_a: lig_42 - ligand_b: lig_34 - atom mapping: {8: 29, 9: 30, 10: 28, 11: 26, 12: 27, 13: 25, 14: 24, 15: 43, 16: 44, - 17: 41, 18: 42, 19: 22, 20: 23, 21: 21, 22: 20, 23: 17, 24: 19, 25: 18} - score: '0.389' - edge_lig_43_lig_25: - ligand_a: lig_43 - ligand_b: lig_25 - atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, - 21: 25, 22: 26, 23: 27, 24: 28, 25: 29, 40: 38, 41: 39, 42: 40, 43: 41} - score: '0.390' + edge_lig_28_lig_14: + ligand_a: lig_28 + ligand_b: lig_14 + atom mapping: {17: 7, 18: 9, 20: 6, 21: 20, 22: 21, 23: 22, 24: 4, 25: 5, 26: 23, + 27: 24, 28: 25, 43: 1, 44: 0, 45: 2, 46: 3} + score: '0.418' + edge_lig_41_lig_45: + ligand_a: lig_41 + ligand_b: lig_45 + atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 47: 41, 48: 42, 49: 43, 50: 44} + score: '0.386' + edge_lig_30_lig_45: + ligand_a: lig_30 + ligand_b: lig_45 + atom mapping: {8: 25, 9: 26, 10: 24, 11: 22, 12: 23, 13: 21, 14: 20, 15: 43, 16: 44, + 17: 41, 18: 42, 19: 18, 20: 19, 21: 17, 22: 16, 23: 13, 24: 15, 25: 14} + score: '0.388' + edge_lig_26_lig_45: + ligand_a: lig_26 + ligand_b: lig_45 + atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 41: 41, 42: 42, 43: 43, 44: 44} + score: '0.356' + edge_lig_13_lig_45: + ligand_a: lig_13 + ligand_b: lig_45 + atom mapping: {2: 41, 3: 24, 4: 25, 5: 26, 20: 22, 21: 23, 22: 21, 23: 16, 24: 13, + 25: 15, 26: 14, 41: 17, 42: 18, 43: 19, 44: 20, 45: 43, 46: 44} + score: '0.395' edge_lig_43_lig_15: ligand_a: lig_43 ligand_b: lig_15 atom mapping: {13: 5, 14: 6, 15: 7, 16: 8, 17: 9, 18: 10, 19: 11, 20: 12, 21: 13, 22: 14, 23: 15, 24: 16, 25: 17, 26: 18, 40: 25, 41: 26, 42: 27, 43: 28} score: '0.425' + edge_lig_28_lig_18: + ligand_a: lig_28 + ligand_b: lig_18 + atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 43: 33, 44: 34, 45: 35, 46: 36} + score: '0.392' + edge_lig_28_lig_44: + ligand_a: lig_28 + ligand_b: lig_44 + atom mapping: {17: 23, 18: 25, 19: 24, 20: 22, 21: 21, 22: 19, 23: 20, 24: 14, + 25: 13, 26: 11, 27: 12, 28: 10, 43: 17, 44: 18, 45: 15, 46: 16} + score: '0.368' + edge_lig_42_lig_36: + ligand_a: lig_42 + ligand_b: lig_36 + atom mapping: {8: 29, 9: 30, 10: 28, 11: 26, 12: 27, 13: 25, 14: 24, 15: 47, 16: 48, + 17: 45, 18: 46, 19: 22, 20: 23, 21: 21, 22: 20, 23: 17, 24: 19, 25: 18} + score: '0.389' + edge_lig_37_lig_45: + ligand_a: lig_37 + ligand_b: lig_45 + atom mapping: {17: 13, 18: 14, 19: 15, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 44: 41, 45: 42, 46: 43, 47: 44} + score: '0.390' + edge_lig_43_lig_24: + ligand_a: lig_43 + ligand_b: lig_24 + atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, + 21: 25, 22: 26, 23: 27, 24: 28, 25: 29, 40: 37, 41: 38, 42: 39, 43: 40} + score: '0.395' + edge_lig_43_lig_28: + ligand_a: lig_43 + ligand_b: lig_28 + atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, + 21: 25, 22: 26, 23: 27, 24: 28, 40: 43, 41: 44, 42: 45, 43: 46} + score: '0.356' edge_lig_42_lig_27: ligand_a: lig_42 ligand_b: lig_27 atom mapping: {8: 29, 10: 28, 11: 26, 12: 27, 13: 25, 14: 24, 15: 47, 16: 48, 17: 45, 18: 46, 19: 22, 20: 23, 21: 21, 22: 20, 23: 17, 24: 19, 25: 18} score: '0.375' - edge_lig_43_lig_23: + edge_lig_43_lig_16: + ligand_a: lig_43 + ligand_b: lig_16 + atom mapping: {13: 5, 14: 6, 15: 7, 16: 8, 17: 9, 18: 10, 19: 11, 20: 12, 21: 13, + 22: 14, 23: 15, 24: 16, 25: 17, 26: 18, 40: 25, 41: 26, 42: 27, 43: 28} + score: '0.454' + edge_lig_29_lig_45: + ligand_a: lig_29 + ligand_b: lig_45 + atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 31: 26, 42: 41, 43: 42, 44: 43, 45: 44} + score: '0.394' + edge_lig_42_lig_34: + ligand_a: lig_42 + ligand_b: lig_34 + atom mapping: {8: 29, 9: 30, 10: 28, 11: 26, 12: 27, 13: 25, 14: 24, 15: 43, 16: 44, + 17: 41, 18: 42, 19: 22, 20: 23, 21: 21, 22: 20, 23: 17, 24: 19, 25: 18} + score: '0.389' + edge_lig_42_lig_35: + ligand_a: lig_42 + ligand_b: lig_35 + atom mapping: {8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, + 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, 22: 22, 23: 23, 24: 25, 25: 24} + score: '0.392' + edge_lig_43_lig_25: ligand_a: lig_43 - ligand_b: lig_23 + ligand_b: lig_25 atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, - 21: 25, 22: 26, 23: 27, 24: 28, 40: 41, 41: 42, 42: 43, 43: 44} - score: '0.337' + 21: 25, 22: 26, 23: 27, 24: 28, 25: 29, 40: 38, 41: 39, 42: 40, 43: 41} + score: '0.390' edge_lig_28_lig_45: ligand_a: lig_28 ligand_b: lig_45 atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, 25: 21, 26: 22, 27: 23, 28: 24, 43: 41, 44: 42, 45: 43, 46: 44} score: '0.354' - edge_lig_44_lig_23: - ligand_a: lig_44 - ligand_b: lig_23 - atom mapping: {10: 28, 11: 26, 12: 27, 13: 25, 14: 24, 15: 43, 16: 44, 17: 41, - 18: 42, 19: 22, 20: 23, 21: 21, 22: 20, 23: 17, 24: 19, 25: 18} - score: '0.345' - edge_lig_41_lig_45: - ligand_a: lig_41 - ligand_b: lig_45 - atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, - 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 47: 41, 48: 42, 49: 43, 50: 44} - score: '0.386' - edge_lig_37_lig_45: - ligand_a: lig_37 - ligand_b: lig_45 - atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, - 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 44: 41, 45: 42, 46: 43, 47: 44} - score: '0.390' - edge_lig_18_lig_23: - ligand_a: lig_18 - ligand_b: lig_23 - atom mapping: {13: 17, 14: 18, 15: 19, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, - 21: 25, 22: 26, 23: 27, 24: 28, 33: 41, 34: 42, 35: 43, 36: 44} - score: '0.366' edge_lig_43_lig_19: ligand_a: lig_43 ligand_b: lig_19 atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, 21: 25, 22: 26, 23: 27, 24: 28, 25: 29, 26: 30, 40: 37, 41: 38, 42: 39, 43: 40} score: '0.414' - edge_lig_33_lig_45: - ligand_a: lig_33 - ligand_b: lig_45 - atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, - 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 41: 41, 42: 42, 43: 43, 44: 44} - score: '0.396' - edge_lig_29_lig_45: - ligand_a: lig_29 - ligand_b: lig_45 - atom mapping: {17: 13, 18: 14, 19: 15, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, - 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 42: 41, 43: 42, 44: 43, 45: 44} - score: '0.394' - edge_lig_43_lig_24: - ligand_a: lig_43 - ligand_b: lig_24 - atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, - 21: 25, 22: 26, 23: 27, 24: 28, 25: 29, 40: 37, 41: 38, 42: 39, 43: 40} - score: '0.395' - edge_lig_43_lig_32: - ligand_a: lig_43 - ligand_b: lig_32 - atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, - 21: 25, 22: 26, 23: 27, 24: 28, 25: 29, 26: 30, 40: 34, 41: 35, 42: 36, 43: 37} - score: '0.430' - edge_lig_13_lig_45: - ligand_a: lig_13 - ligand_b: lig_45 - atom mapping: {2: 41, 3: 24, 4: 25, 5: 26, 20: 22, 21: 23, 22: 21, 23: 16, 24: 13, - 25: 15, 26: 14, 41: 17, 42: 18, 43: 19, 44: 20, 45: 43, 46: 44} - score: '0.395' - edge_lig_30_lig_45: - ligand_a: lig_30 - ligand_b: lig_45 - atom mapping: {8: 25, 9: 26, 10: 24, 11: 22, 12: 23, 13: 21, 14: 20, 15: 43, 16: 44, - 17: 41, 18: 42, 19: 18, 20: 19, 21: 17, 22: 16, 23: 13, 24: 14, 25: 15} - score: '0.388' + edge_lig_42_lig_28: + ligand_a: lig_42 + ligand_b: lig_28 + atom mapping: {10: 28, 11: 26, 12: 27, 13: 25, 14: 24, 15: 45, 16: 46, 17: 43, + 18: 44, 19: 22, 20: 23, 21: 21, 22: 20, 23: 17, 24: 19, 25: 18} + score: '0.354' diff --git a/data/cmet/03_edges/01_perses_openfe.yml b/data/cmet/03_edges/01_perses_openfe.yml index 323b566b8..129f22a94 100644 --- a/data/cmet/03_edges/01_perses_openfe.yml +++ b/data/cmet/03_edges/01_perses_openfe.yml @@ -1,23 +1,15 @@ mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph +planner: openfe v0.5 minimal_spanning_graph edges: - edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402761_1_21: + edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402754_40_14: ligand_a: lig_CHEMBL3402745_200_5 - ligand_b: lig_CHEMBL3402761_1_21 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 15, 7: 16, 8: 12, 9: 13, - 10: 10, 11: 11, 12: 8, 14: 6, 15: 7, 16: 17, 17: 18, 18: 19, 19: 20, 20: 21, - 21: 22, 22: 59, 23: 60, 24: 29, 26: 27, 27: 28, 28: 25, 41: 23, 42: 24, 43: 61, - 44: 62} - score: '0.648' - edge_lig_CHEMBL3402744_300_4_lig_CHEMBL3402761_1_21: - ligand_a: lig_CHEMBL3402744_300_4 - ligand_b: lig_CHEMBL3402761_1_21 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 15, 7: 16, 8: 12, 9: 13, - 10: 10, 11: 11, 12: 8, 14: 6, 15: 7, 16: 17, 17: 18, 18: 19, 19: 20, 20: 21, - 21: 22, 22: 59, 23: 60, 24: 29, 26: 27, 27: 28, 28: 25, 38: 23, 39: 24, 40: 61, - 41: 62} - score: '0.671' + ligand_b: lig_CHEMBL3402754_40_14 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 14, 7: 15, 8: 12, 9: 13, + 10: 10, 11: 11, 12: 8, 13: 9, 14: 6, 15: 7, 16: 16, 17: 17, 18: 18, 19: 19, + 20: 20, 21: 21, 22: 41, 23: 42, 24: 28, 26: 26, 27: 27, 28: 24, 41: 22, 42: 23, + 43: 43, 44: 44} + score: '0.716' edge_lig_CHEMBL3402761_1_21_lig_CHEMBL3402749_500_9: ligand_a: lig_CHEMBL3402761_1_21 ligand_b: lig_CHEMBL3402749_500_9 @@ -26,3 +18,19 @@ edges: 21: 19, 22: 16, 23: 14, 24: 15, 25: 12, 26: 13, 27: 10, 28: 11, 29: 9, 59: 40, 60: 41, 61: 38, 62: 39} score: '0.675' + edge_lig_CHEMBL3402744_300_4_lig_CHEMBL3402761_1_21: + ligand_a: lig_CHEMBL3402744_300_4 + ligand_b: lig_CHEMBL3402761_1_21 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 15, 7: 16, 8: 12, 9: 13, + 10: 10, 11: 11, 12: 8, 14: 6, 15: 7, 16: 17, 17: 18, 18: 19, 19: 20, 20: 21, + 21: 22, 22: 59, 23: 60, 24: 29, 26: 27, 27: 28, 28: 25, 38: 23, 39: 24, 40: 61, + 41: 62} + score: '0.671' + edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402761_1_21: + ligand_a: lig_CHEMBL3402745_200_5 + ligand_b: lig_CHEMBL3402761_1_21 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 15, 7: 16, 8: 12, 9: 13, + 10: 10, 11: 11, 12: 8, 14: 6, 15: 7, 16: 17, 17: 18, 18: 19, 19: 20, 20: 21, + 21: 22, 22: 59, 23: 60, 24: 29, 26: 27, 27: 28, 28: 25, 41: 23, 42: 24, 43: 61, + 44: 62} + score: '0.648' diff --git a/data/eg5/03_edges/01_perses_openfe.yml b/data/eg5/03_edges/01_perses_openfe.yml index 98d166b4b..fd212f12f 100644 --- a/data/eg5/03_edges/01_perses_openfe.yml +++ b/data/eg5/03_edges/01_perses_openfe.yml @@ -1,21 +1,54 @@ mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph +planner: openfe v0.5 minimal_spanning_graph edges: - edge_lig_CHEMBL1083836_lig_CHEMBL1084115: - ligand_a: lig_CHEMBL1083836 - ligand_b: lig_CHEMBL1084115 - atom mapping: {7: 5, 8: 6, 9: 7, 10: 8, 11: 9, 12: 10, 13: 11, 14: 12, 15: 13, - 16: 14, 25: 28, 26: 29, 27: 30, 28: 31, 29: 32, 30: 33, 31: 34, 32: 36, 42: 37, - 43: 38, 44: 39, 45: 40, 46: 41, 47: 42, 48: 43, 49: 44} + edge_lig_CHEMBL1084676_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1084676 + ligand_b: lig_CHEMBL1078998 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 17: 17, 18: 18, 19: 22, 20: 26, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, + 26: 35, 27: 36, 28: 38, 52: 39, 53: 40, 54: 41, 55: 42, 56: 43, 57: 44, 58: 45, + 59: 46} + score: '0.598' + edge_lig_CHEMBL1084678_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1084678 + ligand_b: lig_CHEMBL1078998 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 17: 17, 18: 18, 19: 22, 20: 26, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, + 26: 35, 27: 36, 28: 38, 52: 39, 53: 40, 54: 41, 55: 42, 56: 43, 57: 44, 58: 45, + 59: 46} + score: '0.598' + edge_lig_CHEMBL1078998_lig_CHEMBL1083836: + ligand_a: lig_CHEMBL1078998 + ligand_b: lig_CHEMBL1083836 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 30: 25, 31: 26, 32: 27, 33: 28, 34: 29, 35: 30, 36: 31, 37: 32, 39: 42, + 40: 43, 41: 44, 42: 45, 43: 46, 44: 47, 45: 48, 46: 49} score: '0.544' - edge_lig_CHEMBL1096003_lig_CHEMBL1084115: - ligand_a: lig_CHEMBL1096003 - ligand_b: lig_CHEMBL1084115 - atom mapping: {7: 5, 8: 6, 9: 7, 10: 8, 11: 9, 12: 10, 14: 12, 15: 13, 16: 14, - 17: 15, 18: 28, 19: 29, 20: 30, 21: 31, 22: 32, 23: 33, 24: 34, 25: 35, 49: 37, - 50: 39, 51: 38, 52: 40, 53: 42, 54: 41, 55: 43, 56: 44} - score: '0.538' + edge_lig_CHEMBL1085895_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1085895 + ligand_b: lig_CHEMBL1078998 + atom mapping: {20: 36, 21: 38, 22: 35, 23: 33, 24: 34, 25: 32, 26: 30, 27: 31, + 28: 16, 29: 17, 30: 26, 31: 22, 32: 18, 33: 14, 34: 15, 35: 12, 36: 13, 37: 11, + 38: 9, 39: 10, 40: 7, 41: 8, 53: 45, 54: 46, 55: 42, 56: 44, 57: 43, 58: 39, + 59: 41, 60: 40} + score: '0.602' + edge_lig_CHEMBL1084143_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1084143 + ligand_b: lig_CHEMBL1078998 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 17: 17, 19: 26, 20: 27, 21: 28, 22: 29, 23: 18, 24: 19, 25: 20, 26: 21, + 27: 30, 28: 31, 29: 32, 30: 33, 31: 34, 32: 35, 33: 36, 34: 37, 61: 39, 62: 41, + 63: 40, 64: 42, 65: 44, 66: 43, 67: 45, 68: 46} + score: '0.653' + edge_lig_CHEMBL1085666_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1085666 + ligand_b: lig_CHEMBL1078998 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 17: 17, 18: 26, 19: 22, 20: 18, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, + 26: 35, 27: 36, 28: 37, 35: 39, 36: 41, 37: 40, 38: 42, 39: 44, 40: 43, 41: 45, + 42: 46} + score: '0.628' edge_lig_CHEMBL1084677_lig_CHEMBL1078998: ligand_a: lig_CHEMBL1084677 ligand_b: lig_CHEMBL1078998 @@ -24,36 +57,23 @@ edges: 26: 35, 27: 36, 28: 37, 49: 39, 50: 41, 51: 40, 52: 42, 53: 44, 54: 43, 55: 45, 56: 46} score: '0.602' - edge_lig_CHEMBL1088740_lig_CHEMBL1077227: - ligand_a: lig_CHEMBL1088740 - ligand_b: lig_CHEMBL1077227 - atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, - 16: 16, 17: 17, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, 26: 35, 27: 36, 28: 37, - 30: 47, 31: 49, 32: 48, 33: 50, 34: 52, 35: 51, 36: 53, 37: 54} - score: '0.618' - edge_lig_CHEMBL1093087_lig_CHEMBL1084115: - ligand_a: lig_CHEMBL1093087 - ligand_b: lig_CHEMBL1084115 - atom mapping: {20: 34, 21: 36, 22: 33, 23: 31, 24: 32, 25: 30, 26: 28, 27: 29, - 28: 14, 29: 15, 30: 16, 31: 20, 32: 24, 33: 12, 34: 13, 35: 10, 36: 11, 37: 9, - 38: 7, 39: 8, 40: 5, 41: 6, 53: 43, 54: 44, 55: 40, 56: 41, 57: 42, 58: 37, - 59: 39, 60: 38} - score: '0.547' - edge_lig_CHEMBL1086409_lig_CHEMBL1084115: - ligand_a: lig_CHEMBL1086409 - ligand_b: lig_CHEMBL1084115 - atom mapping: {5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, - 15: 15, 16: 16, 17: 20, 18: 24, 19: 28, 20: 29, 21: 30, 22: 31, 23: 32, 24: 33, - 25: 34, 26: 36, 36: 37, 37: 39, 38: 38, 39: 40, 40: 42, 41: 41, 42: 43, 43: 44} - score: '0.621' - edge_lig_CHEMBL1089056_lig_CHEMBL1077227: - ligand_a: lig_CHEMBL1089056 - ligand_b: lig_CHEMBL1077227 + edge_lig_CHEMBL1077204_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1077204 + ligand_b: lig_CHEMBL1078998 atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, - 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, - 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, 31: 31, 32: 32, 33: 33, 34: 34, 35: 35, - 36: 36, 38: 37, 39: 47, 40: 48, 41: 49, 42: 50, 43: 51, 44: 52, 45: 53, 46: 54} - score: '0.716' + 16: 16, 17: 17, 18: 26, 19: 22, 20: 18, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, + 26: 35, 27: 36, 28: 37, 53: 39, 54: 41, 55: 40, 56: 42, 57: 44, 58: 43, 59: 45, + 60: 46} + score: '0.598' + edge_lig_CHEMBL1084935_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1084935 + ligand_b: lig_CHEMBL1078998 + atom mapping: {19: 36, 20: 38, 21: 35, 22: 33, 23: 34, 24: 32, 25: 30, 26: 31, + 27: 16, 28: 17, 29: 18, 30: 19, 31: 20, 32: 21, 33: 22, 34: 25, 35: 24, 36: 23, + 37: 26, 38: 27, 39: 28, 40: 29, 41: 14, 42: 15, 43: 12, 44: 13, 45: 11, 46: 9, + 47: 10, 48: 7, 49: 8, 61: 45, 62: 46, 63: 42, 64: 44, 65: 43, 66: 39, 67: 41, + 68: 40} + score: '0.720' edge_lig_CHEMBL1078691_lig_CHEMBL1077227: ligand_a: lig_CHEMBL1078691 ligand_b: lig_CHEMBL1077227 @@ -62,6 +82,36 @@ edges: 27: 18, 28: 19, 29: 20, 30: 21, 31: 30, 32: 31, 33: 32, 34: 33, 35: 34, 36: 35, 37: 36, 38: 37, 40: 47, 41: 48, 42: 49, 43: 50, 44: 51, 45: 52, 46: 53, 47: 54} score: '0.707' + edge_lig_CHEMBL1078774_lig_CHEMBL1077227: + ligand_a: lig_CHEMBL1078774 + ligand_b: lig_CHEMBL1077227 + atom mapping: {8: 7, 9: 8, 10: 9, 11: 10, 12: 11, 13: 12, 14: 13, 15: 14, 16: 15, + 17: 16, 18: 17, 19: 26, 20: 27, 21: 28, 22: 29, 23: 22, 24: 25, 25: 24, 26: 23, + 27: 18, 28: 19, 29: 20, 30: 21, 31: 30, 32: 31, 33: 32, 34: 33, 35: 34, 36: 35, + 37: 36, 38: 37, 40: 47, 41: 48, 42: 49, 43: 50, 44: 51, 45: 52, 46: 53, 47: 54} + score: '0.707' + edge_lig_CHEMBL1089056_lig_CHEMBL1077227: + ligand_a: lig_CHEMBL1089056 + ligand_b: lig_CHEMBL1077227 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, + 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, 31: 31, 32: 32, 33: 33, 34: 34, 35: 35, + 36: 36, 38: 37, 39: 47, 40: 48, 41: 49, 42: 50, 43: 51, 44: 52, 45: 53, 46: 54} + score: '0.716' + edge_lig_CHEMBL1078998_lig_CHEMBL1082248: + ligand_a: lig_CHEMBL1078998 + ligand_b: lig_CHEMBL1082248 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 14: 14, 15: 15, 16: 16, + 17: 17, 30: 18, 31: 19, 32: 20, 33: 21, 34: 22, 35: 23, 36: 24, 37: 25, 39: 35, + 40: 36, 41: 37, 42: 38, 43: 39, 44: 40, 45: 41, 46: 42} + score: '0.562' + edge_lig_CHEMBL1078998_lig_CHEMBL1085692: + ligand_a: lig_CHEMBL1078998 + ligand_b: lig_CHEMBL1085692 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 14: 14, 15: 15, 16: 16, + 17: 17, 30: 18, 31: 19, 32: 20, 33: 21, 34: 22, 35: 23, 36: 24, 37: 25, 39: 51, + 40: 52, 41: 53, 42: 54, 43: 55, 44: 56, 45: 57, 46: 58} + score: '0.538' edge_lig_CHEMBL1089393_lig_CHEMBL1077227: ligand_a: lig_CHEMBL1089393 ligand_b: lig_CHEMBL1077227 @@ -69,30 +119,36 @@ edges: 16: 16, 17: 17, 18: 30, 19: 31, 20: 32, 21: 33, 22: 34, 23: 35, 24: 36, 26: 37, 27: 47, 28: 48, 29: 49, 30: 50, 31: 51, 32: 52, 33: 53, 34: 54} score: '0.645' - edge_lig_CHEMBL1077204_lig_CHEMBL1078998: - ligand_a: lig_CHEMBL1077204 - ligand_b: lig_CHEMBL1078998 + edge_lig_CHEMBL1088740_lig_CHEMBL1077227: + ligand_a: lig_CHEMBL1088740 + ligand_b: lig_CHEMBL1077227 atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, - 16: 16, 17: 17, 18: 26, 19: 22, 20: 18, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, - 26: 35, 27: 36, 28: 37, 53: 39, 54: 41, 55: 40, 56: 42, 57: 44, 58: 43, 59: 45, - 60: 46} - score: '0.598' - edge_lig_CHEMBL1093088_lig_CHEMBL1084115: + 16: 16, 17: 17, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, 26: 35, 27: 36, 28: 37, + 30: 47, 31: 49, 32: 48, 33: 50, 34: 52, 35: 51, 36: 53, 37: 54} + score: '0.618' + edge_lig_CHEMBL1093088_lig_CHEMBL1078998: ligand_a: lig_CHEMBL1093088 - ligand_b: lig_CHEMBL1084115 - atom mapping: {7: 34, 8: 35, 9: 33, 10: 31, 11: 32, 12: 30, 13: 28, 14: 29, 15: 14, - 16: 15, 17: 24, 18: 20, 19: 16, 20: 12, 21: 13, 22: 10, 23: 11, 24: 9, 25: 7, - 26: 8, 27: 5, 28: 6, 40: 43, 41: 44, 42: 40, 43: 42, 44: 41, 45: 37, 46: 39, - 47: 38} - score: '0.598' - edge_lig_CHEMBL1084676_lig_CHEMBL1084115: - ligand_a: lig_CHEMBL1084676 - ligand_b: lig_CHEMBL1084115 - atom mapping: {7: 5, 8: 6, 9: 7, 10: 8, 11: 9, 12: 10, 13: 11, 14: 12, 15: 13, - 16: 14, 17: 15, 18: 16, 19: 20, 20: 24, 21: 28, 22: 29, 23: 30, 24: 31, 25: 32, - 26: 33, 27: 34, 28: 36, 52: 37, 53: 38, 54: 39, 55: 40, 56: 41, 57: 42, 58: 43, - 59: 44} + ligand_b: lig_CHEMBL1078998 + atom mapping: {7: 36, 8: 37, 9: 35, 10: 33, 11: 34, 12: 32, 13: 30, 14: 31, 15: 16, + 16: 17, 17: 26, 18: 22, 19: 18, 20: 14, 21: 15, 22: 12, 23: 13, 24: 11, 25: 9, + 26: 10, 27: 7, 28: 8, 40: 45, 41: 46, 42: 42, 43: 44, 44: 43, 45: 39, 46: 41, + 47: 40} score: '0.598' + edge_lig_CHEMBL1083517_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1083517 + ligand_b: lig_CHEMBL1078998 + atom mapping: {8: 7, 9: 8, 10: 9, 11: 10, 12: 11, 13: 12, 14: 13, 15: 14, 16: 15, + 17: 16, 18: 17, 19: 18, 20: 22, 21: 26, 22: 30, 23: 31, 24: 32, 25: 33, 26: 34, + 27: 35, 28: 36, 29: 37, 39: 39, 40: 40, 41: 41, 42: 42, 43: 43, 44: 44, 45: 45, + 46: 46} + score: '0.621' + edge_lig_CHEMBL1084115_lig_CHEMBL1085692: + ligand_a: lig_CHEMBL1084115 + ligand_b: lig_CHEMBL1085692 + atom mapping: {5: 7, 6: 8, 7: 9, 8: 10, 9: 11, 10: 12, 12: 14, 13: 15, 14: 16, + 15: 17, 28: 18, 29: 19, 30: 20, 31: 21, 32: 22, 33: 23, 34: 24, 36: 25, 37: 51, + 38: 53, 39: 52, 40: 54, 41: 55, 42: 56, 43: 57, 44: 58} + score: '0.538' edge_lig_CHEMBL1096003_lig_CHEMBL1078998: ligand_a: lig_CHEMBL1096003 ligand_b: lig_CHEMBL1078998 @@ -100,29 +156,44 @@ edges: 17: 17, 18: 30, 19: 31, 20: 32, 21: 33, 22: 34, 23: 35, 24: 36, 25: 37, 49: 39, 50: 41, 51: 40, 52: 42, 53: 44, 54: 43, 55: 45, 56: 46} score: '0.538' - edge_lig_CHEMBL1096002_lig_CHEMBL1084115: - ligand_a: lig_CHEMBL1096002 - ligand_b: lig_CHEMBL1084115 - atom mapping: {13: 34, 14: 36, 15: 33, 16: 31, 17: 32, 18: 30, 19: 28, 20: 29, - 21: 14, 22: 15, 23: 12, 24: 13, 25: 10, 27: 9, 28: 7, 29: 8, 30: 5, 31: 6, 43: 43, - 44: 44, 45: 40, 46: 41, 47: 42, 48: 37, 49: 39, 50: 38} + edge_lig_CHEMBL1078998_lig_CHEMBL1096002: + ligand_a: lig_CHEMBL1078998 + ligand_b: lig_CHEMBL1096002 + atom mapping: {7: 30, 8: 31, 9: 28, 10: 29, 11: 27, 12: 25, 14: 23, 15: 24, 16: 21, + 17: 22, 30: 19, 31: 20, 32: 18, 33: 16, 34: 17, 35: 15, 36: 13, 38: 14, 39: 48, + 40: 49, 41: 50, 42: 45, 43: 46, 44: 47, 45: 43, 46: 44} score: '0.555' - edge_lig_CHEMBL1084935_lig_CHEMBL1084115: - ligand_a: lig_CHEMBL1084935 + edge_lig_CHEMBL1078998_lig_CHEMBL1082249: + ligand_a: lig_CHEMBL1078998 + ligand_b: lig_CHEMBL1082249 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 14: 14, 15: 15, 16: 16, + 17: 17, 30: 18, 31: 19, 32: 20, 33: 21, 34: 22, 35: 23, 36: 24, 37: 25, 39: 45, + 40: 46, 41: 47, 42: 48, 43: 49, 44: 50, 45: 51, 46: 52} + score: '0.545' + edge_lig_CHEMBL1086409_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1086409 + ligand_b: lig_CHEMBL1078998 + atom mapping: {5: 7, 6: 8, 7: 9, 8: 10, 9: 11, 10: 12, 11: 13, 12: 14, 13: 15, + 14: 16, 15: 17, 16: 18, 17: 22, 18: 26, 19: 30, 20: 31, 21: 32, 22: 33, 23: 34, + 24: 35, 25: 36, 26: 38, 36: 39, 37: 41, 38: 40, 39: 42, 40: 44, 41: 43, 42: 45, + 43: 46} + score: '0.621' + edge_lig_CHEMBL1077227_lig_CHEMBL1085692: + ligand_a: lig_CHEMBL1077227 + ligand_b: lig_CHEMBL1085692 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 14: 14, 15: 15, 16: 16, + 17: 17, 30: 18, 31: 19, 32: 20, 33: 21, 34: 22, 35: 23, 36: 24, 37: 25, 38: 26, + 39: 28, 40: 27, 41: 29, 42: 30, 43: 31, 47: 51, 48: 53, 49: 52, 50: 54, 51: 56, + 52: 55, 53: 57, 54: 58} + score: '0.567' + edge_lig_CHEMBL1093087_lig_CHEMBL1084115: + ligand_a: lig_CHEMBL1093087 ligand_b: lig_CHEMBL1084115 - atom mapping: {19: 34, 20: 36, 21: 33, 22: 31, 23: 32, 24: 30, 25: 28, 26: 29, - 27: 14, 28: 15, 29: 16, 30: 17, 31: 18, 32: 19, 33: 20, 34: 23, 35: 22, 36: 21, - 37: 24, 38: 25, 39: 26, 40: 27, 41: 12, 42: 13, 43: 10, 44: 11, 45: 9, 46: 7, - 47: 8, 48: 5, 49: 6, 61: 43, 62: 44, 63: 40, 64: 42, 65: 41, 66: 37, 67: 39, - 68: 38} - score: '0.720' - edge_lig_CHEMBL1084115_lig_CHEMBL1082248: - ligand_a: lig_CHEMBL1084115 - ligand_b: lig_CHEMBL1082248 - atom mapping: {5: 7, 6: 8, 7: 9, 8: 10, 9: 11, 10: 12, 12: 14, 13: 15, 14: 16, - 15: 17, 28: 18, 29: 19, 30: 20, 31: 21, 32: 22, 33: 23, 34: 24, 36: 25, 37: 35, - 38: 37, 39: 36, 40: 38, 41: 39, 42: 40, 43: 41, 44: 42} - score: '0.562' + atom mapping: {20: 34, 21: 36, 22: 33, 23: 31, 24: 32, 25: 30, 26: 28, 27: 29, + 28: 14, 29: 15, 30: 16, 31: 20, 32: 24, 33: 12, 34: 13, 35: 10, 36: 11, 37: 9, + 38: 7, 39: 8, 40: 5, 41: 6, 53: 43, 54: 44, 55: 40, 56: 41, 57: 42, 58: 37, + 59: 39, 60: 38} + score: '0.547' edge_lig_CHEMBL1086410_lig_CHEMBL1078998: ligand_a: lig_CHEMBL1086410 ligand_b: lig_CHEMBL1078998 @@ -131,73 +202,3 @@ edges: 26: 18, 27: 21, 28: 20, 29: 19, 30: 30, 31: 31, 32: 32, 33: 33, 34: 34, 35: 35, 36: 36, 37: 37, 47: 39, 48: 41, 49: 40, 50: 42, 51: 44, 52: 43, 53: 45, 54: 46} score: '0.738' - edge_lig_CHEMBL1085895_lig_CHEMBL1084115: - ligand_a: lig_CHEMBL1085895 - ligand_b: lig_CHEMBL1084115 - atom mapping: {20: 34, 21: 36, 22: 33, 23: 31, 24: 32, 25: 30, 26: 28, 27: 29, - 28: 14, 29: 15, 30: 24, 31: 20, 32: 16, 33: 12, 34: 13, 35: 10, 36: 11, 37: 9, - 38: 7, 39: 8, 40: 5, 41: 6, 53: 43, 54: 44, 55: 40, 56: 42, 57: 41, 58: 37, - 59: 39, 60: 38} - score: '0.602' - edge_lig_CHEMBL1082249_lig_CHEMBL1084115: - ligand_a: lig_CHEMBL1082249 - ligand_b: lig_CHEMBL1084115 - atom mapping: {7: 5, 8: 6, 9: 7, 10: 8, 11: 9, 12: 10, 14: 12, 15: 13, 16: 14, - 17: 15, 18: 28, 19: 29, 20: 30, 21: 31, 22: 32, 23: 33, 24: 34, 25: 35, 45: 37, - 46: 39, 47: 38, 48: 40, 49: 42, 50: 41, 51: 43, 52: 44} - score: '0.545' - edge_lig_CHEMBL1085692_lig_CHEMBL1084115: - ligand_a: lig_CHEMBL1085692 - ligand_b: lig_CHEMBL1084115 - atom mapping: {7: 5, 8: 6, 9: 7, 10: 8, 11: 9, 12: 10, 14: 12, 15: 13, 16: 14, - 17: 15, 18: 28, 19: 29, 20: 30, 21: 31, 22: 32, 23: 33, 24: 34, 25: 35, 51: 37, - 52: 39, 53: 38, 54: 40, 55: 42, 56: 41, 57: 43, 58: 44} - score: '0.538' - edge_lig_CHEMBL1084143_lig_CHEMBL1084115: - ligand_a: lig_CHEMBL1084143 - ligand_b: lig_CHEMBL1084115 - atom mapping: {7: 5, 8: 6, 9: 7, 10: 8, 11: 9, 12: 10, 13: 11, 14: 12, 15: 13, - 16: 14, 17: 15, 19: 20, 20: 21, 21: 22, 22: 23, 23: 16, 24: 17, 25: 18, 26: 19, - 27: 28, 28: 29, 29: 30, 30: 31, 31: 32, 32: 33, 33: 34, 34: 35, 61: 37, 62: 39, - 63: 38, 64: 40, 65: 42, 66: 41, 67: 43, 68: 44} - score: '0.653' - edge_lig_CHEMBL1083517_lig_CHEMBL1084115: - ligand_a: lig_CHEMBL1083517 - ligand_b: lig_CHEMBL1084115 - atom mapping: {8: 5, 9: 6, 10: 7, 11: 8, 12: 9, 13: 10, 14: 11, 15: 12, 16: 13, - 17: 14, 18: 15, 19: 16, 20: 20, 21: 24, 22: 28, 23: 29, 24: 30, 25: 31, 26: 32, - 27: 33, 28: 34, 29: 35, 39: 37, 40: 38, 41: 39, 42: 40, 43: 41, 44: 42, 45: 43, - 46: 44} - score: '0.621' - edge_lig_CHEMBL1078774_lig_CHEMBL1077227: - ligand_a: lig_CHEMBL1078774 - ligand_b: lig_CHEMBL1077227 - atom mapping: {8: 7, 9: 8, 10: 9, 11: 10, 12: 11, 13: 12, 14: 13, 15: 14, 16: 15, - 17: 16, 18: 17, 19: 26, 20: 27, 21: 28, 22: 29, 23: 22, 24: 25, 25: 24, 26: 23, - 27: 18, 28: 19, 29: 20, 30: 21, 31: 30, 32: 31, 33: 32, 34: 33, 35: 34, 36: 35, - 37: 36, 38: 37, 40: 47, 41: 48, 42: 49, 43: 50, 44: 51, 45: 52, 46: 53, 47: 54} - score: '0.707' - edge_lig_CHEMBL1084678_lig_CHEMBL1078998: - ligand_a: lig_CHEMBL1084678 - ligand_b: lig_CHEMBL1078998 - atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, - 16: 16, 17: 17, 18: 18, 19: 22, 20: 26, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, - 26: 35, 27: 36, 28: 38, 52: 39, 53: 40, 54: 41, 55: 42, 56: 43, 57: 44, 58: 45, - 59: 46} - score: '0.598' - edge_lig_CHEMBL1096003_lig_CHEMBL1077227: - ligand_a: lig_CHEMBL1096003 - ligand_b: lig_CHEMBL1077227 - atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 14: 14, 15: 15, 16: 16, - 17: 17, 18: 30, 19: 31, 20: 32, 21: 33, 22: 34, 23: 35, 24: 36, 25: 37, 26: 38, - 27: 40, 28: 39, 29: 41, 30: 42, 31: 43, 49: 47, 50: 49, 51: 48, 52: 50, 53: 52, - 54: 51, 55: 53, 56: 54} - score: '0.567' - edge_lig_CHEMBL1085666_lig_CHEMBL1084115: - ligand_a: lig_CHEMBL1085666 - ligand_b: lig_CHEMBL1084115 - atom mapping: {7: 5, 8: 6, 9: 7, 10: 8, 11: 9, 12: 10, 13: 11, 14: 12, 15: 13, - 16: 14, 17: 15, 18: 24, 19: 20, 20: 16, 21: 28, 22: 29, 23: 30, 24: 31, 25: 32, - 26: 33, 27: 34, 28: 35, 35: 37, 36: 39, 37: 38, 38: 40, 39: 42, 40: 41, 41: 43, - 42: 44} - score: '0.628' diff --git a/data/hif2a/03_edges/01_perses_openfe.yml b/data/hif2a/03_edges/01_perses_openfe.yml index e5a43a353..1070dce53 100644 --- a/data/hif2a/03_edges/01_perses_openfe.yml +++ b/data/hif2a/03_edges/01_perses_openfe.yml @@ -1,59 +1,102 @@ mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph +planner: openfe v0.5 minimal_spanning_graph edges: + edge_lig_165_lig_54: + ligand_a: lig_165 + ligand_b: lig_54 + atom mapping: {0: 19, 1: 18, 2: 16, 3: 17, 4: 14, 5: 15, 6: 13, 7: 12, 34: 22, + 35: 23, 36: 20, 37: 21} + score: '0.367' + edge_lig_43_lig_84: + ligand_a: lig_43 + ligand_b: lig_84 + atom mapping: {9: 7, 10: 6, 11: 4, 12: 5, 13: 2, 15: 1, 16: 0, 17: 31, 18: 32, + 20: 29, 21: 30} + score: '0.363' + edge_lig_124_lig_224: + ligand_a: lig_124 + ligand_b: lig_224 + atom mapping: {14: 24, 15: 26, 16: 25, 17: 27, 18: 28, 19: 29, 20: 30} + score: '0.174' + edge_lig_1_lig_43: + ligand_a: lig_1 + ligand_b: lig_43 + atom mapping: {7: 9, 8: 10, 9: 20, 10: 21, 11: 17, 12: 18, 13: 15, 14: 16, 15: 13, + 17: 11, 18: 12} + score: '0.357' + edge_lig_156_lig_54: + ligand_a: lig_156 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 13: 18, 14: 19, 15: 16, 16: 17, + 18: 14, 19: 15} + score: '0.346' + edge_lig_57_lig_54: + ligand_a: lig_57 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.364' + edge_lig_30_lig_224: + ligand_a: lig_30 + ligand_b: lig_224 + atom mapping: {14: 24, 15: 26, 16: 25, 17: 27, 19: 29, 20: 28} + score: '0.152' + edge_lig_206_lig_54: + ligand_a: lig_206 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.364' + edge_lig_54_lig_224: + ligand_a: lig_54 + ligand_b: lig_224 + atom mapping: {29: 24, 30: 26, 31: 25, 32: 27} + score: '0.093' edge_lig_67_lig_124: ligand_a: lig_67 ligand_b: lig_124 atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 13: 13, 15: 21, 17: 23} score: '0.311' - edge_lig_42_lig_224: - ligand_a: lig_42 + edge_lig_35_lig_224: + ligand_a: lig_35 ligand_b: lig_224 - atom mapping: {27: 24, 28: 25, 29: 26, 30: 27, 32: 29, 33: 30} + atom mapping: {27: 24, 28: 26, 29: 25, 30: 27, 32: 29, 33: 28} score: '0.145' - edge_lig_231_lig_54: - ligand_a: lig_231 + edge_lig_227_lig_54: + ligand_a: lig_227 ligand_b: lig_54 atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, 16: 17, 18: 14, 19: 15} - score: '0.370' - edge_lig_54_lig_235: - ligand_a: lig_54 - ligand_b: lig_235 - atom mapping: {12: 7, 13: 8, 14: 17, 15: 18, 16: 14, 17: 15, 18: 12, 19: 13, 20: 11, - 22: 9, 23: 10} - score: '0.338' - edge_lig_1_lig_43: - ligand_a: lig_1 - ligand_b: lig_43 - atom mapping: {7: 9, 8: 10, 9: 20, 10: 21, 11: 17, 12: 18, 13: 15, 14: 16, 15: 13, - 17: 11, 18: 12} - score: '0.357' - edge_lig_23_lig_43: - ligand_a: lig_23 - ligand_b: lig_43 - atom mapping: {7: 9, 8: 10, 9: 20, 10: 21, 11: 17, 12: 18, 13: 15, 14: 16, 15: 13, - 17: 11, 18: 12} - score: '0.355' - edge_lig_61_lig_43: - ligand_a: lig_61 - ligand_b: lig_43 - atom mapping: {7: 9, 8: 10, 9: 20, 10: 21, 11: 17, 12: 18, 13: 15, 14: 16, 15: 13, - 17: 11, 18: 12} - score: '0.360' - edge_lig_215_lig_54: - ligand_a: lig_215 + score: '0.361' + edge_lig_31_lig_224: + ligand_a: lig_31 + ligand_b: lig_224 + atom mapping: {17: 24, 18: 26, 19: 25, 20: 27, 22: 29, 23: 28} + score: '0.145' + edge_lig_338_lig_54: + ligand_a: lig_338 ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, - 16: 17, 18: 14, 19: 15} + atom mapping: {7: 12, 8: 13, 9: 14, 10: 15, 11: 16, 12: 17, 13: 18, 14: 19, 15: 20, + 16: 21, 18: 22, 19: 23} score: '0.364' - edge_lig_252_lig_54: - ligand_a: lig_252 + edge_lig_336_lig_54: + ligand_a: lig_336 ligand_b: lig_54 atom mapping: {7: 12, 8: 13, 9: 14, 10: 15, 11: 16, 12: 17, 13: 18, 14: 19, 15: 20, 16: 21, 18: 22, 19: 23} score: '0.367' + edge_lig_50_lig_224: + ligand_a: lig_50 + ligand_b: lig_224 + atom mapping: {14: 24, 15: 25, 16: 26, 17: 27} + score: '0.098' + edge_lig_231_lig_54: + ligand_a: lig_231 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.370' edge_lig_290_lig_54: ligand_a: lig_290 ligand_b: lig_54 @@ -66,145 +109,102 @@ edges: atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, 16: 17, 18: 14, 19: 15} score: '0.367' - edge_lig_155_lig_54: - ligand_a: lig_155 - ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, - 16: 17, 18: 14, 19: 15} - score: '0.367' - edge_lig_54_lig_224: - ligand_a: lig_54 + edge_lig_42_lig_224: + ligand_a: lig_42 ligand_b: lig_224 - atom mapping: {29: 24, 30: 25, 31: 26, 32: 27} - score: '0.093' - edge_lig_15_lig_54: - ligand_a: lig_15 + atom mapping: {27: 24, 28: 26, 29: 25, 30: 27, 32: 29, 33: 30} + score: '0.145' + edge_lig_215_lig_54: + ligand_a: lig_215 ligand_b: lig_54 atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, 16: 17, 18: 14, 19: 15} - score: '0.361' - edge_lig_165_lig_54: - ligand_a: lig_165 - ligand_b: lig_54 - atom mapping: {0: 19, 1: 18, 2: 16, 3: 17, 4: 14, 5: 15, 6: 13, 7: 12, 34: 22, - 35: 23, 36: 20, 37: 21} - score: '0.367' + score: '0.364' + edge_lig_61_lig_43: + ligand_a: lig_61 + ligand_b: lig_43 + atom mapping: {7: 9, 8: 10, 9: 20, 10: 21, 11: 17, 12: 18, 13: 15, 14: 16, 15: 13, + 17: 11, 18: 12} + score: '0.360' edge_lig_41_lig_224: ligand_a: lig_41 ligand_b: lig_224 - atom mapping: {26: 24, 27: 25, 28: 26, 29: 27, 31: 29, 32: 28} + atom mapping: {26: 24, 27: 25, 28: 26, 29: 27, 31: 29, 32: 30} score: '0.147' - edge_lig_167_lig_54: - ligand_a: lig_167 - ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, - 16: 17, 18: 14, 19: 15} - score: '0.364' - edge_lig_254_lig_54: - ligand_a: lig_254 - ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 14, 10: 15, 11: 16, 12: 17, 13: 18, 14: 19, 15: 20, - 16: 21, 18: 22, 19: 23} - score: '0.364' - edge_lig_35_lig_224: - ligand_a: lig_35 + edge_lig_43_lig_224: + ligand_a: lig_43 ligand_b: lig_224 atom mapping: {27: 24, 28: 25, 29: 26, 30: 27, 32: 29, 33: 30} score: '0.145' - edge_lig_124_lig_224: - ligand_a: lig_124 - ligand_b: lig_224 - atom mapping: {14: 24, 15: 26, 16: 25, 17: 27, 18: 28, 19: 29, 20: 30} - score: '0.174' - edge_lig_31_lig_224: - ligand_a: lig_31 - ligand_b: lig_224 - atom mapping: {17: 24, 18: 26, 19: 25, 20: 27, 22: 29, 23: 28} - score: '0.145' + edge_lig_251_lig_43: + ligand_a: lig_251 + ligand_b: lig_43 + atom mapping: {7: 9, 8: 10, 9: 11, 10: 12, 11: 13, 13: 15, 14: 16, 15: 17, 16: 18, + 17: 20, 18: 21} + score: '0.355' edge_lig_234_lig_54: ligand_a: lig_234 ligand_b: lig_54 atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, 16: 17, 18: 14, 19: 15} score: '0.367' - edge_lig_336_lig_54: - ligand_a: lig_336 + edge_lig_235_lig_54: + ligand_a: lig_235 ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 14, 10: 15, 11: 16, 12: 17, 13: 18, 14: 19, 15: 20, - 16: 21, 18: 22, 19: 23} - score: '0.367' - edge_lig_156_lig_54: - ligand_a: lig_156 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 18, 13: 19, 14: 16, 15: 17, + 17: 14, 18: 15} + score: '0.338' + edge_lig_15_lig_54: + ligand_a: lig_15 ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 13: 18, 14: 19, 15: 16, 16: 17, - 18: 14, 19: 15} - score: '0.346' - edge_lig_289_lig_54: - ligand_a: lig_289 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.361' + edge_lig_155_lig_54: + ligand_a: lig_155 ligand_b: lig_54 atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, 16: 17, 18: 14, 19: 15} score: '0.367' - edge_lig_227_lig_54: - ligand_a: lig_227 + edge_lig_289_lig_54: + ligand_a: lig_289 ligand_b: lig_54 atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, 16: 17, 18: 14, 19: 15} - score: '0.361' - edge_lig_256_lig_43: - ligand_a: lig_256 - ligand_b: lig_43 - atom mapping: {7: 9, 8: 10, 9: 11, 10: 12, 11: 13, 13: 15, 14: 16, 15: 17, 16: 18, - 17: 20, 18: 21} - score: '0.357' - edge_lig_43_lig_84: - ligand_a: lig_43 - ligand_b: lig_84 - atom mapping: {9: 7, 10: 6, 11: 4, 12: 5, 13: 2, 15: 1, 16: 0, 17: 31, 18: 32, - 20: 29, 21: 30} - score: '0.363' - edge_lig_30_lig_224: - ligand_a: lig_30 - ligand_b: lig_224 - atom mapping: {14: 24, 15: 26, 16: 25, 17: 27, 19: 29, 20: 28} - score: '0.152' - edge_lig_338_lig_54: - ligand_a: lig_338 + score: '0.367' + edge_lig_254_lig_54: + ligand_a: lig_254 ligand_b: lig_54 atom mapping: {7: 12, 8: 13, 9: 14, 10: 15, 11: 16, 12: 17, 13: 18, 14: 19, 15: 20, 16: 21, 18: 22, 19: 23} score: '0.364' - edge_lig_50_lig_224: - ligand_a: lig_50 - ligand_b: lig_224 - atom mapping: {14: 24, 15: 25, 16: 26, 17: 27} - score: '0.098' - edge_lig_43_lig_25: - ligand_a: lig_43 - ligand_b: lig_25 - atom mapping: {9: 7, 10: 8, 11: 9, 12: 10, 13: 11, 15: 13, 16: 14, 17: 15, 20: 16, - 21: 17} - score: '0.331' - edge_lig_57_lig_54: - ligand_a: lig_57 + edge_lig_252_lig_54: + ligand_a: lig_252 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 14, 10: 15, 11: 16, 12: 17, 13: 18, 14: 19, 15: 20, + 16: 21, 18: 22, 19: 23} + score: '0.367' + edge_lig_167_lig_54: + ligand_a: lig_167 ligand_b: lig_54 atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, 16: 17, 18: 14, 19: 15} score: '0.364' - edge_lig_251_lig_43: - ligand_a: lig_251 + edge_lig_256_lig_43: + ligand_a: lig_256 ligand_b: lig_43 atom mapping: {7: 9, 8: 10, 9: 11, 10: 12, 11: 13, 13: 15, 14: 16, 15: 17, 16: 18, 17: 20, 18: 21} + score: '0.357' + edge_lig_23_lig_43: + ligand_a: lig_23 + ligand_b: lig_43 + atom mapping: {7: 9, 8: 10, 9: 20, 10: 21, 11: 17, 12: 18, 13: 15, 14: 16, 15: 13, + 17: 11, 18: 12} score: '0.355' - edge_lig_206_lig_54: - ligand_a: lig_206 - ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, - 16: 17, 18: 14, 19: 15} - score: '0.364' - edge_lig_43_lig_224: - ligand_a: lig_43 - ligand_b: lig_224 - atom mapping: {27: 24, 28: 26, 29: 25, 30: 27, 32: 29, 33: 30} - score: '0.145' + edge_lig_25_lig_43: + ligand_a: lig_25 + ligand_b: lig_43 + atom mapping: {7: 9, 8: 10, 9: 11, 10: 12, 11: 13, 13: 15, 14: 16, 15: 17, 16: 20, + 17: 21} + score: '0.331' diff --git a/data/mcl1/03_edges/01_perses_openfe.yml b/data/mcl1/03_edges/01_perses_openfe.yml index d64e38ac2..403c2050f 100644 --- a/data/mcl1/03_edges/01_perses_openfe.yml +++ b/data/mcl1/03_edges/01_perses_openfe.yml @@ -1,77 +1,119 @@ mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph +planner: openfe v0.5 minimal_spanning_graph edges: - edge_lig_67_lig_43: - ligand_a: lig_67 - ligand_b: lig_43 - atom mapping: {0: 35, 1: 30, 2: 31, 3: 32, 4: 27, 5: 28, 6: 29, 7: 36, 8: 24, - 9: 25, 10: 26, 11: 38, 12: 39, 13: 40, 14: 21, 15: 23, 16: 22, 17: 18, 18: 20, - 19: 19, 20: 15, 21: 16, 22: 17, 23: 14, 41: 33, 42: 34} - score: '0.555' - edge_lig_31_lig_43: - ligand_a: lig_31 - ligand_b: lig_43 - atom mapping: {0: 35, 1: 30, 2: 31, 3: 32, 4: 27, 5: 28, 6: 29, 7: 36, 8: 24, - 9: 25, 10: 26, 11: 37, 12: 38, 13: 39, 14: 40, 15: 21, 16: 23, 17: 22, 18: 18, - 19: 19, 20: 20, 21: 15, 22: 17, 23: 16, 24: 14, 39: 33, 40: 34} + edge_lig_47_lig_34: + ligand_a: lig_47 + ligand_b: lig_34 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 23, 23: 22, 24: 24, 41: 39, 42: 40} score: '0.583' - edge_lig_63_lig_43: - ligand_a: lig_63 - ligand_b: lig_43 - atom mapping: {0: 36, 1: 29, 2: 30, 3: 31, 4: 32, 5: 27, 6: 28, 7: 24, 8: 25, - 9: 26, 10: 38, 11: 39, 12: 40, 13: 21, 14: 23, 15: 22, 16: 18, 17: 20, 18: 19, - 19: 15, 20: 16, 21: 17, 22: 14, 40: 33, 42: 35} - score: '0.542' - edge_lig_43_lig_27: - ligand_a: lig_43 + edge_lig_47_lig_52: + ligand_a: lig_47 + ligand_b: lig_52 + atom mapping: {0: 40, 1: 2, 2: 3, 3: 4, 4: 5, 5: 6, 6: 1, 7: 0, 8: 7, 9: 8, 10: 9, + 11: 10, 12: 11, 13: 12, 14: 13, 15: 14, 16: 16, 17: 15, 18: 17, 19: 18, 20: 19, + 21: 20, 22: 22, 23: 21, 24: 23, 41: 38} + score: '0.570' + edge_lig_47_lig_27: + ligand_a: lig_47 ligand_b: lig_27 - atom mapping: {14: 9, 15: 10, 16: 11, 17: 12, 18: 13, 19: 15, 20: 14, 21: 16, - 22: 18, 23: 17, 24: 19, 25: 20, 26: 21, 27: 22, 28: 23, 29: 24, 30: 25, 31: 26, - 32: 27, 33: 28, 34: 29, 35: 30, 36: 31, 37: 32, 38: 33, 39: 34, 40: 35} + atom mapping: {0: 30, 1: 25, 2: 26, 3: 27, 4: 22, 5: 23, 6: 24, 7: 31, 8: 19, + 9: 20, 10: 21, 11: 32, 12: 33, 13: 34, 14: 35, 15: 16, 16: 18, 17: 17, 18: 13, + 19: 14, 20: 15, 21: 10, 22: 12, 23: 11, 24: 9, 41: 28, 42: 29} score: '0.608' - edge_lig_58_lig_43: - ligand_a: lig_58 - ligand_b: lig_43 - atom mapping: {0: 36, 1: 29, 2: 30, 3: 31, 4: 32, 5: 27, 6: 28, 7: 24, 8: 25, - 9: 26, 14: 38, 15: 39, 16: 40, 17: 21, 18: 23, 19: 22, 20: 18, 21: 20, 22: 19, - 23: 15, 24: 17, 25: 16, 26: 14, 44: 33, 46: 35} - score: '0.531' - edge_lig_35_lig_43: - ligand_a: lig_35 - ligand_b: lig_43 - atom mapping: {0: 35, 1: 30, 2: 31, 3: 32, 4: 27, 5: 28, 6: 29, 7: 36, 8: 24, - 9: 25, 10: 26, 11: 37, 12: 38, 13: 39, 14: 40, 15: 21, 16: 23, 17: 22, 18: 18, - 19: 19, 20: 20, 21: 15, 22: 17, 23: 16, 24: 14, 39: 33, 40: 34} - score: '0.583' - edge_lig_36_lig_43: - ligand_a: lig_36 - ligand_b: lig_43 - atom mapping: {0: 35, 1: 30, 2: 31, 3: 32, 4: 27, 5: 28, 6: 29, 7: 36, 8: 24, - 9: 25, 10: 26, 11: 37, 12: 38, 13: 39, 14: 40, 15: 21, 16: 23, 17: 22, 18: 18, - 19: 19, 20: 20, 21: 15, 22: 17, 23: 16, 24: 14, 42: 33, 43: 34} + edge_lig_47_lig_61: + ligand_a: lig_47 + ligand_b: lig_61 + atom mapping: {0: 7, 1: 6, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 8: 9, 9: 10, 10: 11, + 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, 21: 21, + 22: 23, 23: 22, 24: 24, 41: 42, 42: 0} + score: '0.542' + edge_lig_43_lig_56: + ligand_a: lig_43 + ligand_b: lig_56 + atom mapping: {14: 27, 15: 24, 16: 25, 17: 26, 18: 21, 19: 23, 20: 22, 21: 18, + 22: 20, 23: 19, 24: 8, 25: 9, 26: 10, 27: 4, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, + 33: 45, 34: 46, 35: 0, 36: 7, 38: 15, 39: 16, 40: 17} + score: '0.548' + edge_lig_47_lig_63: + ligand_a: lig_47 + ligand_b: lig_63 + atom mapping: {0: 42, 1: 2, 2: 3, 3: 4, 4: 5, 5: 6, 6: 1, 7: 0, 8: 7, 9: 8, 10: 9, + 12: 10, 13: 11, 14: 12, 15: 13, 16: 15, 17: 14, 18: 16, 19: 17, 20: 18, 21: 19, + 22: 21, 23: 20, 24: 22, 41: 40} + score: '0.542' + edge_lig_43_lig_36: + ligand_a: lig_43 + ligand_b: lig_36 + atom mapping: {14: 24, 15: 21, 16: 22, 17: 23, 18: 18, 19: 20, 20: 19, 21: 15, + 22: 17, 23: 16, 24: 8, 25: 9, 26: 10, 27: 4, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, + 33: 42, 34: 43, 35: 0, 36: 7, 37: 11, 38: 12, 39: 13, 40: 14} score: '0.561' - edge_lig_32_lig_43: - ligand_a: lig_32 - ligand_b: lig_43 - atom mapping: {0: 35, 1: 30, 2: 31, 3: 32, 4: 27, 5: 28, 6: 29, 7: 36, 8: 24, - 9: 25, 10: 26, 11: 37, 12: 38, 13: 39, 14: 40, 15: 21, 16: 23, 17: 22, 18: 18, - 19: 19, 20: 20, 21: 15, 22: 17, 23: 16, 24: 14, 39: 33, 40: 34} + edge_lig_46_lig_58: + ligand_a: lig_46 + ligand_b: lig_58 + atom mapping: {0: 46, 1: 2, 2: 3, 3: 4, 4: 5, 5: 6, 6: 1, 7: 0, 8: 7, 9: 8, 10: 9, + 12: 14, 13: 15, 14: 16, 15: 17, 16: 19, 17: 18, 18: 20, 19: 21, 20: 22, 21: 23, + 22: 25, 23: 24, 24: 26, 43: 44} + score: '0.550' + edge_lig_47_lig_30: + ligand_a: lig_47 + ligand_b: lig_30 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 23, 23: 22, 24: 24, 41: 39, 42: 40} score: '0.583' - edge_lig_50_lig_43: - ligand_a: lig_50 - ligand_b: lig_43 - atom mapping: {0: 34, 1: 31, 2: 32, 3: 27, 4: 28, 5: 29, 6: 30, 7: 35, 9: 24, - 10: 25, 11: 26, 12: 37, 13: 38, 14: 39, 15: 40, 16: 21, 17: 23, 18: 22, 19: 18, - 20: 19, 21: 20, 22: 15, 23: 17, 24: 16, 25: 14, 43: 33} + edge_lig_43_lig_37: + ligand_a: lig_43 + ligand_b: lig_37 + atom mapping: {14: 24, 15: 21, 16: 22, 17: 23, 18: 18, 19: 20, 20: 19, 21: 15, + 22: 17, 23: 16, 24: 8, 25: 9, 26: 10, 27: 4, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, + 33: 42, 34: 43, 35: 0, 36: 7, 37: 11, 38: 12, 39: 13, 40: 14} + score: '0.561' + edge_lig_43_lig_50: + ligand_a: lig_43 + ligand_b: lig_50 + atom mapping: {14: 25, 15: 22, 16: 23, 17: 24, 18: 19, 19: 21, 20: 20, 21: 16, + 22: 18, 23: 17, 24: 9, 25: 10, 26: 11, 27: 3, 28: 4, 29: 5, 30: 6, 31: 1, 32: 2, + 33: 43, 34: 0, 35: 7, 37: 12, 38: 13, 39: 14, 40: 15} score: '0.548' - edge_lig_56_lig_43: - ligand_a: lig_56 - ligand_b: lig_43 - atom mapping: {0: 35, 1: 30, 2: 31, 3: 32, 4: 27, 5: 28, 6: 29, 7: 36, 8: 24, - 9: 25, 10: 26, 15: 38, 16: 39, 17: 40, 18: 21, 19: 23, 20: 22, 21: 18, 22: 19, - 23: 20, 24: 15, 25: 16, 26: 17, 27: 14, 45: 33, 46: 34} + edge_lig_47_lig_31: + ligand_a: lig_47 + ligand_b: lig_31 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 23, 23: 22, 24: 24, 41: 39, 42: 40} + score: '0.583' + edge_lig_43_lig_53: + ligand_a: lig_43 + ligand_b: lig_53 + atom mapping: {14: 23, 15: 20, 16: 21, 17: 22, 18: 17, 19: 19, 20: 18, 21: 14, + 22: 16, 23: 15, 24: 7, 25: 8, 26: 9, 27: 5, 28: 6, 29: 1, 30: 2, 31: 3, 32: 4, + 33: 41, 35: 43, 36: 0, 37: 10, 38: 11, 39: 12, 40: 13} score: '0.548' + edge_lig_47_lig_67: + ligand_a: lig_47 + ligand_b: lig_67 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 12: 11, 13: 12, 14: 13, 15: 14, 16: 16, 17: 15, 18: 17, 19: 18, 20: 19, 21: 20, + 22: 22, 23: 21, 24: 23, 41: 41, 42: 42} + score: '0.555' + edge_lig_47_lig_33: + ligand_a: lig_47 + ligand_b: lig_33 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 23, 23: 22, 24: 24, 41: 36, 42: 37} + score: '0.608' + edge_lig_43_lig_58: + ligand_a: lig_43 + ligand_b: lig_58 + atom mapping: {14: 26, 15: 23, 16: 24, 17: 25, 18: 20, 19: 22, 20: 21, 21: 17, + 22: 19, 23: 18, 24: 7, 25: 8, 26: 9, 27: 5, 28: 6, 29: 1, 30: 2, 31: 3, 32: 4, + 33: 44, 35: 46, 36: 0, 38: 14, 39: 15, 40: 16} + score: '0.531' edge_lig_58_lig_48: ligand_a: lig_58 ligand_b: lig_48 @@ -79,94 +121,52 @@ edges: 15: 13, 16: 14, 17: 15, 18: 17, 19: 16, 20: 18, 21: 20, 22: 19, 23: 21, 24: 23, 25: 22, 26: 24, 44: 40, 46: 0} score: '0.573' - edge_lig_28_lig_43: - ligand_a: lig_28 - ligand_b: lig_43 - atom mapping: {0: 35, 1: 30, 2: 31, 3: 32, 4: 27, 5: 28, 6: 29, 7: 36, 8: 24, - 9: 25, 10: 26, 11: 37, 12: 38, 13: 39, 14: 40, 15: 21, 16: 23, 17: 22, 18: 18, - 19: 19, 20: 20, 21: 15, 22: 17, 23: 16, 24: 14, 39: 33, 40: 34} + edge_lig_47_lig_35: + ligand_a: lig_47 + ligand_b: lig_35 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 23, 23: 22, 24: 24, 41: 39, 42: 40} score: '0.583' - edge_lig_37_lig_43: - ligand_a: lig_37 - ligand_b: lig_43 - atom mapping: {0: 35, 1: 30, 2: 31, 3: 32, 4: 27, 5: 28, 6: 29, 7: 36, 8: 24, - 9: 25, 10: 26, 11: 37, 12: 38, 13: 39, 14: 40, 15: 21, 16: 23, 17: 22, 18: 18, - 19: 19, 20: 20, 21: 15, 22: 17, 23: 16, 24: 14, 42: 33, 43: 34} - score: '0.561' - edge_lig_58_lig_47: - ligand_a: lig_58 - ligand_b: lig_47 - atom mapping: {0: 7, 1: 6, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 7: 8, 8: 9, 9: 10, 14: 12, - 15: 13, 16: 14, 17: 15, 18: 17, 19: 16, 20: 18, 21: 20, 22: 19, 23: 21, 24: 23, - 25: 22, 26: 24, 44: 41, 46: 0} + edge_lig_47_lig_58: + ligand_a: lig_47 + ligand_b: lig_58 + atom mapping: {0: 46, 1: 2, 2: 3, 3: 4, 4: 5, 5: 6, 6: 1, 7: 0, 8: 7, 9: 8, 10: 9, + 12: 14, 13: 15, 14: 16, 15: 17, 16: 19, 17: 18, 18: 20, 19: 21, 20: 22, 21: 23, + 22: 25, 23: 24, 24: 26, 41: 44} score: '0.538' - edge_lig_52_lig_47: - ligand_a: lig_52 - ligand_b: lig_47 - atom mapping: {0: 7, 1: 6, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 7: 8, 8: 9, 9: 10, 10: 11, - 11: 12, 12: 13, 13: 14, 14: 15, 15: 17, 16: 16, 17: 18, 18: 20, 19: 19, 20: 21, - 21: 23, 22: 22, 23: 24, 38: 41, 40: 0} + edge_lig_47_lig_49: + ligand_a: lig_47 + ligand_b: lig_49 + atom mapping: {0: 7, 1: 6, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 8: 9, 9: 10, 10: 11, + 11: 12, 12: 13, 13: 14, 14: 15, 15: 16, 16: 18, 17: 17, 18: 19, 19: 20, 20: 21, + 21: 22, 22: 24, 23: 23, 24: 25, 41: 40, 42: 0} score: '0.570' - edge_lig_33_lig_43: - ligand_a: lig_33 - ligand_b: lig_43 - atom mapping: {0: 35, 1: 30, 2: 31, 3: 32, 4: 27, 5: 28, 6: 29, 7: 36, 8: 24, - 9: 25, 10: 26, 11: 37, 12: 38, 13: 39, 14: 40, 15: 21, 16: 23, 17: 22, 18: 18, - 19: 19, 20: 20, 21: 15, 22: 17, 23: 16, 24: 14, 36: 33, 37: 34} - score: '0.608' - edge_lig_53_lig_43: - ligand_a: lig_53 - ligand_b: lig_43 - atom mapping: {0: 36, 1: 29, 2: 30, 3: 31, 4: 32, 5: 27, 6: 28, 7: 24, 8: 25, - 9: 26, 10: 37, 11: 38, 12: 39, 13: 40, 14: 21, 15: 23, 16: 22, 17: 18, 18: 20, - 19: 19, 20: 15, 21: 17, 22: 16, 23: 14, 41: 33, 43: 35} - score: '0.548' - edge_lig_34_lig_43: - ligand_a: lig_34 - ligand_b: lig_43 - atom mapping: {0: 35, 1: 30, 2: 31, 3: 32, 4: 27, 5: 28, 6: 29, 7: 36, 8: 24, - 9: 25, 10: 26, 11: 37, 12: 38, 13: 39, 14: 40, 15: 21, 16: 23, 17: 22, 18: 18, - 19: 19, 20: 20, 21: 15, 22: 17, 23: 16, 24: 14, 39: 33, 40: 34} + edge_lig_47_lig_28: + ligand_a: lig_47 + ligand_b: lig_28 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 23, 23: 22, 24: 24, 41: 39, 42: 40} score: '0.583' - edge_lig_65_lig_43: - ligand_a: lig_65 - ligand_b: lig_43 - atom mapping: {0: 35, 1: 30, 2: 29, 3: 28, 4: 27, 5: 32, 6: 31, 7: 34, 9: 26, - 10: 25, 11: 24, 12: 21, 13: 22, 14: 23, 15: 18, 16: 20, 17: 19, 18: 15, 19: 16, - 20: 17, 21: 14, 39: 38, 40: 39, 41: 40, 42: 36} - score: '0.542' - edge_lig_49_lig_43: - ligand_a: lig_49 - ligand_b: lig_43 - atom mapping: {0: 34, 1: 31, 2: 32, 3: 27, 4: 28, 5: 29, 6: 30, 7: 35, 9: 24, - 10: 25, 11: 26, 12: 37, 13: 38, 14: 39, 15: 40, 16: 21, 17: 23, 18: 22, 19: 18, - 20: 19, 21: 20, 22: 15, 23: 17, 24: 16, 25: 14, 40: 33} - score: '0.570' - edge_lig_58_lig_46: - ligand_a: lig_58 - ligand_b: lig_46 - atom mapping: {0: 7, 1: 6, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 7: 8, 8: 9, 9: 10, 14: 12, - 15: 13, 16: 14, 17: 15, 18: 17, 19: 16, 20: 18, 21: 20, 22: 19, 23: 21, 24: 23, - 25: 22, 26: 24, 44: 43, 46: 0} - score: '0.550' - edge_lig_60_lig_43: - ligand_a: lig_60 - ligand_b: lig_43 - atom mapping: {0: 35, 1: 30, 2: 31, 3: 32, 4: 27, 5: 28, 6: 29, 7: 36, 8: 24, - 9: 25, 10: 26, 11: 38, 12: 39, 13: 40, 14: 21, 15: 23, 16: 22, 17: 18, 18: 20, - 19: 19, 20: 15, 21: 16, 22: 17, 23: 14, 41: 33, 42: 34} - score: '0.555' - edge_lig_61_lig_43: - ligand_a: lig_61 - ligand_b: lig_43 - atom mapping: {0: 34, 1: 31, 2: 32, 3: 27, 4: 28, 5: 29, 6: 30, 7: 35, 9: 24, - 10: 25, 11: 26, 12: 38, 13: 39, 14: 40, 15: 21, 16: 22, 17: 23, 18: 18, 19: 20, - 20: 19, 21: 15, 22: 16, 23: 17, 24: 14, 42: 33} + edge_lig_47_lig_65: + ligand_a: lig_47 + ligand_b: lig_65 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 42, 8: 11, 9: 10, + 10: 9, 12: 39, 13: 40, 14: 41, 15: 12, 16: 14, 17: 13, 18: 15, 19: 16, 20: 17, + 21: 18, 22: 20, 23: 19, 24: 21, 42: 7} score: '0.542' - edge_lig_43_lig_30: - ligand_a: lig_43 - ligand_b: lig_30 - atom mapping: {14: 24, 15: 21, 16: 22, 17: 23, 18: 18, 19: 20, 20: 19, 21: 15, - 22: 17, 23: 16, 24: 8, 25: 9, 26: 10, 27: 4, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, - 33: 39, 34: 40, 35: 0, 36: 7, 37: 11, 38: 12, 39: 13, 40: 14} + edge_lig_47_lig_32: + ligand_a: lig_47 + ligand_b: lig_32 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 23, 23: 22, 24: 24, 41: 39, 42: 40} score: '0.583' + edge_lig_47_lig_60: + ligand_a: lig_47 + ligand_b: lig_60 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 12: 11, 13: 12, 14: 13, 15: 14, 16: 16, 17: 15, 18: 17, 19: 18, 20: 19, 21: 20, + 22: 22, 23: 21, 24: 23, 41: 41, 42: 42} + score: '0.555' diff --git a/data/p38/03_edges/01_perses_openfe.yml b/data/p38/03_edges/01_perses_openfe.yml index 5202799ef..5698988bd 100644 --- a/data/p38/03_edges/01_perses_openfe.yml +++ b/data/p38/03_edges/01_perses_openfe.yml @@ -1,14 +1,35 @@ mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph +planner: openfe v0.5 minimal_spanning_graph edges: - edge_lig_p38a_3flw_lig_p38a_2t: + edge_lig_p38a_3flw_lig_p38a_2m: ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2t + ligand_b: lig_p38a_2m + atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, 19: 41, + 24: 39, 25: 40, 26: 26, 27: 27, 28: 28, 29: 37, 31: 35, 32: 36, 33: 33, 34: 34, + 35: 31, 36: 32, 37: 29, 39: 24, 40: 25} + score: '0.598' + edge_lig_p38a_2y_lig_p38a_2m: + ligand_a: lig_p38a_2y + ligand_b: lig_p38a_2m + atom mapping: {14: 4, 15: 5, 16: 3, 17: 21, 18: 22, 19: 23, 20: 1, 21: 0, 22: 2, + 23: 24, 24: 25, 25: 26, 26: 27, 27: 28, 28: 37, 30: 35, 31: 36, 32: 33, 33: 34, + 34: 31, 35: 32, 36: 29, 38: 39, 39: 40, 40: 41} + score: '0.641' + edge_lig_p38a_2s_lig_p38a_3flw: + ligand_a: lig_p38a_2s + ligand_b: lig_p38a_3flw + atom mapping: {9: 20, 10: 23, 11: 22, 12: 19, 13: 24, 14: 25, 15: 26, 16: 27, + 17: 28, 18: 29, 20: 31, 21: 32, 22: 33, 23: 34, 24: 35, 25: 36, 26: 37, 28: 39, + 29: 40, 30: 16, 31: 17, 32: 18, 33: 12, 34: 10, 51: 13, 52: 14, 53: 15} + score: '0.641' + edge_lig_p38a_3flw_lig_p38a_2o: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2o atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, 19: 41, 20: 42, 22: 44, 23: 43, 24: 39, 25: 40, 26: 26, 27: 27, 28: 28, 29: 37, 31: 35, 32: 36, 33: 33, 34: 34, 35: 31, 36: 32, 37: 29, 39: 24, 40: 25} - score: '0.665' + score: '0.638' edge_lig_p38a_3fmh_lig_p38a_2f: ligand_a: lig_p38a_3fmh ligand_b: lig_p38a_2f @@ -16,13 +37,27 @@ edges: 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, 30: 35, 32: 33, 34: 31, 35: 32, 36: 29, 37: 30, 38: 24, 39: 25} score: '0.668' - edge_lig_p38a_3fmh_lig_p38a_2k: + edge_lig_p38a_3flw_lig_p38a_2i: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2i + atom mapping: {10: 4, 11: 5, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, + 19: 43, 20: 44, 21: 45, 22: 46, 23: 47, 24: 41, 25: 42, 26: 26, 27: 27, 28: 30, + 29: 31, 31: 33, 32: 34, 33: 35, 35: 37, 36: 38, 37: 39, 39: 24, 40: 25} + score: '0.667' + edge_lig_p38a_3fly_lig_p38a_2m: + ligand_a: lig_p38a_3fly + ligand_b: lig_p38a_2m + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 16: 21, 17: 22, 18: 23, 19: 24, 20: 25, + 21: 26, 22: 27, 23: 28, 24: 37, 26: 35, 27: 36, 28: 33, 29: 34, 30: 31, 31: 32, + 32: 29, 34: 39, 35: 40, 36: 41} + score: '0.661' + edge_lig_p38a_3fmh_lig_p38a_2m: ligand_a: lig_p38a_3fmh - ligand_b: lig_p38a_2k + ligand_b: lig_p38a_2m atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, 30: 35, 31: 36, 32: 33, 33: 34, 34: 31, 35: 32, 36: 29, 38: 24, 39: 25} - score: '0.654' + score: '0.620' edge_lig_p38a_3fmh_lig_p38a_2e: ligand_a: lig_p38a_3fmh ligand_b: lig_p38a_2e @@ -30,20 +65,6 @@ edges: 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, 30: 35, 31: 36, 32: 33, 33: 34, 34: 31, 35: 32, 36: 29, 37: 30, 38: 24, 39: 25} score: '0.699' - edge_lig_p38a_3flw_lig_p38a_2ff: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2ff - atom mapping: {10: 12, 12: 14, 13: 20, 14: 18, 15: 19, 16: 17, 17: 16, 18: 15, - 19: 38, 20: 39, 21: 42, 22: 41, 23: 40, 24: 36, 25: 37, 26: 23, 27: 24, 28: 25, - 29: 34, 31: 32, 32: 33, 33: 30, 34: 31, 35: 28, 36: 29, 37: 26, 39: 21, 40: 22} - score: '0.665' - edge_lig_p38a_3flw_lig_p38a_2j: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2j - atom mapping: {10: 4, 11: 5, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, - 19: 43, 20: 44, 21: 45, 22: 46, 23: 47, 24: 41, 25: 42, 26: 26, 27: 27, 28: 30, - 29: 31, 31: 33, 32: 34, 33: 35, 34: 36, 35: 37, 36: 38, 37: 39, 39: 24, 40: 25} - score: '0.686' edge_lig_p38a_3fmh_lig_p38a_2h: ligand_a: lig_p38a_3fmh ligand_b: lig_p38a_2h @@ -51,27 +72,20 @@ edges: 18: 41, 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 29, 30: 31, 31: 32, 32: 33, 34: 35, 35: 36, 36: 37, 38: 24, 39: 25} score: '0.680' - edge_lig_p38a_2aa_lig_p38a_2m: - ligand_a: lig_p38a_2aa + edge_lig_p38a_2x_lig_p38a_2m: + ligand_a: lig_p38a_2x ligand_b: lig_p38a_2m - atom mapping: {7: 4, 9: 3, 10: 21, 11: 22, 12: 23, 13: 1, 14: 0, 15: 2, 16: 24, - 17: 25, 18: 26, 19: 27, 20: 28, 21: 37, 23: 35, 24: 36, 25: 33, 26: 34, 27: 31, - 28: 32, 29: 29, 31: 39, 32: 40, 33: 41} - score: '0.644' - edge_lig_p38a_3flw_lig_p38a_2o: + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 18: 21, 19: 22, 20: 23, 21: 24, + 22: 25, 23: 26, 24: 27, 25: 28, 26: 37, 28: 35, 29: 36, 30: 33, 31: 34, 32: 31, + 33: 32, 34: 29, 36: 39, 37: 40, 38: 41} + score: '0.657' + edge_lig_p38a_3flw_lig_p38a_2ee: ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2o - atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, 19: 41, - 20: 42, 22: 44, 23: 43, 24: 39, 25: 40, 26: 26, 27: 27, 28: 28, 29: 37, 31: 35, - 32: 36, 33: 33, 34: 34, 35: 31, 36: 32, 37: 29, 39: 24, 40: 25} - score: '0.638' - edge_lig_p38a_3fmh_lig_p38a_2m: - ligand_a: lig_p38a_3fmh - ligand_b: lig_p38a_2m - atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, - 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, 30: 35, 31: 36, 32: 33, 33: 34, - 34: 31, 35: 32, 36: 29, 38: 24, 39: 25} - score: '0.620' + ligand_b: lig_p38a_2ee + atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 29, 17: 28, 18: 27, 19: 47, + 20: 48, 21: 51, 22: 50, 23: 49, 24: 45, 25: 46, 26: 32, 27: 33, 28: 34, 29: 43, + 31: 41, 32: 42, 33: 39, 34: 40, 35: 37, 36: 38, 37: 35, 39: 30, 40: 31} + score: '0.657' edge_lig_p38a_2bb_lig_p38a_2m: ligand_a: lig_p38a_2bb ligand_b: lig_p38a_2m @@ -79,27 +93,13 @@ edges: 24: 26, 25: 27, 26: 28, 27: 37, 29: 35, 30: 36, 31: 33, 32: 34, 33: 31, 34: 32, 35: 29, 37: 39, 38: 40, 39: 41} score: '0.636' - edge_lig_p38a_3flw_lig_p38a_2ee: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2ee - atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 29, 17: 28, 18: 27, 19: 47, - 20: 48, 21: 51, 22: 50, 23: 49, 24: 45, 25: 46, 26: 32, 27: 33, 28: 34, 29: 43, - 31: 41, 32: 42, 33: 39, 34: 40, 35: 37, 36: 38, 37: 35, 39: 30, 40: 31} - score: '0.657' - edge_lig_p38a_3flw_lig_p38a_2r: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2r - atom mapping: {10: 36, 12: 35, 13: 53, 14: 54, 15: 55, 16: 32, 17: 33, 18: 34, - 19: 14, 20: 11, 21: 13, 22: 12, 24: 15, 25: 16, 26: 17, 27: 18, 28: 19, 29: 28, - 31: 26, 32: 27, 33: 24, 34: 25, 35: 22, 36: 23, 37: 20, 39: 30, 40: 31} - score: '0.641' - edge_lig_p38a_3flw_lig_p38a_2p: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2p - atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, 19: 41, - 20: 42, 22: 44, 23: 43, 24: 39, 25: 40, 26: 26, 27: 27, 28: 28, 29: 37, 31: 35, - 32: 36, 33: 33, 34: 34, 35: 31, 36: 32, 37: 29, 39: 24, 40: 25} - score: '0.634' + edge_lig_p38a_3fmh_lig_p38a_3fln: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_3fln + atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, + 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, + 30: 35, 31: 36, 32: 33, 33: 34, 34: 31, 35: 32, 36: 29, 38: 24, 39: 25} + score: '0.686' edge_lig_p38a_3flw_lig_p38a_2l: ligand_a: lig_p38a_3flw ligand_b: lig_p38a_2l @@ -121,20 +121,34 @@ edges: 16: 25, 17: 26, 18: 27, 19: 28, 20: 37, 22: 35, 23: 36, 24: 33, 25: 34, 26: 31, 27: 32, 28: 29, 30: 39, 31: 40, 32: 41} score: '0.641' - edge_lig_p38a_2v_lig_p38a_2m: - ligand_a: lig_p38a_2v - ligand_b: lig_p38a_2m - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 10: 21, 11: 22, 12: 23, 13: 24, 14: 25, - 15: 26, 16: 27, 17: 28, 18: 37, 20: 35, 21: 36, 22: 33, 23: 34, 24: 31, 25: 32, - 26: 29, 28: 39, 29: 40, 30: 41} - score: '0.718' - edge_lig_p38a_2y_lig_p38a_2m: - ligand_a: lig_p38a_2y - ligand_b: lig_p38a_2m - atom mapping: {14: 4, 15: 5, 16: 3, 17: 21, 18: 22, 19: 23, 20: 1, 21: 0, 22: 2, - 23: 24, 24: 25, 25: 26, 26: 27, 27: 28, 28: 37, 30: 35, 31: 36, 32: 33, 33: 34, - 34: 31, 35: 32, 36: 29, 38: 39, 39: 40, 40: 41} - score: '0.641' + edge_lig_p38a_3flw_lig_p38a_2gg: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2gg + atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 25, 17: 24, 18: 23, 19: 43, + 20: 44, 21: 47, 22: 46, 23: 45, 24: 41, 25: 42, 26: 28, 27: 29, 28: 30, 29: 39, + 31: 37, 32: 38, 33: 35, 34: 36, 35: 33, 36: 34, 37: 31, 39: 26, 40: 27} + score: '0.670' + edge_lig_p38a_3flw_lig_p38a_2j: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2j + atom mapping: {10: 4, 11: 5, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, + 19: 43, 20: 44, 21: 45, 22: 46, 23: 47, 24: 41, 25: 42, 26: 26, 27: 27, 28: 30, + 29: 31, 31: 33, 32: 34, 33: 35, 34: 36, 35: 37, 36: 38, 37: 39, 39: 24, 40: 25} + score: '0.686' + edge_lig_p38a_3fmh_lig_p38a_2k: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_2k + atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, + 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, 30: 35, 31: 36, 32: 33, 33: 34, + 34: 31, 35: 32, 36: 29, 38: 24, 39: 25} + score: '0.654' + edge_lig_p38a_3flw_lig_p38a_2ff: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2ff + atom mapping: {10: 12, 12: 14, 13: 20, 14: 18, 15: 19, 16: 17, 17: 16, 18: 15, + 19: 38, 20: 39, 21: 42, 22: 41, 23: 40, 24: 36, 25: 37, 26: 23, 27: 24, 28: 25, + 29: 34, 31: 32, 32: 33, 33: 30, 34: 31, 35: 28, 36: 29, 37: 26, 39: 21, 40: 22} + score: '0.665' edge_lig_p38a_3fmh_lig_p38a_3flz: ligand_a: lig_p38a_3fmh ligand_b: lig_p38a_3flz @@ -142,27 +156,6 @@ edges: 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, 30: 35, 31: 36, 32: 33, 34: 31, 35: 32, 36: 29, 37: 30, 38: 24, 39: 25} score: '0.680' - edge_lig_p38a_3fly_lig_p38a_2m: - ligand_a: lig_p38a_3fly - ligand_b: lig_p38a_2m - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 16: 21, 17: 22, 18: 23, 19: 24, 20: 25, - 21: 26, 22: 27, 23: 28, 24: 37, 26: 35, 27: 36, 28: 33, 29: 34, 30: 31, 31: 32, - 32: 29, 34: 39, 35: 40, 36: 41} - score: '0.661' - edge_lig_p38a_3flw_lig_p38a_2i: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2i - atom mapping: {10: 4, 11: 5, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, - 19: 43, 20: 44, 21: 45, 22: 46, 23: 47, 24: 41, 25: 42, 26: 26, 27: 27, 28: 30, - 29: 31, 31: 33, 32: 34, 33: 35, 35: 37, 36: 38, 37: 39, 39: 24, 40: 25} - score: '0.667' - edge_lig_p38a_3flw_lig_p38a_2m: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2m - atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, 19: 41, - 24: 39, 25: 40, 26: 26, 27: 27, 28: 28, 29: 37, 31: 35, 32: 36, 33: 33, 34: 34, - 35: 31, 36: 32, 37: 29, 39: 24, 40: 25} - score: '0.598' edge_lig_p38a_3flw_lig_p38a_2n: ligand_a: lig_p38a_3flw ligand_b: lig_p38a_2n @@ -170,38 +163,39 @@ edges: 18: 31, 19: 11, 20: 8, 22: 9, 23: 10, 24: 12, 25: 13, 26: 14, 27: 15, 28: 16, 29: 17, 31: 19, 32: 20, 33: 21, 34: 22, 35: 23, 36: 24, 37: 25, 39: 27, 40: 28} score: '0.657' - edge_lig_p38a_3flw_lig_p38a_2gg: + edge_lig_p38a_3flw_lig_p38a_2p: ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2gg - atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 25, 17: 24, 18: 23, 19: 43, - 20: 44, 21: 47, 22: 46, 23: 45, 24: 41, 25: 42, 26: 28, 27: 29, 28: 30, 29: 39, - 31: 37, 32: 38, 33: 35, 34: 36, 35: 33, 36: 34, 37: 31, 39: 26, 40: 27} - score: '0.670' - edge_lig_p38a_2x_lig_p38a_2m: - ligand_a: lig_p38a_2x + ligand_b: lig_p38a_2p + atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, 19: 41, + 20: 42, 22: 44, 23: 43, 24: 39, 25: 40, 26: 26, 27: 27, 28: 28, 29: 37, 31: 35, + 32: 36, 33: 33, 34: 34, 35: 31, 36: 32, 37: 29, 39: 24, 40: 25} + score: '0.634' + edge_lig_p38a_3flw_lig_p38a_2t: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2t + atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, 19: 41, + 20: 42, 22: 44, 23: 43, 24: 39, 25: 40, 26: 26, 27: 27, 28: 28, 29: 37, 31: 35, + 32: 36, 33: 33, 34: 34, 35: 31, 36: 32, 37: 29, 39: 24, 40: 25} + score: '0.665' + edge_lig_p38a_2aa_lig_p38a_2m: + ligand_a: lig_p38a_2aa ligand_b: lig_p38a_2m - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 18: 21, 19: 22, 20: 23, 21: 24, - 22: 25, 23: 26, 24: 27, 25: 28, 26: 37, 28: 35, 29: 36, 30: 33, 31: 34, 32: 31, - 33: 32, 34: 29, 36: 39, 37: 40, 38: 41} - score: '0.657' - edge_lig_p38a_2s_lig_p38a_3flw: - ligand_a: lig_p38a_2s + atom mapping: {7: 4, 9: 3, 10: 21, 11: 22, 12: 23, 13: 1, 14: 0, 15: 2, 16: 24, + 17: 25, 18: 26, 19: 27, 20: 28, 21: 37, 23: 35, 24: 36, 25: 33, 26: 34, 27: 31, + 28: 32, 29: 29, 31: 39, 32: 40, 33: 41} + score: '0.644' + edge_lig_p38a_2m_lig_p38a_2v: + ligand_a: lig_p38a_2m + ligand_b: lig_p38a_2v + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 21: 10, 22: 11, 23: 12, 24: 13, 25: 14, + 26: 15, 27: 16, 28: 17, 29: 26, 31: 24, 32: 25, 33: 22, 34: 23, 35: 20, 36: 21, + 37: 18, 39: 28, 40: 29, 41: 30} + score: '0.718' + edge_lig_p38a_2r_lig_p38a_3flw: + ligand_a: lig_p38a_2r ligand_b: lig_p38a_3flw - atom mapping: {9: 20, 10: 23, 11: 22, 12: 19, 13: 24, 14: 25, 15: 26, 16: 27, - 17: 28, 18: 29, 20: 31, 21: 32, 22: 33, 23: 34, 24: 35, 25: 36, 26: 37, 28: 39, - 29: 40, 30: 16, 31: 17, 32: 18, 33: 12, 34: 10, 51: 13, 52: 14, 53: 15} - score: '0.641' - edge_lig_p38a_3fmk_lig_p38a_2m: - ligand_a: lig_p38a_3fmk - ligand_b: lig_p38a_2m - atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, - 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, 30: 35, 31: 36, 32: 33, 33: 34, - 34: 31, 35: 32, 36: 29, 38: 24, 39: 25} - score: '0.620' - edge_lig_p38a_3fmh_lig_p38a_3fln: - ligand_a: lig_p38a_3fmh - ligand_b: lig_p38a_3fln - atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, - 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, - 30: 35, 31: 36, 32: 33, 33: 34, 34: 31, 35: 32, 36: 29, 38: 24, 39: 25} - score: '0.686' + atom mapping: {11: 20, 12: 23, 13: 22, 14: 19, 15: 24, 16: 25, 17: 26, 18: 27, + 19: 28, 20: 29, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, 26: 35, 27: 36, 28: 37, + 29: 38, 30: 39, 31: 40, 32: 16, 33: 17, 34: 18, 35: 12, 36: 10, 53: 13, 54: 14, + 55: 15} + score: '0.671' diff --git a/data/pde2/03_edges/01_perses_openfe.yml b/data/pde2/03_edges/01_perses_openfe.yml index db2317202..2a87e6097 100644 --- a/data/pde2/03_edges/01_perses_openfe.yml +++ b/data/pde2/03_edges/01_perses_openfe.yml @@ -1,133 +1,79 @@ mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph +planner: openfe v0.5 minimal_spanning_graph edges: - edge_lig_49137374_lig_48168913: - ligand_a: lig_49137374 - ligand_b: lig_48168913 - atom mapping: {0: 20, 1: 19, 2: 10, 3: 9, 4: 8, 5: 7, 6: 11, 7: 12, 8: 13, 9: 14, - 10: 15, 11: 16, 12: 17, 13: 18, 14: 21, 15: 22, 16: 27, 17: 26, 18: 25, 19: 24, - 20: 23, 21: 2, 22: 1, 23: 6, 24: 5, 25: 4, 26: 3, 30: 37, 31: 38, 32: 39, 33: 34, - 34: 35, 35: 36, 36: 41, 37: 40, 38: 48, 39: 49, 40: 47, 41: 46, 42: 44, 43: 45, - 44: 43, 45: 42, 47: 33, 48: 32} - score: '0.923' - edge_lig_48271249_lig_48168913: - ligand_a: lig_48271249 - ligand_b: lig_48168913 - atom mapping: {0: 20, 1: 19, 2: 10, 3: 9, 4: 8, 5: 7, 6: 11, 7: 12, 8: 13, 9: 14, - 10: 15, 11: 16, 12: 17, 13: 18, 14: 21, 15: 22, 16: 23, 17: 24, 18: 25, 19: 26, - 20: 27, 21: 2, 22: 3, 23: 4, 24: 5, 25: 6, 26: 1, 29: 37, 30: 38, 31: 39, 32: 34, - 33: 35, 34: 36, 35: 41, 36: 40, 37: 42, 38: 43, 39: 45, 40: 44, 41: 46, 42: 47, - 43: 49, 44: 48, 45: 31, 46: 33} - score: '0.929' - edge_lig_49582390_lig_50107616: + edge_lig_49582390_lig_49585367: ligand_a: lig_49582390 - ligand_b: lig_50107616 + ligand_b: lig_49585367 atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 32, 33: 33, 34: 34, 35: 35, 36: 36, 37: 37, 38: 39, 39: 38, 40: 40, 41: 41, 42: 43, 43: 42, - 44: 44, 45: 45, 46: 47, 47: 46, 48: 48, 49: 49, 50: 50, 52: 53} + 44: 44, 45: 45, 46: 47, 47: 46, 48: 48, 49: 49, 50: 50, 52: 52} score: '0.877' - edge_lig_49582390_lig_50181001: - ligand_a: lig_49582390 - ligand_b: lig_50181001 - atom mapping: {0: 25, 1: 24, 2: 15, 3: 14, 4: 13, 5: 12, 6: 16, 7: 17, 8: 18, - 9: 19, 10: 20, 11: 21, 12: 22, 13: 23, 14: 26, 15: 27, 16: 28, 17: 29, 18: 30, - 19: 31, 20: 32, 21: 7, 22: 6, 23: 5, 24: 10, 25: 9, 26: 8, 27: 4, 28: 3, 32: 47, - 33: 48, 34: 49, 35: 44, 36: 45, 37: 46, 38: 51, 39: 50, 40: 52, 41: 53, 42: 55, - 43: 54, 44: 56, 45: 57, 46: 59, 47: 58, 48: 42, 50: 43, 52: 40} + edge_lig_49175789_lig_49582390: + ligand_a: lig_49175789 + ligand_b: lig_49582390 + atom mapping: {3: 28, 4: 27, 5: 23, 6: 24, 7: 25, 8: 26, 9: 21, 10: 22, 11: 5, + 12: 4, 13: 3, 14: 2, 15: 6, 16: 7, 17: 8, 18: 9, 19: 10, 20: 11, 21: 12, 22: 13, + 23: 1, 24: 0, 25: 14, 26: 15, 27: 20, 28: 19, 29: 18, 30: 17, 31: 16, 40: 52, + 42: 49, 44: 48, 45: 35, 46: 36, 47: 37, 48: 32, 49: 33, 50: 34, 51: 39, 52: 38, + 53: 46, 54: 47, 55: 44, 56: 45, 57: 42, 58: 43, 59: 40, 60: 41} score: '0.861' - edge_lig_49582390_lig_49396360: + edge_lig_49582390_lig_49582468: ligand_a: lig_49582390 - ligand_b: lig_49396360 + ligand_b: lig_49582468 atom mapping: {0: 23, 1: 22, 2: 13, 3: 12, 4: 11, 5: 10, 6: 14, 7: 15, 8: 16, 9: 17, 10: 18, 11: 19, 12: 20, 13: 21, 14: 24, 15: 25, 16: 26, 17: 27, 18: 28, - 19: 29, 20: 30, 21: 6, 22: 5, 23: 4, 24: 9, 25: 8, 26: 7, 27: 3, 28: 2, 32: 44, - 33: 45, 34: 46, 35: 41, 36: 42, 37: 43, 38: 48, 39: 47, 40: 49, 41: 50, 42: 52, - 43: 51, 44: 53, 45: 54, 46: 56, 47: 55, 48: 38, 49: 40, 50: 39, 52: 37} - score: '0.886' - edge_lig_49582390_lig_48009208: + 19: 29, 20: 30, 21: 6, 22: 5, 23: 4, 24: 9, 25: 8, 26: 7, 27: 3, 28: 2, 32: 46, + 33: 45, 34: 44, 35: 41, 36: 42, 37: 43, 38: 47, 39: 48, 40: 49, 41: 50, 42: 52, + 43: 51, 44: 53, 45: 54, 46: 56, 47: 55, 48: 38, 49: 40, 50: 39} + score: '0.875' + edge_lig_49582390_lig_49072088: ligand_a: lig_49582390 - ligand_b: lig_48009208 + ligand_b: lig_49072088 atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 26, 23: 25, 24: 24, 25: 23, 26: 22, 32: 29, 33: 30, 34: 31, 35: 32, - 36: 33, 37: 34, 38: 36, 39: 35, 40: 37, 41: 38, 42: 40, 43: 39, 44: 41, 45: 42, - 46: 44, 47: 43, 50: 45} - score: '0.909' + 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 31, 33: 32, + 34: 33, 35: 34, 36: 35, 37: 36, 38: 38, 39: 37, 40: 39, 41: 40, 42: 42, 43: 41, + 44: 43, 45: 44, 46: 46, 47: 45, 48: 47, 49: 48, 50: 49} + score: '0.875' edge_lig_50181001_lig_43249674: ligand_a: lig_50181001 ligand_b: lig_43249674 - atom mapping: {5: 23, 6: 22, 7: 21, 8: 26, 9: 25, 10: 24, 12: 5, 13: 4, 14: 3, + atom mapping: {5: 25, 6: 26, 7: 21, 8: 22, 9: 23, 10: 24, 12: 5, 13: 4, 14: 3, 15: 2, 16: 6, 17: 7, 18: 8, 19: 9, 20: 10, 21: 11, 22: 12, 23: 13, 24: 1, 25: 0, - 26: 14, 27: 15, 28: 20, 29: 19, 30: 18, 31: 17, 32: 16, 42: 44, 44: 31, 45: 32, + 26: 14, 27: 15, 28: 20, 29: 19, 30: 18, 31: 17, 32: 16, 43: 44, 44: 31, 45: 32, 46: 33, 47: 28, 48: 29, 49: 30, 50: 34, 51: 35, 52: 43, 53: 42, 54: 41, 55: 40, 56: 38, 57: 39, 58: 36, 59: 37} score: '0.917' - edge_lig_50181001_lig_48022468: - ligand_a: lig_50181001 - ligand_b: lig_48022468 - atom mapping: {5: 23, 6: 22, 7: 21, 8: 26, 9: 25, 10: 24, 12: 5, 13: 4, 14: 3, - 15: 2, 16: 6, 17: 7, 18: 8, 19: 9, 20: 10, 21: 11, 22: 12, 23: 13, 24: 1, 25: 0, - 26: 14, 27: 15, 28: 20, 29: 19, 30: 18, 31: 17, 32: 16, 44: 32, 45: 33, 46: 34, - 47: 29, 48: 30, 49: 31, 50: 35, 51: 36, 52: 44, 53: 43, 54: 42, 55: 41, 56: 39, - 57: 40, 58: 37, 59: 38} - score: '0.905' - edge_lig_49582390_lig_49220392: - ligand_a: lig_49582390 - ligand_b: lig_49220392 - atom mapping: {0: 22, 1: 21, 2: 12, 3: 11, 4: 10, 5: 9, 6: 13, 7: 14, 8: 15, 9: 16, - 10: 17, 11: 18, 12: 19, 13: 20, 14: 23, 15: 24, 16: 25, 17: 26, 18: 27, 19: 28, - 20: 29, 21: 7, 22: 8, 23: 3, 24: 4, 25: 5, 26: 6, 27: 2, 28: 1, 32: 42, 33: 43, - 34: 44, 35: 39, 36: 40, 37: 41, 38: 46, 39: 45, 40: 47, 41: 48, 42: 50, 43: 49, - 44: 51, 45: 52, 46: 54, 47: 53, 48: 38, 49: 36, 52: 35} - score: '0.894' - edge_lig_49582390_lig_49137530: + edge_lig_49582390_lig_50107616: ligand_a: lig_49582390 - ligand_b: lig_49137530 - atom mapping: {0: 24, 1: 23, 2: 14, 3: 13, 4: 12, 5: 11, 6: 15, 7: 16, 8: 17, - 9: 18, 10: 19, 11: 20, 12: 21, 13: 22, 14: 25, 15: 26, 16: 27, 17: 28, 18: 29, - 19: 30, 20: 31, 21: 7, 22: 6, 23: 5, 24: 10, 25: 9, 26: 8, 27: 4, 28: 3, 32: 47, - 33: 48, 34: 49, 35: 44, 36: 45, 37: 46, 38: 51, 39: 50, 40: 52, 41: 53, 42: 55, - 43: 54, 44: 56, 45: 57, 46: 59, 47: 58, 48: 41, 49: 43, 50: 42, 52: 39} + ligand_b: lig_50107616 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 32, 33: 33, + 34: 34, 35: 35, 36: 36, 37: 37, 38: 39, 39: 38, 40: 40, 41: 41, 42: 43, 43: 42, + 44: 44, 45: 45, 46: 47, 47: 46, 48: 48, 49: 49, 50: 50, 52: 53} score: '0.877' - edge_lig_49582390_lig_49582468: - ligand_a: lig_49582390 - ligand_b: lig_49582468 - atom mapping: {0: 23, 1: 22, 2: 13, 3: 12, 4: 11, 5: 10, 6: 14, 7: 15, 8: 16, - 9: 17, 10: 18, 11: 19, 12: 20, 13: 21, 14: 24, 15: 25, 16: 26, 17: 27, 18: 28, - 19: 29, 20: 30, 21: 6, 22: 5, 23: 4, 24: 9, 25: 8, 26: 7, 27: 3, 28: 2, 32: 46, - 33: 45, 34: 44, 35: 41, 36: 42, 37: 43, 38: 47, 39: 48, 40: 49, 41: 50, 42: 52, - 43: 51, 44: 53, 45: 54, 46: 56, 47: 55, 48: 38, 49: 40, 50: 39} - score: '0.875' - edge_lig_49582390_lig_49220548: + edge_lig_49582390_lig_49580115: ligand_a: lig_49582390 - ligand_b: lig_49220548 - atom mapping: {0: 23, 1: 22, 2: 13, 3: 12, 4: 11, 5: 10, 6: 14, 7: 15, 8: 16, - 9: 17, 10: 18, 11: 19, 12: 20, 13: 21, 14: 24, 15: 25, 16: 26, 17: 27, 18: 28, - 19: 29, 20: 30, 21: 8, 22: 9, 23: 4, 24: 5, 25: 6, 26: 7, 27: 3, 28: 2, 32: 45, - 33: 46, 34: 47, 35: 42, 36: 43, 37: 44, 38: 49, 39: 48, 40: 50, 41: 51, 42: 53, - 43: 52, 44: 54, 45: 55, 46: 57, 47: 56, 48: 41, 49: 39, 52: 37} - score: '0.866' - edge_lig_50181001_lig_48168913: - ligand_a: lig_50181001 - ligand_b: lig_48168913 - atom mapping: {5: 4, 6: 3, 7: 2, 8: 1, 9: 6, 10: 5, 12: 7, 13: 8, 14: 9, 15: 10, - 16: 11, 17: 12, 18: 13, 19: 14, 20: 15, 21: 16, 22: 17, 23: 18, 24: 19, 25: 20, - 26: 21, 27: 22, 28: 27, 29: 26, 30: 25, 31: 24, 32: 23, 42: 31, 44: 34, 45: 35, - 46: 36, 47: 37, 48: 38, 49: 39, 50: 40, 51: 41, 52: 49, 53: 48, 54: 47, 55: 46, - 56: 44, 57: 45, 58: 42, 59: 43} - score: '0.895' - edge_lig_49582390_lig_49932714: + ligand_b: lig_49580115 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 31, 33: 32, + 34: 33, 35: 34, 36: 35, 37: 36, 38: 38, 39: 37, 40: 39, 41: 40, 42: 42, 43: 41, + 44: 43, 45: 44, 46: 46, 47: 45, 48: 47, 49: 48, 50: 49, 52: 50} + score: '0.915' + edge_lig_49582390_lig_49175828: ligand_a: lig_49582390 - ligand_b: lig_49932714 + ligand_b: lig_49175828 atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 32, 33: 33, + 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 28, 28: 29, 32: 32, 33: 33, 34: 34, 35: 35, 36: 36, 37: 37, 38: 39, 39: 38, 40: 40, 41: 41, 42: 43, 43: 42, - 44: 44, 45: 45, 46: 47, 47: 46, 48: 48, 49: 49, 50: 50, 52: 51} - score: '0.886' + 44: 44, 45: 45, 46: 47, 47: 46, 48: 48, 49: 49} + score: '0.855' edge_lig_49582390_lig_49932129: ligand_a: lig_49582390 ligand_b: lig_49932129 @@ -137,48 +83,102 @@ edges: 34: 33, 35: 34, 36: 35, 37: 36, 38: 38, 39: 37, 40: 39, 41: 40, 42: 42, 43: 41, 44: 43, 45: 44, 46: 46, 47: 45, 48: 47, 49: 48, 50: 49, 52: 53} score: '0.886' - edge_lig_49582390_lig_49072088: - ligand_a: lig_49582390 - ligand_b: lig_49072088 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 31, 33: 32, - 34: 33, 35: 34, 36: 35, 37: 36, 38: 38, 39: 37, 40: 39, 41: 40, 42: 42, 43: 41, - 44: 43, 45: 44, 46: 46, 47: 45, 48: 47, 49: 48, 50: 49} - score: '0.875' - edge_lig_49582390_lig_49580115: + edge_lig_48168913_lig_49137374: + ligand_a: lig_48168913 + ligand_b: lig_49137374 + atom mapping: {1: 22, 2: 21, 3: 26, 4: 25, 5: 24, 6: 23, 7: 5, 8: 4, 9: 3, 10: 2, + 11: 6, 12: 7, 13: 8, 14: 9, 15: 10, 16: 11, 17: 12, 18: 13, 19: 1, 20: 0, 21: 14, + 22: 15, 23: 16, 24: 17, 25: 18, 26: 19, 27: 20, 32: 48, 33: 47, 34: 33, 35: 34, + 36: 35, 37: 30, 38: 31, 39: 32, 40: 37, 41: 36, 42: 38, 43: 39, 44: 40, 45: 41, + 46: 43, 47: 42, 48: 45, 49: 44} + score: '0.923' + edge_lig_49582390_lig_48009208: ligand_a: lig_49582390 - ligand_b: lig_49580115 + ligand_b: lig_48009208 atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 31, 33: 32, - 34: 33, 35: 34, 36: 35, 37: 36, 38: 38, 39: 37, 40: 39, 41: 40, 42: 42, 43: 41, - 44: 43, 45: 44, 46: 46, 47: 45, 48: 47, 49: 48, 50: 49, 52: 50} - score: '0.915' - edge_lig_49582390_lig_49585367: + 21: 21, 22: 26, 23: 25, 24: 24, 25: 23, 26: 22, 32: 29, 33: 30, 34: 31, 35: 32, + 36: 33, 37: 34, 38: 36, 39: 35, 40: 37, 41: 38, 42: 40, 43: 39, 44: 41, 45: 42, + 46: 44, 47: 43, 50: 45} + score: '0.909' + edge_lig_48168913_lig_50181001: + ligand_a: lig_48168913 + ligand_b: lig_50181001 + atom mapping: {1: 8, 2: 7, 3: 6, 4: 5, 5: 10, 6: 9, 7: 12, 8: 13, 9: 14, 10: 15, + 11: 16, 12: 17, 13: 18, 14: 19, 15: 20, 16: 21, 17: 22, 18: 23, 19: 24, 20: 25, + 21: 26, 22: 27, 23: 28, 24: 29, 25: 30, 26: 31, 27: 32, 31: 42, 34: 44, 35: 45, + 36: 46, 37: 47, 38: 48, 39: 49, 40: 51, 41: 50, 42: 52, 43: 53, 44: 54, 45: 55, + 46: 57, 47: 56, 48: 59, 49: 58} + score: '0.895' + edge_lig_50181001_lig_48022468: + ligand_a: lig_50181001 + ligand_b: lig_48022468 + atom mapping: {5: 25, 6: 26, 7: 21, 8: 22, 9: 23, 10: 24, 12: 5, 13: 4, 14: 3, + 15: 2, 16: 6, 17: 7, 18: 8, 19: 9, 20: 10, 21: 11, 22: 12, 23: 13, 24: 1, 25: 0, + 26: 14, 27: 15, 28: 20, 29: 19, 30: 18, 31: 17, 32: 16, 44: 32, 45: 33, 46: 34, + 47: 29, 48: 30, 49: 31, 50: 35, 51: 36, 52: 44, 53: 43, 54: 42, 55: 41, 56: 39, + 57: 40, 58: 37, 59: 38} + score: '0.905' + edge_lig_49220392_lig_49582390: + ligand_a: lig_49220392 + ligand_b: lig_49582390 + atom mapping: {1: 28, 2: 27, 3: 23, 4: 24, 5: 25, 6: 26, 7: 21, 8: 22, 9: 5, 10: 4, + 11: 3, 12: 2, 13: 6, 14: 7, 15: 8, 16: 9, 17: 10, 18: 11, 19: 12, 20: 13, 21: 1, + 22: 0, 23: 14, 24: 15, 25: 16, 26: 17, 27: 18, 28: 19, 29: 20, 34: 52, 36: 49, + 38: 48, 39: 35, 40: 36, 41: 37, 42: 34, 43: 33, 44: 32, 45: 38, 46: 39, 47: 41, + 48: 40, 49: 43, 50: 42, 51: 45, 52: 44, 53: 47, 54: 46} + score: '0.894' + edge_lig_49220548_lig_49582390: + ligand_a: lig_49220548 + ligand_b: lig_49582390 + atom mapping: {2: 28, 3: 27, 4: 23, 5: 24, 6: 25, 7: 26, 8: 21, 9: 22, 10: 5, + 11: 4, 12: 3, 13: 2, 14: 6, 15: 7, 16: 8, 17: 9, 18: 10, 19: 11, 20: 12, 21: 13, + 22: 1, 23: 0, 24: 14, 25: 15, 26: 20, 27: 19, 28: 18, 29: 17, 30: 16, 37: 52, + 39: 49, 41: 48, 42: 35, 43: 36, 44: 37, 45: 32, 46: 33, 47: 34, 48: 39, 49: 38, + 50: 47, 51: 46, 52: 45, 53: 44, 54: 42, 55: 43, 56: 40, 57: 41} + score: '0.866' + edge_lig_48168913_lig_48271249: + ligand_a: lig_48168913 + ligand_b: lig_48271249 + atom mapping: {1: 26, 2: 21, 3: 22, 4: 23, 5: 24, 6: 25, 7: 5, 8: 4, 9: 3, 10: 2, + 11: 6, 12: 7, 13: 8, 14: 9, 15: 10, 16: 11, 17: 12, 18: 13, 19: 1, 20: 0, 21: 14, + 22: 15, 23: 16, 24: 17, 25: 18, 26: 19, 27: 20, 31: 45, 33: 46, 34: 32, 35: 33, + 36: 34, 37: 29, 38: 30, 39: 31, 40: 36, 41: 35, 42: 37, 43: 38, 44: 39, 45: 40, + 46: 42, 47: 41, 48: 44, 49: 43} + score: '0.929' + edge_lig_49582390_lig_49932714: ligand_a: lig_49582390 - ligand_b: lig_49585367 + ligand_b: lig_49932714 atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 32, 33: 33, 34: 34, 35: 35, 36: 36, 37: 37, 38: 39, 39: 38, 40: 40, 41: 41, 42: 43, 43: 42, 44: 44, 45: 45, 46: 47, 47: 46, 48: 48, 49: 49, 50: 50, 52: 52} - score: '0.877' - edge_lig_49582390_lig_49175789: + score: '0.886' + edge_lig_49582390_lig_49137530: ligand_a: lig_49582390 - ligand_b: lig_49175789 + ligand_b: lig_49137530 atom mapping: {0: 24, 1: 23, 2: 14, 3: 13, 4: 12, 5: 11, 6: 15, 7: 16, 8: 17, 9: 18, 10: 19, 11: 20, 12: 21, 13: 22, 14: 25, 15: 26, 16: 27, 17: 28, 18: 29, - 19: 30, 20: 31, 21: 9, 22: 10, 23: 5, 24: 6, 25: 7, 26: 8, 27: 4, 28: 3, 32: 48, - 33: 49, 34: 50, 35: 45, 36: 46, 37: 47, 38: 52, 39: 51, 40: 53, 41: 54, 42: 56, - 43: 55, 44: 57, 45: 58, 46: 60, 47: 59, 48: 44, 49: 42, 52: 40} - score: '0.861' - edge_lig_49582390_lig_49175828: + 19: 30, 20: 31, 21: 7, 22: 6, 23: 5, 24: 10, 25: 9, 26: 8, 27: 4, 28: 3, 32: 47, + 33: 48, 34: 49, 35: 44, 36: 45, 37: 46, 38: 51, 39: 50, 40: 52, 41: 53, 42: 55, + 43: 54, 44: 56, 45: 57, 46: 59, 47: 58, 48: 41, 49: 43, 50: 42, 52: 39} + score: '0.877' + edge_lig_49582390_lig_49396360: ligand_a: lig_49582390 - ligand_b: lig_49175828 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 28, 28: 29, 32: 32, 33: 33, - 34: 34, 35: 35, 36: 36, 37: 37, 38: 39, 39: 38, 40: 40, 41: 41, 42: 43, 43: 42, - 44: 44, 45: 45, 46: 47, 47: 46, 48: 48, 49: 49} - score: '0.855' + ligand_b: lig_49396360 + atom mapping: {0: 23, 1: 22, 2: 13, 3: 12, 4: 11, 5: 10, 6: 14, 7: 15, 8: 16, + 9: 17, 10: 18, 11: 19, 12: 20, 13: 21, 14: 24, 15: 25, 16: 26, 17: 27, 18: 28, + 19: 29, 20: 30, 21: 6, 22: 5, 23: 4, 24: 9, 25: 8, 26: 7, 27: 3, 28: 2, 32: 44, + 33: 45, 34: 46, 35: 41, 36: 42, 37: 43, 38: 48, 39: 47, 40: 49, 41: 50, 42: 52, + 43: 51, 44: 53, 45: 54, 46: 56, 47: 55, 48: 38, 49: 40, 50: 39, 52: 36} + score: '0.886' + edge_lig_50181001_lig_49582390: + ligand_a: lig_50181001 + ligand_b: lig_49582390 + atom mapping: {3: 28, 4: 27, 5: 23, 6: 22, 7: 21, 8: 26, 9: 25, 10: 24, 12: 5, + 13: 4, 14: 3, 15: 2, 16: 6, 17: 7, 18: 8, 19: 9, 20: 10, 21: 11, 22: 12, 23: 13, + 24: 1, 25: 0, 26: 14, 27: 15, 28: 20, 29: 19, 30: 18, 31: 17, 32: 16, 40: 52, + 42: 48, 43: 50, 44: 35, 45: 36, 46: 37, 47: 34, 48: 33, 49: 32, 50: 38, 51: 39, + 52: 47, 53: 46, 54: 45, 55: 44, 56: 43, 57: 42, 58: 41, 59: 40} + score: '0.861' diff --git a/data/pfkfb3/03_edges/01_perses_openfe.yml b/data/pfkfb3/03_edges/01_perses_openfe.yml index 0e07df5f6..6cc3d2211 100644 --- a/data/pfkfb3/03_edges/01_perses_openfe.yml +++ b/data/pfkfb3/03_edges/01_perses_openfe.yml @@ -1,100 +1,35 @@ mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph +planner: openfe v0.5 minimal_spanning_graph edges: - edge_lig_24_lig_44: + edge_lig_24_lig_69: ligand_a: lig_24 - ligand_b: lig_44 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 20, 28: 21, - 29: 22, 30: 23, 31: 24, 32: 25, 33: 33, 35: 31, 36: 32, 37: 29, 38: 30, 39: 28, - 41: 26, 44: 41, 45: 42} - score: '0.608' - edge_lig_19_lig_41: - ligand_a: lig_19 - ligand_b: lig_41 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 45, 5: 46, 6: 26, 7: 27, 8: 28, 9: 29, - 10: 30, 11: 31, 12: 32, 14: 33, 15: 34, 16: 35, 17: 36, 18: 37, 20: 24, 21: 25, - 22: 8, 41: 4, 42: 5, 43: 6, 44: 7} - score: '0.595' - edge_lig_59_lig_31: - ligand_a: lig_59 - ligand_b: lig_31 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 44, 5: 45, 6: 46, 7: 47, 8: 25, 26: 23, - 27: 24, 28: 6, 29: 7, 30: 8, 31: 9, 32: 10, 33: 11, 34: 12, 35: 13, 36: 14, - 37: 15, 38: 16, 39: 17, 40: 18, 43: 19, 44: 22, 45: 21, 46: 20, 47: 4, 48: 5} - score: '0.642' - edge_lig_24_lig_41: - ligand_a: lig_24 - ligand_b: lig_41 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, - 29: 26, 30: 27, 31: 28, 32: 29, 33: 37, 35: 35, 36: 36, 37: 33, 38: 34, 39: 32, - 41: 30, 44: 45, 45: 46} - score: '0.577' - edge_lig_24_lig_20: - ligand_a: lig_24 - ligand_b: lig_20 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, - 29: 26, 30: 27, 31: 28, 32: 29, 33: 37, 35: 35, 36: 36, 37: 33, 38: 34, 39: 32, - 41: 30, 44: 45, 45: 46} - score: '0.587' - edge_lig_24_lig_59: - ligand_a: lig_24 - ligand_b: lig_59 + ligand_b: lig_69 atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 26, 28: 27, - 29: 28, 30: 29, 31: 30, 32: 31, 33: 39, 35: 37, 36: 38, 37: 35, 38: 36, 39: 34, - 41: 32, 44: 47, 45: 48} - score: '0.578' - edge_lig_24_lig_62: + 29: 28, 30: 29, 31: 30, 32: 31, 33: 32, 35: 40, 36: 41, 37: 42, 38: 43, 39: 44, + 41: 45, 44: 47, 45: 48} + score: '0.580' + edge_lig_24_lig_63: ligand_a: lig_24 - ligand_b: lig_62 + ligand_b: lig_63 atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 21, 28: 22, 29: 23, 30: 24, 31: 25, 32: 26, 33: 27, 35: 35, 36: 36, 37: 37, 38: 38, 39: 39, 41: 40, 44: 42, 45: 43} score: '0.597' + edge_lig_24_lig_70: + ligand_a: lig_24 + ligand_b: lig_70 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 26, 28: 27, + 29: 28, 30: 29, 31: 30, 32: 31, 33: 32, 35: 40, 36: 41, 37: 42, 38: 43, 39: 44, + 41: 45, 44: 47, 45: 48} + score: '0.580' edge_lig_26_lig_59: ligand_a: lig_26 ligand_b: lig_59 atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 26, 28: 27, - 29: 28, 30: 29, 31: 30, 32: 31, 33: 39, 34: 40, 35: 42, 36: 43, 39: 37, 40: 38, + 29: 28, 30: 29, 31: 30, 32: 31, 33: 39, 34: 40, 35: 41, 36: 43, 39: 37, 40: 38, 41: 35, 42: 36, 43: 34, 45: 32, 46: 33, 47: 47, 48: 48} score: '0.618' - edge_lig_57_lig_38: - ligand_a: lig_57 - ligand_b: lig_38 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 28, 28: 29, - 29: 30, 30: 31, 31: 32, 32: 33, 33: 34, 34: 35, 35: 36, 36: 37, 37: 38, 38: 39, - 39: 40, 40: 41, 41: 42, 42: 44, 43: 43, 44: 45, 45: 48, 46: 47, 47: 46, 48: 49, - 49: 50} - score: '0.656' - edge_lig_24_lig_43: - ligand_a: lig_24 - ligand_b: lig_43 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 20, 28: 21, - 29: 22, 30: 23, 31: 24, 32: 25, 33: 33, 35: 31, 36: 32, 37: 29, 38: 30, 39: 28, - 41: 26, 44: 41, 45: 42} - score: '0.608' - edge_lig_56_lig_38: - ligand_a: lig_56 - ligand_b: lig_38 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 30: 28, 31: 29, - 32: 30, 33: 31, 34: 32, 35: 33, 36: 34, 37: 35, 38: 36, 39: 37, 40: 38, 41: 39, - 42: 40, 43: 41, 44: 42, 45: 43, 46: 44, 47: 45, 48: 46, 49: 47, 50: 48, 51: 49, - 52: 50} - score: '0.652' - edge_lig_41_lig_23: - ligand_a: lig_41 - ligand_b: lig_23 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 40, 5: 41, 6: 42, 7: 43, 8: 21, 24: 19, - 25: 20, 26: 6, 27: 7, 28: 8, 29: 9, 30: 10, 31: 11, 32: 12, 33: 13, 34: 14, - 35: 15, 36: 16, 37: 17, 45: 4, 46: 5} - score: '0.602' - edge_lig_38_lig_36: - ligand_a: lig_38 - ligand_b: lig_36 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 28: 27, 29: 28, - 30: 29, 31: 30, 33: 31, 34: 45, 35: 46, 36: 44, 37: 42, 38: 43, 39: 40, 40: 41, - 41: 32, 42: 33, 43: 35, 44: 34, 45: 36, 46: 39, 47: 38, 48: 37, 49: 51, 50: 52} - score: '0.642' edge_lig_35_lig_38: ligand_a: lig_35 ligand_b: lig_38 @@ -103,13 +38,6 @@ edges: 20: 37, 21: 38, 22: 36, 23: 34, 24: 35, 25: 28, 26: 29, 27: 8, 46: 4, 47: 5, 48: 6, 49: 7} score: '0.663' - edge_lig_33_lig_41: - ligand_a: lig_33 - ligand_b: lig_41 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 45, 5: 46, 6: 26, 7: 27, 8: 28, 9: 29, - 10: 37, 11: 38, 13: 35, 14: 36, 15: 33, 16: 34, 17: 32, 18: 30, 19: 31, 20: 24, - 21: 25, 22: 8, 41: 4, 42: 5, 43: 6, 44: 7} - score: '0.612' edge_lig_55_lig_38: ligand_a: lig_55 ligand_b: lig_38 @@ -118,49 +46,6 @@ edges: 20: 43, 21: 45, 22: 48, 23: 47, 24: 46, 25: 28, 26: 29, 27: 8, 46: 4, 47: 5, 48: 6, 49: 7} score: '0.659' - edge_lig_54_lig_38: - ligand_a: lig_54 - ligand_b: lig_38 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 49, 5: 50, 6: 30, 7: 31, 8: 32, 9: 33, - 10: 34, 11: 35, 12: 36, 13: 37, 14: 38, 15: 39, 16: 40, 17: 41, 18: 42, 19: 44, - 20: 43, 21: 45, 22: 48, 23: 47, 24: 46, 25: 28, 26: 29, 27: 8, 52: 4, 53: 5, - 54: 6, 55: 7} - score: '0.649' - edge_lig_34_lig_59: - ligand_a: lig_34 - ligand_b: lig_59 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 26, 28: 27, - 29: 28, 30: 29, 31: 30, 32: 31, 33: 39, 34: 40, 35: 41, 36: 43, 39: 37, 40: 38, - 41: 35, 42: 36, 43: 34, 44: 32, 45: 33, 46: 47, 47: 48} - score: '0.625' - edge_lig_46_lig_24: - ligand_a: lig_46 - ligand_b: lig_24 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 23: 27, 24: 28, - 25: 29, 26: 30, 27: 31, 28: 32, 29: 41, 31: 39, 32: 37, 33: 38, 34: 35, 35: 36, - 36: 33, 44: 44, 45: 45} - score: '0.580' - edge_lig_59_lig_30: - ligand_a: lig_59 - ligand_b: lig_30 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 44, 5: 45, 6: 46, 7: 47, 8: 25, 26: 23, - 27: 24, 28: 6, 29: 7, 30: 8, 31: 9, 32: 21, 33: 22, 34: 19, 35: 17, 36: 18, - 37: 16, 39: 10, 40: 11, 43: 12, 44: 15, 45: 14, 46: 13, 47: 4, 48: 5} - score: '0.631' - edge_lig_24_lig_63: - ligand_a: lig_24 - ligand_b: lig_63 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 21, 28: 22, - 29: 23, 30: 24, 31: 25, 32: 26, 33: 27, 35: 35, 36: 36, 37: 37, 38: 38, 39: 39, - 41: 40, 44: 42, 45: 43} - score: '0.597' - edge_lig_24_lig_65: - ligand_a: lig_24 - ligand_b: lig_65 - atom mapping: {0: 37, 1: 36, 2: 38, 3: 31, 4: 32, 5: 33, 6: 34, 7: 35, 8: 7, 27: 8, - 28: 9, 29: 10, 30: 11, 31: 12, 32: 13, 33: 21, 35: 19, 36: 20, 37: 17, 38: 18, - 39: 16, 41: 14, 44: 29, 45: 30} - score: '0.590' edge_lig_24_lig_39: ligand_a: lig_24 ligand_b: lig_39 @@ -168,14 +53,6 @@ edges: 29: 24, 30: 25, 31: 26, 32: 27, 33: 35, 35: 33, 36: 34, 37: 31, 38: 32, 39: 30, 41: 28, 44: 43, 45: 44} score: '0.594' - edge_lig_53_lig_38: - ligand_a: lig_53 - ligand_b: lig_38 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 33: 28, 34: 29, - 35: 30, 36: 31, 37: 32, 38: 33, 39: 34, 40: 35, 41: 36, 42: 37, 43: 38, 44: 39, - 45: 40, 46: 41, 47: 42, 48: 44, 49: 43, 50: 45, 51: 48, 52: 47, 53: 46, 54: 49, - 55: 50} - score: '0.649' edge_lig_24_lig_38: ligand_a: lig_24 ligand_b: lig_38 @@ -183,28 +60,13 @@ edges: 29: 30, 30: 31, 31: 32, 32: 33, 33: 41, 35: 39, 36: 40, 37: 37, 38: 38, 39: 36, 41: 34, 44: 49, 45: 50} score: '0.584' - edge_lig_24_lig_48: + edge_lig_24_lig_47: ligand_a: lig_24 - ligand_b: lig_48 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, - 29: 26, 30: 27, 31: 28, 32: 29, 33: 37, 35: 35, 36: 36, 37: 33, 38: 34, 39: 32, - 41: 30, 44: 45, 45: 46} + ligand_b: lig_47 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 45, 5: 46, 6: 47, 7: 48, 8: 27, 27: 25, + 28: 26, 29: 6, 30: 7, 31: 8, 32: 9, 33: 17, 35: 15, 36: 16, 37: 13, 38: 14, + 39: 12, 41: 10, 44: 4, 45: 5} score: '0.587' - edge_lig_52_lig_38: - ligand_a: lig_52 - ligand_b: lig_38 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 30: 28, 31: 29, - 32: 30, 33: 31, 34: 32, 35: 33, 36: 34, 37: 35, 38: 36, 39: 37, 40: 38, 41: 39, - 42: 40, 43: 41, 44: 42, 45: 44, 46: 43, 47: 45, 48: 48, 49: 47, 50: 46, 51: 49, - 52: 50} - score: '0.652' - edge_lig_70_lig_24: - ligand_a: lig_70 - ligand_b: lig_24 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 26: 27, 27: 28, - 28: 29, 29: 30, 30: 31, 31: 32, 32: 33, 40: 35, 41: 36, 42: 37, 43: 38, 44: 39, - 45: 41, 47: 44, 48: 45} - score: '0.580' edge_lig_58_lig_59: ligand_a: lig_58 ligand_b: lig_59 @@ -213,13 +75,49 @@ edges: 37: 38, 38: 39, 39: 40, 40: 42, 41: 41, 42: 43, 43: 44, 44: 45, 45: 46, 46: 47, 47: 48} score: '0.674' - edge_lig_69_lig_24: - ligand_a: lig_69 - ligand_b: lig_24 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 26: 27, 27: 28, - 28: 29, 29: 30, 30: 31, 31: 32, 32: 33, 40: 35, 41: 36, 42: 37, 43: 38, 44: 39, - 45: 41, 47: 44, 48: 45} - score: '0.580' + edge_lig_24_lig_41: + ligand_a: lig_24 + ligand_b: lig_41 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, + 29: 26, 30: 27, 31: 28, 32: 29, 33: 37, 35: 35, 36: 36, 37: 33, 38: 34, 39: 32, + 41: 30, 44: 45, 45: 46} + score: '0.577' + edge_lig_24_lig_44: + ligand_a: lig_24 + ligand_b: lig_44 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 20, 28: 21, + 29: 22, 30: 23, 31: 24, 32: 25, 33: 33, 35: 31, 36: 32, 37: 29, 38: 30, 39: 28, + 41: 26, 44: 41, 45: 42} + score: '0.608' + edge_lig_24_lig_62: + ligand_a: lig_24 + ligand_b: lig_62 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 21, 28: 22, + 29: 23, 30: 24, 31: 25, 32: 26, 33: 27, 35: 35, 36: 36, 37: 37, 38: 38, 39: 39, + 41: 40, 44: 42, 45: 43} + score: '0.597' + edge_lig_33_lig_41: + ligand_a: lig_33 + ligand_b: lig_41 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 45, 5: 46, 6: 26, 7: 27, 8: 28, 9: 29, + 10: 37, 11: 38, 13: 35, 14: 36, 15: 33, 16: 34, 17: 32, 18: 30, 19: 31, 20: 24, + 21: 25, 22: 8, 41: 4, 42: 5, 43: 6, 44: 7} + score: '0.612' + edge_lig_57_lig_38: + ligand_a: lig_57 + ligand_b: lig_38 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 28, 28: 29, + 29: 30, 30: 31, 31: 32, 32: 33, 33: 34, 34: 35, 35: 36, 36: 37, 37: 38, 38: 39, + 39: 40, 40: 41, 41: 42, 42: 44, 43: 43, 44: 45, 45: 48, 46: 47, 47: 46, 48: 49, + 49: 50} + score: '0.656' + edge_lig_37_lig_38: + ligand_a: lig_37 + ligand_b: lig_38 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 28, 28: 29, + 29: 30, 30: 31, 31: 32, 32: 33, 33: 34, 34: 35, 35: 36, 36: 37, 37: 38, 38: 39, + 39: 40, 40: 41, 41: 42, 42: 43, 43: 45, 60: 49, 61: 50} + score: '0.578' edge_lig_24_lig_49: ligand_a: lig_24 ligand_b: lig_49 @@ -227,13 +125,13 @@ edges: 29: 24, 30: 25, 31: 26, 32: 27, 33: 35, 35: 33, 36: 34, 37: 31, 38: 32, 39: 30, 41: 28, 44: 43, 45: 44} score: '0.594' - edge_lig_24_lig_42: + edge_lig_24_lig_43: ligand_a: lig_24 - ligand_b: lig_42 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, - 29: 26, 30: 27, 31: 28, 32: 29, 33: 37, 35: 35, 36: 36, 37: 33, 38: 34, 39: 32, - 41: 30, 44: 45, 45: 46} - score: '0.587' + ligand_b: lig_43 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 20, 28: 21, + 29: 22, 30: 23, 31: 24, 32: 25, 33: 33, 35: 31, 36: 32, 37: 29, 38: 30, 39: 28, + 41: 26, 44: 41, 45: 42} + score: '0.608' edge_lig_29_lig_38: ligand_a: lig_29 ligand_b: lig_38 @@ -242,32 +140,90 @@ edges: 20: 37, 21: 38, 22: 36, 24: 34, 25: 35, 26: 28, 27: 29, 28: 8, 47: 4, 48: 5, 49: 6, 50: 7} score: '0.656' - edge_lig_41_lig_64: - ligand_a: lig_41 - ligand_b: lig_64 - atom mapping: {0: 39, 1: 38, 2: 40, 3: 33, 4: 34, 5: 35, 6: 36, 7: 37, 8: 9, 24: 10, - 25: 11, 26: 12, 27: 13, 28: 14, 29: 15, 30: 29, 31: 30, 32: 28, 33: 26, 34: 27, - 35: 24, 36: 25, 37: 16, 38: 17, 39: 19, 40: 18, 41: 20, 42: 23, 43: 22, 44: 21, - 45: 31, 46: 32} + edge_lig_23_lig_41: + ligand_a: lig_23 + ligand_b: lig_41 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 45, 5: 46, 6: 26, 7: 27, 8: 28, 9: 29, + 10: 30, 11: 31, 12: 32, 13: 33, 14: 34, 15: 35, 16: 36, 17: 37, 19: 24, 20: 25, + 21: 8, 40: 4, 41: 5, 42: 6, 43: 7} + score: '0.602' + edge_lig_24_lig_42: + ligand_a: lig_24 + ligand_b: lig_42 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, + 29: 26, 30: 27, 31: 28, 32: 29, 33: 37, 35: 35, 36: 36, 37: 33, 38: 34, 39: 32, + 41: 30, 44: 45, 45: 46} + score: '0.587' + edge_lig_24_lig_65: + ligand_a: lig_24 + ligand_b: lig_65 + atom mapping: {0: 37, 1: 36, 2: 38, 3: 31, 4: 32, 5: 33, 6: 34, 7: 35, 8: 7, 27: 8, + 28: 9, 29: 10, 30: 11, 31: 12, 32: 13, 33: 21, 35: 19, 36: 20, 37: 17, 38: 18, + 39: 16, 41: 14, 44: 29, 45: 30} + score: '0.590' + edge_lig_52_lig_38: + ligand_a: lig_52 + ligand_b: lig_38 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 30: 28, 31: 29, + 32: 30, 33: 31, 34: 32, 35: 33, 36: 34, 37: 35, 38: 36, 39: 37, 40: 38, 41: 39, + 42: 40, 43: 41, 44: 42, 45: 44, 46: 43, 47: 45, 48: 48, 49: 47, 50: 46, 51: 49, + 52: 50} + score: '0.652' + edge_lig_34_lig_59: + ligand_a: lig_34 + ligand_b: lig_59 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 26, 28: 27, + 29: 28, 30: 29, 31: 30, 32: 31, 33: 39, 34: 40, 35: 41, 36: 43, 39: 37, 40: 38, + 41: 35, 42: 36, 43: 34, 44: 32, 45: 33, 46: 47, 47: 48} + score: '0.625' + edge_lig_24_lig_20: + ligand_a: lig_24 + ligand_b: lig_20 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, + 29: 26, 30: 27, 31: 28, 32: 29, 33: 37, 35: 35, 36: 36, 37: 33, 38: 34, 39: 32, + 41: 30, 44: 45, 45: 46} + score: '0.587' + edge_lig_64_lig_41: + ligand_a: lig_64 + ligand_b: lig_41 + atom mapping: {9: 8, 10: 24, 11: 25, 12: 26, 13: 27, 14: 28, 15: 29, 16: 37, 17: 38, + 18: 40, 19: 39, 20: 41, 21: 42, 22: 43, 23: 44, 24: 35, 25: 36, 26: 33, 27: 34, + 28: 32, 29: 30, 30: 31, 31: 45, 32: 46, 33: 3, 34: 4, 35: 5, 36: 6, 37: 7, 38: 1, + 39: 0, 40: 2} score: '0.696' - edge_lig_38_lig_37: - ligand_a: lig_38 - ligand_b: lig_37 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 28: 27, 29: 28, - 30: 29, 31: 30, 32: 31, 33: 32, 34: 33, 35: 34, 36: 35, 37: 36, 38: 37, 39: 38, - 40: 39, 41: 40, 42: 41, 43: 42, 45: 43, 49: 60, 50: 61} + edge_lig_56_lig_38: + ligand_a: lig_56 + ligand_b: lig_38 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 30: 28, 31: 29, + 32: 30, 33: 31, 34: 32, 35: 33, 36: 34, 37: 35, 38: 36, 39: 37, 40: 38, 41: 39, + 42: 40, 43: 41, 44: 42, 45: 43, 46: 44, 47: 45, 48: 46, 49: 47, 50: 48, 51: 49, + 52: 50} + score: '0.652' + edge_lig_19_lig_41: + ligand_a: lig_19 + ligand_b: lig_41 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 45, 5: 46, 6: 26, 7: 27, 8: 28, 9: 29, + 10: 30, 11: 31, 12: 32, 14: 33, 15: 34, 16: 35, 17: 36, 18: 37, 20: 24, 21: 25, + 22: 8, 41: 4, 42: 5, 43: 6, 44: 7} + score: '0.595' + edge_lig_59_lig_31: + ligand_a: lig_59 + ligand_b: lig_31 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 44, 5: 45, 6: 46, 7: 47, 8: 25, 26: 23, + 27: 24, 28: 6, 29: 7, 30: 8, 31: 9, 32: 10, 33: 11, 34: 12, 35: 13, 36: 14, + 37: 15, 38: 16, 39: 17, 40: 18, 43: 19, 44: 22, 45: 21, 46: 20, 47: 4, 48: 5} + score: '0.642' + edge_lig_24_lig_59: + ligand_a: lig_24 + ligand_b: lig_59 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 26, 28: 27, + 29: 28, 30: 29, 31: 30, 32: 31, 33: 39, 35: 37, 36: 38, 37: 35, 38: 36, 39: 34, + 41: 32, 44: 47, 45: 48} score: '0.578' - edge_lig_24_lig_47: + edge_lig_24_lig_48: ligand_a: lig_24 - ligand_b: lig_47 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 45, 5: 46, 6: 47, 7: 48, 8: 27, 27: 25, - 28: 26, 29: 6, 30: 7, 31: 8, 32: 9, 33: 17, 35: 15, 36: 16, 37: 13, 38: 14, - 39: 12, 41: 10, 44: 4, 45: 5} + ligand_b: lig_48 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, + 29: 26, 30: 27, 31: 28, 32: 29, 33: 37, 35: 35, 36: 36, 37: 33, 38: 34, 39: 32, + 41: 30, 44: 45, 45: 46} score: '0.587' - edge_lig_67_lig_24: - ligand_a: lig_67 - ligand_b: lig_24 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 24: 27, 25: 28, - 26: 29, 27: 30, 28: 31, 29: 32, 30: 41, 32: 39, 33: 37, 34: 38, 35: 35, 36: 36, - 37: 33, 45: 44, 46: 45} - score: '0.580' diff --git a/data/ptp1b/03_edges/01_perses_openfe.yml b/data/ptp1b/03_edges/01_perses_openfe.yml index 03f8e8105..4720cb656 100644 --- a/data/ptp1b/03_edges/01_perses_openfe.yml +++ b/data/ptp1b/03_edges/01_perses_openfe.yml @@ -1,42 +1,21 @@ mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph +planner: openfe v0.5 minimal_spanning_graph edges: - edge_lig_23480_lig_23485: - ligand_a: lig_23480 - ligand_b: lig_23485 - atom mapping: {0: 62, 1: 2, 2: 1, 3: 6, 4: 5, 5: 4, 6: 3, 7: 61, 8: 9, 10: 12, - 13: 15, 14: 20, 15: 19, 16: 18, 17: 17, 18: 16, 19: 59, 20: 60, 21: 58, 22: 57, - 23: 26, 30: 23, 31: 24, 32: 22, 33: 21, 35: 8, 52: 0} + edge_lig_23485_lig_23480: + ligand_a: lig_23485 + ligand_b: lig_23480 + atom mapping: {0: 52, 1: 2, 2: 1, 3: 6, 4: 5, 5: 4, 6: 3, 8: 35, 9: 8, 12: 10, + 15: 13, 16: 18, 17: 17, 18: 16, 19: 15, 20: 14, 21: 33, 22: 32, 23: 31, 24: 30, + 26: 23, 57: 22, 58: 21, 59: 20, 60: 19, 61: 7, 62: 0} score: '0.488' - edge_lig_20667_2qbp_lig_23474: - ligand_a: lig_20667_2qbp - ligand_b: lig_23474 - atom mapping: {0: 47, 1: 2, 2: 1, 3: 6, 4: 5, 5: 4, 6: 3, 8: 30, 9: 8, 12: 10, - 15: 13, 16: 18, 17: 17, 18: 16, 19: 15, 20: 14, 21: 28, 22: 27, 23: 26, 24: 25, - 25: 23, 54: 21, 55: 22, 56: 19, 57: 20, 58: 7, 59: 0} - score: '0.511' - edge_lig_23484_lig_23469: - ligand_a: lig_23484 - ligand_b: lig_23469 - atom mapping: {26: 11, 28: 13, 29: 14, 30: 15, 31: 16, 32: 17, 33: 18, 34: 19, - 35: 20, 36: 21, 37: 22, 38: 23, 39: 24, 40: 25, 41: 26, 42: 27, 43: 28, 44: 29, - 45: 31, 46: 30, 47: 32, 48: 33, 49: 34, 51: 36, 52: 37, 53: 38} - score: '0.581' - edge_lig_23473_lig_23484: - ligand_a: lig_23473 + edge_lig_23476_lig_23484: + ligand_a: lig_23476 ligand_b: lig_23484 - atom mapping: {12: 26, 13: 28, 14: 29, 15: 30, 16: 31, 17: 32, 18: 33, 19: 34, - 20: 35, 21: 36, 22: 37, 23: 38, 24: 39, 25: 40, 26: 41, 27: 42, 28: 43, 29: 44, - 30: 46, 31: 45, 32: 47, 33: 48, 34: 49, 36: 51, 37: 52, 38: 53} - score: '0.581' - edge_lig_23466_lig_23483: - ligand_a: lig_23466 - ligand_b: lig_23483 - atom mapping: {0: 49, 1: 27, 2: 28, 3: 29, 4: 30, 5: 25, 6: 26, 7: 50, 8: 23, - 10: 24, 11: 31, 12: 32, 13: 33, 14: 34, 15: 35, 16: 36, 17: 37, 18: 38, 19: 39, - 20: 40, 21: 41, 22: 42, 23: 43, 24: 44, 25: 45, 26: 46, 27: 47, 28: 48} - score: '0.725' + atom mapping: {0: 52, 1: 30, 2: 31, 3: 32, 4: 33, 5: 28, 6: 29, 7: 53, 8: 26, + 9: 27, 30: 34, 31: 35, 32: 36, 33: 37, 34: 38, 35: 39, 36: 40, 37: 41, 38: 42, + 39: 43, 40: 44, 41: 45, 42: 46, 43: 47, 44: 48, 45: 49, 47: 51} + score: '0.545' edge_lig_23484_lig_20669_2qbr: ligand_a: lig_23484 ligand_b: lig_20669_2qbr @@ -44,13 +23,13 @@ edges: 35: 21, 36: 22, 37: 23, 38: 24, 39: 25, 40: 26, 41: 27, 42: 28, 43: 29, 44: 30, 45: 32, 46: 31, 47: 33, 48: 34, 49: 35, 51: 37, 52: 38, 53: 39} score: '0.574' - edge_lig_23482_lig_23480: - ligand_a: lig_23482 + edge_lig_20667_2qbp_lig_23480: + ligand_a: lig_20667_2qbp ligand_b: lig_23480 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 32: 35, 33: 36, - 34: 37, 35: 38, 36: 39, 37: 40, 38: 41, 39: 42, 40: 43, 41: 44, 42: 45, 43: 46, - 44: 47, 45: 48, 46: 49, 47: 50, 48: 51, 49: 52} - score: '0.602' + atom mapping: {0: 52, 1: 2, 2: 3, 3: 4, 4: 5, 5: 6, 6: 1, 7: 0, 8: 7, 9: 8, 12: 10, + 15: 13, 16: 14, 17: 15, 18: 16, 19: 17, 20: 18, 21: 20, 22: 19, 23: 22, 24: 21, + 26: 23, 54: 30, 55: 31, 56: 32, 57: 33, 58: 35} + score: '0.488' edge_lig_23484_lig_23468: ligand_a: lig_23484 ligand_b: lig_23468 @@ -58,20 +37,48 @@ edges: 36: 21, 37: 22, 38: 23, 39: 24, 40: 25, 41: 26, 42: 27, 43: 28, 44: 29, 45: 31, 46: 30, 47: 32, 48: 33, 49: 34, 51: 36, 52: 0, 53: 7} score: '0.612' - edge_lig_23479_lig_23480: - ligand_a: lig_23479 - ligand_b: lig_23480 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 31: 35, 32: 36, - 33: 37, 34: 38, 35: 39, 36: 40, 37: 41, 38: 42, 39: 43, 40: 44, 41: 45, 42: 46, - 43: 47, 44: 48, 45: 49, 46: 50, 47: 51, 48: 52} + edge_lig_23480_lig_23484: + ligand_a: lig_23480 + ligand_b: lig_23484 + atom mapping: {0: 7, 1: 6, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 7: 8, 8: 9, 10: 12, 13: 15, + 14: 20, 15: 19, 16: 18, 17: 17, 18: 16, 19: 56, 20: 57, 21: 55, 22: 54, 23: 26, + 30: 23, 31: 24, 32: 22, 33: 21, 35: 58, 52: 0} + score: '0.491' + edge_lig_23480_lig_23479: + ligand_a: lig_23480 + ligand_b: lig_23479 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 35: 31, 36: 32, + 37: 33, 38: 34, 39: 35, 40: 36, 41: 37, 42: 38, 43: 39, 44: 40, 45: 41, 46: 43, + 47: 42, 48: 44, 49: 45, 50: 46, 51: 47, 52: 48} score: '0.610' - edge_lig_20667_2qbp_lig_23480: - ligand_a: lig_20667_2qbp - ligand_b: lig_23480 - atom mapping: {0: 52, 1: 2, 2: 3, 3: 4, 4: 5, 5: 6, 6: 1, 7: 0, 8: 7, 9: 8, 12: 10, - 15: 13, 16: 18, 17: 17, 18: 16, 19: 15, 20: 14, 21: 33, 22: 32, 23: 30, 24: 31, - 26: 23, 54: 22, 55: 21, 56: 19, 57: 20, 58: 35} - score: '0.488' + edge_lig_23477_lig_23472: + ligand_a: lig_23477 + ligand_b: lig_23472 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 25: 24, 26: 25, + 27: 26, 28: 27, 29: 28, 30: 29, 31: 30, 32: 31, 33: 32, 34: 33, 35: 34, 36: 35, + 37: 36, 38: 37, 39: 38, 40: 39, 41: 40, 42: 41} + score: '0.632' + edge_lig_23480_lig_23482: + ligand_a: lig_23480 + ligand_b: lig_23482 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 35: 32, 36: 33, + 37: 34, 38: 35, 39: 36, 40: 37, 41: 38, 42: 39, 43: 40, 44: 41, 45: 42, 46: 44, + 47: 43, 48: 45, 49: 46, 50: 47, 51: 48, 52: 49} + score: '0.602' + edge_lig_23484_lig_23472: + ligand_a: lig_23484 + ligand_b: lig_23472 + atom mapping: {26: 8, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, 33: 4, 34: 24, 35: 25, + 36: 26, 37: 27, 38: 28, 39: 29, 40: 30, 41: 31, 42: 32, 43: 33, 44: 34, 45: 36, + 46: 35, 47: 37, 48: 38, 49: 39, 51: 41, 52: 0, 53: 7} + score: '0.574' + edge_lig_23466_lig_23472: + ligand_a: lig_23466 + ligand_b: lig_23472 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 11: 24, + 12: 25, 13: 26, 14: 27, 15: 28, 16: 29, 17: 30, 18: 31, 19: 32, 20: 33, 21: 34, + 22: 36, 23: 35, 24: 37, 25: 38, 26: 39, 27: 40, 28: 41} + score: '0.783' edge_lig_20670_2qbs_lig_23472: ligand_a: lig_20670_2qbs ligand_b: lig_23472 @@ -79,20 +86,34 @@ edges: 29: 26, 30: 27, 31: 28, 32: 29, 33: 30, 34: 31, 35: 32, 36: 33, 37: 34, 38: 35, 39: 36, 40: 37, 41: 38, 42: 39, 43: 40, 44: 41} score: '0.632' - edge_lig_23471_lig_23483: - ligand_a: lig_23471 - ligand_b: lig_23483 - atom mapping: {0: 49, 1: 27, 2: 28, 3: 29, 4: 30, 5: 25, 6: 26, 7: 50, 8: 23, - 17: 31, 18: 32, 19: 33, 20: 34, 21: 35, 22: 36, 23: 37, 24: 38, 25: 39, 26: 40, - 27: 41, 28: 43, 29: 42, 30: 44, 31: 45, 32: 46, 33: 47, 34: 48} - score: '0.650' - edge_lig_23477_lig_23472: - ligand_a: lig_23477 + edge_lig_23485_lig_23474: + ligand_a: lig_23485 + ligand_b: lig_23474 + atom mapping: {0: 47, 1: 2, 2: 1, 3: 6, 4: 5, 5: 4, 6: 3, 8: 30, 9: 8, 12: 10, + 15: 13, 16: 18, 17: 17, 18: 16, 19: 15, 20: 14, 21: 28, 22: 27, 23: 26, 24: 25, + 25: 24, 57: 21, 58: 22, 59: 19, 60: 20, 61: 7, 62: 0} + score: '0.511' + edge_lig_23467_lig_23472: + ligand_a: lig_23467 ligand_b: lig_23472 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 25: 24, 26: 25, - 27: 26, 28: 27, 29: 28, 30: 29, 31: 30, 32: 31, 33: 32, 34: 33, 35: 34, 36: 35, - 37: 36, 38: 37, 39: 38, 40: 39, 41: 40, 42: 41} - score: '0.632' + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 13: 24, 14: 25, + 15: 26, 16: 27, 17: 28, 18: 29, 19: 30, 20: 31, 21: 32, 22: 33, 23: 34, 24: 36, + 25: 35, 26: 37, 27: 38, 28: 39, 29: 40, 30: 41} + score: '0.742' + edge_lig_23484_lig_23471: + ligand_a: lig_23484 + ligand_b: lig_23471 + atom mapping: {26: 8, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, 33: 4, 34: 17, 35: 18, + 36: 19, 37: 20, 38: 21, 39: 22, 40: 23, 41: 24, 42: 25, 43: 26, 44: 27, 45: 29, + 46: 28, 47: 30, 48: 31, 49: 32, 51: 34, 52: 0, 53: 7} + score: '0.682' + edge_lig_23484_lig_23473: + ligand_a: lig_23484 + ligand_b: lig_23473 + atom mapping: {26: 12, 28: 13, 29: 14, 30: 15, 31: 16, 32: 17, 33: 18, 34: 19, + 35: 20, 36: 21, 37: 22, 38: 23, 39: 24, 40: 25, 41: 26, 42: 27, 43: 28, 44: 29, + 45: 31, 46: 30, 47: 32, 48: 33, 49: 34, 51: 36, 52: 37, 53: 38} + score: '0.581' edge_lig_23480_lig_23483: ligand_a: lig_23480 ligand_b: lig_23483 @@ -100,20 +121,13 @@ edges: 35: 31, 36: 32, 37: 33, 38: 34, 39: 35, 40: 36, 41: 37, 42: 38, 43: 39, 44: 40, 45: 41, 46: 43, 47: 42, 48: 44, 49: 45, 50: 46, 51: 47, 52: 48} score: '0.520' - edge_lig_23480_lig_23486: - ligand_a: lig_23480 - ligand_b: lig_23486 - atom mapping: {0: 7, 1: 6, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 7: 8, 8: 9, 10: 12, 13: 15, - 14: 20, 15: 19, 16: 18, 17: 17, 18: 16, 19: 56, 20: 57, 21: 55, 22: 54, 23: 26, - 30: 23, 31: 24, 32: 22, 33: 21, 35: 58, 52: 0} - score: '0.488' - edge_lig_23484_lig_23480: + edge_lig_23484_lig_23469: ligand_a: lig_23484 - ligand_b: lig_23480 - atom mapping: {0: 52, 1: 2, 2: 3, 3: 4, 4: 5, 5: 6, 6: 1, 7: 0, 8: 7, 9: 8, 12: 10, - 15: 13, 16: 18, 17: 17, 18: 16, 19: 15, 20: 14, 21: 33, 22: 32, 23: 30, 24: 31, - 26: 23, 54: 22, 55: 21, 56: 19, 57: 20, 58: 35} - score: '0.491' + ligand_b: lig_23469 + atom mapping: {26: 11, 28: 13, 29: 14, 30: 15, 31: 16, 32: 17, 33: 18, 34: 19, + 35: 20, 36: 21, 37: 22, 38: 23, 39: 24, 40: 25, 41: 26, 42: 27, 43: 28, 44: 29, + 45: 31, 46: 30, 47: 32, 48: 33, 49: 34, 51: 36, 52: 37, 53: 38} + score: '0.581' edge_lig_23484_lig_23475: ligand_a: lig_23484 ligand_b: lig_23475 @@ -128,24 +142,10 @@ edges: 36: 26, 37: 27, 38: 28, 39: 29, 40: 30, 41: 31, 42: 32, 43: 33, 44: 34, 45: 36, 46: 35, 47: 37, 48: 38, 49: 39, 51: 41, 52: 0, 53: 7} score: '0.574' - edge_lig_23484_lig_23476: - ligand_a: lig_23484 - ligand_b: lig_23476 - atom mapping: {26: 8, 27: 9, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, 33: 4, 34: 30, - 35: 31, 36: 32, 37: 33, 38: 34, 39: 35, 40: 36, 41: 37, 42: 38, 43: 39, 44: 40, - 45: 41, 46: 42, 47: 43, 48: 44, 49: 45, 51: 47, 52: 0, 53: 7} - score: '0.545' - edge_lig_23484_lig_23472: - ligand_a: lig_23484 - ligand_b: lig_23472 - atom mapping: {26: 8, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, 33: 4, 34: 24, 35: 25, - 36: 26, 37: 27, 38: 28, 39: 29, 40: 30, 41: 31, 42: 32, 43: 33, 44: 34, 45: 36, - 46: 35, 47: 37, 48: 38, 49: 39, 51: 41, 52: 0, 53: 7} - score: '0.574' - edge_lig_23467_lig_23485: - ligand_a: lig_23467 - ligand_b: lig_23485 - atom mapping: {0: 55, 1: 30, 2: 31, 3: 32, 4: 33, 5: 28, 6: 29, 7: 56, 8: 26, - 13: 34, 14: 35, 15: 36, 16: 37, 17: 38, 18: 39, 19: 40, 20: 41, 21: 42, 22: 43, - 23: 44, 24: 46, 25: 45, 26: 47, 27: 48, 28: 49, 29: 50, 30: 54} - score: '0.684' + edge_lig_23480_lig_23486: + ligand_a: lig_23480 + ligand_b: lig_23486 + atom mapping: {0: 59, 1: 2, 2: 1, 3: 6, 4: 5, 5: 4, 6: 3, 7: 58, 8: 9, 10: 12, + 13: 15, 14: 20, 15: 19, 16: 18, 17: 17, 18: 16, 19: 56, 20: 57, 21: 55, 22: 54, + 23: 26, 30: 23, 31: 24, 32: 22, 33: 21, 35: 8, 52: 0} + score: '0.488' diff --git a/data/shp2/03_edges/01_perses_openfe.yml b/data/shp2/03_edges/01_perses_openfe.yml index 559c2a728..3831570c5 100644 --- a/data/shp2/03_edges/01_perses_openfe.yml +++ b/data/shp2/03_edges/01_perses_openfe.yml @@ -1,37 +1,67 @@ mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph +planner: openfe v0.5 minimal_spanning_graph edges: - edge_lig_E14_lig_E29: - ligand_a: lig_E14 - ligand_b: lig_E29 - atom mapping: {0: 6, 1: 5, 2: 4, 3: 3, 15: 30, 16: 31, 17: 32, 18: 33, 19: 29, - 20: 7} - score: '0.305' - edge_lig_E14_lig_E6: - ligand_a: lig_E14 - ligand_b: lig_E6 - atom mapping: {1: 13, 2: 11, 3: 10, 4: 9, 5: 7, 7: 5, 9: 3, 10: 4, 11: 2, 12: 1, - 13: 41, 15: 37, 16: 38, 17: 40, 18: 39, 19: 36, 20: 14} - score: '0.558' edge_lig_E14_lig_10: ligand_a: lig_E14 ligand_b: lig_10 atom mapping: {0: 26, 1: 25, 2: 27, 3: 28, 4: 29, 5: 38, 7: 36, 9: 34, 10: 35, 11: 32, 13: 30, 15: 1, 19: 2, 20: 3} score: '0.507' + edge_lig_E14_lig_E30: + ligand_a: lig_E14 + ligand_b: lig_E30 + atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 39, + 15: 35, 16: 36, 17: 38, 18: 37, 19: 34, 20: 12} + score: '0.540' + edge_lig_E14_lig_SHP099-1: + ligand_a: lig_E14 + ligand_b: lig_SHP099-1 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 13, 7: 11, 9: 9, 10: 10, 11: 7, + 13: 5, 15: 15, 16: 16, 17: 18, 18: 17, 19: 19, 20: 20} + score: '0.555' + edge_lig_E3_lig_E14: + ligand_a: lig_E3 + ligand_b: lig_E14 + atom mapping: {6: 3, 7: 2, 9: 1, 10: 20, 32: 19, 33: 15, 34: 16, 35: 17, 36: 18} + score: '0.292' + edge_lig_E28_lig_7: + ligand_a: lig_E28 + ligand_b: lig_7 + atom mapping: {15: 33, 16: 1, 17: 2, 19: 3, 20: 4, 21: 5, 22: 6, 23: 7, 24: 8, + 25: 9, 26: 10, 27: 11, 28: 13, 35: 22, 36: 24, 37: 23, 38: 25, 39: 27, 40: 26, + 41: 28, 42: 29, 43: 30, 44: 32, 45: 31} + score: '0.534' + edge_lig_6_lig_E14: + ligand_a: lig_6 + ligand_b: lig_E14 + atom mapping: {1: 2, 2: 1, 3: 20, 22: 19, 23: 15, 24: 16, 25: 18, 26: 17, 27: 3, + 28: 4, 29: 13, 31: 11, 33: 9, 34: 10, 35: 7, 37: 5} + score: '0.544' + edge_lig_E8_lig_E14: + ligand_a: lig_E8 + ligand_b: lig_E14 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 13, 7: 11, 9: 9, 10: 10, 11: 7, + 13: 5, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20} + score: '0.551' edge_lig_E14_lig_E2: ligand_a: lig_E14 ligand_b: lig_E2 atom mapping: {1: 2, 2: 1, 3: 30, 4: 31, 5: 43, 7: 38, 9: 36, 10: 37, 11: 34, 13: 32, 15: 26, 16: 27, 17: 29, 18: 28, 19: 25, 20: 3} score: '0.540' - edge_lig_E14_lig_E1: + edge_lig_E14_lig_E22: ligand_a: lig_E14 - ligand_b: lig_E1 - atom mapping: {1: 2, 2: 1, 3: 30, 4: 31, 5: 40, 7: 38, 9: 36, 10: 37, 11: 34, - 13: 32, 15: 26, 16: 27, 17: 29, 18: 28, 19: 25, 20: 3} - score: '0.540' + ligand_b: lig_E22 + atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 40, + 15: 36, 16: 37, 17: 39, 18: 38, 19: 35, 20: 13} + score: '0.536' + edge_lig_E14_lig_E28: + ligand_a: lig_E14 + ligand_b: lig_E28 + atom mapping: {0: 18, 1: 17, 2: 16, 3: 15, 15: 42, 16: 43, 17: 44, 18: 45, 19: 41, + 20: 19} + score: '0.296' edge_lig_E4_lig_E27: ligand_a: lig_E4 ligand_b: lig_E27 @@ -39,113 +69,77 @@ edges: 14: 34, 15: 31, 23: 25, 25: 26, 26: 22, 27: 24, 28: 23, 29: 19, 30: 15, 31: 16, 32: 18, 33: 17} score: '0.520' - edge_lig_E14_lig_E3: - ligand_a: lig_E14 - ligand_b: lig_E3 - atom mapping: {1: 9, 2: 7, 3: 6, 15: 33, 16: 34, 17: 35, 18: 36, 19: 32, 20: 10} - score: '0.292' - edge_lig_E14_lig_E26: - ligand_a: lig_E14 - ligand_b: lig_E26 - atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 44, - 15: 40, 16: 41, 17: 43, 18: 42, 19: 39, 20: 17} - score: '0.529' - edge_lig_E14_lig_E28: + edge_lig_E14_lig_E6: ligand_a: lig_E14 - ligand_b: lig_E28 - atom mapping: {0: 18, 1: 17, 2: 16, 3: 15, 15: 42, 16: 43, 17: 44, 18: 45, 19: 41, - 20: 19} - score: '0.296' - edge_lig_E8_lig_E14: - ligand_a: lig_E8 - ligand_b: lig_E14 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 13, 7: 11, 9: 9, 10: 10, 11: 7, - 13: 5, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20} - score: '0.551' - edge_lig_7_lig_E28: - ligand_a: lig_7 - ligand_b: lig_E28 - atom mapping: {1: 16, 2: 17, 3: 19, 4: 20, 5: 21, 6: 23, 7: 22, 8: 24, 9: 26, - 10: 25, 11: 27, 13: 28, 22: 35, 23: 37, 24: 36, 25: 38, 26: 40, 27: 39, 28: 41, - 29: 42, 30: 43, 31: 44, 32: 45, 33: 15} - score: '0.534' - edge_lig_E9_lig_E14: - ligand_a: lig_E9 - ligand_b: lig_E14 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 13, 7: 11, 9: 9, 10: 10, 11: 7, - 13: 5, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20} - score: '0.555' - edge_lig_3_lig_E28: - ligand_a: lig_3 + ligand_b: lig_E6 + atom mapping: {1: 13, 2: 11, 3: 10, 4: 9, 5: 7, 7: 5, 9: 3, 10: 4, 11: 2, 12: 1, + 13: 41, 15: 37, 16: 38, 17: 40, 18: 39, 19: 36, 20: 14} + score: '0.558' + edge_lig_SHP836-2_lig_E28: + ligand_a: lig_SHP836-2 ligand_b: lig_E28 atom mapping: {1: 16, 2: 17, 3: 19, 4: 20, 5: 38, 6: 40, 7: 39, 8: 35, 9: 36, 14: 27, 16: 24, 17: 25, 22: 21, 23: 23, 24: 22, 25: 41, 26: 42, 27: 43, 28: 45, 29: 44, 30: 15} score: '0.508' - edge_lig_E14_lig_E24: + edge_lig_E14_lig_E25: ligand_a: lig_E14 - ligand_b: lig_E24 - atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 43, - 15: 39, 16: 40, 17: 42, 18: 41, 19: 38, 20: 16} - score: '0.536' - edge_lig_E28_lig_E5: - ligand_a: lig_E28 - ligand_b: lig_E5 - atom mapping: {15: 30, 16: 1, 17: 2, 19: 3, 20: 4, 21: 5, 22: 6, 23: 7, 24: 8, - 25: 9, 26: 10, 27: 11, 28: 16, 32: 12, 35: 19, 36: 21, 37: 20, 38: 22, 39: 24, - 40: 23, 41: 25, 42: 26, 43: 27, 44: 29, 45: 28} - score: '0.543' - edge_lig_SHP836-2_lig_E28: - ligand_a: lig_SHP836-2 + ligand_b: lig_E25 + atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 41, + 15: 37, 16: 38, 17: 40, 18: 39, 19: 36, 20: 14} + score: '0.532' + edge_lig_3_lig_E28: + ligand_a: lig_3 ligand_b: lig_E28 atom mapping: {1: 16, 2: 17, 3: 19, 4: 20, 5: 38, 6: 40, 7: 39, 8: 35, 9: 36, 14: 27, 16: 24, 17: 25, 22: 21, 23: 23, 24: 22, 25: 41, 26: 42, 27: 43, 28: 45, 29: 44, 30: 15} score: '0.508' - edge_lig_E14_lig_11: - ligand_a: lig_E14 - ligand_b: lig_11 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 13, 7: 11, 9: 9, 10: 10, 11: 7, - 13: 5, 15: 15, 16: 16, 18: 17, 19: 22, 20: 23} - score: '0.536' edge_lig_E14_lig_E23: ligand_a: lig_E14 ligand_b: lig_E23 atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 40, 15: 36, 16: 37, 17: 39, 18: 38, 19: 35, 20: 13} score: '0.536' - edge_lig_E14_lig_SHP099-1: + edge_lig_E14_lig_E24: ligand_a: lig_E14 - ligand_b: lig_SHP099-1 + ligand_b: lig_E24 + atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 43, + 15: 39, 16: 40, 17: 42, 18: 41, 19: 38, 20: 16} + score: '0.536' + edge_lig_E9_lig_E14: + ligand_a: lig_E9 + ligand_b: lig_E14 atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 13, 7: 11, 9: 9, 10: 10, 11: 7, - 13: 5, 15: 15, 16: 16, 17: 18, 18: 17, 19: 19, 20: 20} + 13: 5, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20} score: '0.555' - edge_lig_E14_lig_E30: - ligand_a: lig_E14 - ligand_b: lig_E30 - atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 39, - 15: 35, 16: 36, 17: 38, 18: 37, 19: 34, 20: 12} - score: '0.540' - edge_lig_E14_lig_E25: + edge_lig_E14_lig_11: ligand_a: lig_E14 - ligand_b: lig_E25 - atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 41, - 15: 37, 16: 38, 17: 40, 18: 39, 19: 36, 20: 14} - score: '0.532' - edge_lig_E14_lig_E4: + ligand_b: lig_11 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 13, 7: 11, 9: 9, 10: 10, 11: 7, + 13: 5, 15: 15, 16: 16, 18: 17, 19: 22, 20: 23} + score: '0.536' + edge_lig_E14_lig_E29: ligand_a: lig_E14 - ligand_b: lig_E4 - atom mapping: {1: 6, 2: 4, 3: 3, 15: 30, 16: 31, 17: 33, 18: 32, 19: 29, 20: 7} + ligand_b: lig_E29 + atom mapping: {0: 6, 1: 5, 2: 4, 3: 3, 15: 30, 16: 31, 17: 32, 18: 33, 19: 29, + 20: 7} + score: '0.305' + edge_lig_E28_lig_E5: + ligand_a: lig_E28 + ligand_b: lig_E5 + atom mapping: {15: 30, 16: 1, 17: 2, 19: 3, 20: 4, 21: 5, 22: 6, 23: 7, 24: 8, + 25: 9, 26: 10, 27: 11, 28: 16, 32: 12, 35: 19, 36: 21, 37: 20, 38: 22, 39: 24, + 40: 23, 41: 25, 42: 26, 43: 27, 44: 29, 45: 28} + score: '0.543' + edge_lig_E4_lig_E14: + ligand_a: lig_E4 + ligand_b: lig_E14 + atom mapping: {3: 3, 4: 2, 6: 1, 7: 20, 29: 19, 30: 15, 31: 16, 32: 17, 33: 18} score: '0.292' - edge_lig_E14_lig_E22: - ligand_a: lig_E14 - ligand_b: lig_E22 - atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 40, - 15: 36, 16: 37, 17: 39, 18: 38, 19: 35, 20: 13} - score: '0.536' - edge_lig_6_lig_E14: - ligand_a: lig_6 + edge_lig_E1_lig_E14: + ligand_a: lig_E1 ligand_b: lig_E14 - atom mapping: {1: 2, 2: 1, 3: 20, 22: 19, 23: 15, 24: 16, 25: 18, 26: 17, 27: 3, - 28: 4, 29: 13, 31: 11, 33: 9, 34: 10, 35: 7, 37: 5} - score: '0.544' + atom mapping: {1: 2, 2: 1, 3: 20, 25: 19, 26: 15, 27: 16, 28: 17, 29: 18, 30: 3, + 31: 4, 32: 13, 34: 11, 36: 9, 37: 10, 38: 7, 40: 5} + score: '0.540' diff --git a/data/syk/03_edges/01_perses_openfe.yml b/data/syk/03_edges/01_perses_openfe.yml index 0ae6d65aa..2a7975a12 100644 --- a/data/syk/03_edges/01_perses_openfe.yml +++ b/data/syk/03_edges/01_perses_openfe.yml @@ -1,126 +1,168 @@ mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph +planner: openfe v0.5 minimal_spanning_graph edges: - edge_lig_CHEMBL3265014_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265014 + edge_lig_CHEMBL3264994_lig_CHEMBL3265022: + ligand_a: lig_CHEMBL3264994 + ligand_b: lig_CHEMBL3265022 + atom mapping: {0: 19, 1: 18, 2: 20, 3: 21, 4: 15, 5: 16, 6: 17, 7: 22, 8: 23, + 9: 24, 10: 25, 11: 42, 12: 43, 13: 36, 15: 30, 16: 31, 21: 32, 22: 33, 23: 34, + 24: 35, 29: 28, 30: 29, 31: 26, 32: 27, 33: 44, 34: 12, 62: 13, 63: 14} + score: '0.507' + edge_lig_CHEMBL3265002_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265002 ligand_b: lig_CHEMBL3265031 - atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, - 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 50: 39, 51: 40} - score: '0.464' - edge_lig_CHEMBL3265018_lig_CHEMBL3264994: - ligand_a: lig_CHEMBL3265018 - ligand_b: lig_CHEMBL3264994 - atom mapping: {9: 34, 10: 62, 11: 63, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, - 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, - 28: 16, 29: 17, 30: 18, 31: 19, 32: 20, 33: 29, 39: 31, 40: 32, 41: 33} - score: '0.524' - edge_lig_CHEMBL3264998_lig_CHEMBL3265031: + atom mapping: {25: 24, 26: 39, 27: 40, 28: 41, 29: 42, 30: 43, 31: 44, 32: 45, + 33: 46, 34: 47, 35: 22, 36: 20, 37: 21, 38: 19, 39: 48, 40: 49, 41: 50, 42: 51, + 43: 14, 49: 15, 55: 17, 56: 18, 57: 23} + score: '0.397' + edge_lig_CHEMBL3265003_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265003 + ligand_b: lig_CHEMBL3265031 + atom mapping: {24: 24, 25: 39, 26: 40, 27: 41, 28: 42, 29: 43, 30: 44, 31: 45, + 32: 46, 33: 47, 34: 22, 35: 20, 36: 21, 37: 19, 38: 17, 39: 18, 40: 15, 41: 16, + 42: 14, 48: 50, 54: 48, 55: 49, 56: 23} + score: '0.397' + edge_lig_CHEMBL3264998_lig_CHEMBL3265027: ligand_a: lig_CHEMBL3264998 + ligand_b: lig_CHEMBL3265027 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 29, 27: 31, 28: 32, + 29: 33, 30: 9, 61: 10, 62: 11} + score: '0.499' + edge_lig_CHEMBL3264994_lig_CHEMBL3265019: + ligand_a: lig_CHEMBL3264994 + ligand_b: lig_CHEMBL3265019 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 25: 17, 26: 18, 27: 19, 28: 20, + 29: 21, 31: 27, 32: 28, 33: 29, 34: 30, 62: 44, 63: 45} + score: '0.530' + edge_lig_CHEMBL3265033_lig_CHEMBL3265024: + ligand_a: lig_CHEMBL3265033 + ligand_b: lig_CHEMBL3265024 + atom mapping: {9: 30, 10: 48, 11: 49, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, + 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, + 44: 21, 46: 27, 47: 28, 48: 29} + score: '0.474' + edge_lig_CHEMBL3265012_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265012 ligand_b: lig_CHEMBL3265031 atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 61: 39, 62: 40} - score: '0.402' - edge_lig_CHEMBL3265021_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265021 - ligand_b: lig_CHEMBL3265031 - atom mapping: {11: 24, 12: 39, 13: 40, 14: 41, 15: 42, 16: 43, 17: 44, 18: 45, - 19: 46, 20: 47, 21: 22, 22: 20, 23: 21, 24: 19, 25: 17, 26: 18, 27: 15, 28: 16, - 29: 14, 35: 50, 41: 48, 42: 49, 43: 23} - score: '0.491' - edge_lig_CHEMBL3265005_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265005 + 29: 23, 30: 24, 46: 39, 47: 40} + score: '0.485' + edge_lig_CHEMBL3265001_lig_CHEMBL3265030_n: + ligand_a: lig_CHEMBL3265001 + ligand_b: lig_CHEMBL3265030_n + atom mapping: {0: 42, 1: 41, 2: 43, 3: 44, 4: 38, 5: 39, 6: 40, 7: 19, 8: 17, + 9: 18, 10: 16, 11: 45, 12: 46, 13: 47, 14: 48, 15: 11, 21: 12, 27: 14, 28: 15, + 29: 20, 30: 21, 60: 36, 61: 37} + score: '0.417' + edge_lig_CHEMBL3264995_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3264995 ligand_b: lig_CHEMBL3265031 atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 46: 39, 47: 40} - score: '0.485' - edge_lig_CHEMBL3265031_lig_CHEMBL3264999: - ligand_a: lig_CHEMBL3265031 - ligand_b: lig_CHEMBL3264999 - atom mapping: {14: 15, 15: 13, 16: 14, 17: 11, 18: 12, 19: 10, 20: 8, 21: 9, 22: 7, - 23: 29, 24: 30, 39: 60, 40: 61, 41: 4, 42: 5, 43: 6, 44: 1, 45: 0, 46: 2, 47: 3, - 48: 27, 49: 28, 50: 21} + 29: 23, 30: 24, 58: 39, 59: 40} score: '0.404' - edge_lig_CHEMBL3265015_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265015 + edge_lig_CHEMBL3265000_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265000 + ligand_b: lig_CHEMBL3265033 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 44, 27: 46, 28: 47, + 29: 48, 30: 9, 65: 10, 66: 11} + score: '0.412' + edge_lig_CHEMBL3264999_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3264999 ligand_b: lig_CHEMBL3265031 atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 49: 39, 50: 40} - score: '0.469' - edge_lig_CHEMBL3265024_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265024 + 29: 23, 30: 24, 60: 39, 61: 40} + score: '0.404' + edge_lig_CHEMBL3265001_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265001 ligand_b: lig_CHEMBL3265031 atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 48: 39, 49: 40} - score: '0.474' - edge_lig_CHEMBL3264996_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3264996 + 29: 23, 30: 24, 60: 39, 61: 40} + score: '0.397' + edge_lig_CHEMBL3264998_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3264998 ligand_b: lig_CHEMBL3265031 atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 62: 39, 63: 40} + 29: 23, 30: 24, 61: 39, 62: 40} score: '0.402' - edge_lig_CHEMBL3265000_lig_CHEMBL3265032: - ligand_a: lig_CHEMBL3265000 - ligand_b: lig_CHEMBL3265032 - atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, - 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 42, 27: 44, 28: 45, - 29: 46, 30: 9, 65: 10, 66: 11} - score: '0.421' - edge_lig_CHEMBL3265002_lig_CHEMBL3265035: - ligand_a: lig_CHEMBL3265002 - ligand_b: lig_CHEMBL3265035 - atom mapping: {25: 19, 26: 34, 27: 35, 28: 36, 29: 37, 30: 38, 31: 39, 32: 40, - 33: 41, 34: 42, 35: 17, 36: 15, 37: 16, 38: 14, 39: 12, 40: 13, 41: 10, 42: 11, - 43: 9, 44: 8, 45: 5, 46: 7, 47: 6, 49: 45, 55: 43, 56: 44, 57: 18} - score: '0.472' - edge_lig_CHEMBL3265011_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265011 + edge_lig_CHEMBL3265006_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265006 ligand_b: lig_CHEMBL3265031 atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, 29: 23, 30: 24, 49: 39, 50: 40} score: '0.469' - edge_lig_CHEMBL3265000_lig_CHEMBL3265034: + edge_lig_CHEMBL3265000_lig_CHEMBL3265036: ligand_a: lig_CHEMBL3265000 - ligand_b: lig_CHEMBL3265034 + ligand_b: lig_CHEMBL3265036 atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, - 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 43, 27: 45, 28: 46, - 29: 47, 30: 9, 65: 10, 66: 11} - score: '0.416' - edge_lig_CHEMBL3265028_lig_CHEMBL3264994: - ligand_a: lig_CHEMBL3265028 - ligand_b: lig_CHEMBL3264994 - atom mapping: {9: 34, 10: 62, 11: 63, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, - 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, - 29: 29, 35: 31, 36: 32, 37: 33} - score: '0.479' - edge_lig_CHEMBL3259820_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3259820 - ligand_b: lig_CHEMBL3265031 - atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, - 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 46: 39, 47: 40} - score: '0.485' - edge_lig_CHEMBL3265025_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265025 - ligand_b: lig_CHEMBL3265031 - atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, - 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 48: 39, 49: 40} - score: '0.474' + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 45, 27: 47, 28: 48, + 29: 49, 30: 9, 65: 10, 66: 11} + score: '0.407' + edge_lig_CHEMBL3264994_lig_CHEMBL3265018: + ligand_a: lig_CHEMBL3264994 + ligand_b: lig_CHEMBL3265018 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 16: 28, 25: 29, 26: 30, + 27: 31, 28: 32, 29: 33, 31: 39, 32: 40, 33: 41, 34: 9, 62: 10, 63: 11} + score: '0.524' + edge_lig_CHEMBL3265001_lig_CHEMBL3265029: + ligand_a: lig_CHEMBL3265001 + ligand_b: lig_CHEMBL3265029 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 16: 28, 17: 29, 18: 32, + 19: 31, 20: 30, 21: 33, 27: 35, 28: 36, 29: 37, 30: 9, 60: 10, 61: 11} + score: '0.530' + edge_lig_CHEMBL3265009_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265009 + ligand_b: lig_CHEMBL3265033 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 44, 27: 46, 28: 47, + 29: 48, 30: 9, 49: 10, 50: 11} + score: '0.469' edge_lig_CHEMBL3265004_lig_CHEMBL3265031: ligand_a: lig_CHEMBL3265004 ligand_b: lig_CHEMBL3265031 atom mapping: {26: 24, 27: 39, 28: 40, 29: 41, 30: 42, 31: 43, 32: 44, 33: 45, - 34: 46, 35: 47, 36: 22, 37: 20, 38: 21, 39: 19, 40: 48, 41: 49, 42: 50, 43: 51, - 44: 14, 50: 15, 56: 17, 57: 18, 58: 23} + 34: 46, 35: 47, 36: 22, 37: 20, 38: 21, 39: 19, 40: 17, 41: 18, 42: 15, 43: 16, + 44: 14, 50: 50, 56: 48, 57: 49, 58: 23} score: '0.397' + edge_lig_CHEMBL3265001_lig_CHEMBL3265035: + ligand_a: lig_CHEMBL3265001 + ligand_b: lig_CHEMBL3265035 + atom mapping: {0: 40, 1: 39, 2: 41, 3: 42, 4: 36, 5: 37, 6: 38, 7: 17, 8: 15, + 9: 16, 10: 14, 11: 43, 12: 44, 13: 45, 14: 46, 15: 9, 16: 8, 17: 5, 18: 7, 19: 6, + 21: 10, 27: 12, 28: 13, 29: 18, 30: 19, 60: 34, 61: 35} + score: '0.472' + edge_lig_CHEMBL3265033_lig_CHEMBL3265025: + ligand_a: lig_CHEMBL3265033 + ligand_b: lig_CHEMBL3265025 + atom mapping: {9: 30, 10: 48, 11: 49, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, + 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, + 44: 21, 46: 27, 47: 28, 48: 29} + score: '0.474' + edge_lig_CHEMBL3265023_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265023 + ligand_b: lig_CHEMBL3265031 + atom mapping: {14: 24, 15: 39, 16: 40, 17: 41, 18: 42, 19: 43, 20: 44, 21: 45, + 22: 46, 23: 47, 24: 22, 25: 20, 26: 21, 27: 19, 28: 48, 29: 49, 30: 50, 31: 51, + 32: 14, 38: 15, 44: 17, 45: 18, 46: 23} + score: '0.474' + edge_lig_CHEMBL3265033_lig_CHEMBL3265026: + ligand_a: lig_CHEMBL3265033 + ligand_b: lig_CHEMBL3265026 + atom mapping: {9: 30, 10: 49, 11: 50, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, + 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, + 44: 21, 46: 27, 47: 28, 48: 29} + score: '0.469' edge_lig_CHEMBL3265000_lig_CHEMBL3265031: ligand_a: lig_CHEMBL3265000 ligand_b: lig_CHEMBL3265031 @@ -128,111 +170,83 @@ edges: 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, 29: 23, 30: 24, 65: 39, 66: 40} score: '0.397' - edge_lig_CHEMBL3265016_lig_CHEMBL3264994: - ligand_a: lig_CHEMBL3265016 - ligand_b: lig_CHEMBL3264994 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 20, 19: 19, 20: 18, - 21: 29, 27: 31, 28: 32, 29: 33, 30: 34, 46: 62, 47: 63} - score: '0.518' - edge_lig_CHEMBL3265020_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265020 - ligand_b: lig_CHEMBL3265031 - atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, - 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 46: 39, 47: 40} - score: '0.485' - edge_lig_CHEMBL3265008_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265008 - ligand_b: lig_CHEMBL3265031 - atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, - 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 46: 39, 47: 40} + edge_lig_CHEMBL3265033_lig_CHEMBL3265020: + ligand_a: lig_CHEMBL3265033 + ligand_b: lig_CHEMBL3265020 + atom mapping: {9: 30, 10: 46, 11: 47, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, + 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, + 44: 21, 46: 27, 47: 28, 48: 29} score: '0.485' - edge_lig_CHEMBL3265023_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3265023 - ligand_b: lig_CHEMBL3265033 - atom mapping: {14: 9, 15: 10, 16: 11, 17: 12, 18: 13, 19: 14, 20: 15, 21: 16, - 22: 17, 23: 18, 24: 19, 25: 20, 26: 21, 27: 22, 28: 23, 29: 24, 30: 25, 31: 26, - 32: 27, 38: 44, 44: 46, 45: 47, 46: 48} - score: '0.474' - edge_lig_CHEMBL3265000_lig_CHEMBL3265033: + edge_lig_CHEMBL3265000_lig_CHEMBL3265034: ligand_a: lig_CHEMBL3265000 + ligand_b: lig_CHEMBL3265034 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 43, 27: 45, 28: 46, + 29: 47, 30: 9, 65: 10, 66: 11} + score: '0.416' + edge_lig_CHEMBL3265033_lig_CHEMBL3265021: + ligand_a: lig_CHEMBL3265033 + ligand_b: lig_CHEMBL3265021 + atom mapping: {9: 11, 10: 12, 11: 13, 12: 14, 13: 15, 14: 16, 15: 17, 16: 18, + 17: 19, 18: 20, 19: 21, 20: 22, 21: 23, 22: 24, 23: 25, 24: 26, 25: 27, 26: 28, + 27: 29, 44: 35, 46: 41, 47: 42, 48: 43} + score: '0.491' + edge_lig_CHEMBL3265011_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265011 ligand_b: lig_CHEMBL3265033 atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 44, 27: 46, 28: 47, - 29: 48, 30: 9, 65: 10, 66: 11} - score: '0.412' - edge_lig_CHEMBL3265013_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265013 - ligand_b: lig_CHEMBL3265031 - atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, - 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 49: 39, 50: 40} + 29: 48, 30: 9, 49: 10, 50: 11} score: '0.469' - edge_lig_CHEMBL3265037_lig_CHEMBL3264994: - ligand_a: lig_CHEMBL3265037 - ligand_b: lig_CHEMBL3264994 - atom mapping: {9: 34, 10: 62, 11: 63, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, - 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, - 42: 29, 48: 31, 49: 32, 50: 33} - score: '0.412' - edge_lig_CHEMBL3265002_lig_CHEMBL3265030_n: - ligand_a: lig_CHEMBL3265002 - ligand_b: lig_CHEMBL3265030_n - atom mapping: {25: 21, 26: 36, 27: 37, 28: 38, 29: 39, 30: 40, 31: 41, 32: 42, - 33: 43, 34: 44, 35: 19, 36: 17, 37: 18, 38: 16, 39: 45, 40: 46, 41: 47, 42: 48, - 43: 11, 49: 12, 55: 14, 56: 15, 57: 20} - score: '0.417' - edge_lig_CHEMBL3265001_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265001 - ligand_b: lig_CHEMBL3265031 - atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, - 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 60: 39, 61: 40} - score: '0.397' - edge_lig_CHEMBL3265002_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265002 - ligand_b: lig_CHEMBL3265031 - atom mapping: {25: 24, 26: 39, 27: 40, 28: 41, 29: 42, 30: 43, 31: 44, 32: 45, - 33: 46, 34: 47, 35: 22, 36: 20, 37: 21, 38: 19, 39: 17, 40: 18, 41: 15, 42: 16, - 43: 14, 49: 50, 55: 48, 56: 49, 57: 23} - score: '0.397' - edge_lig_CHEMBL3265012_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265012 + edge_lig_CHEMBL3264994_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3264994 ligand_b: lig_CHEMBL3265031 atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, - 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 46: 39, 47: 40} + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 29: 15, 30: 16, 31: 17, + 32: 18, 33: 23, 34: 24, 62: 39, 63: 40} + score: '0.414' + edge_lig_CHEMBL3265033_lig_CHEMBL3265013: + ligand_a: lig_CHEMBL3265033 + ligand_b: lig_CHEMBL3265013 + atom mapping: {9: 30, 10: 49, 11: 50, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, + 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, + 44: 21, 46: 27, 47: 28, 48: 29} + score: '0.469' + edge_lig_CHEMBL3265010_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265010 + ligand_b: lig_CHEMBL3265033 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 44, 27: 46, 28: 47, + 29: 48, 30: 9, 50: 10, 51: 11} + score: '0.464' + edge_lig_CHEMBL3264994_lig_CHEMBL3265028: + ligand_a: lig_CHEMBL3264994 + ligand_b: lig_CHEMBL3265028 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 29: 29, 31: 35, 32: 36, + 33: 37, 34: 9, 62: 10, 63: 11} + score: '0.479' + edge_lig_CHEMBL3264994_lig_CHEMBL3265016: + ligand_a: lig_CHEMBL3264994 + ligand_b: lig_CHEMBL3265016 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 27, 12: 28, 13: 21, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 29: 13, + 30: 14, 31: 11, 32: 12, 33: 29, 34: 30, 62: 46, 63: 47} + score: '0.518' + edge_lig_CHEMBL3265005_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265005 + ligand_b: lig_CHEMBL3265033 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 44, 27: 46, 28: 47, + 29: 48, 30: 9, 46: 10, 47: 11} score: '0.485' - edge_lig_CHEMBL3265009_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265009 + edge_lig_CHEMBL3264996_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3264996 ligand_b: lig_CHEMBL3265031 atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 49: 39, 50: 40} - score: '0.469' - edge_lig_CHEMBL3265017_lig_CHEMBL3264994: - ligand_a: lig_CHEMBL3265017 - ligand_b: lig_CHEMBL3264994 - atom mapping: {9: 34, 10: 62, 11: 63, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, - 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, - 28: 16, 29: 21, 30: 24, 31: 23, 32: 22, 33: 29, 39: 31, 40: 32, 41: 33} - score: '0.524' - edge_lig_CHEMBL3265019_lig_CHEMBL3264994: - ligand_a: lig_CHEMBL3265019 - ligand_b: lig_CHEMBL3264994 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 21, 18: 24, 19: 23, 20: 22, - 21: 29, 27: 31, 28: 32, 29: 33, 30: 34, 44: 62, 45: 63} - score: '0.530' - edge_lig_CHEMBL3265022_lig_CHEMBL3264994: - ligand_a: lig_CHEMBL3265022 - ligand_b: lig_CHEMBL3264994 - atom mapping: {12: 34, 13: 62, 14: 63, 15: 4, 16: 5, 17: 6, 18: 1, 19: 0, 20: 2, - 21: 3, 22: 7, 23: 8, 24: 9, 25: 10, 26: 31, 27: 32, 28: 29, 29: 30, 30: 15, - 31: 16, 32: 25, 33: 28, 34: 27, 35: 26, 36: 13, 42: 11, 43: 12, 44: 33} - score: '0.507' + 29: 23, 30: 24, 62: 39, 63: 40} + score: '0.402' edge_lig_CHEMBL3264997_lig_CHEMBL3265031: ligand_a: lig_CHEMBL3264997 ligand_b: lig_CHEMBL3265031 @@ -240,66 +254,52 @@ edges: 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, 29: 23, 30: 24, 58: 39, 59: 40} score: '0.404' - edge_lig_CHEMBL3265000_lig_CHEMBL3265036: + edge_lig_CHEMBL3264994_lig_CHEMBL3265017: + ligand_a: lig_CHEMBL3264994 + ligand_b: lig_CHEMBL3265017 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 39, 12: 40, 13: 33, 15: 27, 16: 28, 21: 29, 22: 30, 23: 31, + 24: 32, 29: 25, 30: 26, 31: 23, 32: 24, 33: 41, 34: 9, 62: 10, 63: 11} + score: '0.524' + edge_lig_CHEMBL3265000_lig_CHEMBL3265032: ligand_a: lig_CHEMBL3265000 - ligand_b: lig_CHEMBL3265036 + ligand_b: lig_CHEMBL3265032 atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, - 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 45, 27: 47, 28: 48, - 29: 49, 30: 9, 65: 10, 66: 11} - score: '0.407' - edge_lig_CHEMBL3265026_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3265026 + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 42, 27: 44, 28: 45, + 29: 46, 30: 9, 65: 10, 66: 11} + score: '0.421' + edge_lig_CHEMBL3264994_lig_CHEMBL3265037: + ligand_a: lig_CHEMBL3264994 + ligand_b: lig_CHEMBL3265037 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 29: 42, 31: 48, 32: 49, + 33: 50, 34: 9, 62: 10, 63: 11} + score: '0.412' + edge_lig_CHEMBL3265008_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265008 ligand_b: lig_CHEMBL3265033 atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 44, 27: 46, 28: 47, - 29: 48, 30: 9, 49: 10, 50: 11} - score: '0.469' - edge_lig_CHEMBL3265002_lig_CHEMBL3265029: - ligand_a: lig_CHEMBL3265002 - ligand_b: lig_CHEMBL3265029 - atom mapping: {25: 9, 26: 10, 27: 11, 28: 12, 29: 13, 30: 14, 31: 15, 32: 16, - 33: 17, 34: 18, 35: 19, 36: 20, 37: 21, 38: 22, 39: 23, 40: 24, 41: 25, 42: 26, - 43: 27, 44: 28, 45: 29, 46: 32, 47: 31, 48: 30, 49: 33, 55: 35, 56: 36, 57: 37} - score: '0.530' - edge_lig_CHEMBL3265031_lig_CHEMBL3264994: - ligand_a: lig_CHEMBL3265031 - ligand_b: lig_CHEMBL3264994 - atom mapping: {14: 15, 15: 13, 16: 14, 17: 11, 18: 12, 19: 10, 20: 8, 21: 9, 22: 7, - 23: 33, 24: 34, 39: 62, 40: 63, 41: 4, 42: 5, 43: 6, 44: 1, 45: 0, 46: 2, 47: 3, - 48: 31, 49: 32, 50: 29, 51: 30} - score: '0.414' - edge_lig_CHEMBL3265010_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265010 - ligand_b: lig_CHEMBL3265031 - atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, - 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 50: 39, 51: 40} + 29: 48, 30: 9, 46: 10, 47: 11} + score: '0.485' + edge_lig_CHEMBL3265033_lig_CHEMBL3265014: + ligand_a: lig_CHEMBL3265033 + ligand_b: lig_CHEMBL3265014 + atom mapping: {9: 30, 10: 50, 11: 51, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, + 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, + 44: 21, 46: 27, 47: 28, 48: 29} score: '0.464' - edge_lig_CHEMBL3264995_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3264995 - ligand_b: lig_CHEMBL3265031 - atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, - 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 58: 39, 59: 40} - score: '0.404' - edge_lig_CHEMBL3265006_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265006 - ligand_b: lig_CHEMBL3265031 - atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, - 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 49: 39, 50: 40} + edge_lig_CHEMBL3265033_lig_CHEMBL3265015: + ligand_a: lig_CHEMBL3265033 + ligand_b: lig_CHEMBL3265015 + atom mapping: {9: 30, 10: 49, 11: 50, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, + 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, + 44: 21, 46: 27, 47: 28, 48: 29} score: '0.469' - edge_lig_CHEMBL3264996_lig_CHEMBL3265027: - ligand_a: lig_CHEMBL3264996 - ligand_b: lig_CHEMBL3265027 - atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, - 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 29, 27: 31, 28: 32, - 29: 33, 30: 9, 62: 10, 63: 11} - score: '0.499' - edge_lig_CHEMBL3265003_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265003 - ligand_b: lig_CHEMBL3265031 - atom mapping: {24: 24, 25: 39, 26: 40, 27: 41, 28: 42, 29: 43, 30: 44, 31: 45, - 32: 46, 33: 47, 34: 22, 35: 20, 36: 21, 37: 19, 38: 17, 39: 18, 40: 15, 41: 16, - 42: 14, 48: 50, 54: 48, 55: 49, 56: 23} - score: '0.397' + edge_lig_CHEMBL3265033_lig_CHEMBL3259820: + ligand_a: lig_CHEMBL3265033 + ligand_b: lig_CHEMBL3259820 + atom mapping: {9: 30, 10: 46, 11: 47, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, + 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, + 44: 21, 46: 27, 47: 28, 48: 29} + score: '0.485' diff --git a/data/thrombin/03_edges/01_perses_openfe.yml b/data/thrombin/03_edges/01_perses_openfe.yml index 26e40c135..58b7f6625 100644 --- a/data/thrombin/03_edges/01_perses_openfe.yml +++ b/data/thrombin/03_edges/01_perses_openfe.yml @@ -1,85 +1,180 @@ mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph +planner: openfe v0.5 minimal_spanning_graph edges: - edge_lig_1d_lig_5: - ligand_a: lig_1d - ligand_b: lig_5 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 24, - 21: 23, 22: 22, 23: 21, 24: 20, 26: 25, 27: 26, 28: 27, 29: 51, 30: 29, 31: 30, - 32: 31, 33: 32, 34: 33, 35: 34, 36: 36, 37: 35, 38: 38, 39: 37, 40: 40, 41: 39, - 42: 41, 43: 42, 44: 43, 45: 45, 46: 44, 47: 50, 48: 49, 49: 48, 50: 46, 51: 28} - score: '0.982' - edge_lig_7a_lig_5: - ligand_a: lig_7a - ligand_b: lig_5 - atom mapping: {1: 21, 2: 22, 3: 23, 4: 24, 5: 19, 6: 20, 7: 18, 8: 17, 9: 15, - 10: 16, 11: 14, 12: 13, 13: 12, 14: 11, 15: 10, 16: 8, 17: 9, 18: 7, 19: 6, - 20: 3, 21: 2, 22: 1, 23: 0, 24: 5, 25: 4, 26: 25, 28: 27, 29: 26, 30: 51, 31: 29, - 35: 48, 36: 49, 37: 46, 38: 45, 39: 44, 40: 43, 41: 42, 42: 41, 43: 39, 44: 40, - 45: 37, 46: 38, 47: 35, 48: 36, 49: 32, 50: 31, 51: 30, 52: 34, 53: 33, 57: 28} - score: '0.964' - edge_lig_6b_lig_5: + edge_lig_7e_lig_7d: + ligand_a: lig_7e + ligand_b: lig_7d + atom mapping: {0: 17, 1: 7, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 1, 8: 18, 9: 19, + 10: 20, 11: 21, 12: 26, 13: 25, 14: 24, 15: 23, 16: 22, 17: 0, 18: 8, 19: 9, + 28: 27, 29: 28, 30: 29, 31: 30, 32: 35, 33: 36, 34: 33, 35: 34, 36: 31, 37: 32, + 38: 53, 39: 52, 40: 58, 41: 57, 42: 56, 43: 55, 44: 54, 45: 37, 46: 38, 47: 39} + score: '0.693' + edge_lig_2e_lig_7d: + ligand_a: lig_2e + ligand_b: lig_7d + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 19: 17, + 20: 18, 21: 19, 22: 20, 23: 21, 24: 26, 25: 25, 26: 24, 27: 23, 28: 22, 29: 27, + 30: 28, 31: 30, 32: 29, 33: 32, 34: 31, 35: 33, 36: 34, 37: 36, 38: 35, 39: 37, + 40: 39, 41: 38, 46: 52, 47: 53, 48: 58, 49: 57, 50: 56, 51: 55, 52: 54} + score: '0.706' + edge_lig_6b_lig_7d: ligand_a: lig_6b - ligand_b: lig_5 - atom mapping: {1: 20, 2: 21, 3: 22, 4: 23, 5: 24, 6: 19, 7: 18, 8: 17, 9: 15, - 10: 16, 11: 14, 12: 13, 13: 12, 14: 11, 15: 10, 16: 8, 17: 9, 18: 7, 19: 6, - 20: 3, 21: 4, 22: 5, 23: 0, 24: 1, 25: 2, 26: 25, 28: 27, 29: 26, 30: 28, 31: 29, - 35: 47, 36: 48, 37: 50, 38: 44, 39: 45, 40: 43, 41: 41, 42: 42, 43: 40, 44: 39, - 45: 38, 46: 37, 47: 36, 48: 35, 49: 33, 50: 34, 51: 30, 52: 31, 53: 32, 54: 51} - score: '0.964' - edge_lig_6a_lig_6e: - ligand_a: lig_6a - ligand_b: lig_6e - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 24, - 21: 23, 22: 22, 23: 21, 24: 20, 27: 27, 28: 28, 29: 29, 30: 51, 31: 31, 32: 32, - 33: 33, 34: 34, 35: 35, 36: 36, 37: 38, 38: 37, 39: 40, 40: 39, 41: 42, 42: 41, - 43: 43, 44: 44, 45: 45, 46: 47, 47: 46, 49: 49, 51: 30} - score: '0.939' - edge_lig_6a_lig_3a: + ligand_b: lig_7d + atom mapping: {7: 9, 8: 8, 9: 7, 10: 17, 11: 6, 12: 5, 13: 4, 14: 3, 15: 2, 16: 1, + 17: 0, 18: 18, 19: 20, 20: 21, 21: 22, 22: 23, 23: 24, 24: 25, 25: 26, 26: 19, + 28: 27, 29: 28, 30: 29, 31: 30, 38: 39, 39: 38, 40: 37, 41: 36, 42: 35, 43: 34, + 44: 33, 45: 32, 46: 31, 47: 52, 48: 53, 49: 54, 50: 55, 51: 56, 52: 57, 53: 58} + score: '0.701' + edge_lig_6a_lig_7d: ligand_a: lig_6a - ligand_b: lig_3a - atom mapping: {0: 23, 1: 24, 2: 25, 3: 20, 4: 21, 5: 22, 6: 19, 7: 18, 8: 16, - 9: 17, 10: 15, 11: 14, 12: 13, 13: 12, 14: 11, 15: 9, 16: 10, 17: 8, 18: 7, - 19: 5, 20: 4, 21: 3, 22: 2, 23: 1, 24: 6, 27: 26, 28: 28, 29: 27, 30: 54, 31: 30, - 32: 51, 33: 52, 34: 53, 35: 49, 36: 50, 37: 48, 38: 47, 39: 46, 40: 45, 41: 44, - 42: 43, 43: 41, 44: 42, 45: 40, 46: 39, 47: 38, 48: 36, 49: 34, 51: 29} - score: '0.951' - edge_lig_1d_lig_1b: - ligand_a: lig_1d - ligand_b: lig_1b - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 24, - 21: 23, 22: 22, 23: 21, 24: 20, 26: 26, 27: 27, 28: 28, 29: 51, 30: 30, 31: 31, - 32: 32, 33: 33, 34: 34, 35: 35, 36: 37, 37: 36, 38: 39, 39: 38, 40: 41, 41: 40, - 42: 42, 43: 43, 44: 44, 45: 46, 46: 45, 47: 50, 49: 49, 50: 47, 51: 29} - score: '0.969' - edge_lig_1d_lig_1a: - ligand_a: lig_1d - ligand_b: lig_1a - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 24, - 21: 23, 22: 22, 23: 21, 24: 20, 26: 26, 27: 27, 28: 28, 29: 51, 30: 30, 31: 31, - 32: 32, 33: 33, 34: 34, 35: 35, 36: 37, 37: 36, 38: 39, 39: 38, 40: 41, 41: 40, - 42: 42, 43: 43, 44: 44, 45: 46, 46: 45, 47: 50, 49: 49, 50: 47, 51: 29} - score: '0.969' - edge_lig_1c_lig_1d: + ligand_b: lig_7d + atom mapping: {0: 24, 1: 25, 2: 26, 3: 21, 4: 22, 5: 23, 6: 20, 7: 18, 8: 1, 9: 0, + 10: 2, 11: 3, 12: 4, 13: 5, 14: 6, 15: 7, 16: 17, 17: 8, 18: 9, 27: 19, 28: 28, + 29: 27, 30: 30, 31: 29, 32: 56, 33: 57, 34: 58, 35: 54, 36: 55, 37: 53, 38: 52, + 39: 31, 40: 32, 41: 33, 42: 34, 43: 36, 44: 35, 45: 37, 46: 38, 47: 39} + score: '0.727' + edge_lig_2b_lig_7d: + ligand_a: lig_2b + ligand_b: lig_7d + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 18: 17, + 19: 18, 20: 19, 21: 20, 22: 21, 23: 26, 24: 25, 25: 24, 26: 23, 27: 22, 28: 27, + 29: 28, 30: 30, 31: 29, 32: 32, 33: 31, 34: 33, 35: 34, 36: 36, 37: 35, 38: 37, + 39: 39, 40: 38, 48: 52, 49: 53, 50: 58, 51: 57, 52: 56, 53: 55, 54: 54} + score: '0.693' + edge_lig_2d_lig_7d: + ligand_a: lig_2d + ligand_b: lig_7d + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 17: 17, + 18: 18, 19: 19, 20: 20, 21: 21, 22: 26, 23: 25, 24: 24, 25: 23, 26: 22, 27: 27, + 28: 28, 29: 30, 30: 29, 31: 32, 32: 31, 33: 33, 34: 34, 35: 36, 36: 35, 37: 37, + 38: 39, 39: 38, 46: 52, 47: 53, 48: 58, 49: 57, 50: 56, 51: 55, 52: 54} + score: '0.714' + edge_lig_7d_lig_7b: + ligand_a: lig_7d + ligand_b: lig_7b + atom mapping: {0: 17, 1: 7, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 1, 8: 18, 9: 19, + 17: 0, 18: 8, 19: 9, 20: 10, 21: 11, 22: 16, 23: 15, 24: 14, 25: 13, 26: 12, + 27: 27, 28: 28, 29: 30, 30: 29, 31: 36, 32: 35, 33: 33, 34: 34, 35: 32, 36: 31, + 37: 44, 38: 46, 39: 45, 52: 37, 53: 38, 54: 43, 55: 42, 56: 41, 57: 40, 58: 39} + score: '0.732' + edge_lig_1c_lig_7d: ligand_a: lig_1c - ligand_b: lig_1d - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 24, - 21: 23, 22: 22, 23: 21, 24: 20, 26: 26, 27: 27, 28: 28, 29: 51, 30: 30, 31: 31, - 32: 32, 33: 33, 34: 34, 35: 35, 36: 37, 37: 36, 38: 39, 39: 38, 40: 41, 41: 40, - 42: 42, 43: 43, 44: 44, 45: 46, 46: 45, 47: 50, 49: 49, 50: 47, 51: 29} - score: '0.969' - edge_lig_6b_lig_3a: - ligand_a: lig_6b - ligand_b: lig_3a - atom mapping: {1: 4, 2: 3, 3: 2, 4: 1, 5: 6, 6: 5, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, - 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, - 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 0, 28: 27, 29: 28, 30: 29, 31: 30, - 35: 35, 36: 34, 37: 37, 38: 38, 39: 39, 40: 40, 41: 41, 42: 42, 43: 44, 44: 43, - 45: 46, 46: 45, 47: 48, 48: 47, 49: 49, 50: 50, 51: 51, 52: 52, 53: 53, 54: 54} - score: '0.947' + ligand_b: lig_7d + atom mapping: {0: 24, 1: 25, 2: 26, 3: 21, 4: 22, 5: 23, 6: 20, 7: 18, 8: 1, 9: 0, + 10: 2, 11: 3, 12: 4, 13: 5, 14: 6, 15: 7, 16: 17, 17: 8, 18: 9, 26: 19, 27: 28, + 28: 27, 29: 30, 30: 29, 31: 56, 32: 57, 33: 58, 34: 54, 35: 55, 36: 53, 37: 52, + 38: 31, 39: 32, 40: 33, 41: 34, 42: 36, 43: 35, 44: 37, 45: 38, 46: 39} + score: '0.732' + edge_lig_6c_lig_7d: + ligand_a: lig_6c + ligand_b: lig_7d + atom mapping: {0: 17, 1: 7, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 1, 8: 18, 9: 19, + 10: 20, 11: 21, 12: 22, 13: 23, 14: 24, 15: 25, 16: 26, 17: 0, 18: 8, 19: 9, + 29: 27, 30: 28, 31: 29, 32: 30, 33: 35, 34: 36, 35: 33, 36: 34, 37: 31, 38: 32, + 39: 53, 40: 52, 41: 54, 42: 55, 43: 56, 44: 57, 45: 58, 46: 37, 47: 38, 48: 39} + score: '0.689' + edge_lig_7d_lig_5: + ligand_a: lig_7d + ligand_b: lig_5 + atom mapping: {0: 9, 1: 8, 2: 10, 3: 11, 4: 12, 5: 13, 6: 14, 7: 15, 8: 17, 9: 18, + 17: 16, 18: 7, 19: 25, 20: 6, 21: 3, 22: 2, 23: 1, 24: 0, 25: 5, 26: 4, 27: 27, + 28: 26, 29: 29, 30: 28, 31: 38, 32: 37, 33: 39, 34: 40, 35: 42, 36: 41, 37: 43, + 38: 45, 39: 44, 52: 35, 53: 36, 54: 32, 55: 31, 56: 30, 57: 34, 58: 33} + score: '0.732' + edge_lig_4_lig_7d: + ligand_a: lig_4 + ligand_b: lig_7d + atom mapping: {0: 17, 1: 7, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 1, 8: 18, 9: 19, + 10: 20, 11: 21, 12: 26, 13: 25, 14: 24, 15: 23, 16: 22, 17: 0, 18: 8, 19: 9, + 29: 27, 30: 28, 31: 29, 32: 30, 33: 35, 34: 36, 35: 33, 36: 34, 37: 31, 38: 32, + 39: 53, 40: 52, 41: 58, 42: 57, 43: 56, 44: 55, 45: 54, 46: 37, 47: 38, 48: 39} + score: '0.673' + edge_lig_3a_lig_7d: + ligand_a: lig_3a + ligand_b: lig_7d + atom mapping: {7: 9, 8: 8, 9: 7, 10: 17, 11: 6, 12: 5, 13: 4, 14: 3, 15: 2, 16: 1, + 17: 0, 18: 18, 19: 20, 20: 21, 21: 22, 22: 23, 23: 24, 24: 25, 25: 26, 26: 19, + 27: 27, 28: 28, 29: 29, 30: 30, 38: 39, 39: 38, 40: 37, 41: 36, 42: 35, 43: 33, + 44: 34, 45: 32, 46: 31, 47: 52, 48: 53, 49: 54, 50: 55, 51: 56, 52: 57, 53: 58} + score: '0.706' + edge_lig_7d_lig_2a: + ligand_a: lig_7d + ligand_b: lig_2a + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 17: 20, + 18: 21, 19: 22, 20: 23, 21: 24, 22: 29, 23: 28, 24: 27, 25: 26, 26: 25, 27: 30, + 28: 31, 29: 33, 30: 32, 31: 35, 32: 34, 33: 36, 34: 37, 35: 39, 36: 38, 37: 40, + 38: 42, 39: 41, 52: 47, 53: 48, 54: 53, 55: 52, 56: 51, 57: 50, 58: 49} + score: '0.693' + edge_lig_6d_lig_7d: + ligand_a: lig_6d + ligand_b: lig_7d + atom mapping: {3: 9, 4: 8, 5: 7, 6: 6, 7: 5, 8: 4, 9: 3, 10: 2, 11: 1, 12: 18, + 13: 19, 14: 20, 15: 21, 16: 22, 17: 23, 18: 24, 19: 25, 20: 26, 21: 0, 22: 17, + 28: 27, 29: 28, 30: 29, 31: 30, 33: 38, 34: 39, 35: 37, 36: 36, 37: 35, 38: 33, + 39: 34, 40: 32, 41: 31, 42: 52, 43: 53, 44: 54, 45: 55, 46: 56, 47: 57, 48: 58} + score: '0.718' + edge_lig_1b_lig_7d: + ligand_a: lig_1b + ligand_b: lig_7d + atom mapping: {0: 24, 1: 25, 2: 26, 3: 21, 4: 22, 5: 23, 6: 20, 7: 18, 8: 1, 9: 0, + 10: 2, 11: 3, 12: 4, 13: 5, 14: 6, 15: 7, 16: 17, 17: 8, 18: 9, 26: 19, 27: 28, + 28: 27, 29: 30, 30: 29, 31: 56, 32: 57, 33: 58, 34: 54, 35: 55, 36: 53, 37: 52, + 38: 31, 39: 32, 40: 33, 41: 34, 42: 36, 43: 35, 44: 37, 45: 38, 46: 39} + score: '0.732' + edge_lig_2c_lig_7d: + ligand_a: lig_2c + ligand_b: lig_7d + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 17: 17, + 18: 18, 19: 19, 20: 20, 21: 21, 22: 26, 23: 25, 24: 24, 25: 23, 26: 22, 27: 27, + 28: 28, 29: 30, 30: 29, 31: 32, 32: 31, 33: 33, 34: 34, 35: 36, 36: 35, 37: 37, + 38: 39, 39: 38, 45: 52, 46: 53, 47: 58, 48: 57, 49: 56, 50: 55, 51: 54} + score: '0.723' + edge_lig_7d_lig_3b: + ligand_a: lig_7d + ligand_b: lig_3b + atom mapping: {0: 18, 1: 17, 2: 16, 3: 15, 4: 14, 5: 13, 6: 12, 7: 10, 8: 9, 9: 8, + 17: 11, 18: 19, 19: 27, 20: 20, 21: 21, 22: 26, 23: 25, 24: 24, 25: 23, 26: 22, + 27: 28, 28: 29, 29: 31, 30: 30, 31: 49, 32: 48, 33: 46, 34: 47, 35: 45, 36: 44, + 37: 43, 38: 42, 39: 41, 52: 50, 53: 51, 54: 56, 55: 55, 56: 54, 57: 53, 58: 52} + score: '0.677' + edge_lig_7f_lig_7d: + ligand_a: lig_7f + ligand_b: lig_7d + atom mapping: {0: 17, 1: 7, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 1, 8: 18, 9: 19, + 10: 20, 11: 21, 12: 26, 13: 25, 14: 24, 15: 23, 16: 22, 17: 0, 18: 8, 19: 9, + 28: 27, 29: 28, 30: 29, 31: 30, 32: 35, 33: 36, 34: 33, 35: 34, 36: 31, 37: 32, + 38: 53, 39: 52, 40: 58, 41: 57, 42: 56, 43: 55, 44: 54, 45: 37, 46: 38, 47: 39} + score: '0.693' + edge_lig_1d_lig_7d: + ligand_a: lig_1d + ligand_b: lig_7d + atom mapping: {0: 24, 1: 25, 2: 26, 3: 21, 4: 22, 5: 23, 6: 20, 7: 18, 8: 1, 9: 0, + 10: 2, 11: 3, 12: 4, 13: 5, 14: 6, 15: 7, 16: 17, 17: 8, 18: 9, 26: 19, 27: 28, + 28: 27, 29: 30, 30: 29, 31: 56, 32: 57, 33: 58, 34: 54, 35: 55, 36: 53, 37: 52, + 38: 31, 39: 32, 40: 33, 41: 34, 42: 36, 43: 35, 44: 37, 45: 38, 46: 39} + score: '0.732' + edge_lig_6e_lig_7d: + ligand_a: lig_6e + ligand_b: lig_7d + atom mapping: {0: 24, 1: 25, 2: 26, 3: 21, 4: 22, 5: 23, 6: 20, 7: 18, 8: 1, 9: 0, + 10: 2, 11: 3, 12: 4, 13: 5, 14: 6, 15: 7, 16: 17, 17: 8, 18: 9, 27: 19, 28: 28, + 29: 27, 30: 30, 31: 29, 32: 56, 33: 57, 34: 58, 35: 54, 36: 55, 37: 53, 38: 52, + 39: 31, 40: 32, 41: 33, 42: 34, 43: 36, 44: 35, 45: 37, 46: 38, 47: 39} + score: '0.727' + edge_lig_7c_lig_7d: + ligand_a: lig_7c + ligand_b: lig_7d + atom mapping: {0: 17, 1: 7, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 1, 8: 18, 9: 19, + 10: 20, 11: 21, 12: 26, 13: 25, 14: 24, 15: 23, 16: 22, 17: 0, 18: 8, 19: 9, + 27: 27, 28: 28, 29: 29, 30: 30, 31: 35, 32: 36, 33: 33, 34: 34, 35: 31, 36: 32, + 37: 53, 38: 52, 39: 58, 40: 57, 41: 56, 42: 55, 43: 54, 44: 37, 45: 38, 46: 39} + score: '0.732' + edge_lig_1a_lig_7d: + ligand_a: lig_1a + ligand_b: lig_7d + atom mapping: {0: 24, 1: 25, 2: 26, 3: 21, 4: 22, 5: 23, 6: 20, 7: 18, 8: 1, 9: 0, + 10: 2, 11: 3, 12: 4, 13: 5, 14: 6, 15: 7, 16: 17, 17: 8, 18: 9, 26: 19, 27: 28, + 28: 27, 29: 30, 30: 29, 31: 56, 32: 57, 33: 58, 34: 54, 35: 55, 36: 53, 37: 52, + 38: 31, 39: 32, 40: 33, 41: 34, 42: 36, 43: 35, 44: 37, 45: 38, 46: 39} + score: '0.732' diff --git a/data/tnks2/03_edges/01_perses_openfe.yml b/data/tnks2/03_edges/01_perses_openfe.yml index beaece8aa..02e60b372 100644 --- a/data/tnks2/03_edges/01_perses_openfe.yml +++ b/data/tnks2/03_edges/01_perses_openfe.yml @@ -1,56 +1,21 @@ mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph +planner: openfe v0.5 minimal_spanning_graph edges: - edge_lig_8e_lig_7: - ligand_a: lig_8e - ligand_b: lig_7 - atom mapping: {0: 14, 1: 13, 2: 15, 3: 16, 4: 17, 5: 18, 6: 19, 7: 10, 8: 11, - 10: 9, 11: 8, 12: 7, 13: 6, 15: 4, 16: 5, 17: 3, 37: 25, 38: 26, 39: 23, 40: 24, - 41: 22, 43: 20, 44: 21} - score: '0.723' - edge_lig_5m_lig_8a: - ligand_a: lig_5m - ligand_b: lig_8a - atom mapping: {3: 20, 4: 18, 5: 19, 6: 16, 7: 17, 8: 15, 9: 14, 10: 43, 11: 4, - 12: 5, 13: 6, 14: 7, 15: 8, 16: 9, 17: 1, 18: 0, 19: 2, 24: 10, 25: 11, 26: 12, - 27: 13, 28: 41, 29: 42, 30: 39, 31: 40} + edge_lig_8a_lig_5m: + ligand_a: lig_8a + ligand_b: lig_5m + atom mapping: {0: 18, 1: 17, 2: 19, 4: 11, 5: 12, 6: 13, 7: 14, 8: 15, 9: 16, + 10: 24, 11: 25, 12: 26, 13: 27, 14: 9, 15: 8, 16: 6, 17: 7, 18: 4, 19: 5, 20: 3, + 39: 30, 40: 31, 41: 28, 42: 29, 43: 10} score: '0.705' - edge_lig_5l_lig_8a: - ligand_a: lig_5l + edge_lig_5g_lig_8a: + ligand_a: lig_5g ligand_b: lig_8a atom mapping: {3: 20, 4: 18, 5: 19, 6: 16, 7: 17, 8: 15, 9: 14, 10: 43, 11: 4, - 12: 2, 14: 1, 15: 0, 16: 8, 18: 6, 20: 5, 21: 10, 22: 11, 23: 12, 24: 13, 25: 41, - 26: 42, 27: 39, 28: 40} - score: '0.700' - edge_lig_5c_lig_8e: - ligand_a: lig_5c - ligand_b: lig_8e - atom mapping: {3: 17, 4: 15, 5: 16, 6: 13, 7: 14, 8: 12, 9: 11, 10: 10, 11: 7, - 12: 8, 14: 1, 15: 0, 16: 2, 18: 4, 20: 6, 21: 43, 22: 44, 23: 41, 24: 42, 25: 39, - 26: 40, 27: 37, 28: 38} - score: '0.694' - edge_lig_8e_lig_1b: - ligand_a: lig_8e - ligand_b: lig_1b - atom mapping: {0: 0, 1: 1, 2: 2, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 10: 10, 11: 11, - 12: 12, 13: 25, 14: 26, 15: 23, 16: 24, 17: 17, 37: 15, 38: 16, 39: 13, 40: 14, - 41: 27, 42: 28, 43: 29, 44: 30} - score: '0.777' - edge_lig_5j_lig_8e: - ligand_a: lig_5j - ligand_b: lig_8e - atom mapping: {3: 17, 4: 15, 5: 16, 6: 13, 7: 14, 8: 12, 9: 11, 10: 10, 11: 7, - 12: 8, 14: 1, 15: 0, 16: 2, 17: 3, 18: 4, 20: 6, 21: 43, 22: 44, 23: 41, 24: 42, - 25: 39, 26: 40, 27: 37, 28: 38} - score: '0.716' - edge_lig_5n_lig_8e: - ligand_a: lig_5n - ligand_b: lig_8e - atom mapping: {10: 17, 11: 15, 12: 16, 13: 13, 14: 14, 15: 12, 16: 11, 17: 10, - 18: 7, 19: 8, 21: 1, 22: 0, 23: 2, 24: 3, 25: 4, 26: 5, 27: 6, 28: 43, 29: 44, - 30: 41, 31: 42, 32: 39, 33: 40, 34: 37, 35: 38} - score: '0.663' + 12: 2, 14: 1, 15: 0, 16: 8, 18: 6, 19: 7, 20: 5, 21: 10, 22: 11, 23: 12, 24: 13, + 25: 41, 26: 42, 27: 39, 28: 40} + score: '0.714' edge_lig_5f_lig_8a: ligand_a: lig_5f ligand_b: lig_8a @@ -58,27 +23,20 @@ edges: 12: 2, 14: 1, 15: 0, 16: 8, 18: 6, 19: 7, 20: 5, 21: 10, 22: 11, 23: 12, 24: 13, 25: 41, 26: 42, 27: 39, 28: 40} score: '0.714' - edge_lig_3a_lig_8e: - ligand_a: lig_3a - ligand_b: lig_8e - atom mapping: {0: 0, 1: 1, 2: 2, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 10: 10, 11: 11, - 12: 12, 13: 39, 14: 40, 15: 37, 16: 38, 17: 17, 31: 15, 32: 16, 33: 13, 34: 14, - 35: 41, 36: 42, 37: 43, 38: 44} - score: '0.689' - edge_lig_3b_lig_8e: - ligand_a: lig_3b - ligand_b: lig_8e - atom mapping: {0: 0, 1: 1, 2: 8, 4: 7, 5: 6, 6: 4, 7: 5, 8: 2, 9: 3, 10: 43, 11: 44, - 12: 41, 13: 42, 14: 11, 15: 12, 16: 39, 17: 40, 18: 37, 19: 38, 20: 17, 34: 15, - 35: 16, 36: 13, 37: 14, 38: 10} - score: '0.710' - edge_lig_5p_lig_8e: - ligand_a: lig_5p - ligand_b: lig_8e - atom mapping: {0: 0, 1: 1, 2: 8, 4: 7, 5: 6, 6: 4, 7: 5, 8: 2, 9: 3, 10: 43, 11: 44, - 12: 41, 13: 42, 14: 11, 15: 12, 16: 39, 17: 40, 18: 37, 19: 38, 20: 17, 42: 15, - 43: 16, 44: 13, 45: 14, 46: 10} - score: '0.646' + edge_lig_8e_lig_5j: + ligand_a: lig_8e + ligand_b: lig_5j + atom mapping: {0: 15, 1: 14, 2: 16, 3: 17, 4: 18, 6: 20, 7: 11, 8: 12, 10: 10, + 11: 9, 12: 8, 13: 6, 14: 7, 15: 4, 16: 5, 17: 3, 37: 27, 38: 28, 39: 25, 40: 26, + 41: 23, 42: 24, 43: 21, 44: 22} + score: '0.716' + edge_lig_8a_lig_5k: + ligand_a: lig_8a + ligand_b: lig_5k + atom mapping: {0: 15, 1: 14, 2: 12, 4: 11, 5: 20, 6: 18, 7: 19, 8: 16, 9: 17, + 10: 21, 11: 22, 12: 23, 13: 24, 14: 9, 15: 8, 16: 6, 17: 7, 18: 4, 19: 5, 20: 3, + 39: 27, 40: 28, 41: 25, 42: 26, 43: 10} + score: '0.736' edge_lig_8e_lig_1a: ligand_a: lig_8e ligand_b: lig_1a @@ -86,48 +44,41 @@ edges: 12: 6, 13: 4, 14: 5, 15: 2, 16: 3, 17: 1, 37: 25, 38: 26, 39: 23, 40: 24, 41: 21, 42: 22, 43: 19, 44: 20} score: '0.830' - edge_lig_5p_lig_8f: - ligand_a: lig_5p - ligand_b: lig_8f - atom mapping: {0: 38, 1: 37, 2: 39, 4: 31, 5: 32, 6: 33, 7: 34, 8: 35, 9: 36, - 10: 44, 11: 45, 12: 46, 13: 47, 14: 29, 15: 28, 16: 1, 17: 0, 18: 2, 19: 3, - 20: 4, 42: 24, 43: 25, 44: 26, 45: 27, 46: 30} + edge_lig_8e_lig_5a: + ligand_a: lig_8e + ligand_b: lig_5a + atom mapping: {0: 15, 1: 14, 2: 16, 4: 18, 5: 19, 6: 20, 7: 11, 8: 12, 10: 10, + 11: 9, 12: 8, 13: 6, 14: 7, 15: 4, 16: 5, 17: 3, 37: 27, 38: 28, 39: 25, 40: 26, + 41: 23, 42: 24, 43: 21, 44: 22} + score: '0.709' + edge_lig_8e_lig_7: + ligand_a: lig_8e + ligand_b: lig_7 + atom mapping: {0: 14, 1: 13, 2: 15, 3: 16, 4: 17, 5: 18, 6: 19, 7: 10, 8: 11, + 10: 9, 11: 8, 12: 7, 13: 23, 14: 24, 15: 25, 16: 26, 17: 3, 37: 4, 38: 5, 39: 6, + 41: 22, 43: 20, 44: 21} + score: '0.723' + edge_lig_8b_lig_5p: + ligand_a: lig_8b + ligand_b: lig_5p + atom mapping: {0: 17, 1: 16, 2: 18, 3: 19, 4: 20, 23: 42, 24: 43, 25: 44, 26: 45, + 27: 15, 28: 14, 29: 46, 30: 4, 31: 5, 32: 6, 33: 7, 34: 8, 35: 9, 36: 1, 37: 0, + 38: 2, 43: 10, 44: 11, 45: 12, 46: 13} score: '0.638' - edge_lig_5d_lig_8e: - ligand_a: lig_5d - ligand_b: lig_8e - atom mapping: {3: 17, 4: 15, 5: 16, 6: 13, 7: 14, 8: 12, 9: 11, 10: 10, 11: 7, - 12: 8, 14: 1, 15: 0, 16: 2, 17: 3, 18: 4, 19: 5, 20: 6, 21: 43, 22: 44, 23: 41, - 24: 42, 25: 39, 26: 40, 27: 37, 28: 38} + edge_lig_8e_lig_5d: + ligand_a: lig_8e + ligand_b: lig_5d + atom mapping: {0: 15, 1: 14, 2: 16, 3: 17, 4: 18, 5: 19, 6: 20, 7: 11, 8: 12, + 10: 10, 11: 9, 12: 8, 13: 6, 14: 7, 15: 4, 16: 5, 17: 3, 37: 27, 38: 28, 39: 25, + 40: 26, 41: 23, 42: 24, 43: 21, 44: 22} score: '0.731' - edge_lig_5b_lig_8e: - ligand_a: lig_5b - ligand_b: lig_8e - atom mapping: {3: 17, 4: 15, 5: 16, 6: 13, 7: 14, 8: 12, 9: 11, 10: 10, 11: 7, - 12: 8, 14: 1, 15: 0, 16: 2, 18: 4, 20: 6, 21: 43, 22: 44, 23: 41, 24: 42, 25: 39, - 26: 40, 27: 37, 28: 38} - score: '0.694' - edge_lig_5h_lig_8a: - ligand_a: lig_5h - ligand_b: lig_8a - atom mapping: {3: 20, 4: 18, 5: 19, 6: 16, 7: 17, 8: 15, 9: 14, 10: 43, 11: 4, - 12: 2, 18: 1, 19: 0, 20: 8, 22: 6, 23: 7, 24: 5, 25: 10, 26: 11, 27: 12, 28: 13, - 29: 41, 30: 42, 31: 39, 32: 40} - score: '0.675' - edge_lig_8c_lig_5p: - ligand_a: lig_8c + edge_lig_8f_lig_5p: + ligand_a: lig_8f ligand_b: lig_5p - atom mapping: {0: 0, 1: 1, 2: 8, 3: 9, 4: 6, 5: 7, 6: 5, 7: 4, 8: 2, 10: 46, 11: 14, - 12: 15, 13: 44, 14: 45, 15: 42, 16: 43, 17: 20, 34: 18, 35: 19, 36: 16, 37: 17, - 38: 12, 39: 13, 40: 10, 41: 11} - score: '0.672' - edge_lig_5i_lig_8a: - ligand_a: lig_5i - ligand_b: lig_8a - atom mapping: {3: 20, 4: 18, 5: 19, 6: 16, 7: 17, 8: 15, 9: 14, 10: 43, 11: 4, - 12: 5, 13: 6, 14: 7, 15: 8, 17: 1, 18: 0, 19: 2, 24: 10, 25: 11, 26: 12, 27: 13, - 28: 41, 29: 42, 30: 39, 31: 40} - score: '0.684' + atom mapping: {0: 17, 1: 16, 2: 18, 3: 19, 4: 20, 24: 42, 25: 43, 26: 44, 27: 45, + 28: 15, 29: 14, 30: 46, 31: 4, 32: 5, 33: 6, 34: 7, 35: 8, 36: 9, 37: 1, 38: 0, + 39: 2, 44: 10, 45: 11, 46: 12, 47: 13} + score: '0.638' edge_lig_5o_lig_8a: ligand_a: lig_5o ligand_b: lig_8a @@ -135,34 +86,90 @@ edges: 18: 4, 19: 5, 20: 6, 21: 7, 22: 8, 23: 9, 24: 1, 25: 0, 26: 2, 31: 10, 32: 11, 33: 12, 34: 13, 35: 41, 36: 42, 37: 39, 38: 40} score: '0.654' - edge_lig_5p_lig_8b: - ligand_a: lig_5p - ligand_b: lig_8b - atom mapping: {0: 37, 1: 36, 2: 38, 4: 30, 5: 31, 6: 32, 7: 33, 8: 34, 9: 35, - 10: 43, 11: 44, 12: 45, 13: 46, 14: 28, 15: 27, 16: 1, 17: 0, 18: 2, 19: 3, - 20: 4, 42: 23, 43: 24, 44: 25, 45: 26, 46: 29} - score: '0.638' - edge_lig_5k_lig_8a: - ligand_a: lig_5k - ligand_b: lig_8a - atom mapping: {3: 20, 4: 18, 5: 19, 6: 16, 7: 17, 8: 15, 9: 14, 10: 43, 11: 4, - 12: 2, 14: 1, 15: 0, 16: 8, 17: 9, 18: 6, 19: 7, 20: 5, 21: 10, 22: 11, 23: 12, - 24: 13, 25: 41, 26: 42, 27: 39, 28: 40} - score: '0.736' - edge_lig_5a_lig_8e: - ligand_a: lig_5a + edge_lig_5o_lig_8e: + ligand_a: lig_5o ligand_b: lig_8e - atom mapping: {3: 17, 4: 15, 5: 16, 6: 13, 7: 14, 8: 12, 9: 11, 10: 10, 11: 7, - 12: 8, 14: 1, 15: 0, 16: 2, 18: 4, 19: 5, 20: 6, 21: 43, 22: 44, 23: 41, 24: 42, - 25: 39, 26: 40, 27: 37, 28: 38} - score: '0.709' - edge_lig_5g_lig_8a: - ligand_a: lig_5g + atom mapping: {10: 17, 11: 15, 12: 16, 13: 13, 14: 14, 15: 12, 16: 11, 17: 10, + 18: 7, 19: 6, 20: 4, 21: 5, 22: 2, 23: 3, 24: 1, 25: 0, 26: 8, 27: 9, 31: 43, + 32: 44, 33: 41, 34: 42, 35: 39, 36: 40, 37: 37, 38: 38} + score: '0.665' + edge_lig_8a_lig_5h: + ligand_a: lig_8a + ligand_b: lig_5h + atom mapping: {0: 19, 1: 18, 2: 12, 4: 11, 5: 24, 6: 22, 7: 23, 8: 20, 10: 25, + 11: 26, 12: 27, 13: 28, 14: 9, 15: 8, 16: 6, 17: 7, 18: 4, 19: 5, 20: 3, 39: 31, + 40: 32, 41: 29, 42: 30, 43: 10} + score: '0.675' + edge_lig_5i_lig_8a: + ligand_a: lig_5i ligand_b: lig_8a atom mapping: {3: 20, 4: 18, 5: 19, 6: 16, 7: 17, 8: 15, 9: 14, 10: 43, 11: 4, - 12: 2, 14: 1, 15: 0, 16: 8, 18: 6, 19: 7, 20: 5, 21: 10, 22: 11, 23: 12, 24: 13, - 25: 41, 26: 42, 27: 39, 28: 40} - score: '0.714' + 12: 5, 13: 6, 14: 7, 15: 8, 17: 1, 18: 0, 19: 2, 24: 10, 25: 11, 26: 12, 27: 13, + 28: 41, 29: 42, 30: 39, 31: 40} + score: '0.684' + edge_lig_8e_lig_5e: + ligand_a: lig_8e + ligand_b: lig_5e + atom mapping: {0: 15, 1: 14, 2: 16, 3: 17, 4: 18, 5: 19, 6: 20, 7: 11, 8: 12, + 10: 10, 11: 9, 12: 8, 13: 6, 14: 7, 15: 4, 16: 5, 17: 3, 37: 27, 38: 28, 39: 25, + 40: 26, 41: 23, 42: 24, 43: 21, 44: 22} + score: '0.731' + edge_lig_8c_lig_5p: + ligand_a: lig_8c + ligand_b: lig_5p + atom mapping: {0: 0, 1: 1, 2: 8, 3: 9, 4: 6, 5: 7, 6: 5, 7: 4, 8: 2, 10: 46, 11: 14, + 12: 15, 13: 44, 14: 45, 15: 42, 16: 43, 17: 20, 34: 18, 35: 19, 36: 16, 37: 17, + 38: 12, 39: 13, 40: 10, 41: 11} + score: '0.672' + edge_lig_8e_lig_5p: + ligand_a: lig_8e + ligand_b: lig_5p + atom mapping: {0: 0, 1: 1, 2: 8, 3: 9, 4: 6, 5: 7, 6: 5, 7: 4, 8: 2, 10: 46, 11: 14, + 12: 15, 13: 44, 14: 45, 15: 42, 16: 43, 17: 20, 37: 18, 38: 19, 39: 16, 40: 17, + 41: 12, 42: 13, 43: 10, 44: 11} + score: '0.646' + edge_lig_8e_lig_5n: + ligand_a: lig_8e + ligand_b: lig_5n + atom mapping: {0: 22, 1: 21, 2: 23, 3: 24, 4: 25, 5: 26, 6: 27, 7: 18, 8: 19, + 10: 17, 11: 16, 12: 15, 13: 13, 14: 14, 15: 11, 16: 12, 17: 10, 37: 34, 38: 35, + 39: 32, 40: 33, 41: 30, 42: 31, 43: 28, 44: 29} + score: '0.663' + edge_lig_8e_lig_1b: + ligand_a: lig_8e + ligand_b: lig_1b + atom mapping: {0: 0, 1: 1, 2: 2, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 10: 10, 11: 11, + 12: 12, 13: 25, 14: 26, 15: 23, 16: 24, 17: 17, 37: 15, 38: 16, 39: 13, 40: 14, + 41: 27, 42: 28, 43: 29, 44: 30} + score: '0.777' + edge_lig_8a_lig_5l: + ligand_a: lig_8a + ligand_b: lig_5l + atom mapping: {0: 15, 1: 14, 2: 12, 4: 11, 5: 20, 6: 18, 8: 16, 10: 21, 11: 22, + 12: 23, 13: 24, 14: 9, 15: 8, 16: 6, 17: 7, 18: 4, 19: 5, 20: 3, 39: 27, 40: 28, + 41: 25, 42: 26, 43: 10} + score: '0.700' + edge_lig_8e_lig_3a: + ligand_a: lig_8e + ligand_b: lig_3a + atom mapping: {0: 0, 1: 1, 2: 2, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 10: 10, 11: 11, + 12: 12, 13: 33, 14: 34, 15: 31, 16: 32, 17: 17, 37: 15, 38: 16, 39: 13, 40: 14, + 41: 35, 42: 36, 43: 37, 44: 38} + score: '0.689' + edge_lig_8e_lig_5b: + ligand_a: lig_8e + ligand_b: lig_5b + atom mapping: {0: 15, 1: 14, 2: 16, 4: 18, 6: 20, 7: 11, 8: 12, 10: 10, 11: 9, + 12: 8, 13: 6, 14: 7, 15: 4, 16: 5, 17: 3, 37: 27, 38: 28, 39: 25, 40: 26, 41: 23, + 42: 24, 43: 21, 44: 22} + score: '0.694' + edge_lig_8e_lig_3b: + ligand_a: lig_8e + ligand_b: lig_3b + atom mapping: {0: 0, 1: 1, 2: 8, 3: 9, 4: 6, 5: 7, 6: 5, 7: 4, 8: 2, 10: 38, 11: 14, + 12: 15, 13: 36, 14: 37, 15: 34, 16: 35, 17: 20, 37: 18, 38: 19, 39: 16, 40: 17, + 41: 12, 42: 13, 43: 10, 44: 11} + score: '0.710' edge_lig_8d_lig_5p: ligand_a: lig_8d ligand_b: lig_5p @@ -170,10 +177,10 @@ edges: 25: 15, 26: 14, 27: 46, 28: 4, 29: 5, 30: 6, 31: 7, 32: 8, 33: 9, 34: 1, 35: 0, 36: 2, 41: 10, 42: 11, 43: 12, 44: 13} score: '0.646' - edge_lig_5o_lig_8e: - ligand_a: lig_5o - ligand_b: lig_8e - atom mapping: {10: 17, 11: 15, 12: 16, 13: 13, 14: 14, 15: 12, 16: 11, 17: 10, - 18: 7, 19: 6, 20: 4, 21: 5, 22: 2, 23: 3, 24: 1, 25: 0, 26: 8, 27: 9, 31: 43, - 32: 44, 33: 41, 34: 42, 35: 39, 36: 40, 37: 37, 38: 38} - score: '0.665' + edge_lig_8e_lig_5c: + ligand_a: lig_8e + ligand_b: lig_5c + atom mapping: {0: 15, 1: 14, 2: 16, 4: 18, 6: 20, 7: 11, 8: 12, 10: 10, 11: 9, + 12: 8, 13: 6, 14: 7, 15: 4, 16: 5, 17: 3, 37: 27, 38: 28, 39: 25, 40: 26, 41: 23, + 42: 24, 43: 21, 44: 22} + score: '0.694' diff --git a/data/tyk2/03_edges/01_perses_openfe.yml b/data/tyk2/03_edges/01_perses_openfe.yml index 9f32ac7e5..f86683f32 100644 --- a/data/tyk2/03_edges/01_perses_openfe.yml +++ b/data/tyk2/03_edges/01_perses_openfe.yml @@ -1,28 +1,21 @@ mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.4 minimal_spanning_graph +planner: openfe v0.5 minimal_spanning_graph edges: - edge_lig_ejm_45_lig_ejm_48: - ligand_a: lig_ejm_45 + edge_lig_ejm_55_lig_ejm_48: + ligand_a: lig_ejm_55 ligand_b: lig_ejm_48 atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 35: 38, 36: 39, 37: 8, 38: 7} - score: '0.772' - edge_lig_ejm_48_lig_ejm_43: - ligand_a: lig_ejm_48 - ligand_b: lig_ejm_43 - atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 37, 8: 36, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 38: 34, 39: 35, 40: 8, 41: 7} - score: '0.783' - edge_lig_jmc_30_lig_ejm_48: - ligand_a: lig_jmc_30 + 21: 21, 22: 22, 23: 23, 29: 38, 30: 39, 31: 8, 32: 7} + score: '0.847' + edge_lig_jmc_27_lig_ejm_48: + ligand_a: lig_jmc_27 ligand_b: lig_ejm_48 atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 33: 38, 34: 39, 35: 40, 36: 41} - score: '0.795' + 21: 21, 22: 22, 23: 23, 32: 38, 33: 39, 34: 40, 35: 41} + score: '0.807' edge_lig_ejm_46_lig_ejm_48: ligand_a: lig_ejm_46 ligand_b: lig_ejm_48 @@ -37,6 +30,20 @@ edges: 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, 22: 22, 23: 23, 28: 38, 29: 39, 30: 8, 31: 7} score: '0.860' + edge_lig_jmc_28_lig_ejm_48: + ligand_a: lig_jmc_28 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 35: 38, 36: 39, 37: 8, 38: 7} + score: '0.772' + edge_lig_ejm_43_lig_ejm_48: + ligand_a: lig_ejm_43 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 34: 38, 35: 39, 36: 8, 37: 7} + score: '0.783' edge_lig_ejm_50_lig_ejm_48: ligand_a: lig_ejm_50 ligand_b: lig_ejm_48 @@ -44,6 +51,13 @@ edges: 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, 22: 22, 23: 23, 29: 38, 30: 39, 31: 8, 32: 7} score: '0.847' + edge_lig_ejm_45_lig_ejm_48: + ligand_a: lig_ejm_45 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 35: 38, 36: 39, 37: 8, 38: 7} + score: '0.772' edge_lig_ejm_54_lig_ejm_48: ligand_a: lig_ejm_54 ligand_b: lig_ejm_48 @@ -51,13 +65,6 @@ edges: 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, 22: 22, 23: 23, 33: 38, 34: 39, 35: 8, 36: 7} score: '0.795' - edge_lig_jmc_27_lig_ejm_48: - ligand_a: lig_jmc_27 - ligand_b: lig_ejm_48 - atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 32: 38, 33: 39, 34: 8, 35: 7} - score: '0.807' edge_lig_jmc_23_lig_ejm_48: ligand_a: lig_jmc_23 ligand_b: lig_ejm_48 @@ -65,20 +72,6 @@ edges: 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, 22: 22, 23: 23, 32: 38, 33: 39, 34: 8, 35: 7} score: '0.807' - edge_lig_ejm_55_lig_ejm_48: - ligand_a: lig_ejm_55 - ligand_b: lig_ejm_48 - atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 29: 38, 30: 39, 31: 8, 32: 7} - score: '0.847' - edge_lig_ejm_47_lig_ejm_48: - ligand_a: lig_ejm_47 - ligand_b: lig_ejm_48 - atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 35: 38, 36: 39, 37: 8, 38: 7} - score: '0.772' edge_lig_ejm_42_lig_ejm_48: ligand_a: lig_ejm_42 ligand_b: lig_ejm_48 @@ -86,8 +79,8 @@ edges: 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, 22: 22, 23: 23, 31: 38, 32: 39, 33: 8, 34: 7} score: '0.820' - edge_lig_jmc_28_lig_ejm_48: - ligand_a: lig_jmc_28 + edge_lig_ejm_47_lig_ejm_48: + ligand_a: lig_ejm_47 ligand_b: lig_ejm_48 atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, diff --git a/preparation/mappers/perses-mapper.py b/preparation/mappers/perses-mapper.py index 6d0513476..3ace11377 100644 --- a/preparation/mappers/perses-mapper.py +++ b/preparation/mappers/perses-mapper.py @@ -29,7 +29,7 @@ output = {} output['mapper'] = "Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, coordinate_tolerance=0.2), default non geometric scorer" -output['planner'] = "openfe v0.4 minimal_spanning_graph" +output['planner'] = "openfe v0.5 minimal_spanning_graph" edges_dict = dict() From b18c0b1bda9ff4a96410e91dbb0a3364ead3bd8d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Iv=C3=A1n=20Pulido?= <2949729+ijpulidos@users.noreply.github.com> Date: Mon, 5 Jun 2023 11:55:48 -0400 Subject: [PATCH 5/6] Removing current edges file to merge to main. --- data/cdk2/03_edges/01_perses_openfe.yml | 85 ------ data/cdk8/03_edges/01_perses_openfe.yml | 184 ------------ data/cmet/03_edges/01_perses_openfe.yml | 36 --- data/eg5/03_edges/01_perses_openfe.yml | 204 ------------- data/hif2a/03_edges/01_perses_openfe.yml | 210 -------------- data/mcl1/03_edges/01_perses_openfe.yml | 172 ----------- data/p38/03_edges/01_perses_openfe.yml | 201 ------------- data/pde2/03_edges/01_perses_openfe.yml | 184 ------------ data/pfkfb3/03_edges/01_perses_openfe.yml | 229 --------------- data/ptp1b/03_edges/01_perses_openfe.yml | 151 ---------- data/shp2/03_edges/01_perses_openfe.yml | 145 ---------- data/syk/03_edges/01_perses_openfe.yml | 305 -------------------- data/thrombin/03_edges/01_perses_openfe.yml | 180 ------------ data/tnks2/03_edges/01_perses_openfe.yml | 186 ------------ data/tyk2/03_edges/01_perses_openfe.yml | 88 ------ 15 files changed, 2560 deletions(-) delete mode 100644 data/cdk2/03_edges/01_perses_openfe.yml delete mode 100644 data/cdk8/03_edges/01_perses_openfe.yml delete mode 100644 data/cmet/03_edges/01_perses_openfe.yml delete mode 100644 data/eg5/03_edges/01_perses_openfe.yml delete mode 100644 data/hif2a/03_edges/01_perses_openfe.yml delete mode 100644 data/mcl1/03_edges/01_perses_openfe.yml delete mode 100644 data/p38/03_edges/01_perses_openfe.yml delete mode 100644 data/pde2/03_edges/01_perses_openfe.yml delete mode 100644 data/pfkfb3/03_edges/01_perses_openfe.yml delete mode 100644 data/ptp1b/03_edges/01_perses_openfe.yml delete mode 100644 data/shp2/03_edges/01_perses_openfe.yml delete mode 100644 data/syk/03_edges/01_perses_openfe.yml delete mode 100644 data/thrombin/03_edges/01_perses_openfe.yml delete mode 100644 data/tnks2/03_edges/01_perses_openfe.yml delete mode 100644 data/tyk2/03_edges/01_perses_openfe.yml diff --git a/data/cdk2/03_edges/01_perses_openfe.yml b/data/cdk2/03_edges/01_perses_openfe.yml deleted file mode 100644 index e4edf0035..000000000 --- a/data/cdk2/03_edges/01_perses_openfe.yml +++ /dev/null @@ -1,85 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.5 minimal_spanning_graph -edges: - edge_lig_22_lig_1oiy: - ligand_a: lig_22 - ligand_b: lig_1oiy - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, - 31: 43, 32: 44, 33: 41, 34: 42, 35: 35, 37: 33, 43: 31, 44: 32, 45: 45, 46: 46, - 47: 47, 48: 48} - score: '0.907' - edge_lig_20_lig_1oiy: - ligand_a: lig_20 - ligand_b: lig_1oiy - atom mapping: {5: 33, 6: 35, 8: 41, 9: 42, 10: 43, 11: 44, 12: 30, 13: 28, 14: 29, - 15: 27, 16: 26, 17: 4, 18: 5, 19: 6, 20: 8, 21: 7, 22: 9, 23: 10, 24: 23, 25: 24, - 26: 25, 27: 20, 28: 21, 29: 22, 30: 17, 31: 19, 32: 18, 33: 14, 34: 16, 35: 15, - 36: 11, 37: 12, 38: 13, 39: 3, 40: 2, 41: 1, 42: 0, 43: 47, 44: 48, 45: 46, - 46: 45, 47: 31, 48: 32} - score: '0.907' - edge_lig_17_lig_1oiy: - ligand_a: lig_17 - ligand_b: lig_1oiy - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, - 31: 43, 32: 44, 33: 41, 34: 42, 35: 35, 37: 33, 39: 31, 40: 32, 41: 45, 42: 46, - 43: 47, 44: 48} - score: '0.954' - edge_lig_21_lig_1oiy: - ligand_a: lig_21 - ligand_b: lig_1oiy - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, - 31: 43, 32: 44, 33: 41, 34: 42, 35: 35, 37: 33, 43: 31, 44: 32, 45: 45, 46: 46, - 47: 47, 48: 48} - score: '0.907' - edge_lig_1oiu_lig_1h1r: - ligand_a: lig_1oiu - ligand_b: lig_1h1r - atom mapping: {0: 43, 1: 40, 2: 39, 3: 15, 4: 16, 5: 18, 6: 19, 7: 20, 8: 21, - 9: 22, 10: 38, 11: 23, 12: 37, 13: 36, 14: 24, 15: 35, 16: 34, 17: 25, 18: 32, - 19: 33, 20: 26, 21: 30, 22: 31, 23: 27, 24: 29, 25: 28, 26: 17, 27: 12, 28: 10, - 29: 11, 30: 3, 31: 2, 32: 44, 33: 1, 40: 6, 41: 7, 42: 5, 44: 4, 45: 9, 46: 13, - 47: 14, 48: 41, 49: 42} - score: '0.948' - edge_lig_1oiu_lig_1oiy: - ligand_a: lig_1oiu - ligand_b: lig_1oiy - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, - 31: 43, 32: 44, 33: 41, 40: 35, 42: 33, 43: 34, 44: 31, 45: 32, 46: 45, 47: 46, - 48: 47, 49: 48} - score: '0.901' - edge_lig_1oiu_lig_1h1q: - ligand_a: lig_1oiu - ligand_b: lig_1h1q - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, - 31: 39, 32: 40, 33: 37, 40: 35, 41: 36, 42: 33, 43: 34, 44: 31, 45: 32, 46: 41, - 47: 42, 48: 43, 49: 44} - score: '0.961' - edge_lig_1oi9_lig_1oiu: - ligand_a: lig_1oi9 - ligand_b: lig_1oiu - atom mapping: {2: 40, 3: 33, 5: 31, 6: 32, 7: 30, 8: 28, 9: 29, 10: 27, 11: 26, - 12: 4, 13: 5, 14: 6, 15: 7, 16: 8, 17: 9, 18: 10, 19: 11, 20: 12, 21: 13, 22: 14, - 23: 16, 24: 15, 25: 17, 26: 18, 27: 19, 28: 20, 29: 22, 30: 21, 31: 23, 32: 24, - 33: 25, 34: 3, 35: 2, 36: 1, 37: 0, 38: 48, 39: 49, 40: 47, 41: 46, 42: 44, - 43: 45, 44: 42, 45: 43} - score: '0.936' - edge_lig_26_lig_1oiu: - ligand_a: lig_26 - ligand_b: lig_1oiu - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, - 31: 44, 32: 45, 33: 42, 34: 43, 35: 40, 41: 33, 43: 31, 44: 32, 45: 46, 46: 47, - 47: 48, 48: 49} - score: '0.901' diff --git a/data/cdk8/03_edges/01_perses_openfe.yml b/data/cdk8/03_edges/01_perses_openfe.yml deleted file mode 100644 index 2ee334fc2..000000000 --- a/data/cdk8/03_edges/01_perses_openfe.yml +++ /dev/null @@ -1,184 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.5 minimal_spanning_graph -edges: - edge_lig_22_lig_43: - ligand_a: lig_22 - ligand_b: lig_43 - atom mapping: {17: 13, 18: 14, 19: 15, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, - 25: 21, 26: 22, 27: 23, 28: 24, 40: 40, 41: 41, 42: 42, 43: 43} - score: '0.358' - edge_lig_33_lig_45: - ligand_a: lig_33 - ligand_b: lig_45 - atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, - 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 41: 41, 42: 42, 43: 43, 44: 44} - score: '0.396' - edge_lig_40_lig_45: - ligand_a: lig_40 - ligand_b: lig_45 - atom mapping: {17: 13, 18: 14, 19: 15, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, - 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 46: 41, 47: 42, 48: 43, 49: 44} - score: '0.386' - edge_lig_42_lig_20: - ligand_a: lig_42 - ligand_b: lig_20 - atom mapping: {8: 37, 9: 38, 10: 36, 11: 34, 12: 35, 13: 33, 14: 32, 15: 47, 16: 48, - 17: 45, 18: 46, 19: 30, 20: 31, 21: 29, 22: 28, 23: 25, 24: 27, 25: 26} - score: '0.391' - edge_lig_43_lig_32: - ligand_a: lig_43 - ligand_b: lig_32 - atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, - 21: 25, 22: 26, 23: 27, 24: 28, 25: 29, 26: 30, 40: 34, 41: 35, 42: 36, 43: 37} - score: '0.430' - edge_lig_39_lig_45: - ligand_a: lig_39 - ligand_b: lig_45 - atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, - 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 45: 41, 46: 42, 47: 43, 48: 44} - score: '0.386' - edge_lig_38_lig_45: - ligand_a: lig_38 - ligand_b: lig_45 - atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, - 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 44: 41, 45: 42, 46: 43, 47: 44} - score: '0.385' - edge_lig_28_lig_17: - ligand_a: lig_28 - ligand_b: lig_17 - atom mapping: {17: 15, 18: 17, 19: 16, 20: 18, 21: 19, 22: 20, 23: 21, 24: 22, - 25: 23, 26: 24, 27: 25, 28: 26, 43: 35, 44: 36, 45: 37, 46: 38} - score: '0.392' - edge_lig_21_lig_43: - ligand_a: lig_21 - ligand_b: lig_43 - atom mapping: {17: 13, 18: 14, 19: 15, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, - 25: 21, 26: 22, 27: 23, 28: 24, 40: 40, 41: 41, 42: 42, 43: 43} - score: '0.358' - edge_lig_28_lig_14: - ligand_a: lig_28 - ligand_b: lig_14 - atom mapping: {17: 7, 18: 9, 20: 6, 21: 20, 22: 21, 23: 22, 24: 4, 25: 5, 26: 23, - 27: 24, 28: 25, 43: 1, 44: 0, 45: 2, 46: 3} - score: '0.418' - edge_lig_41_lig_45: - ligand_a: lig_41 - ligand_b: lig_45 - atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, - 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 47: 41, 48: 42, 49: 43, 50: 44} - score: '0.386' - edge_lig_30_lig_45: - ligand_a: lig_30 - ligand_b: lig_45 - atom mapping: {8: 25, 9: 26, 10: 24, 11: 22, 12: 23, 13: 21, 14: 20, 15: 43, 16: 44, - 17: 41, 18: 42, 19: 18, 20: 19, 21: 17, 22: 16, 23: 13, 24: 15, 25: 14} - score: '0.388' - edge_lig_26_lig_45: - ligand_a: lig_26 - ligand_b: lig_45 - atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, - 25: 21, 26: 22, 27: 23, 28: 24, 41: 41, 42: 42, 43: 43, 44: 44} - score: '0.356' - edge_lig_13_lig_45: - ligand_a: lig_13 - ligand_b: lig_45 - atom mapping: {2: 41, 3: 24, 4: 25, 5: 26, 20: 22, 21: 23, 22: 21, 23: 16, 24: 13, - 25: 15, 26: 14, 41: 17, 42: 18, 43: 19, 44: 20, 45: 43, 46: 44} - score: '0.395' - edge_lig_43_lig_15: - ligand_a: lig_43 - ligand_b: lig_15 - atom mapping: {13: 5, 14: 6, 15: 7, 16: 8, 17: 9, 18: 10, 19: 11, 20: 12, 21: 13, - 22: 14, 23: 15, 24: 16, 25: 17, 26: 18, 40: 25, 41: 26, 42: 27, 43: 28} - score: '0.425' - edge_lig_28_lig_18: - ligand_a: lig_28 - ligand_b: lig_18 - atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, - 25: 21, 26: 22, 27: 23, 28: 24, 43: 33, 44: 34, 45: 35, 46: 36} - score: '0.392' - edge_lig_28_lig_44: - ligand_a: lig_28 - ligand_b: lig_44 - atom mapping: {17: 23, 18: 25, 19: 24, 20: 22, 21: 21, 22: 19, 23: 20, 24: 14, - 25: 13, 26: 11, 27: 12, 28: 10, 43: 17, 44: 18, 45: 15, 46: 16} - score: '0.368' - edge_lig_42_lig_36: - ligand_a: lig_42 - ligand_b: lig_36 - atom mapping: {8: 29, 9: 30, 10: 28, 11: 26, 12: 27, 13: 25, 14: 24, 15: 47, 16: 48, - 17: 45, 18: 46, 19: 22, 20: 23, 21: 21, 22: 20, 23: 17, 24: 19, 25: 18} - score: '0.389' - edge_lig_37_lig_45: - ligand_a: lig_37 - ligand_b: lig_45 - atom mapping: {17: 13, 18: 14, 19: 15, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, - 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 44: 41, 45: 42, 46: 43, 47: 44} - score: '0.390' - edge_lig_43_lig_24: - ligand_a: lig_43 - ligand_b: lig_24 - atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, - 21: 25, 22: 26, 23: 27, 24: 28, 25: 29, 40: 37, 41: 38, 42: 39, 43: 40} - score: '0.395' - edge_lig_43_lig_28: - ligand_a: lig_43 - ligand_b: lig_28 - atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, - 21: 25, 22: 26, 23: 27, 24: 28, 40: 43, 41: 44, 42: 45, 43: 46} - score: '0.356' - edge_lig_42_lig_27: - ligand_a: lig_42 - ligand_b: lig_27 - atom mapping: {8: 29, 10: 28, 11: 26, 12: 27, 13: 25, 14: 24, 15: 47, 16: 48, - 17: 45, 18: 46, 19: 22, 20: 23, 21: 21, 22: 20, 23: 17, 24: 19, 25: 18} - score: '0.375' - edge_lig_43_lig_16: - ligand_a: lig_43 - ligand_b: lig_16 - atom mapping: {13: 5, 14: 6, 15: 7, 16: 8, 17: 9, 18: 10, 19: 11, 20: 12, 21: 13, - 22: 14, 23: 15, 24: 16, 25: 17, 26: 18, 40: 25, 41: 26, 42: 27, 43: 28} - score: '0.454' - edge_lig_29_lig_45: - ligand_a: lig_29 - ligand_b: lig_45 - atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, - 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 31: 26, 42: 41, 43: 42, 44: 43, 45: 44} - score: '0.394' - edge_lig_42_lig_34: - ligand_a: lig_42 - ligand_b: lig_34 - atom mapping: {8: 29, 9: 30, 10: 28, 11: 26, 12: 27, 13: 25, 14: 24, 15: 43, 16: 44, - 17: 41, 18: 42, 19: 22, 20: 23, 21: 21, 22: 20, 23: 17, 24: 19, 25: 18} - score: '0.389' - edge_lig_42_lig_35: - ligand_a: lig_42 - ligand_b: lig_35 - atom mapping: {8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, - 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, 22: 22, 23: 23, 24: 25, 25: 24} - score: '0.392' - edge_lig_43_lig_25: - ligand_a: lig_43 - ligand_b: lig_25 - atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, - 21: 25, 22: 26, 23: 27, 24: 28, 25: 29, 40: 38, 41: 39, 42: 40, 43: 41} - score: '0.390' - edge_lig_28_lig_45: - ligand_a: lig_28 - ligand_b: lig_45 - atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, - 25: 21, 26: 22, 27: 23, 28: 24, 43: 41, 44: 42, 45: 43, 46: 44} - score: '0.354' - edge_lig_43_lig_19: - ligand_a: lig_43 - ligand_b: lig_19 - atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, - 21: 25, 22: 26, 23: 27, 24: 28, 25: 29, 26: 30, 40: 37, 41: 38, 42: 39, 43: 40} - score: '0.414' - edge_lig_42_lig_28: - ligand_a: lig_42 - ligand_b: lig_28 - atom mapping: {10: 28, 11: 26, 12: 27, 13: 25, 14: 24, 15: 45, 16: 46, 17: 43, - 18: 44, 19: 22, 20: 23, 21: 21, 22: 20, 23: 17, 24: 19, 25: 18} - score: '0.354' diff --git a/data/cmet/03_edges/01_perses_openfe.yml b/data/cmet/03_edges/01_perses_openfe.yml deleted file mode 100644 index 129f22a94..000000000 --- a/data/cmet/03_edges/01_perses_openfe.yml +++ /dev/null @@ -1,36 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.5 minimal_spanning_graph -edges: - edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402754_40_14: - ligand_a: lig_CHEMBL3402745_200_5 - ligand_b: lig_CHEMBL3402754_40_14 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 14, 7: 15, 8: 12, 9: 13, - 10: 10, 11: 11, 12: 8, 13: 9, 14: 6, 15: 7, 16: 16, 17: 17, 18: 18, 19: 19, - 20: 20, 21: 21, 22: 41, 23: 42, 24: 28, 26: 26, 27: 27, 28: 24, 41: 22, 42: 23, - 43: 43, 44: 44} - score: '0.716' - edge_lig_CHEMBL3402761_1_21_lig_CHEMBL3402749_500_9: - ligand_a: lig_CHEMBL3402761_1_21 - ligand_b: lig_CHEMBL3402749_500_9 - atom mapping: {0: 37, 1: 36, 2: 34, 3: 35, 4: 22, 5: 23, 6: 32, 7: 33, 8: 30, - 10: 28, 11: 29, 12: 26, 13: 27, 15: 24, 16: 25, 17: 21, 18: 20, 19: 17, 20: 18, - 21: 19, 22: 16, 23: 14, 24: 15, 25: 12, 26: 13, 27: 10, 28: 11, 29: 9, 59: 40, - 60: 41, 61: 38, 62: 39} - score: '0.675' - edge_lig_CHEMBL3402744_300_4_lig_CHEMBL3402761_1_21: - ligand_a: lig_CHEMBL3402744_300_4 - ligand_b: lig_CHEMBL3402761_1_21 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 15, 7: 16, 8: 12, 9: 13, - 10: 10, 11: 11, 12: 8, 14: 6, 15: 7, 16: 17, 17: 18, 18: 19, 19: 20, 20: 21, - 21: 22, 22: 59, 23: 60, 24: 29, 26: 27, 27: 28, 28: 25, 38: 23, 39: 24, 40: 61, - 41: 62} - score: '0.671' - edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402761_1_21: - ligand_a: lig_CHEMBL3402745_200_5 - ligand_b: lig_CHEMBL3402761_1_21 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 15, 7: 16, 8: 12, 9: 13, - 10: 10, 11: 11, 12: 8, 14: 6, 15: 7, 16: 17, 17: 18, 18: 19, 19: 20, 20: 21, - 21: 22, 22: 59, 23: 60, 24: 29, 26: 27, 27: 28, 28: 25, 41: 23, 42: 24, 43: 61, - 44: 62} - score: '0.648' diff --git a/data/eg5/03_edges/01_perses_openfe.yml b/data/eg5/03_edges/01_perses_openfe.yml deleted file mode 100644 index fd212f12f..000000000 --- a/data/eg5/03_edges/01_perses_openfe.yml +++ /dev/null @@ -1,204 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.5 minimal_spanning_graph -edges: - edge_lig_CHEMBL1084676_lig_CHEMBL1078998: - ligand_a: lig_CHEMBL1084676 - ligand_b: lig_CHEMBL1078998 - atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, - 16: 16, 17: 17, 18: 18, 19: 22, 20: 26, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, - 26: 35, 27: 36, 28: 38, 52: 39, 53: 40, 54: 41, 55: 42, 56: 43, 57: 44, 58: 45, - 59: 46} - score: '0.598' - edge_lig_CHEMBL1084678_lig_CHEMBL1078998: - ligand_a: lig_CHEMBL1084678 - ligand_b: lig_CHEMBL1078998 - atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, - 16: 16, 17: 17, 18: 18, 19: 22, 20: 26, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, - 26: 35, 27: 36, 28: 38, 52: 39, 53: 40, 54: 41, 55: 42, 56: 43, 57: 44, 58: 45, - 59: 46} - score: '0.598' - edge_lig_CHEMBL1078998_lig_CHEMBL1083836: - ligand_a: lig_CHEMBL1078998 - ligand_b: lig_CHEMBL1083836 - atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, - 16: 16, 30: 25, 31: 26, 32: 27, 33: 28, 34: 29, 35: 30, 36: 31, 37: 32, 39: 42, - 40: 43, 41: 44, 42: 45, 43: 46, 44: 47, 45: 48, 46: 49} - score: '0.544' - edge_lig_CHEMBL1085895_lig_CHEMBL1078998: - ligand_a: lig_CHEMBL1085895 - ligand_b: lig_CHEMBL1078998 - atom mapping: {20: 36, 21: 38, 22: 35, 23: 33, 24: 34, 25: 32, 26: 30, 27: 31, - 28: 16, 29: 17, 30: 26, 31: 22, 32: 18, 33: 14, 34: 15, 35: 12, 36: 13, 37: 11, - 38: 9, 39: 10, 40: 7, 41: 8, 53: 45, 54: 46, 55: 42, 56: 44, 57: 43, 58: 39, - 59: 41, 60: 40} - score: '0.602' - edge_lig_CHEMBL1084143_lig_CHEMBL1078998: - ligand_a: lig_CHEMBL1084143 - ligand_b: lig_CHEMBL1078998 - atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, - 16: 16, 17: 17, 19: 26, 20: 27, 21: 28, 22: 29, 23: 18, 24: 19, 25: 20, 26: 21, - 27: 30, 28: 31, 29: 32, 30: 33, 31: 34, 32: 35, 33: 36, 34: 37, 61: 39, 62: 41, - 63: 40, 64: 42, 65: 44, 66: 43, 67: 45, 68: 46} - score: '0.653' - edge_lig_CHEMBL1085666_lig_CHEMBL1078998: - ligand_a: lig_CHEMBL1085666 - ligand_b: lig_CHEMBL1078998 - atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, - 16: 16, 17: 17, 18: 26, 19: 22, 20: 18, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, - 26: 35, 27: 36, 28: 37, 35: 39, 36: 41, 37: 40, 38: 42, 39: 44, 40: 43, 41: 45, - 42: 46} - score: '0.628' - edge_lig_CHEMBL1084677_lig_CHEMBL1078998: - ligand_a: lig_CHEMBL1084677 - ligand_b: lig_CHEMBL1078998 - atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, - 16: 16, 17: 17, 18: 26, 19: 22, 20: 18, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, - 26: 35, 27: 36, 28: 37, 49: 39, 50: 41, 51: 40, 52: 42, 53: 44, 54: 43, 55: 45, - 56: 46} - score: '0.602' - edge_lig_CHEMBL1077204_lig_CHEMBL1078998: - ligand_a: lig_CHEMBL1077204 - ligand_b: lig_CHEMBL1078998 - atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, - 16: 16, 17: 17, 18: 26, 19: 22, 20: 18, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, - 26: 35, 27: 36, 28: 37, 53: 39, 54: 41, 55: 40, 56: 42, 57: 44, 58: 43, 59: 45, - 60: 46} - score: '0.598' - edge_lig_CHEMBL1084935_lig_CHEMBL1078998: - ligand_a: lig_CHEMBL1084935 - ligand_b: lig_CHEMBL1078998 - atom mapping: {19: 36, 20: 38, 21: 35, 22: 33, 23: 34, 24: 32, 25: 30, 26: 31, - 27: 16, 28: 17, 29: 18, 30: 19, 31: 20, 32: 21, 33: 22, 34: 25, 35: 24, 36: 23, - 37: 26, 38: 27, 39: 28, 40: 29, 41: 14, 42: 15, 43: 12, 44: 13, 45: 11, 46: 9, - 47: 10, 48: 7, 49: 8, 61: 45, 62: 46, 63: 42, 64: 44, 65: 43, 66: 39, 67: 41, - 68: 40} - score: '0.720' - edge_lig_CHEMBL1078691_lig_CHEMBL1077227: - ligand_a: lig_CHEMBL1078691 - ligand_b: lig_CHEMBL1077227 - atom mapping: {8: 7, 9: 8, 10: 9, 11: 10, 12: 11, 13: 12, 14: 13, 15: 14, 16: 15, - 17: 16, 18: 17, 19: 26, 20: 27, 21: 28, 22: 29, 23: 22, 24: 25, 25: 24, 26: 23, - 27: 18, 28: 19, 29: 20, 30: 21, 31: 30, 32: 31, 33: 32, 34: 33, 35: 34, 36: 35, - 37: 36, 38: 37, 40: 47, 41: 48, 42: 49, 43: 50, 44: 51, 45: 52, 46: 53, 47: 54} - score: '0.707' - edge_lig_CHEMBL1078774_lig_CHEMBL1077227: - ligand_a: lig_CHEMBL1078774 - ligand_b: lig_CHEMBL1077227 - atom mapping: {8: 7, 9: 8, 10: 9, 11: 10, 12: 11, 13: 12, 14: 13, 15: 14, 16: 15, - 17: 16, 18: 17, 19: 26, 20: 27, 21: 28, 22: 29, 23: 22, 24: 25, 25: 24, 26: 23, - 27: 18, 28: 19, 29: 20, 30: 21, 31: 30, 32: 31, 33: 32, 34: 33, 35: 34, 36: 35, - 37: 36, 38: 37, 40: 47, 41: 48, 42: 49, 43: 50, 44: 51, 45: 52, 46: 53, 47: 54} - score: '0.707' - edge_lig_CHEMBL1089056_lig_CHEMBL1077227: - ligand_a: lig_CHEMBL1089056 - ligand_b: lig_CHEMBL1077227 - atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, - 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, - 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, 31: 31, 32: 32, 33: 33, 34: 34, 35: 35, - 36: 36, 38: 37, 39: 47, 40: 48, 41: 49, 42: 50, 43: 51, 44: 52, 45: 53, 46: 54} - score: '0.716' - edge_lig_CHEMBL1078998_lig_CHEMBL1082248: - ligand_a: lig_CHEMBL1078998 - ligand_b: lig_CHEMBL1082248 - atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 14: 14, 15: 15, 16: 16, - 17: 17, 30: 18, 31: 19, 32: 20, 33: 21, 34: 22, 35: 23, 36: 24, 37: 25, 39: 35, - 40: 36, 41: 37, 42: 38, 43: 39, 44: 40, 45: 41, 46: 42} - score: '0.562' - edge_lig_CHEMBL1078998_lig_CHEMBL1085692: - ligand_a: lig_CHEMBL1078998 - ligand_b: lig_CHEMBL1085692 - atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 14: 14, 15: 15, 16: 16, - 17: 17, 30: 18, 31: 19, 32: 20, 33: 21, 34: 22, 35: 23, 36: 24, 37: 25, 39: 51, - 40: 52, 41: 53, 42: 54, 43: 55, 44: 56, 45: 57, 46: 58} - score: '0.538' - edge_lig_CHEMBL1089393_lig_CHEMBL1077227: - ligand_a: lig_CHEMBL1089393 - ligand_b: lig_CHEMBL1077227 - atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, - 16: 16, 17: 17, 18: 30, 19: 31, 20: 32, 21: 33, 22: 34, 23: 35, 24: 36, 26: 37, - 27: 47, 28: 48, 29: 49, 30: 50, 31: 51, 32: 52, 33: 53, 34: 54} - score: '0.645' - edge_lig_CHEMBL1088740_lig_CHEMBL1077227: - ligand_a: lig_CHEMBL1088740 - ligand_b: lig_CHEMBL1077227 - atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, - 16: 16, 17: 17, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, 26: 35, 27: 36, 28: 37, - 30: 47, 31: 49, 32: 48, 33: 50, 34: 52, 35: 51, 36: 53, 37: 54} - score: '0.618' - edge_lig_CHEMBL1093088_lig_CHEMBL1078998: - ligand_a: lig_CHEMBL1093088 - ligand_b: lig_CHEMBL1078998 - atom mapping: {7: 36, 8: 37, 9: 35, 10: 33, 11: 34, 12: 32, 13: 30, 14: 31, 15: 16, - 16: 17, 17: 26, 18: 22, 19: 18, 20: 14, 21: 15, 22: 12, 23: 13, 24: 11, 25: 9, - 26: 10, 27: 7, 28: 8, 40: 45, 41: 46, 42: 42, 43: 44, 44: 43, 45: 39, 46: 41, - 47: 40} - score: '0.598' - edge_lig_CHEMBL1083517_lig_CHEMBL1078998: - ligand_a: lig_CHEMBL1083517 - ligand_b: lig_CHEMBL1078998 - atom mapping: {8: 7, 9: 8, 10: 9, 11: 10, 12: 11, 13: 12, 14: 13, 15: 14, 16: 15, - 17: 16, 18: 17, 19: 18, 20: 22, 21: 26, 22: 30, 23: 31, 24: 32, 25: 33, 26: 34, - 27: 35, 28: 36, 29: 37, 39: 39, 40: 40, 41: 41, 42: 42, 43: 43, 44: 44, 45: 45, - 46: 46} - score: '0.621' - edge_lig_CHEMBL1084115_lig_CHEMBL1085692: - ligand_a: lig_CHEMBL1084115 - ligand_b: lig_CHEMBL1085692 - atom mapping: {5: 7, 6: 8, 7: 9, 8: 10, 9: 11, 10: 12, 12: 14, 13: 15, 14: 16, - 15: 17, 28: 18, 29: 19, 30: 20, 31: 21, 32: 22, 33: 23, 34: 24, 36: 25, 37: 51, - 38: 53, 39: 52, 40: 54, 41: 55, 42: 56, 43: 57, 44: 58} - score: '0.538' - edge_lig_CHEMBL1096003_lig_CHEMBL1078998: - ligand_a: lig_CHEMBL1096003 - ligand_b: lig_CHEMBL1078998 - atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 14: 14, 15: 15, 16: 16, - 17: 17, 18: 30, 19: 31, 20: 32, 21: 33, 22: 34, 23: 35, 24: 36, 25: 37, 49: 39, - 50: 41, 51: 40, 52: 42, 53: 44, 54: 43, 55: 45, 56: 46} - score: '0.538' - edge_lig_CHEMBL1078998_lig_CHEMBL1096002: - ligand_a: lig_CHEMBL1078998 - ligand_b: lig_CHEMBL1096002 - atom mapping: {7: 30, 8: 31, 9: 28, 10: 29, 11: 27, 12: 25, 14: 23, 15: 24, 16: 21, - 17: 22, 30: 19, 31: 20, 32: 18, 33: 16, 34: 17, 35: 15, 36: 13, 38: 14, 39: 48, - 40: 49, 41: 50, 42: 45, 43: 46, 44: 47, 45: 43, 46: 44} - score: '0.555' - edge_lig_CHEMBL1078998_lig_CHEMBL1082249: - ligand_a: lig_CHEMBL1078998 - ligand_b: lig_CHEMBL1082249 - atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 14: 14, 15: 15, 16: 16, - 17: 17, 30: 18, 31: 19, 32: 20, 33: 21, 34: 22, 35: 23, 36: 24, 37: 25, 39: 45, - 40: 46, 41: 47, 42: 48, 43: 49, 44: 50, 45: 51, 46: 52} - score: '0.545' - edge_lig_CHEMBL1086409_lig_CHEMBL1078998: - ligand_a: lig_CHEMBL1086409 - ligand_b: lig_CHEMBL1078998 - atom mapping: {5: 7, 6: 8, 7: 9, 8: 10, 9: 11, 10: 12, 11: 13, 12: 14, 13: 15, - 14: 16, 15: 17, 16: 18, 17: 22, 18: 26, 19: 30, 20: 31, 21: 32, 22: 33, 23: 34, - 24: 35, 25: 36, 26: 38, 36: 39, 37: 41, 38: 40, 39: 42, 40: 44, 41: 43, 42: 45, - 43: 46} - score: '0.621' - edge_lig_CHEMBL1077227_lig_CHEMBL1085692: - ligand_a: lig_CHEMBL1077227 - ligand_b: lig_CHEMBL1085692 - atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 14: 14, 15: 15, 16: 16, - 17: 17, 30: 18, 31: 19, 32: 20, 33: 21, 34: 22, 35: 23, 36: 24, 37: 25, 38: 26, - 39: 28, 40: 27, 41: 29, 42: 30, 43: 31, 47: 51, 48: 53, 49: 52, 50: 54, 51: 56, - 52: 55, 53: 57, 54: 58} - score: '0.567' - edge_lig_CHEMBL1093087_lig_CHEMBL1084115: - ligand_a: lig_CHEMBL1093087 - ligand_b: lig_CHEMBL1084115 - atom mapping: {20: 34, 21: 36, 22: 33, 23: 31, 24: 32, 25: 30, 26: 28, 27: 29, - 28: 14, 29: 15, 30: 16, 31: 20, 32: 24, 33: 12, 34: 13, 35: 10, 36: 11, 37: 9, - 38: 7, 39: 8, 40: 5, 41: 6, 53: 43, 54: 44, 55: 40, 56: 41, 57: 42, 58: 37, - 59: 39, 60: 38} - score: '0.547' - edge_lig_CHEMBL1086410_lig_CHEMBL1078998: - ligand_a: lig_CHEMBL1086410 - ligand_b: lig_CHEMBL1078998 - atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, - 16: 16, 17: 17, 18: 26, 19: 29, 20: 28, 21: 27, 22: 22, 23: 25, 24: 24, 25: 23, - 26: 18, 27: 21, 28: 20, 29: 19, 30: 30, 31: 31, 32: 32, 33: 33, 34: 34, 35: 35, - 36: 36, 37: 37, 47: 39, 48: 41, 49: 40, 50: 42, 51: 44, 52: 43, 53: 45, 54: 46} - score: '0.738' diff --git a/data/hif2a/03_edges/01_perses_openfe.yml b/data/hif2a/03_edges/01_perses_openfe.yml deleted file mode 100644 index 1070dce53..000000000 --- a/data/hif2a/03_edges/01_perses_openfe.yml +++ /dev/null @@ -1,210 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.5 minimal_spanning_graph -edges: - edge_lig_165_lig_54: - ligand_a: lig_165 - ligand_b: lig_54 - atom mapping: {0: 19, 1: 18, 2: 16, 3: 17, 4: 14, 5: 15, 6: 13, 7: 12, 34: 22, - 35: 23, 36: 20, 37: 21} - score: '0.367' - edge_lig_43_lig_84: - ligand_a: lig_43 - ligand_b: lig_84 - atom mapping: {9: 7, 10: 6, 11: 4, 12: 5, 13: 2, 15: 1, 16: 0, 17: 31, 18: 32, - 20: 29, 21: 30} - score: '0.363' - edge_lig_124_lig_224: - ligand_a: lig_124 - ligand_b: lig_224 - atom mapping: {14: 24, 15: 26, 16: 25, 17: 27, 18: 28, 19: 29, 20: 30} - score: '0.174' - edge_lig_1_lig_43: - ligand_a: lig_1 - ligand_b: lig_43 - atom mapping: {7: 9, 8: 10, 9: 20, 10: 21, 11: 17, 12: 18, 13: 15, 14: 16, 15: 13, - 17: 11, 18: 12} - score: '0.357' - edge_lig_156_lig_54: - ligand_a: lig_156 - ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 13: 18, 14: 19, 15: 16, 16: 17, - 18: 14, 19: 15} - score: '0.346' - edge_lig_57_lig_54: - ligand_a: lig_57 - ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, - 16: 17, 18: 14, 19: 15} - score: '0.364' - edge_lig_30_lig_224: - ligand_a: lig_30 - ligand_b: lig_224 - atom mapping: {14: 24, 15: 26, 16: 25, 17: 27, 19: 29, 20: 28} - score: '0.152' - edge_lig_206_lig_54: - ligand_a: lig_206 - ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, - 16: 17, 18: 14, 19: 15} - score: '0.364' - edge_lig_54_lig_224: - ligand_a: lig_54 - ligand_b: lig_224 - atom mapping: {29: 24, 30: 26, 31: 25, 32: 27} - score: '0.093' - edge_lig_67_lig_124: - ligand_a: lig_67 - ligand_b: lig_124 - atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 13: 13, 15: 21, 17: 23} - score: '0.311' - edge_lig_35_lig_224: - ligand_a: lig_35 - ligand_b: lig_224 - atom mapping: {27: 24, 28: 26, 29: 25, 30: 27, 32: 29, 33: 28} - score: '0.145' - edge_lig_227_lig_54: - ligand_a: lig_227 - ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, - 16: 17, 18: 14, 19: 15} - score: '0.361' - edge_lig_31_lig_224: - ligand_a: lig_31 - ligand_b: lig_224 - atom mapping: {17: 24, 18: 26, 19: 25, 20: 27, 22: 29, 23: 28} - score: '0.145' - edge_lig_338_lig_54: - ligand_a: lig_338 - ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 14, 10: 15, 11: 16, 12: 17, 13: 18, 14: 19, 15: 20, - 16: 21, 18: 22, 19: 23} - score: '0.364' - edge_lig_336_lig_54: - ligand_a: lig_336 - ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 14, 10: 15, 11: 16, 12: 17, 13: 18, 14: 19, 15: 20, - 16: 21, 18: 22, 19: 23} - score: '0.367' - edge_lig_50_lig_224: - ligand_a: lig_50 - ligand_b: lig_224 - atom mapping: {14: 24, 15: 25, 16: 26, 17: 27} - score: '0.098' - edge_lig_231_lig_54: - ligand_a: lig_231 - ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, - 16: 17, 18: 14, 19: 15} - score: '0.370' - edge_lig_290_lig_54: - ligand_a: lig_290 - ligand_b: lig_54 - atom mapping: {0: 19, 1: 18, 2: 16, 3: 17, 4: 14, 5: 15, 6: 13, 7: 12, 34: 22, - 35: 23, 36: 20, 37: 21} - score: '0.359' - edge_lig_163_lig_54: - ligand_a: lig_163 - ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, - 16: 17, 18: 14, 19: 15} - score: '0.367' - edge_lig_42_lig_224: - ligand_a: lig_42 - ligand_b: lig_224 - atom mapping: {27: 24, 28: 26, 29: 25, 30: 27, 32: 29, 33: 30} - score: '0.145' - edge_lig_215_lig_54: - ligand_a: lig_215 - ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, - 16: 17, 18: 14, 19: 15} - score: '0.364' - edge_lig_61_lig_43: - ligand_a: lig_61 - ligand_b: lig_43 - atom mapping: {7: 9, 8: 10, 9: 20, 10: 21, 11: 17, 12: 18, 13: 15, 14: 16, 15: 13, - 17: 11, 18: 12} - score: '0.360' - edge_lig_41_lig_224: - ligand_a: lig_41 - ligand_b: lig_224 - atom mapping: {26: 24, 27: 25, 28: 26, 29: 27, 31: 29, 32: 30} - score: '0.147' - edge_lig_43_lig_224: - ligand_a: lig_43 - ligand_b: lig_224 - atom mapping: {27: 24, 28: 25, 29: 26, 30: 27, 32: 29, 33: 30} - score: '0.145' - edge_lig_251_lig_43: - ligand_a: lig_251 - ligand_b: lig_43 - atom mapping: {7: 9, 8: 10, 9: 11, 10: 12, 11: 13, 13: 15, 14: 16, 15: 17, 16: 18, - 17: 20, 18: 21} - score: '0.355' - edge_lig_234_lig_54: - ligand_a: lig_234 - ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, - 16: 17, 18: 14, 19: 15} - score: '0.367' - edge_lig_235_lig_54: - ligand_a: lig_235 - ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 18, 13: 19, 14: 16, 15: 17, - 17: 14, 18: 15} - score: '0.338' - edge_lig_15_lig_54: - ligand_a: lig_15 - ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, - 16: 17, 18: 14, 19: 15} - score: '0.361' - edge_lig_155_lig_54: - ligand_a: lig_155 - ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, - 16: 17, 18: 14, 19: 15} - score: '0.367' - edge_lig_289_lig_54: - ligand_a: lig_289 - ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, - 16: 17, 18: 14, 19: 15} - score: '0.367' - edge_lig_254_lig_54: - ligand_a: lig_254 - ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 14, 10: 15, 11: 16, 12: 17, 13: 18, 14: 19, 15: 20, - 16: 21, 18: 22, 19: 23} - score: '0.364' - edge_lig_252_lig_54: - ligand_a: lig_252 - ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 14, 10: 15, 11: 16, 12: 17, 13: 18, 14: 19, 15: 20, - 16: 21, 18: 22, 19: 23} - score: '0.367' - edge_lig_167_lig_54: - ligand_a: lig_167 - ligand_b: lig_54 - atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, - 16: 17, 18: 14, 19: 15} - score: '0.364' - edge_lig_256_lig_43: - ligand_a: lig_256 - ligand_b: lig_43 - atom mapping: {7: 9, 8: 10, 9: 11, 10: 12, 11: 13, 13: 15, 14: 16, 15: 17, 16: 18, - 17: 20, 18: 21} - score: '0.357' - edge_lig_23_lig_43: - ligand_a: lig_23 - ligand_b: lig_43 - atom mapping: {7: 9, 8: 10, 9: 20, 10: 21, 11: 17, 12: 18, 13: 15, 14: 16, 15: 13, - 17: 11, 18: 12} - score: '0.355' - edge_lig_25_lig_43: - ligand_a: lig_25 - ligand_b: lig_43 - atom mapping: {7: 9, 8: 10, 9: 11, 10: 12, 11: 13, 13: 15, 14: 16, 15: 17, 16: 20, - 17: 21} - score: '0.331' diff --git a/data/mcl1/03_edges/01_perses_openfe.yml b/data/mcl1/03_edges/01_perses_openfe.yml deleted file mode 100644 index 403c2050f..000000000 --- a/data/mcl1/03_edges/01_perses_openfe.yml +++ /dev/null @@ -1,172 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.5 minimal_spanning_graph -edges: - edge_lig_47_lig_34: - ligand_a: lig_47 - ligand_b: lig_34 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 23, 23: 22, 24: 24, 41: 39, 42: 40} - score: '0.583' - edge_lig_47_lig_52: - ligand_a: lig_47 - ligand_b: lig_52 - atom mapping: {0: 40, 1: 2, 2: 3, 3: 4, 4: 5, 5: 6, 6: 1, 7: 0, 8: 7, 9: 8, 10: 9, - 11: 10, 12: 11, 13: 12, 14: 13, 15: 14, 16: 16, 17: 15, 18: 17, 19: 18, 20: 19, - 21: 20, 22: 22, 23: 21, 24: 23, 41: 38} - score: '0.570' - edge_lig_47_lig_27: - ligand_a: lig_47 - ligand_b: lig_27 - atom mapping: {0: 30, 1: 25, 2: 26, 3: 27, 4: 22, 5: 23, 6: 24, 7: 31, 8: 19, - 9: 20, 10: 21, 11: 32, 12: 33, 13: 34, 14: 35, 15: 16, 16: 18, 17: 17, 18: 13, - 19: 14, 20: 15, 21: 10, 22: 12, 23: 11, 24: 9, 41: 28, 42: 29} - score: '0.608' - edge_lig_47_lig_61: - ligand_a: lig_47 - ligand_b: lig_61 - atom mapping: {0: 7, 1: 6, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 8: 9, 9: 10, 10: 11, - 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, 21: 21, - 22: 23, 23: 22, 24: 24, 41: 42, 42: 0} - score: '0.542' - edge_lig_43_lig_56: - ligand_a: lig_43 - ligand_b: lig_56 - atom mapping: {14: 27, 15: 24, 16: 25, 17: 26, 18: 21, 19: 23, 20: 22, 21: 18, - 22: 20, 23: 19, 24: 8, 25: 9, 26: 10, 27: 4, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, - 33: 45, 34: 46, 35: 0, 36: 7, 38: 15, 39: 16, 40: 17} - score: '0.548' - edge_lig_47_lig_63: - ligand_a: lig_47 - ligand_b: lig_63 - atom mapping: {0: 42, 1: 2, 2: 3, 3: 4, 4: 5, 5: 6, 6: 1, 7: 0, 8: 7, 9: 8, 10: 9, - 12: 10, 13: 11, 14: 12, 15: 13, 16: 15, 17: 14, 18: 16, 19: 17, 20: 18, 21: 19, - 22: 21, 23: 20, 24: 22, 41: 40} - score: '0.542' - edge_lig_43_lig_36: - ligand_a: lig_43 - ligand_b: lig_36 - atom mapping: {14: 24, 15: 21, 16: 22, 17: 23, 18: 18, 19: 20, 20: 19, 21: 15, - 22: 17, 23: 16, 24: 8, 25: 9, 26: 10, 27: 4, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, - 33: 42, 34: 43, 35: 0, 36: 7, 37: 11, 38: 12, 39: 13, 40: 14} - score: '0.561' - edge_lig_46_lig_58: - ligand_a: lig_46 - ligand_b: lig_58 - atom mapping: {0: 46, 1: 2, 2: 3, 3: 4, 4: 5, 5: 6, 6: 1, 7: 0, 8: 7, 9: 8, 10: 9, - 12: 14, 13: 15, 14: 16, 15: 17, 16: 19, 17: 18, 18: 20, 19: 21, 20: 22, 21: 23, - 22: 25, 23: 24, 24: 26, 43: 44} - score: '0.550' - edge_lig_47_lig_30: - ligand_a: lig_47 - ligand_b: lig_30 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 23, 23: 22, 24: 24, 41: 39, 42: 40} - score: '0.583' - edge_lig_43_lig_37: - ligand_a: lig_43 - ligand_b: lig_37 - atom mapping: {14: 24, 15: 21, 16: 22, 17: 23, 18: 18, 19: 20, 20: 19, 21: 15, - 22: 17, 23: 16, 24: 8, 25: 9, 26: 10, 27: 4, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, - 33: 42, 34: 43, 35: 0, 36: 7, 37: 11, 38: 12, 39: 13, 40: 14} - score: '0.561' - edge_lig_43_lig_50: - ligand_a: lig_43 - ligand_b: lig_50 - atom mapping: {14: 25, 15: 22, 16: 23, 17: 24, 18: 19, 19: 21, 20: 20, 21: 16, - 22: 18, 23: 17, 24: 9, 25: 10, 26: 11, 27: 3, 28: 4, 29: 5, 30: 6, 31: 1, 32: 2, - 33: 43, 34: 0, 35: 7, 37: 12, 38: 13, 39: 14, 40: 15} - score: '0.548' - edge_lig_47_lig_31: - ligand_a: lig_47 - ligand_b: lig_31 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 23, 23: 22, 24: 24, 41: 39, 42: 40} - score: '0.583' - edge_lig_43_lig_53: - ligand_a: lig_43 - ligand_b: lig_53 - atom mapping: {14: 23, 15: 20, 16: 21, 17: 22, 18: 17, 19: 19, 20: 18, 21: 14, - 22: 16, 23: 15, 24: 7, 25: 8, 26: 9, 27: 5, 28: 6, 29: 1, 30: 2, 31: 3, 32: 4, - 33: 41, 35: 43, 36: 0, 37: 10, 38: 11, 39: 12, 40: 13} - score: '0.548' - edge_lig_47_lig_67: - ligand_a: lig_47 - ligand_b: lig_67 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 12: 11, 13: 12, 14: 13, 15: 14, 16: 16, 17: 15, 18: 17, 19: 18, 20: 19, 21: 20, - 22: 22, 23: 21, 24: 23, 41: 41, 42: 42} - score: '0.555' - edge_lig_47_lig_33: - ligand_a: lig_47 - ligand_b: lig_33 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 23, 23: 22, 24: 24, 41: 36, 42: 37} - score: '0.608' - edge_lig_43_lig_58: - ligand_a: lig_43 - ligand_b: lig_58 - atom mapping: {14: 26, 15: 23, 16: 24, 17: 25, 18: 20, 19: 22, 20: 21, 21: 17, - 22: 19, 23: 18, 24: 7, 25: 8, 26: 9, 27: 5, 28: 6, 29: 1, 30: 2, 31: 3, 32: 4, - 33: 44, 35: 46, 36: 0, 38: 14, 39: 15, 40: 16} - score: '0.531' - edge_lig_58_lig_48: - ligand_a: lig_58 - ligand_b: lig_48 - atom mapping: {0: 7, 1: 6, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 7: 8, 8: 9, 9: 10, 14: 12, - 15: 13, 16: 14, 17: 15, 18: 17, 19: 16, 20: 18, 21: 20, 22: 19, 23: 21, 24: 23, - 25: 22, 26: 24, 44: 40, 46: 0} - score: '0.573' - edge_lig_47_lig_35: - ligand_a: lig_47 - ligand_b: lig_35 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 23, 23: 22, 24: 24, 41: 39, 42: 40} - score: '0.583' - edge_lig_47_lig_58: - ligand_a: lig_47 - ligand_b: lig_58 - atom mapping: {0: 46, 1: 2, 2: 3, 3: 4, 4: 5, 5: 6, 6: 1, 7: 0, 8: 7, 9: 8, 10: 9, - 12: 14, 13: 15, 14: 16, 15: 17, 16: 19, 17: 18, 18: 20, 19: 21, 20: 22, 21: 23, - 22: 25, 23: 24, 24: 26, 41: 44} - score: '0.538' - edge_lig_47_lig_49: - ligand_a: lig_47 - ligand_b: lig_49 - atom mapping: {0: 7, 1: 6, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 8: 9, 9: 10, 10: 11, - 11: 12, 12: 13, 13: 14, 14: 15, 15: 16, 16: 18, 17: 17, 18: 19, 19: 20, 20: 21, - 21: 22, 22: 24, 23: 23, 24: 25, 41: 40, 42: 0} - score: '0.570' - edge_lig_47_lig_28: - ligand_a: lig_47 - ligand_b: lig_28 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 23, 23: 22, 24: 24, 41: 39, 42: 40} - score: '0.583' - edge_lig_47_lig_65: - ligand_a: lig_47 - ligand_b: lig_65 - atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 42, 8: 11, 9: 10, - 10: 9, 12: 39, 13: 40, 14: 41, 15: 12, 16: 14, 17: 13, 18: 15, 19: 16, 20: 17, - 21: 18, 22: 20, 23: 19, 24: 21, 42: 7} - score: '0.542' - edge_lig_47_lig_32: - ligand_a: lig_47 - ligand_b: lig_32 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 23, 23: 22, 24: 24, 41: 39, 42: 40} - score: '0.583' - edge_lig_47_lig_60: - ligand_a: lig_47 - ligand_b: lig_60 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 12: 11, 13: 12, 14: 13, 15: 14, 16: 16, 17: 15, 18: 17, 19: 18, 20: 19, 21: 20, - 22: 22, 23: 21, 24: 23, 41: 41, 42: 42} - score: '0.555' diff --git a/data/p38/03_edges/01_perses_openfe.yml b/data/p38/03_edges/01_perses_openfe.yml deleted file mode 100644 index 5698988bd..000000000 --- a/data/p38/03_edges/01_perses_openfe.yml +++ /dev/null @@ -1,201 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.5 minimal_spanning_graph -edges: - edge_lig_p38a_3flw_lig_p38a_2m: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2m - atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, 19: 41, - 24: 39, 25: 40, 26: 26, 27: 27, 28: 28, 29: 37, 31: 35, 32: 36, 33: 33, 34: 34, - 35: 31, 36: 32, 37: 29, 39: 24, 40: 25} - score: '0.598' - edge_lig_p38a_2y_lig_p38a_2m: - ligand_a: lig_p38a_2y - ligand_b: lig_p38a_2m - atom mapping: {14: 4, 15: 5, 16: 3, 17: 21, 18: 22, 19: 23, 20: 1, 21: 0, 22: 2, - 23: 24, 24: 25, 25: 26, 26: 27, 27: 28, 28: 37, 30: 35, 31: 36, 32: 33, 33: 34, - 34: 31, 35: 32, 36: 29, 38: 39, 39: 40, 40: 41} - score: '0.641' - edge_lig_p38a_2s_lig_p38a_3flw: - ligand_a: lig_p38a_2s - ligand_b: lig_p38a_3flw - atom mapping: {9: 20, 10: 23, 11: 22, 12: 19, 13: 24, 14: 25, 15: 26, 16: 27, - 17: 28, 18: 29, 20: 31, 21: 32, 22: 33, 23: 34, 24: 35, 25: 36, 26: 37, 28: 39, - 29: 40, 30: 16, 31: 17, 32: 18, 33: 12, 34: 10, 51: 13, 52: 14, 53: 15} - score: '0.641' - edge_lig_p38a_3flw_lig_p38a_2o: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2o - atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, 19: 41, - 20: 42, 22: 44, 23: 43, 24: 39, 25: 40, 26: 26, 27: 27, 28: 28, 29: 37, 31: 35, - 32: 36, 33: 33, 34: 34, 35: 31, 36: 32, 37: 29, 39: 24, 40: 25} - score: '0.638' - edge_lig_p38a_3fmh_lig_p38a_2f: - ligand_a: lig_p38a_3fmh - ligand_b: lig_p38a_2f - atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, - 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, - 30: 35, 32: 33, 34: 31, 35: 32, 36: 29, 37: 30, 38: 24, 39: 25} - score: '0.668' - edge_lig_p38a_3flw_lig_p38a_2i: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2i - atom mapping: {10: 4, 11: 5, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, - 19: 43, 20: 44, 21: 45, 22: 46, 23: 47, 24: 41, 25: 42, 26: 26, 27: 27, 28: 30, - 29: 31, 31: 33, 32: 34, 33: 35, 35: 37, 36: 38, 37: 39, 39: 24, 40: 25} - score: '0.667' - edge_lig_p38a_3fly_lig_p38a_2m: - ligand_a: lig_p38a_3fly - ligand_b: lig_p38a_2m - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 16: 21, 17: 22, 18: 23, 19: 24, 20: 25, - 21: 26, 22: 27, 23: 28, 24: 37, 26: 35, 27: 36, 28: 33, 29: 34, 30: 31, 31: 32, - 32: 29, 34: 39, 35: 40, 36: 41} - score: '0.661' - edge_lig_p38a_3fmh_lig_p38a_2m: - ligand_a: lig_p38a_3fmh - ligand_b: lig_p38a_2m - atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, - 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, 30: 35, 31: 36, 32: 33, 33: 34, - 34: 31, 35: 32, 36: 29, 38: 24, 39: 25} - score: '0.620' - edge_lig_p38a_3fmh_lig_p38a_2e: - ligand_a: lig_p38a_3fmh - ligand_b: lig_p38a_2e - atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, - 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, - 30: 35, 31: 36, 32: 33, 33: 34, 34: 31, 35: 32, 36: 29, 37: 30, 38: 24, 39: 25} - score: '0.699' - edge_lig_p38a_3fmh_lig_p38a_2h: - ligand_a: lig_p38a_3fmh - ligand_b: lig_p38a_2h - atom mapping: {9: 4, 10: 5, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, - 18: 41, 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, - 28: 29, 30: 31, 31: 32, 32: 33, 34: 35, 35: 36, 36: 37, 38: 24, 39: 25} - score: '0.680' - edge_lig_p38a_2x_lig_p38a_2m: - ligand_a: lig_p38a_2x - ligand_b: lig_p38a_2m - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 18: 21, 19: 22, 20: 23, 21: 24, - 22: 25, 23: 26, 24: 27, 25: 28, 26: 37, 28: 35, 29: 36, 30: 33, 31: 34, 32: 31, - 33: 32, 34: 29, 36: 39, 37: 40, 38: 41} - score: '0.657' - edge_lig_p38a_3flw_lig_p38a_2ee: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2ee - atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 29, 17: 28, 18: 27, 19: 47, - 20: 48, 21: 51, 22: 50, 23: 49, 24: 45, 25: 46, 26: 32, 27: 33, 28: 34, 29: 43, - 31: 41, 32: 42, 33: 39, 34: 40, 35: 37, 36: 38, 37: 35, 39: 30, 40: 31} - score: '0.657' - edge_lig_p38a_2bb_lig_p38a_2m: - ligand_a: lig_p38a_2bb - ligand_b: lig_p38a_2m - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 19: 21, 20: 22, 21: 23, 22: 24, 23: 25, - 24: 26, 25: 27, 26: 28, 27: 37, 29: 35, 30: 36, 31: 33, 32: 34, 33: 31, 34: 32, - 35: 29, 37: 39, 38: 40, 39: 41} - score: '0.636' - edge_lig_p38a_3fmh_lig_p38a_3fln: - ligand_a: lig_p38a_3fmh - ligand_b: lig_p38a_3fln - atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, - 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, - 30: 35, 31: 36, 32: 33, 33: 34, 34: 31, 35: 32, 36: 29, 38: 24, 39: 25} - score: '0.686' - edge_lig_p38a_3flw_lig_p38a_2l: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2l - atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, 19: 41, - 20: 42, 22: 44, 23: 43, 24: 39, 25: 40, 26: 26, 27: 27, 28: 28, 29: 37, 31: 35, - 32: 36, 33: 33, 34: 34, 35: 31, 36: 32, 37: 29, 39: 24, 40: 25} - score: '0.653' - edge_lig_p38a_3fmh_lig_p38a_2g: - ligand_a: lig_p38a_3fmh - ligand_b: lig_p38a_2g - atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, - 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, - 30: 35, 31: 36, 32: 33, 34: 31, 35: 32, 36: 29, 38: 24, 39: 25} - score: '0.668' - edge_lig_p38a_2z_lig_p38a_2m: - ligand_a: lig_p38a_2z - ligand_b: lig_p38a_2m - atom mapping: {6: 4, 7: 5, 8: 3, 9: 21, 10: 22, 11: 23, 12: 1, 13: 0, 14: 2, 15: 24, - 16: 25, 17: 26, 18: 27, 19: 28, 20: 37, 22: 35, 23: 36, 24: 33, 25: 34, 26: 31, - 27: 32, 28: 29, 30: 39, 31: 40, 32: 41} - score: '0.641' - edge_lig_p38a_3flw_lig_p38a_2gg: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2gg - atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 25, 17: 24, 18: 23, 19: 43, - 20: 44, 21: 47, 22: 46, 23: 45, 24: 41, 25: 42, 26: 28, 27: 29, 28: 30, 29: 39, - 31: 37, 32: 38, 33: 35, 34: 36, 35: 33, 36: 34, 37: 31, 39: 26, 40: 27} - score: '0.670' - edge_lig_p38a_3flw_lig_p38a_2j: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2j - atom mapping: {10: 4, 11: 5, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, - 19: 43, 20: 44, 21: 45, 22: 46, 23: 47, 24: 41, 25: 42, 26: 26, 27: 27, 28: 30, - 29: 31, 31: 33, 32: 34, 33: 35, 34: 36, 35: 37, 36: 38, 37: 39, 39: 24, 40: 25} - score: '0.686' - edge_lig_p38a_3fmh_lig_p38a_2k: - ligand_a: lig_p38a_3fmh - ligand_b: lig_p38a_2k - atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, - 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, 30: 35, 31: 36, 32: 33, 33: 34, - 34: 31, 35: 32, 36: 29, 38: 24, 39: 25} - score: '0.654' - edge_lig_p38a_3flw_lig_p38a_2ff: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2ff - atom mapping: {10: 12, 12: 14, 13: 20, 14: 18, 15: 19, 16: 17, 17: 16, 18: 15, - 19: 38, 20: 39, 21: 42, 22: 41, 23: 40, 24: 36, 25: 37, 26: 23, 27: 24, 28: 25, - 29: 34, 31: 32, 32: 33, 33: 30, 34: 31, 35: 28, 36: 29, 37: 26, 39: 21, 40: 22} - score: '0.665' - edge_lig_p38a_3fmh_lig_p38a_3flz: - ligand_a: lig_p38a_3fmh - ligand_b: lig_p38a_3flz - atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, - 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, - 30: 35, 31: 36, 32: 33, 34: 31, 35: 32, 36: 29, 37: 30, 38: 24, 39: 25} - score: '0.680' - edge_lig_p38a_3flw_lig_p38a_2n: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2n - atom mapping: {10: 33, 11: 34, 12: 32, 13: 50, 14: 51, 15: 52, 16: 29, 17: 30, - 18: 31, 19: 11, 20: 8, 22: 9, 23: 10, 24: 12, 25: 13, 26: 14, 27: 15, 28: 16, - 29: 17, 31: 19, 32: 20, 33: 21, 34: 22, 35: 23, 36: 24, 37: 25, 39: 27, 40: 28} - score: '0.657' - edge_lig_p38a_3flw_lig_p38a_2p: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2p - atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, 19: 41, - 20: 42, 22: 44, 23: 43, 24: 39, 25: 40, 26: 26, 27: 27, 28: 28, 29: 37, 31: 35, - 32: 36, 33: 33, 34: 34, 35: 31, 36: 32, 37: 29, 39: 24, 40: 25} - score: '0.634' - edge_lig_p38a_3flw_lig_p38a_2t: - ligand_a: lig_p38a_3flw - ligand_b: lig_p38a_2t - atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, 19: 41, - 20: 42, 22: 44, 23: 43, 24: 39, 25: 40, 26: 26, 27: 27, 28: 28, 29: 37, 31: 35, - 32: 36, 33: 33, 34: 34, 35: 31, 36: 32, 37: 29, 39: 24, 40: 25} - score: '0.665' - edge_lig_p38a_2aa_lig_p38a_2m: - ligand_a: lig_p38a_2aa - ligand_b: lig_p38a_2m - atom mapping: {7: 4, 9: 3, 10: 21, 11: 22, 12: 23, 13: 1, 14: 0, 15: 2, 16: 24, - 17: 25, 18: 26, 19: 27, 20: 28, 21: 37, 23: 35, 24: 36, 25: 33, 26: 34, 27: 31, - 28: 32, 29: 29, 31: 39, 32: 40, 33: 41} - score: '0.644' - edge_lig_p38a_2m_lig_p38a_2v: - ligand_a: lig_p38a_2m - ligand_b: lig_p38a_2v - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 21: 10, 22: 11, 23: 12, 24: 13, 25: 14, - 26: 15, 27: 16, 28: 17, 29: 26, 31: 24, 32: 25, 33: 22, 34: 23, 35: 20, 36: 21, - 37: 18, 39: 28, 40: 29, 41: 30} - score: '0.718' - edge_lig_p38a_2r_lig_p38a_3flw: - ligand_a: lig_p38a_2r - ligand_b: lig_p38a_3flw - atom mapping: {11: 20, 12: 23, 13: 22, 14: 19, 15: 24, 16: 25, 17: 26, 18: 27, - 19: 28, 20: 29, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, 26: 35, 27: 36, 28: 37, - 29: 38, 30: 39, 31: 40, 32: 16, 33: 17, 34: 18, 35: 12, 36: 10, 53: 13, 54: 14, - 55: 15} - score: '0.671' diff --git a/data/pde2/03_edges/01_perses_openfe.yml b/data/pde2/03_edges/01_perses_openfe.yml deleted file mode 100644 index 2a87e6097..000000000 --- a/data/pde2/03_edges/01_perses_openfe.yml +++ /dev/null @@ -1,184 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.5 minimal_spanning_graph -edges: - edge_lig_49582390_lig_49585367: - ligand_a: lig_49582390 - ligand_b: lig_49585367 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 32, 33: 33, - 34: 34, 35: 35, 36: 36, 37: 37, 38: 39, 39: 38, 40: 40, 41: 41, 42: 43, 43: 42, - 44: 44, 45: 45, 46: 47, 47: 46, 48: 48, 49: 49, 50: 50, 52: 52} - score: '0.877' - edge_lig_49175789_lig_49582390: - ligand_a: lig_49175789 - ligand_b: lig_49582390 - atom mapping: {3: 28, 4: 27, 5: 23, 6: 24, 7: 25, 8: 26, 9: 21, 10: 22, 11: 5, - 12: 4, 13: 3, 14: 2, 15: 6, 16: 7, 17: 8, 18: 9, 19: 10, 20: 11, 21: 12, 22: 13, - 23: 1, 24: 0, 25: 14, 26: 15, 27: 20, 28: 19, 29: 18, 30: 17, 31: 16, 40: 52, - 42: 49, 44: 48, 45: 35, 46: 36, 47: 37, 48: 32, 49: 33, 50: 34, 51: 39, 52: 38, - 53: 46, 54: 47, 55: 44, 56: 45, 57: 42, 58: 43, 59: 40, 60: 41} - score: '0.861' - edge_lig_49582390_lig_49582468: - ligand_a: lig_49582390 - ligand_b: lig_49582468 - atom mapping: {0: 23, 1: 22, 2: 13, 3: 12, 4: 11, 5: 10, 6: 14, 7: 15, 8: 16, - 9: 17, 10: 18, 11: 19, 12: 20, 13: 21, 14: 24, 15: 25, 16: 26, 17: 27, 18: 28, - 19: 29, 20: 30, 21: 6, 22: 5, 23: 4, 24: 9, 25: 8, 26: 7, 27: 3, 28: 2, 32: 46, - 33: 45, 34: 44, 35: 41, 36: 42, 37: 43, 38: 47, 39: 48, 40: 49, 41: 50, 42: 52, - 43: 51, 44: 53, 45: 54, 46: 56, 47: 55, 48: 38, 49: 40, 50: 39} - score: '0.875' - edge_lig_49582390_lig_49072088: - ligand_a: lig_49582390 - ligand_b: lig_49072088 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 31, 33: 32, - 34: 33, 35: 34, 36: 35, 37: 36, 38: 38, 39: 37, 40: 39, 41: 40, 42: 42, 43: 41, - 44: 43, 45: 44, 46: 46, 47: 45, 48: 47, 49: 48, 50: 49} - score: '0.875' - edge_lig_50181001_lig_43249674: - ligand_a: lig_50181001 - ligand_b: lig_43249674 - atom mapping: {5: 25, 6: 26, 7: 21, 8: 22, 9: 23, 10: 24, 12: 5, 13: 4, 14: 3, - 15: 2, 16: 6, 17: 7, 18: 8, 19: 9, 20: 10, 21: 11, 22: 12, 23: 13, 24: 1, 25: 0, - 26: 14, 27: 15, 28: 20, 29: 19, 30: 18, 31: 17, 32: 16, 43: 44, 44: 31, 45: 32, - 46: 33, 47: 28, 48: 29, 49: 30, 50: 34, 51: 35, 52: 43, 53: 42, 54: 41, 55: 40, - 56: 38, 57: 39, 58: 36, 59: 37} - score: '0.917' - edge_lig_49582390_lig_50107616: - ligand_a: lig_49582390 - ligand_b: lig_50107616 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 32, 33: 33, - 34: 34, 35: 35, 36: 36, 37: 37, 38: 39, 39: 38, 40: 40, 41: 41, 42: 43, 43: 42, - 44: 44, 45: 45, 46: 47, 47: 46, 48: 48, 49: 49, 50: 50, 52: 53} - score: '0.877' - edge_lig_49582390_lig_49580115: - ligand_a: lig_49582390 - ligand_b: lig_49580115 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 31, 33: 32, - 34: 33, 35: 34, 36: 35, 37: 36, 38: 38, 39: 37, 40: 39, 41: 40, 42: 42, 43: 41, - 44: 43, 45: 44, 46: 46, 47: 45, 48: 47, 49: 48, 50: 49, 52: 50} - score: '0.915' - edge_lig_49582390_lig_49175828: - ligand_a: lig_49582390 - ligand_b: lig_49175828 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 28, 28: 29, 32: 32, 33: 33, - 34: 34, 35: 35, 36: 36, 37: 37, 38: 39, 39: 38, 40: 40, 41: 41, 42: 43, 43: 42, - 44: 44, 45: 45, 46: 47, 47: 46, 48: 48, 49: 49} - score: '0.855' - edge_lig_49582390_lig_49932129: - ligand_a: lig_49582390 - ligand_b: lig_49932129 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 31, 33: 32, - 34: 33, 35: 34, 36: 35, 37: 36, 38: 38, 39: 37, 40: 39, 41: 40, 42: 42, 43: 41, - 44: 43, 45: 44, 46: 46, 47: 45, 48: 47, 49: 48, 50: 49, 52: 53} - score: '0.886' - edge_lig_48168913_lig_49137374: - ligand_a: lig_48168913 - ligand_b: lig_49137374 - atom mapping: {1: 22, 2: 21, 3: 26, 4: 25, 5: 24, 6: 23, 7: 5, 8: 4, 9: 3, 10: 2, - 11: 6, 12: 7, 13: 8, 14: 9, 15: 10, 16: 11, 17: 12, 18: 13, 19: 1, 20: 0, 21: 14, - 22: 15, 23: 16, 24: 17, 25: 18, 26: 19, 27: 20, 32: 48, 33: 47, 34: 33, 35: 34, - 36: 35, 37: 30, 38: 31, 39: 32, 40: 37, 41: 36, 42: 38, 43: 39, 44: 40, 45: 41, - 46: 43, 47: 42, 48: 45, 49: 44} - score: '0.923' - edge_lig_49582390_lig_48009208: - ligand_a: lig_49582390 - ligand_b: lig_48009208 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 26, 23: 25, 24: 24, 25: 23, 26: 22, 32: 29, 33: 30, 34: 31, 35: 32, - 36: 33, 37: 34, 38: 36, 39: 35, 40: 37, 41: 38, 42: 40, 43: 39, 44: 41, 45: 42, - 46: 44, 47: 43, 50: 45} - score: '0.909' - edge_lig_48168913_lig_50181001: - ligand_a: lig_48168913 - ligand_b: lig_50181001 - atom mapping: {1: 8, 2: 7, 3: 6, 4: 5, 5: 10, 6: 9, 7: 12, 8: 13, 9: 14, 10: 15, - 11: 16, 12: 17, 13: 18, 14: 19, 15: 20, 16: 21, 17: 22, 18: 23, 19: 24, 20: 25, - 21: 26, 22: 27, 23: 28, 24: 29, 25: 30, 26: 31, 27: 32, 31: 42, 34: 44, 35: 45, - 36: 46, 37: 47, 38: 48, 39: 49, 40: 51, 41: 50, 42: 52, 43: 53, 44: 54, 45: 55, - 46: 57, 47: 56, 48: 59, 49: 58} - score: '0.895' - edge_lig_50181001_lig_48022468: - ligand_a: lig_50181001 - ligand_b: lig_48022468 - atom mapping: {5: 25, 6: 26, 7: 21, 8: 22, 9: 23, 10: 24, 12: 5, 13: 4, 14: 3, - 15: 2, 16: 6, 17: 7, 18: 8, 19: 9, 20: 10, 21: 11, 22: 12, 23: 13, 24: 1, 25: 0, - 26: 14, 27: 15, 28: 20, 29: 19, 30: 18, 31: 17, 32: 16, 44: 32, 45: 33, 46: 34, - 47: 29, 48: 30, 49: 31, 50: 35, 51: 36, 52: 44, 53: 43, 54: 42, 55: 41, 56: 39, - 57: 40, 58: 37, 59: 38} - score: '0.905' - edge_lig_49220392_lig_49582390: - ligand_a: lig_49220392 - ligand_b: lig_49582390 - atom mapping: {1: 28, 2: 27, 3: 23, 4: 24, 5: 25, 6: 26, 7: 21, 8: 22, 9: 5, 10: 4, - 11: 3, 12: 2, 13: 6, 14: 7, 15: 8, 16: 9, 17: 10, 18: 11, 19: 12, 20: 13, 21: 1, - 22: 0, 23: 14, 24: 15, 25: 16, 26: 17, 27: 18, 28: 19, 29: 20, 34: 52, 36: 49, - 38: 48, 39: 35, 40: 36, 41: 37, 42: 34, 43: 33, 44: 32, 45: 38, 46: 39, 47: 41, - 48: 40, 49: 43, 50: 42, 51: 45, 52: 44, 53: 47, 54: 46} - score: '0.894' - edge_lig_49220548_lig_49582390: - ligand_a: lig_49220548 - ligand_b: lig_49582390 - atom mapping: {2: 28, 3: 27, 4: 23, 5: 24, 6: 25, 7: 26, 8: 21, 9: 22, 10: 5, - 11: 4, 12: 3, 13: 2, 14: 6, 15: 7, 16: 8, 17: 9, 18: 10, 19: 11, 20: 12, 21: 13, - 22: 1, 23: 0, 24: 14, 25: 15, 26: 20, 27: 19, 28: 18, 29: 17, 30: 16, 37: 52, - 39: 49, 41: 48, 42: 35, 43: 36, 44: 37, 45: 32, 46: 33, 47: 34, 48: 39, 49: 38, - 50: 47, 51: 46, 52: 45, 53: 44, 54: 42, 55: 43, 56: 40, 57: 41} - score: '0.866' - edge_lig_48168913_lig_48271249: - ligand_a: lig_48168913 - ligand_b: lig_48271249 - atom mapping: {1: 26, 2: 21, 3: 22, 4: 23, 5: 24, 6: 25, 7: 5, 8: 4, 9: 3, 10: 2, - 11: 6, 12: 7, 13: 8, 14: 9, 15: 10, 16: 11, 17: 12, 18: 13, 19: 1, 20: 0, 21: 14, - 22: 15, 23: 16, 24: 17, 25: 18, 26: 19, 27: 20, 31: 45, 33: 46, 34: 32, 35: 33, - 36: 34, 37: 29, 38: 30, 39: 31, 40: 36, 41: 35, 42: 37, 43: 38, 44: 39, 45: 40, - 46: 42, 47: 41, 48: 44, 49: 43} - score: '0.929' - edge_lig_49582390_lig_49932714: - ligand_a: lig_49582390 - ligand_b: lig_49932714 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 32, 33: 33, - 34: 34, 35: 35, 36: 36, 37: 37, 38: 39, 39: 38, 40: 40, 41: 41, 42: 43, 43: 42, - 44: 44, 45: 45, 46: 47, 47: 46, 48: 48, 49: 49, 50: 50, 52: 52} - score: '0.886' - edge_lig_49582390_lig_49137530: - ligand_a: lig_49582390 - ligand_b: lig_49137530 - atom mapping: {0: 24, 1: 23, 2: 14, 3: 13, 4: 12, 5: 11, 6: 15, 7: 16, 8: 17, - 9: 18, 10: 19, 11: 20, 12: 21, 13: 22, 14: 25, 15: 26, 16: 27, 17: 28, 18: 29, - 19: 30, 20: 31, 21: 7, 22: 6, 23: 5, 24: 10, 25: 9, 26: 8, 27: 4, 28: 3, 32: 47, - 33: 48, 34: 49, 35: 44, 36: 45, 37: 46, 38: 51, 39: 50, 40: 52, 41: 53, 42: 55, - 43: 54, 44: 56, 45: 57, 46: 59, 47: 58, 48: 41, 49: 43, 50: 42, 52: 39} - score: '0.877' - edge_lig_49582390_lig_49396360: - ligand_a: lig_49582390 - ligand_b: lig_49396360 - atom mapping: {0: 23, 1: 22, 2: 13, 3: 12, 4: 11, 5: 10, 6: 14, 7: 15, 8: 16, - 9: 17, 10: 18, 11: 19, 12: 20, 13: 21, 14: 24, 15: 25, 16: 26, 17: 27, 18: 28, - 19: 29, 20: 30, 21: 6, 22: 5, 23: 4, 24: 9, 25: 8, 26: 7, 27: 3, 28: 2, 32: 44, - 33: 45, 34: 46, 35: 41, 36: 42, 37: 43, 38: 48, 39: 47, 40: 49, 41: 50, 42: 52, - 43: 51, 44: 53, 45: 54, 46: 56, 47: 55, 48: 38, 49: 40, 50: 39, 52: 36} - score: '0.886' - edge_lig_50181001_lig_49582390: - ligand_a: lig_50181001 - ligand_b: lig_49582390 - atom mapping: {3: 28, 4: 27, 5: 23, 6: 22, 7: 21, 8: 26, 9: 25, 10: 24, 12: 5, - 13: 4, 14: 3, 15: 2, 16: 6, 17: 7, 18: 8, 19: 9, 20: 10, 21: 11, 22: 12, 23: 13, - 24: 1, 25: 0, 26: 14, 27: 15, 28: 20, 29: 19, 30: 18, 31: 17, 32: 16, 40: 52, - 42: 48, 43: 50, 44: 35, 45: 36, 46: 37, 47: 34, 48: 33, 49: 32, 50: 38, 51: 39, - 52: 47, 53: 46, 54: 45, 55: 44, 56: 43, 57: 42, 58: 41, 59: 40} - score: '0.861' diff --git a/data/pfkfb3/03_edges/01_perses_openfe.yml b/data/pfkfb3/03_edges/01_perses_openfe.yml deleted file mode 100644 index 6cc3d2211..000000000 --- a/data/pfkfb3/03_edges/01_perses_openfe.yml +++ /dev/null @@ -1,229 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.5 minimal_spanning_graph -edges: - edge_lig_24_lig_69: - ligand_a: lig_24 - ligand_b: lig_69 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 26, 28: 27, - 29: 28, 30: 29, 31: 30, 32: 31, 33: 32, 35: 40, 36: 41, 37: 42, 38: 43, 39: 44, - 41: 45, 44: 47, 45: 48} - score: '0.580' - edge_lig_24_lig_63: - ligand_a: lig_24 - ligand_b: lig_63 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 21, 28: 22, - 29: 23, 30: 24, 31: 25, 32: 26, 33: 27, 35: 35, 36: 36, 37: 37, 38: 38, 39: 39, - 41: 40, 44: 42, 45: 43} - score: '0.597' - edge_lig_24_lig_70: - ligand_a: lig_24 - ligand_b: lig_70 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 26, 28: 27, - 29: 28, 30: 29, 31: 30, 32: 31, 33: 32, 35: 40, 36: 41, 37: 42, 38: 43, 39: 44, - 41: 45, 44: 47, 45: 48} - score: '0.580' - edge_lig_26_lig_59: - ligand_a: lig_26 - ligand_b: lig_59 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 26, 28: 27, - 29: 28, 30: 29, 31: 30, 32: 31, 33: 39, 34: 40, 35: 41, 36: 43, 39: 37, 40: 38, - 41: 35, 42: 36, 43: 34, 45: 32, 46: 33, 47: 47, 48: 48} - score: '0.618' - edge_lig_35_lig_38: - ligand_a: lig_35 - ligand_b: lig_38 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 49, 5: 50, 6: 30, 7: 31, 8: 32, 9: 33, - 10: 41, 11: 42, 12: 44, 13: 43, 14: 45, 15: 46, 16: 47, 17: 48, 18: 39, 19: 40, - 20: 37, 21: 38, 22: 36, 23: 34, 24: 35, 25: 28, 26: 29, 27: 8, 46: 4, 47: 5, - 48: 6, 49: 7} - score: '0.663' - edge_lig_55_lig_38: - ligand_a: lig_55 - ligand_b: lig_38 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 49, 5: 50, 6: 30, 7: 31, 8: 32, 9: 33, - 10: 34, 11: 35, 12: 36, 13: 37, 14: 38, 15: 39, 16: 40, 17: 41, 18: 42, 19: 44, - 20: 43, 21: 45, 22: 48, 23: 47, 24: 46, 25: 28, 26: 29, 27: 8, 46: 4, 47: 5, - 48: 6, 49: 7} - score: '0.659' - edge_lig_24_lig_39: - ligand_a: lig_24 - ligand_b: lig_39 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 22, 28: 23, - 29: 24, 30: 25, 31: 26, 32: 27, 33: 35, 35: 33, 36: 34, 37: 31, 38: 32, 39: 30, - 41: 28, 44: 43, 45: 44} - score: '0.594' - edge_lig_24_lig_38: - ligand_a: lig_24 - ligand_b: lig_38 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 28, 28: 29, - 29: 30, 30: 31, 31: 32, 32: 33, 33: 41, 35: 39, 36: 40, 37: 37, 38: 38, 39: 36, - 41: 34, 44: 49, 45: 50} - score: '0.584' - edge_lig_24_lig_47: - ligand_a: lig_24 - ligand_b: lig_47 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 45, 5: 46, 6: 47, 7: 48, 8: 27, 27: 25, - 28: 26, 29: 6, 30: 7, 31: 8, 32: 9, 33: 17, 35: 15, 36: 16, 37: 13, 38: 14, - 39: 12, 41: 10, 44: 4, 45: 5} - score: '0.587' - edge_lig_58_lig_59: - ligand_a: lig_58 - ligand_b: lig_59 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 25: 26, 26: 27, - 27: 28, 28: 29, 29: 30, 30: 31, 31: 32, 32: 33, 33: 34, 34: 35, 35: 36, 36: 37, - 37: 38, 38: 39, 39: 40, 40: 42, 41: 41, 42: 43, 43: 44, 44: 45, 45: 46, 46: 47, - 47: 48} - score: '0.674' - edge_lig_24_lig_41: - ligand_a: lig_24 - ligand_b: lig_41 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, - 29: 26, 30: 27, 31: 28, 32: 29, 33: 37, 35: 35, 36: 36, 37: 33, 38: 34, 39: 32, - 41: 30, 44: 45, 45: 46} - score: '0.577' - edge_lig_24_lig_44: - ligand_a: lig_24 - ligand_b: lig_44 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 20, 28: 21, - 29: 22, 30: 23, 31: 24, 32: 25, 33: 33, 35: 31, 36: 32, 37: 29, 38: 30, 39: 28, - 41: 26, 44: 41, 45: 42} - score: '0.608' - edge_lig_24_lig_62: - ligand_a: lig_24 - ligand_b: lig_62 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 21, 28: 22, - 29: 23, 30: 24, 31: 25, 32: 26, 33: 27, 35: 35, 36: 36, 37: 37, 38: 38, 39: 39, - 41: 40, 44: 42, 45: 43} - score: '0.597' - edge_lig_33_lig_41: - ligand_a: lig_33 - ligand_b: lig_41 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 45, 5: 46, 6: 26, 7: 27, 8: 28, 9: 29, - 10: 37, 11: 38, 13: 35, 14: 36, 15: 33, 16: 34, 17: 32, 18: 30, 19: 31, 20: 24, - 21: 25, 22: 8, 41: 4, 42: 5, 43: 6, 44: 7} - score: '0.612' - edge_lig_57_lig_38: - ligand_a: lig_57 - ligand_b: lig_38 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 28, 28: 29, - 29: 30, 30: 31, 31: 32, 32: 33, 33: 34, 34: 35, 35: 36, 36: 37, 37: 38, 38: 39, - 39: 40, 40: 41, 41: 42, 42: 44, 43: 43, 44: 45, 45: 48, 46: 47, 47: 46, 48: 49, - 49: 50} - score: '0.656' - edge_lig_37_lig_38: - ligand_a: lig_37 - ligand_b: lig_38 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 28, 28: 29, - 29: 30, 30: 31, 31: 32, 32: 33, 33: 34, 34: 35, 35: 36, 36: 37, 37: 38, 38: 39, - 39: 40, 40: 41, 41: 42, 42: 43, 43: 45, 60: 49, 61: 50} - score: '0.578' - edge_lig_24_lig_49: - ligand_a: lig_24 - ligand_b: lig_49 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 22, 28: 23, - 29: 24, 30: 25, 31: 26, 32: 27, 33: 35, 35: 33, 36: 34, 37: 31, 38: 32, 39: 30, - 41: 28, 44: 43, 45: 44} - score: '0.594' - edge_lig_24_lig_43: - ligand_a: lig_24 - ligand_b: lig_43 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 20, 28: 21, - 29: 22, 30: 23, 31: 24, 32: 25, 33: 33, 35: 31, 36: 32, 37: 29, 38: 30, 39: 28, - 41: 26, 44: 41, 45: 42} - score: '0.608' - edge_lig_29_lig_38: - ligand_a: lig_29 - ligand_b: lig_38 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 49, 5: 50, 6: 30, 7: 31, 8: 32, 9: 33, - 10: 41, 11: 42, 12: 44, 13: 43, 14: 45, 15: 46, 16: 47, 17: 48, 18: 39, 19: 40, - 20: 37, 21: 38, 22: 36, 24: 34, 25: 35, 26: 28, 27: 29, 28: 8, 47: 4, 48: 5, - 49: 6, 50: 7} - score: '0.656' - edge_lig_23_lig_41: - ligand_a: lig_23 - ligand_b: lig_41 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 45, 5: 46, 6: 26, 7: 27, 8: 28, 9: 29, - 10: 30, 11: 31, 12: 32, 13: 33, 14: 34, 15: 35, 16: 36, 17: 37, 19: 24, 20: 25, - 21: 8, 40: 4, 41: 5, 42: 6, 43: 7} - score: '0.602' - edge_lig_24_lig_42: - ligand_a: lig_24 - ligand_b: lig_42 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, - 29: 26, 30: 27, 31: 28, 32: 29, 33: 37, 35: 35, 36: 36, 37: 33, 38: 34, 39: 32, - 41: 30, 44: 45, 45: 46} - score: '0.587' - edge_lig_24_lig_65: - ligand_a: lig_24 - ligand_b: lig_65 - atom mapping: {0: 37, 1: 36, 2: 38, 3: 31, 4: 32, 5: 33, 6: 34, 7: 35, 8: 7, 27: 8, - 28: 9, 29: 10, 30: 11, 31: 12, 32: 13, 33: 21, 35: 19, 36: 20, 37: 17, 38: 18, - 39: 16, 41: 14, 44: 29, 45: 30} - score: '0.590' - edge_lig_52_lig_38: - ligand_a: lig_52 - ligand_b: lig_38 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 30: 28, 31: 29, - 32: 30, 33: 31, 34: 32, 35: 33, 36: 34, 37: 35, 38: 36, 39: 37, 40: 38, 41: 39, - 42: 40, 43: 41, 44: 42, 45: 44, 46: 43, 47: 45, 48: 48, 49: 47, 50: 46, 51: 49, - 52: 50} - score: '0.652' - edge_lig_34_lig_59: - ligand_a: lig_34 - ligand_b: lig_59 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 26, 28: 27, - 29: 28, 30: 29, 31: 30, 32: 31, 33: 39, 34: 40, 35: 41, 36: 43, 39: 37, 40: 38, - 41: 35, 42: 36, 43: 34, 44: 32, 45: 33, 46: 47, 47: 48} - score: '0.625' - edge_lig_24_lig_20: - ligand_a: lig_24 - ligand_b: lig_20 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, - 29: 26, 30: 27, 31: 28, 32: 29, 33: 37, 35: 35, 36: 36, 37: 33, 38: 34, 39: 32, - 41: 30, 44: 45, 45: 46} - score: '0.587' - edge_lig_64_lig_41: - ligand_a: lig_64 - ligand_b: lig_41 - atom mapping: {9: 8, 10: 24, 11: 25, 12: 26, 13: 27, 14: 28, 15: 29, 16: 37, 17: 38, - 18: 40, 19: 39, 20: 41, 21: 42, 22: 43, 23: 44, 24: 35, 25: 36, 26: 33, 27: 34, - 28: 32, 29: 30, 30: 31, 31: 45, 32: 46, 33: 3, 34: 4, 35: 5, 36: 6, 37: 7, 38: 1, - 39: 0, 40: 2} - score: '0.696' - edge_lig_56_lig_38: - ligand_a: lig_56 - ligand_b: lig_38 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 30: 28, 31: 29, - 32: 30, 33: 31, 34: 32, 35: 33, 36: 34, 37: 35, 38: 36, 39: 37, 40: 38, 41: 39, - 42: 40, 43: 41, 44: 42, 45: 43, 46: 44, 47: 45, 48: 46, 49: 47, 50: 48, 51: 49, - 52: 50} - score: '0.652' - edge_lig_19_lig_41: - ligand_a: lig_19 - ligand_b: lig_41 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 45, 5: 46, 6: 26, 7: 27, 8: 28, 9: 29, - 10: 30, 11: 31, 12: 32, 14: 33, 15: 34, 16: 35, 17: 36, 18: 37, 20: 24, 21: 25, - 22: 8, 41: 4, 42: 5, 43: 6, 44: 7} - score: '0.595' - edge_lig_59_lig_31: - ligand_a: lig_59 - ligand_b: lig_31 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 44, 5: 45, 6: 46, 7: 47, 8: 25, 26: 23, - 27: 24, 28: 6, 29: 7, 30: 8, 31: 9, 32: 10, 33: 11, 34: 12, 35: 13, 36: 14, - 37: 15, 38: 16, 39: 17, 40: 18, 43: 19, 44: 22, 45: 21, 46: 20, 47: 4, 48: 5} - score: '0.642' - edge_lig_24_lig_59: - ligand_a: lig_24 - ligand_b: lig_59 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 26, 28: 27, - 29: 28, 30: 29, 31: 30, 32: 31, 33: 39, 35: 37, 36: 38, 37: 35, 38: 36, 39: 34, - 41: 32, 44: 47, 45: 48} - score: '0.578' - edge_lig_24_lig_48: - ligand_a: lig_24 - ligand_b: lig_48 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, - 29: 26, 30: 27, 31: 28, 32: 29, 33: 37, 35: 35, 36: 36, 37: 33, 38: 34, 39: 32, - 41: 30, 44: 45, 45: 46} - score: '0.587' diff --git a/data/ptp1b/03_edges/01_perses_openfe.yml b/data/ptp1b/03_edges/01_perses_openfe.yml deleted file mode 100644 index 4720cb656..000000000 --- a/data/ptp1b/03_edges/01_perses_openfe.yml +++ /dev/null @@ -1,151 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.5 minimal_spanning_graph -edges: - edge_lig_23485_lig_23480: - ligand_a: lig_23485 - ligand_b: lig_23480 - atom mapping: {0: 52, 1: 2, 2: 1, 3: 6, 4: 5, 5: 4, 6: 3, 8: 35, 9: 8, 12: 10, - 15: 13, 16: 18, 17: 17, 18: 16, 19: 15, 20: 14, 21: 33, 22: 32, 23: 31, 24: 30, - 26: 23, 57: 22, 58: 21, 59: 20, 60: 19, 61: 7, 62: 0} - score: '0.488' - edge_lig_23476_lig_23484: - ligand_a: lig_23476 - ligand_b: lig_23484 - atom mapping: {0: 52, 1: 30, 2: 31, 3: 32, 4: 33, 5: 28, 6: 29, 7: 53, 8: 26, - 9: 27, 30: 34, 31: 35, 32: 36, 33: 37, 34: 38, 35: 39, 36: 40, 37: 41, 38: 42, - 39: 43, 40: 44, 41: 45, 42: 46, 43: 47, 44: 48, 45: 49, 47: 51} - score: '0.545' - edge_lig_23484_lig_20669_2qbr: - ligand_a: lig_23484 - ligand_b: lig_20669_2qbr - atom mapping: {26: 12, 28: 14, 29: 15, 30: 16, 31: 17, 32: 18, 33: 19, 34: 20, - 35: 21, 36: 22, 37: 23, 38: 24, 39: 25, 40: 26, 41: 27, 42: 28, 43: 29, 44: 30, - 45: 32, 46: 31, 47: 33, 48: 34, 49: 35, 51: 37, 52: 38, 53: 39} - score: '0.574' - edge_lig_20667_2qbp_lig_23480: - ligand_a: lig_20667_2qbp - ligand_b: lig_23480 - atom mapping: {0: 52, 1: 2, 2: 3, 3: 4, 4: 5, 5: 6, 6: 1, 7: 0, 8: 7, 9: 8, 12: 10, - 15: 13, 16: 14, 17: 15, 18: 16, 19: 17, 20: 18, 21: 20, 22: 19, 23: 22, 24: 21, - 26: 23, 54: 30, 55: 31, 56: 32, 57: 33, 58: 35} - score: '0.488' - edge_lig_23484_lig_23468: - ligand_a: lig_23484 - ligand_b: lig_23468 - atom mapping: {26: 8, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, 33: 4, 34: 19, 35: 20, - 36: 21, 37: 22, 38: 23, 39: 24, 40: 25, 41: 26, 42: 27, 43: 28, 44: 29, 45: 31, - 46: 30, 47: 32, 48: 33, 49: 34, 51: 36, 52: 0, 53: 7} - score: '0.612' - edge_lig_23480_lig_23484: - ligand_a: lig_23480 - ligand_b: lig_23484 - atom mapping: {0: 7, 1: 6, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 7: 8, 8: 9, 10: 12, 13: 15, - 14: 20, 15: 19, 16: 18, 17: 17, 18: 16, 19: 56, 20: 57, 21: 55, 22: 54, 23: 26, - 30: 23, 31: 24, 32: 22, 33: 21, 35: 58, 52: 0} - score: '0.491' - edge_lig_23480_lig_23479: - ligand_a: lig_23480 - ligand_b: lig_23479 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 35: 31, 36: 32, - 37: 33, 38: 34, 39: 35, 40: 36, 41: 37, 42: 38, 43: 39, 44: 40, 45: 41, 46: 43, - 47: 42, 48: 44, 49: 45, 50: 46, 51: 47, 52: 48} - score: '0.610' - edge_lig_23477_lig_23472: - ligand_a: lig_23477 - ligand_b: lig_23472 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 25: 24, 26: 25, - 27: 26, 28: 27, 29: 28, 30: 29, 31: 30, 32: 31, 33: 32, 34: 33, 35: 34, 36: 35, - 37: 36, 38: 37, 39: 38, 40: 39, 41: 40, 42: 41} - score: '0.632' - edge_lig_23480_lig_23482: - ligand_a: lig_23480 - ligand_b: lig_23482 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 35: 32, 36: 33, - 37: 34, 38: 35, 39: 36, 40: 37, 41: 38, 42: 39, 43: 40, 44: 41, 45: 42, 46: 44, - 47: 43, 48: 45, 49: 46, 50: 47, 51: 48, 52: 49} - score: '0.602' - edge_lig_23484_lig_23472: - ligand_a: lig_23484 - ligand_b: lig_23472 - atom mapping: {26: 8, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, 33: 4, 34: 24, 35: 25, - 36: 26, 37: 27, 38: 28, 39: 29, 40: 30, 41: 31, 42: 32, 43: 33, 44: 34, 45: 36, - 46: 35, 47: 37, 48: 38, 49: 39, 51: 41, 52: 0, 53: 7} - score: '0.574' - edge_lig_23466_lig_23472: - ligand_a: lig_23466 - ligand_b: lig_23472 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 11: 24, - 12: 25, 13: 26, 14: 27, 15: 28, 16: 29, 17: 30, 18: 31, 19: 32, 20: 33, 21: 34, - 22: 36, 23: 35, 24: 37, 25: 38, 26: 39, 27: 40, 28: 41} - score: '0.783' - edge_lig_20670_2qbs_lig_23472: - ligand_a: lig_20670_2qbs - ligand_b: lig_23472 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, - 29: 26, 30: 27, 31: 28, 32: 29, 33: 30, 34: 31, 35: 32, 36: 33, 37: 34, 38: 35, - 39: 36, 40: 37, 41: 38, 42: 39, 43: 40, 44: 41} - score: '0.632' - edge_lig_23485_lig_23474: - ligand_a: lig_23485 - ligand_b: lig_23474 - atom mapping: {0: 47, 1: 2, 2: 1, 3: 6, 4: 5, 5: 4, 6: 3, 8: 30, 9: 8, 12: 10, - 15: 13, 16: 18, 17: 17, 18: 16, 19: 15, 20: 14, 21: 28, 22: 27, 23: 26, 24: 25, - 25: 24, 57: 21, 58: 22, 59: 19, 60: 20, 61: 7, 62: 0} - score: '0.511' - edge_lig_23467_lig_23472: - ligand_a: lig_23467 - ligand_b: lig_23472 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 13: 24, 14: 25, - 15: 26, 16: 27, 17: 28, 18: 29, 19: 30, 20: 31, 21: 32, 22: 33, 23: 34, 24: 36, - 25: 35, 26: 37, 27: 38, 28: 39, 29: 40, 30: 41} - score: '0.742' - edge_lig_23484_lig_23471: - ligand_a: lig_23484 - ligand_b: lig_23471 - atom mapping: {26: 8, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, 33: 4, 34: 17, 35: 18, - 36: 19, 37: 20, 38: 21, 39: 22, 40: 23, 41: 24, 42: 25, 43: 26, 44: 27, 45: 29, - 46: 28, 47: 30, 48: 31, 49: 32, 51: 34, 52: 0, 53: 7} - score: '0.682' - edge_lig_23484_lig_23473: - ligand_a: lig_23484 - ligand_b: lig_23473 - atom mapping: {26: 12, 28: 13, 29: 14, 30: 15, 31: 16, 32: 17, 33: 18, 34: 19, - 35: 20, 36: 21, 37: 22, 38: 23, 39: 24, 40: 25, 41: 26, 42: 27, 43: 28, 44: 29, - 45: 31, 46: 30, 47: 32, 48: 33, 49: 34, 51: 36, 52: 37, 53: 38} - score: '0.581' - edge_lig_23480_lig_23483: - ligand_a: lig_23480 - ligand_b: lig_23483 - atom mapping: {0: 49, 1: 27, 2: 28, 3: 29, 4: 30, 5: 25, 6: 26, 7: 50, 8: 23, - 35: 31, 36: 32, 37: 33, 38: 34, 39: 35, 40: 36, 41: 37, 42: 38, 43: 39, 44: 40, - 45: 41, 46: 43, 47: 42, 48: 44, 49: 45, 50: 46, 51: 47, 52: 48} - score: '0.520' - edge_lig_23484_lig_23469: - ligand_a: lig_23484 - ligand_b: lig_23469 - atom mapping: {26: 11, 28: 13, 29: 14, 30: 15, 31: 16, 32: 17, 33: 18, 34: 19, - 35: 20, 36: 21, 37: 22, 38: 23, 39: 24, 40: 25, 41: 26, 42: 27, 43: 28, 44: 29, - 45: 31, 46: 30, 47: 32, 48: 33, 49: 34, 51: 36, 52: 37, 53: 38} - score: '0.581' - edge_lig_23484_lig_23475: - ligand_a: lig_23484 - ligand_b: lig_23475 - atom mapping: {26: 8, 27: 9, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, 33: 4, 34: 24, - 35: 25, 36: 26, 37: 27, 38: 28, 39: 29, 40: 30, 41: 31, 42: 32, 43: 33, 44: 34, - 45: 36, 46: 35, 47: 37, 48: 38, 49: 39, 51: 41, 52: 0, 53: 7} - score: '0.586' - edge_lig_23484_lig_23470: - ligand_a: lig_23484 - ligand_b: lig_23470 - atom mapping: {26: 8, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, 33: 4, 34: 24, 35: 25, - 36: 26, 37: 27, 38: 28, 39: 29, 40: 30, 41: 31, 42: 32, 43: 33, 44: 34, 45: 36, - 46: 35, 47: 37, 48: 38, 49: 39, 51: 41, 52: 0, 53: 7} - score: '0.574' - edge_lig_23480_lig_23486: - ligand_a: lig_23480 - ligand_b: lig_23486 - atom mapping: {0: 59, 1: 2, 2: 1, 3: 6, 4: 5, 5: 4, 6: 3, 7: 58, 8: 9, 10: 12, - 13: 15, 14: 20, 15: 19, 16: 18, 17: 17, 18: 16, 19: 56, 20: 57, 21: 55, 22: 54, - 23: 26, 30: 23, 31: 24, 32: 22, 33: 21, 35: 8, 52: 0} - score: '0.488' diff --git a/data/shp2/03_edges/01_perses_openfe.yml b/data/shp2/03_edges/01_perses_openfe.yml deleted file mode 100644 index 3831570c5..000000000 --- a/data/shp2/03_edges/01_perses_openfe.yml +++ /dev/null @@ -1,145 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.5 minimal_spanning_graph -edges: - edge_lig_E14_lig_10: - ligand_a: lig_E14 - ligand_b: lig_10 - atom mapping: {0: 26, 1: 25, 2: 27, 3: 28, 4: 29, 5: 38, 7: 36, 9: 34, 10: 35, - 11: 32, 13: 30, 15: 1, 19: 2, 20: 3} - score: '0.507' - edge_lig_E14_lig_E30: - ligand_a: lig_E14 - ligand_b: lig_E30 - atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 39, - 15: 35, 16: 36, 17: 38, 18: 37, 19: 34, 20: 12} - score: '0.540' - edge_lig_E14_lig_SHP099-1: - ligand_a: lig_E14 - ligand_b: lig_SHP099-1 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 13, 7: 11, 9: 9, 10: 10, 11: 7, - 13: 5, 15: 15, 16: 16, 17: 18, 18: 17, 19: 19, 20: 20} - score: '0.555' - edge_lig_E3_lig_E14: - ligand_a: lig_E3 - ligand_b: lig_E14 - atom mapping: {6: 3, 7: 2, 9: 1, 10: 20, 32: 19, 33: 15, 34: 16, 35: 17, 36: 18} - score: '0.292' - edge_lig_E28_lig_7: - ligand_a: lig_E28 - ligand_b: lig_7 - atom mapping: {15: 33, 16: 1, 17: 2, 19: 3, 20: 4, 21: 5, 22: 6, 23: 7, 24: 8, - 25: 9, 26: 10, 27: 11, 28: 13, 35: 22, 36: 24, 37: 23, 38: 25, 39: 27, 40: 26, - 41: 28, 42: 29, 43: 30, 44: 32, 45: 31} - score: '0.534' - edge_lig_6_lig_E14: - ligand_a: lig_6 - ligand_b: lig_E14 - atom mapping: {1: 2, 2: 1, 3: 20, 22: 19, 23: 15, 24: 16, 25: 18, 26: 17, 27: 3, - 28: 4, 29: 13, 31: 11, 33: 9, 34: 10, 35: 7, 37: 5} - score: '0.544' - edge_lig_E8_lig_E14: - ligand_a: lig_E8 - ligand_b: lig_E14 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 13, 7: 11, 9: 9, 10: 10, 11: 7, - 13: 5, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20} - score: '0.551' - edge_lig_E14_lig_E2: - ligand_a: lig_E14 - ligand_b: lig_E2 - atom mapping: {1: 2, 2: 1, 3: 30, 4: 31, 5: 43, 7: 38, 9: 36, 10: 37, 11: 34, - 13: 32, 15: 26, 16: 27, 17: 29, 18: 28, 19: 25, 20: 3} - score: '0.540' - edge_lig_E14_lig_E22: - ligand_a: lig_E14 - ligand_b: lig_E22 - atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 40, - 15: 36, 16: 37, 17: 39, 18: 38, 19: 35, 20: 13} - score: '0.536' - edge_lig_E14_lig_E28: - ligand_a: lig_E14 - ligand_b: lig_E28 - atom mapping: {0: 18, 1: 17, 2: 16, 3: 15, 15: 42, 16: 43, 17: 44, 18: 45, 19: 41, - 20: 19} - score: '0.296' - edge_lig_E4_lig_E27: - ligand_a: lig_E4 - ligand_b: lig_E27 - atom mapping: {3: 3, 4: 2, 6: 1, 7: 20, 8: 21, 9: 39, 10: 41, 11: 40, 12: 33, - 14: 34, 15: 31, 23: 25, 25: 26, 26: 22, 27: 24, 28: 23, 29: 19, 30: 15, 31: 16, - 32: 18, 33: 17} - score: '0.520' - edge_lig_E14_lig_E6: - ligand_a: lig_E14 - ligand_b: lig_E6 - atom mapping: {1: 13, 2: 11, 3: 10, 4: 9, 5: 7, 7: 5, 9: 3, 10: 4, 11: 2, 12: 1, - 13: 41, 15: 37, 16: 38, 17: 40, 18: 39, 19: 36, 20: 14} - score: '0.558' - edge_lig_SHP836-2_lig_E28: - ligand_a: lig_SHP836-2 - ligand_b: lig_E28 - atom mapping: {1: 16, 2: 17, 3: 19, 4: 20, 5: 38, 6: 40, 7: 39, 8: 35, 9: 36, - 14: 27, 16: 24, 17: 25, 22: 21, 23: 23, 24: 22, 25: 41, 26: 42, 27: 43, 28: 45, - 29: 44, 30: 15} - score: '0.508' - edge_lig_E14_lig_E25: - ligand_a: lig_E14 - ligand_b: lig_E25 - atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 41, - 15: 37, 16: 38, 17: 40, 18: 39, 19: 36, 20: 14} - score: '0.532' - edge_lig_3_lig_E28: - ligand_a: lig_3 - ligand_b: lig_E28 - atom mapping: {1: 16, 2: 17, 3: 19, 4: 20, 5: 38, 6: 40, 7: 39, 8: 35, 9: 36, - 14: 27, 16: 24, 17: 25, 22: 21, 23: 23, 24: 22, 25: 41, 26: 42, 27: 43, 28: 45, - 29: 44, 30: 15} - score: '0.508' - edge_lig_E14_lig_E23: - ligand_a: lig_E14 - ligand_b: lig_E23 - atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 40, - 15: 36, 16: 37, 17: 39, 18: 38, 19: 35, 20: 13} - score: '0.536' - edge_lig_E14_lig_E24: - ligand_a: lig_E14 - ligand_b: lig_E24 - atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 43, - 15: 39, 16: 40, 17: 42, 18: 41, 19: 38, 20: 16} - score: '0.536' - edge_lig_E9_lig_E14: - ligand_a: lig_E9 - ligand_b: lig_E14 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 13, 7: 11, 9: 9, 10: 10, 11: 7, - 13: 5, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20} - score: '0.555' - edge_lig_E14_lig_11: - ligand_a: lig_E14 - ligand_b: lig_11 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 13, 7: 11, 9: 9, 10: 10, 11: 7, - 13: 5, 15: 15, 16: 16, 18: 17, 19: 22, 20: 23} - score: '0.536' - edge_lig_E14_lig_E29: - ligand_a: lig_E14 - ligand_b: lig_E29 - atom mapping: {0: 6, 1: 5, 2: 4, 3: 3, 15: 30, 16: 31, 17: 32, 18: 33, 19: 29, - 20: 7} - score: '0.305' - edge_lig_E28_lig_E5: - ligand_a: lig_E28 - ligand_b: lig_E5 - atom mapping: {15: 30, 16: 1, 17: 2, 19: 3, 20: 4, 21: 5, 22: 6, 23: 7, 24: 8, - 25: 9, 26: 10, 27: 11, 28: 16, 32: 12, 35: 19, 36: 21, 37: 20, 38: 22, 39: 24, - 40: 23, 41: 25, 42: 26, 43: 27, 44: 29, 45: 28} - score: '0.543' - edge_lig_E4_lig_E14: - ligand_a: lig_E4 - ligand_b: lig_E14 - atom mapping: {3: 3, 4: 2, 6: 1, 7: 20, 29: 19, 30: 15, 31: 16, 32: 17, 33: 18} - score: '0.292' - edge_lig_E1_lig_E14: - ligand_a: lig_E1 - ligand_b: lig_E14 - atom mapping: {1: 2, 2: 1, 3: 20, 25: 19, 26: 15, 27: 16, 28: 17, 29: 18, 30: 3, - 31: 4, 32: 13, 34: 11, 36: 9, 37: 10, 38: 7, 40: 5} - score: '0.540' diff --git a/data/syk/03_edges/01_perses_openfe.yml b/data/syk/03_edges/01_perses_openfe.yml deleted file mode 100644 index 2a7975a12..000000000 --- a/data/syk/03_edges/01_perses_openfe.yml +++ /dev/null @@ -1,305 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.5 minimal_spanning_graph -edges: - edge_lig_CHEMBL3264994_lig_CHEMBL3265022: - ligand_a: lig_CHEMBL3264994 - ligand_b: lig_CHEMBL3265022 - atom mapping: {0: 19, 1: 18, 2: 20, 3: 21, 4: 15, 5: 16, 6: 17, 7: 22, 8: 23, - 9: 24, 10: 25, 11: 42, 12: 43, 13: 36, 15: 30, 16: 31, 21: 32, 22: 33, 23: 34, - 24: 35, 29: 28, 30: 29, 31: 26, 32: 27, 33: 44, 34: 12, 62: 13, 63: 14} - score: '0.507' - edge_lig_CHEMBL3265002_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265002 - ligand_b: lig_CHEMBL3265031 - atom mapping: {25: 24, 26: 39, 27: 40, 28: 41, 29: 42, 30: 43, 31: 44, 32: 45, - 33: 46, 34: 47, 35: 22, 36: 20, 37: 21, 38: 19, 39: 48, 40: 49, 41: 50, 42: 51, - 43: 14, 49: 15, 55: 17, 56: 18, 57: 23} - score: '0.397' - edge_lig_CHEMBL3265003_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265003 - ligand_b: lig_CHEMBL3265031 - atom mapping: {24: 24, 25: 39, 26: 40, 27: 41, 28: 42, 29: 43, 30: 44, 31: 45, - 32: 46, 33: 47, 34: 22, 35: 20, 36: 21, 37: 19, 38: 17, 39: 18, 40: 15, 41: 16, - 42: 14, 48: 50, 54: 48, 55: 49, 56: 23} - score: '0.397' - edge_lig_CHEMBL3264998_lig_CHEMBL3265027: - ligand_a: lig_CHEMBL3264998 - ligand_b: lig_CHEMBL3265027 - atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, - 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 29, 27: 31, 28: 32, - 29: 33, 30: 9, 61: 10, 62: 11} - score: '0.499' - edge_lig_CHEMBL3264994_lig_CHEMBL3265019: - ligand_a: lig_CHEMBL3264994 - ligand_b: lig_CHEMBL3265019 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 25: 17, 26: 18, 27: 19, 28: 20, - 29: 21, 31: 27, 32: 28, 33: 29, 34: 30, 62: 44, 63: 45} - score: '0.530' - edge_lig_CHEMBL3265033_lig_CHEMBL3265024: - ligand_a: lig_CHEMBL3265033 - ligand_b: lig_CHEMBL3265024 - atom mapping: {9: 30, 10: 48, 11: 49, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, - 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, - 44: 21, 46: 27, 47: 28, 48: 29} - score: '0.474' - edge_lig_CHEMBL3265012_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265012 - ligand_b: lig_CHEMBL3265031 - atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, - 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 46: 39, 47: 40} - score: '0.485' - edge_lig_CHEMBL3265001_lig_CHEMBL3265030_n: - ligand_a: lig_CHEMBL3265001 - ligand_b: lig_CHEMBL3265030_n - atom mapping: {0: 42, 1: 41, 2: 43, 3: 44, 4: 38, 5: 39, 6: 40, 7: 19, 8: 17, - 9: 18, 10: 16, 11: 45, 12: 46, 13: 47, 14: 48, 15: 11, 21: 12, 27: 14, 28: 15, - 29: 20, 30: 21, 60: 36, 61: 37} - score: '0.417' - edge_lig_CHEMBL3264995_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3264995 - ligand_b: lig_CHEMBL3265031 - atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, - 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 58: 39, 59: 40} - score: '0.404' - edge_lig_CHEMBL3265000_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3265000 - ligand_b: lig_CHEMBL3265033 - atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, - 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 44, 27: 46, 28: 47, - 29: 48, 30: 9, 65: 10, 66: 11} - score: '0.412' - edge_lig_CHEMBL3264999_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3264999 - ligand_b: lig_CHEMBL3265031 - atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, - 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 60: 39, 61: 40} - score: '0.404' - edge_lig_CHEMBL3265001_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265001 - ligand_b: lig_CHEMBL3265031 - atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, - 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 60: 39, 61: 40} - score: '0.397' - edge_lig_CHEMBL3264998_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3264998 - ligand_b: lig_CHEMBL3265031 - atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, - 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 61: 39, 62: 40} - score: '0.402' - edge_lig_CHEMBL3265006_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265006 - ligand_b: lig_CHEMBL3265031 - atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, - 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 49: 39, 50: 40} - score: '0.469' - edge_lig_CHEMBL3265000_lig_CHEMBL3265036: - ligand_a: lig_CHEMBL3265000 - ligand_b: lig_CHEMBL3265036 - atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, - 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 45, 27: 47, 28: 48, - 29: 49, 30: 9, 65: 10, 66: 11} - score: '0.407' - edge_lig_CHEMBL3264994_lig_CHEMBL3265018: - ligand_a: lig_CHEMBL3264994 - ligand_b: lig_CHEMBL3265018 - atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, - 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 16: 28, 25: 29, 26: 30, - 27: 31, 28: 32, 29: 33, 31: 39, 32: 40, 33: 41, 34: 9, 62: 10, 63: 11} - score: '0.524' - edge_lig_CHEMBL3265001_lig_CHEMBL3265029: - ligand_a: lig_CHEMBL3265001 - ligand_b: lig_CHEMBL3265029 - atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, - 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 16: 28, 17: 29, 18: 32, - 19: 31, 20: 30, 21: 33, 27: 35, 28: 36, 29: 37, 30: 9, 60: 10, 61: 11} - score: '0.530' - edge_lig_CHEMBL3265009_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3265009 - ligand_b: lig_CHEMBL3265033 - atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, - 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 44, 27: 46, 28: 47, - 29: 48, 30: 9, 49: 10, 50: 11} - score: '0.469' - edge_lig_CHEMBL3265004_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265004 - ligand_b: lig_CHEMBL3265031 - atom mapping: {26: 24, 27: 39, 28: 40, 29: 41, 30: 42, 31: 43, 32: 44, 33: 45, - 34: 46, 35: 47, 36: 22, 37: 20, 38: 21, 39: 19, 40: 17, 41: 18, 42: 15, 43: 16, - 44: 14, 50: 50, 56: 48, 57: 49, 58: 23} - score: '0.397' - edge_lig_CHEMBL3265001_lig_CHEMBL3265035: - ligand_a: lig_CHEMBL3265001 - ligand_b: lig_CHEMBL3265035 - atom mapping: {0: 40, 1: 39, 2: 41, 3: 42, 4: 36, 5: 37, 6: 38, 7: 17, 8: 15, - 9: 16, 10: 14, 11: 43, 12: 44, 13: 45, 14: 46, 15: 9, 16: 8, 17: 5, 18: 7, 19: 6, - 21: 10, 27: 12, 28: 13, 29: 18, 30: 19, 60: 34, 61: 35} - score: '0.472' - edge_lig_CHEMBL3265033_lig_CHEMBL3265025: - ligand_a: lig_CHEMBL3265033 - ligand_b: lig_CHEMBL3265025 - atom mapping: {9: 30, 10: 48, 11: 49, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, - 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, - 44: 21, 46: 27, 47: 28, 48: 29} - score: '0.474' - edge_lig_CHEMBL3265023_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265023 - ligand_b: lig_CHEMBL3265031 - atom mapping: {14: 24, 15: 39, 16: 40, 17: 41, 18: 42, 19: 43, 20: 44, 21: 45, - 22: 46, 23: 47, 24: 22, 25: 20, 26: 21, 27: 19, 28: 48, 29: 49, 30: 50, 31: 51, - 32: 14, 38: 15, 44: 17, 45: 18, 46: 23} - score: '0.474' - edge_lig_CHEMBL3265033_lig_CHEMBL3265026: - ligand_a: lig_CHEMBL3265033 - ligand_b: lig_CHEMBL3265026 - atom mapping: {9: 30, 10: 49, 11: 50, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, - 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, - 44: 21, 46: 27, 47: 28, 48: 29} - score: '0.469' - edge_lig_CHEMBL3265000_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3265000 - ligand_b: lig_CHEMBL3265031 - atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, - 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 65: 39, 66: 40} - score: '0.397' - edge_lig_CHEMBL3265033_lig_CHEMBL3265020: - ligand_a: lig_CHEMBL3265033 - ligand_b: lig_CHEMBL3265020 - atom mapping: {9: 30, 10: 46, 11: 47, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, - 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, - 44: 21, 46: 27, 47: 28, 48: 29} - score: '0.485' - edge_lig_CHEMBL3265000_lig_CHEMBL3265034: - ligand_a: lig_CHEMBL3265000 - ligand_b: lig_CHEMBL3265034 - atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, - 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 43, 27: 45, 28: 46, - 29: 47, 30: 9, 65: 10, 66: 11} - score: '0.416' - edge_lig_CHEMBL3265033_lig_CHEMBL3265021: - ligand_a: lig_CHEMBL3265033 - ligand_b: lig_CHEMBL3265021 - atom mapping: {9: 11, 10: 12, 11: 13, 12: 14, 13: 15, 14: 16, 15: 17, 16: 18, - 17: 19, 18: 20, 19: 21, 20: 22, 21: 23, 22: 24, 23: 25, 24: 26, 25: 27, 26: 28, - 27: 29, 44: 35, 46: 41, 47: 42, 48: 43} - score: '0.491' - edge_lig_CHEMBL3265011_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3265011 - ligand_b: lig_CHEMBL3265033 - atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, - 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 44, 27: 46, 28: 47, - 29: 48, 30: 9, 49: 10, 50: 11} - score: '0.469' - edge_lig_CHEMBL3264994_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3264994 - ligand_b: lig_CHEMBL3265031 - atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, - 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 29: 15, 30: 16, 31: 17, - 32: 18, 33: 23, 34: 24, 62: 39, 63: 40} - score: '0.414' - edge_lig_CHEMBL3265033_lig_CHEMBL3265013: - ligand_a: lig_CHEMBL3265033 - ligand_b: lig_CHEMBL3265013 - atom mapping: {9: 30, 10: 49, 11: 50, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, - 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, - 44: 21, 46: 27, 47: 28, 48: 29} - score: '0.469' - edge_lig_CHEMBL3265010_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3265010 - ligand_b: lig_CHEMBL3265033 - atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, - 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 44, 27: 46, 28: 47, - 29: 48, 30: 9, 50: 10, 51: 11} - score: '0.464' - edge_lig_CHEMBL3264994_lig_CHEMBL3265028: - ligand_a: lig_CHEMBL3264994 - ligand_b: lig_CHEMBL3265028 - atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, - 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 29: 29, 31: 35, 32: 36, - 33: 37, 34: 9, 62: 10, 63: 11} - score: '0.479' - edge_lig_CHEMBL3264994_lig_CHEMBL3265016: - ligand_a: lig_CHEMBL3264994 - ligand_b: lig_CHEMBL3265016 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 27, 12: 28, 13: 21, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 29: 13, - 30: 14, 31: 11, 32: 12, 33: 29, 34: 30, 62: 46, 63: 47} - score: '0.518' - edge_lig_CHEMBL3265005_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3265005 - ligand_b: lig_CHEMBL3265033 - atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, - 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 44, 27: 46, 28: 47, - 29: 48, 30: 9, 46: 10, 47: 11} - score: '0.485' - edge_lig_CHEMBL3264996_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3264996 - ligand_b: lig_CHEMBL3265031 - atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, - 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 62: 39, 63: 40} - score: '0.402' - edge_lig_CHEMBL3264997_lig_CHEMBL3265031: - ligand_a: lig_CHEMBL3264997 - ligand_b: lig_CHEMBL3265031 - atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, - 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, - 29: 23, 30: 24, 58: 39, 59: 40} - score: '0.404' - edge_lig_CHEMBL3264994_lig_CHEMBL3265017: - ligand_a: lig_CHEMBL3264994 - ligand_b: lig_CHEMBL3265017 - atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, - 9: 21, 10: 22, 11: 39, 12: 40, 13: 33, 15: 27, 16: 28, 21: 29, 22: 30, 23: 31, - 24: 32, 29: 25, 30: 26, 31: 23, 32: 24, 33: 41, 34: 9, 62: 10, 63: 11} - score: '0.524' - edge_lig_CHEMBL3265000_lig_CHEMBL3265032: - ligand_a: lig_CHEMBL3265000 - ligand_b: lig_CHEMBL3265032 - atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, - 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 42, 27: 44, 28: 45, - 29: 46, 30: 9, 65: 10, 66: 11} - score: '0.421' - edge_lig_CHEMBL3264994_lig_CHEMBL3265037: - ligand_a: lig_CHEMBL3264994 - ligand_b: lig_CHEMBL3265037 - atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, - 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 29: 42, 31: 48, 32: 49, - 33: 50, 34: 9, 62: 10, 63: 11} - score: '0.412' - edge_lig_CHEMBL3265008_lig_CHEMBL3265033: - ligand_a: lig_CHEMBL3265008 - ligand_b: lig_CHEMBL3265033 - atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, - 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 44, 27: 46, 28: 47, - 29: 48, 30: 9, 46: 10, 47: 11} - score: '0.485' - edge_lig_CHEMBL3265033_lig_CHEMBL3265014: - ligand_a: lig_CHEMBL3265033 - ligand_b: lig_CHEMBL3265014 - atom mapping: {9: 30, 10: 50, 11: 51, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, - 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, - 44: 21, 46: 27, 47: 28, 48: 29} - score: '0.464' - edge_lig_CHEMBL3265033_lig_CHEMBL3265015: - ligand_a: lig_CHEMBL3265033 - ligand_b: lig_CHEMBL3265015 - atom mapping: {9: 30, 10: 49, 11: 50, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, - 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, - 44: 21, 46: 27, 47: 28, 48: 29} - score: '0.469' - edge_lig_CHEMBL3265033_lig_CHEMBL3259820: - ligand_a: lig_CHEMBL3265033 - ligand_b: lig_CHEMBL3259820 - atom mapping: {9: 30, 10: 46, 11: 47, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, - 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, - 44: 21, 46: 27, 47: 28, 48: 29} - score: '0.485' diff --git a/data/thrombin/03_edges/01_perses_openfe.yml b/data/thrombin/03_edges/01_perses_openfe.yml deleted file mode 100644 index 58b7f6625..000000000 --- a/data/thrombin/03_edges/01_perses_openfe.yml +++ /dev/null @@ -1,180 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.5 minimal_spanning_graph -edges: - edge_lig_7e_lig_7d: - ligand_a: lig_7e - ligand_b: lig_7d - atom mapping: {0: 17, 1: 7, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 1, 8: 18, 9: 19, - 10: 20, 11: 21, 12: 26, 13: 25, 14: 24, 15: 23, 16: 22, 17: 0, 18: 8, 19: 9, - 28: 27, 29: 28, 30: 29, 31: 30, 32: 35, 33: 36, 34: 33, 35: 34, 36: 31, 37: 32, - 38: 53, 39: 52, 40: 58, 41: 57, 42: 56, 43: 55, 44: 54, 45: 37, 46: 38, 47: 39} - score: '0.693' - edge_lig_2e_lig_7d: - ligand_a: lig_2e - ligand_b: lig_7d - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 19: 17, - 20: 18, 21: 19, 22: 20, 23: 21, 24: 26, 25: 25, 26: 24, 27: 23, 28: 22, 29: 27, - 30: 28, 31: 30, 32: 29, 33: 32, 34: 31, 35: 33, 36: 34, 37: 36, 38: 35, 39: 37, - 40: 39, 41: 38, 46: 52, 47: 53, 48: 58, 49: 57, 50: 56, 51: 55, 52: 54} - score: '0.706' - edge_lig_6b_lig_7d: - ligand_a: lig_6b - ligand_b: lig_7d - atom mapping: {7: 9, 8: 8, 9: 7, 10: 17, 11: 6, 12: 5, 13: 4, 14: 3, 15: 2, 16: 1, - 17: 0, 18: 18, 19: 20, 20: 21, 21: 22, 22: 23, 23: 24, 24: 25, 25: 26, 26: 19, - 28: 27, 29: 28, 30: 29, 31: 30, 38: 39, 39: 38, 40: 37, 41: 36, 42: 35, 43: 34, - 44: 33, 45: 32, 46: 31, 47: 52, 48: 53, 49: 54, 50: 55, 51: 56, 52: 57, 53: 58} - score: '0.701' - edge_lig_6a_lig_7d: - ligand_a: lig_6a - ligand_b: lig_7d - atom mapping: {0: 24, 1: 25, 2: 26, 3: 21, 4: 22, 5: 23, 6: 20, 7: 18, 8: 1, 9: 0, - 10: 2, 11: 3, 12: 4, 13: 5, 14: 6, 15: 7, 16: 17, 17: 8, 18: 9, 27: 19, 28: 28, - 29: 27, 30: 30, 31: 29, 32: 56, 33: 57, 34: 58, 35: 54, 36: 55, 37: 53, 38: 52, - 39: 31, 40: 32, 41: 33, 42: 34, 43: 36, 44: 35, 45: 37, 46: 38, 47: 39} - score: '0.727' - edge_lig_2b_lig_7d: - ligand_a: lig_2b - ligand_b: lig_7d - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 18: 17, - 19: 18, 20: 19, 21: 20, 22: 21, 23: 26, 24: 25, 25: 24, 26: 23, 27: 22, 28: 27, - 29: 28, 30: 30, 31: 29, 32: 32, 33: 31, 34: 33, 35: 34, 36: 36, 37: 35, 38: 37, - 39: 39, 40: 38, 48: 52, 49: 53, 50: 58, 51: 57, 52: 56, 53: 55, 54: 54} - score: '0.693' - edge_lig_2d_lig_7d: - ligand_a: lig_2d - ligand_b: lig_7d - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 17: 17, - 18: 18, 19: 19, 20: 20, 21: 21, 22: 26, 23: 25, 24: 24, 25: 23, 26: 22, 27: 27, - 28: 28, 29: 30, 30: 29, 31: 32, 32: 31, 33: 33, 34: 34, 35: 36, 36: 35, 37: 37, - 38: 39, 39: 38, 46: 52, 47: 53, 48: 58, 49: 57, 50: 56, 51: 55, 52: 54} - score: '0.714' - edge_lig_7d_lig_7b: - ligand_a: lig_7d - ligand_b: lig_7b - atom mapping: {0: 17, 1: 7, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 1, 8: 18, 9: 19, - 17: 0, 18: 8, 19: 9, 20: 10, 21: 11, 22: 16, 23: 15, 24: 14, 25: 13, 26: 12, - 27: 27, 28: 28, 29: 30, 30: 29, 31: 36, 32: 35, 33: 33, 34: 34, 35: 32, 36: 31, - 37: 44, 38: 46, 39: 45, 52: 37, 53: 38, 54: 43, 55: 42, 56: 41, 57: 40, 58: 39} - score: '0.732' - edge_lig_1c_lig_7d: - ligand_a: lig_1c - ligand_b: lig_7d - atom mapping: {0: 24, 1: 25, 2: 26, 3: 21, 4: 22, 5: 23, 6: 20, 7: 18, 8: 1, 9: 0, - 10: 2, 11: 3, 12: 4, 13: 5, 14: 6, 15: 7, 16: 17, 17: 8, 18: 9, 26: 19, 27: 28, - 28: 27, 29: 30, 30: 29, 31: 56, 32: 57, 33: 58, 34: 54, 35: 55, 36: 53, 37: 52, - 38: 31, 39: 32, 40: 33, 41: 34, 42: 36, 43: 35, 44: 37, 45: 38, 46: 39} - score: '0.732' - edge_lig_6c_lig_7d: - ligand_a: lig_6c - ligand_b: lig_7d - atom mapping: {0: 17, 1: 7, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 1, 8: 18, 9: 19, - 10: 20, 11: 21, 12: 22, 13: 23, 14: 24, 15: 25, 16: 26, 17: 0, 18: 8, 19: 9, - 29: 27, 30: 28, 31: 29, 32: 30, 33: 35, 34: 36, 35: 33, 36: 34, 37: 31, 38: 32, - 39: 53, 40: 52, 41: 54, 42: 55, 43: 56, 44: 57, 45: 58, 46: 37, 47: 38, 48: 39} - score: '0.689' - edge_lig_7d_lig_5: - ligand_a: lig_7d - ligand_b: lig_5 - atom mapping: {0: 9, 1: 8, 2: 10, 3: 11, 4: 12, 5: 13, 6: 14, 7: 15, 8: 17, 9: 18, - 17: 16, 18: 7, 19: 25, 20: 6, 21: 3, 22: 2, 23: 1, 24: 0, 25: 5, 26: 4, 27: 27, - 28: 26, 29: 29, 30: 28, 31: 38, 32: 37, 33: 39, 34: 40, 35: 42, 36: 41, 37: 43, - 38: 45, 39: 44, 52: 35, 53: 36, 54: 32, 55: 31, 56: 30, 57: 34, 58: 33} - score: '0.732' - edge_lig_4_lig_7d: - ligand_a: lig_4 - ligand_b: lig_7d - atom mapping: {0: 17, 1: 7, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 1, 8: 18, 9: 19, - 10: 20, 11: 21, 12: 26, 13: 25, 14: 24, 15: 23, 16: 22, 17: 0, 18: 8, 19: 9, - 29: 27, 30: 28, 31: 29, 32: 30, 33: 35, 34: 36, 35: 33, 36: 34, 37: 31, 38: 32, - 39: 53, 40: 52, 41: 58, 42: 57, 43: 56, 44: 55, 45: 54, 46: 37, 47: 38, 48: 39} - score: '0.673' - edge_lig_3a_lig_7d: - ligand_a: lig_3a - ligand_b: lig_7d - atom mapping: {7: 9, 8: 8, 9: 7, 10: 17, 11: 6, 12: 5, 13: 4, 14: 3, 15: 2, 16: 1, - 17: 0, 18: 18, 19: 20, 20: 21, 21: 22, 22: 23, 23: 24, 24: 25, 25: 26, 26: 19, - 27: 27, 28: 28, 29: 29, 30: 30, 38: 39, 39: 38, 40: 37, 41: 36, 42: 35, 43: 33, - 44: 34, 45: 32, 46: 31, 47: 52, 48: 53, 49: 54, 50: 55, 51: 56, 52: 57, 53: 58} - score: '0.706' - edge_lig_7d_lig_2a: - ligand_a: lig_7d - ligand_b: lig_2a - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 17: 20, - 18: 21, 19: 22, 20: 23, 21: 24, 22: 29, 23: 28, 24: 27, 25: 26, 26: 25, 27: 30, - 28: 31, 29: 33, 30: 32, 31: 35, 32: 34, 33: 36, 34: 37, 35: 39, 36: 38, 37: 40, - 38: 42, 39: 41, 52: 47, 53: 48, 54: 53, 55: 52, 56: 51, 57: 50, 58: 49} - score: '0.693' - edge_lig_6d_lig_7d: - ligand_a: lig_6d - ligand_b: lig_7d - atom mapping: {3: 9, 4: 8, 5: 7, 6: 6, 7: 5, 8: 4, 9: 3, 10: 2, 11: 1, 12: 18, - 13: 19, 14: 20, 15: 21, 16: 22, 17: 23, 18: 24, 19: 25, 20: 26, 21: 0, 22: 17, - 28: 27, 29: 28, 30: 29, 31: 30, 33: 38, 34: 39, 35: 37, 36: 36, 37: 35, 38: 33, - 39: 34, 40: 32, 41: 31, 42: 52, 43: 53, 44: 54, 45: 55, 46: 56, 47: 57, 48: 58} - score: '0.718' - edge_lig_1b_lig_7d: - ligand_a: lig_1b - ligand_b: lig_7d - atom mapping: {0: 24, 1: 25, 2: 26, 3: 21, 4: 22, 5: 23, 6: 20, 7: 18, 8: 1, 9: 0, - 10: 2, 11: 3, 12: 4, 13: 5, 14: 6, 15: 7, 16: 17, 17: 8, 18: 9, 26: 19, 27: 28, - 28: 27, 29: 30, 30: 29, 31: 56, 32: 57, 33: 58, 34: 54, 35: 55, 36: 53, 37: 52, - 38: 31, 39: 32, 40: 33, 41: 34, 42: 36, 43: 35, 44: 37, 45: 38, 46: 39} - score: '0.732' - edge_lig_2c_lig_7d: - ligand_a: lig_2c - ligand_b: lig_7d - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 17: 17, - 18: 18, 19: 19, 20: 20, 21: 21, 22: 26, 23: 25, 24: 24, 25: 23, 26: 22, 27: 27, - 28: 28, 29: 30, 30: 29, 31: 32, 32: 31, 33: 33, 34: 34, 35: 36, 36: 35, 37: 37, - 38: 39, 39: 38, 45: 52, 46: 53, 47: 58, 48: 57, 49: 56, 50: 55, 51: 54} - score: '0.723' - edge_lig_7d_lig_3b: - ligand_a: lig_7d - ligand_b: lig_3b - atom mapping: {0: 18, 1: 17, 2: 16, 3: 15, 4: 14, 5: 13, 6: 12, 7: 10, 8: 9, 9: 8, - 17: 11, 18: 19, 19: 27, 20: 20, 21: 21, 22: 26, 23: 25, 24: 24, 25: 23, 26: 22, - 27: 28, 28: 29, 29: 31, 30: 30, 31: 49, 32: 48, 33: 46, 34: 47, 35: 45, 36: 44, - 37: 43, 38: 42, 39: 41, 52: 50, 53: 51, 54: 56, 55: 55, 56: 54, 57: 53, 58: 52} - score: '0.677' - edge_lig_7f_lig_7d: - ligand_a: lig_7f - ligand_b: lig_7d - atom mapping: {0: 17, 1: 7, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 1, 8: 18, 9: 19, - 10: 20, 11: 21, 12: 26, 13: 25, 14: 24, 15: 23, 16: 22, 17: 0, 18: 8, 19: 9, - 28: 27, 29: 28, 30: 29, 31: 30, 32: 35, 33: 36, 34: 33, 35: 34, 36: 31, 37: 32, - 38: 53, 39: 52, 40: 58, 41: 57, 42: 56, 43: 55, 44: 54, 45: 37, 46: 38, 47: 39} - score: '0.693' - edge_lig_1d_lig_7d: - ligand_a: lig_1d - ligand_b: lig_7d - atom mapping: {0: 24, 1: 25, 2: 26, 3: 21, 4: 22, 5: 23, 6: 20, 7: 18, 8: 1, 9: 0, - 10: 2, 11: 3, 12: 4, 13: 5, 14: 6, 15: 7, 16: 17, 17: 8, 18: 9, 26: 19, 27: 28, - 28: 27, 29: 30, 30: 29, 31: 56, 32: 57, 33: 58, 34: 54, 35: 55, 36: 53, 37: 52, - 38: 31, 39: 32, 40: 33, 41: 34, 42: 36, 43: 35, 44: 37, 45: 38, 46: 39} - score: '0.732' - edge_lig_6e_lig_7d: - ligand_a: lig_6e - ligand_b: lig_7d - atom mapping: {0: 24, 1: 25, 2: 26, 3: 21, 4: 22, 5: 23, 6: 20, 7: 18, 8: 1, 9: 0, - 10: 2, 11: 3, 12: 4, 13: 5, 14: 6, 15: 7, 16: 17, 17: 8, 18: 9, 27: 19, 28: 28, - 29: 27, 30: 30, 31: 29, 32: 56, 33: 57, 34: 58, 35: 54, 36: 55, 37: 53, 38: 52, - 39: 31, 40: 32, 41: 33, 42: 34, 43: 36, 44: 35, 45: 37, 46: 38, 47: 39} - score: '0.727' - edge_lig_7c_lig_7d: - ligand_a: lig_7c - ligand_b: lig_7d - atom mapping: {0: 17, 1: 7, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 1, 8: 18, 9: 19, - 10: 20, 11: 21, 12: 26, 13: 25, 14: 24, 15: 23, 16: 22, 17: 0, 18: 8, 19: 9, - 27: 27, 28: 28, 29: 29, 30: 30, 31: 35, 32: 36, 33: 33, 34: 34, 35: 31, 36: 32, - 37: 53, 38: 52, 39: 58, 40: 57, 41: 56, 42: 55, 43: 54, 44: 37, 45: 38, 46: 39} - score: '0.732' - edge_lig_1a_lig_7d: - ligand_a: lig_1a - ligand_b: lig_7d - atom mapping: {0: 24, 1: 25, 2: 26, 3: 21, 4: 22, 5: 23, 6: 20, 7: 18, 8: 1, 9: 0, - 10: 2, 11: 3, 12: 4, 13: 5, 14: 6, 15: 7, 16: 17, 17: 8, 18: 9, 26: 19, 27: 28, - 28: 27, 29: 30, 30: 29, 31: 56, 32: 57, 33: 58, 34: 54, 35: 55, 36: 53, 37: 52, - 38: 31, 39: 32, 40: 33, 41: 34, 42: 36, 43: 35, 44: 37, 45: 38, 46: 39} - score: '0.732' diff --git a/data/tnks2/03_edges/01_perses_openfe.yml b/data/tnks2/03_edges/01_perses_openfe.yml deleted file mode 100644 index 02e60b372..000000000 --- a/data/tnks2/03_edges/01_perses_openfe.yml +++ /dev/null @@ -1,186 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.5 minimal_spanning_graph -edges: - edge_lig_8a_lig_5m: - ligand_a: lig_8a - ligand_b: lig_5m - atom mapping: {0: 18, 1: 17, 2: 19, 4: 11, 5: 12, 6: 13, 7: 14, 8: 15, 9: 16, - 10: 24, 11: 25, 12: 26, 13: 27, 14: 9, 15: 8, 16: 6, 17: 7, 18: 4, 19: 5, 20: 3, - 39: 30, 40: 31, 41: 28, 42: 29, 43: 10} - score: '0.705' - edge_lig_5g_lig_8a: - ligand_a: lig_5g - ligand_b: lig_8a - atom mapping: {3: 20, 4: 18, 5: 19, 6: 16, 7: 17, 8: 15, 9: 14, 10: 43, 11: 4, - 12: 2, 14: 1, 15: 0, 16: 8, 18: 6, 19: 7, 20: 5, 21: 10, 22: 11, 23: 12, 24: 13, - 25: 41, 26: 42, 27: 39, 28: 40} - score: '0.714' - edge_lig_5f_lig_8a: - ligand_a: lig_5f - ligand_b: lig_8a - atom mapping: {3: 20, 4: 18, 5: 19, 6: 16, 7: 17, 8: 15, 9: 14, 10: 43, 11: 4, - 12: 2, 14: 1, 15: 0, 16: 8, 18: 6, 19: 7, 20: 5, 21: 10, 22: 11, 23: 12, 24: 13, - 25: 41, 26: 42, 27: 39, 28: 40} - score: '0.714' - edge_lig_8e_lig_5j: - ligand_a: lig_8e - ligand_b: lig_5j - atom mapping: {0: 15, 1: 14, 2: 16, 3: 17, 4: 18, 6: 20, 7: 11, 8: 12, 10: 10, - 11: 9, 12: 8, 13: 6, 14: 7, 15: 4, 16: 5, 17: 3, 37: 27, 38: 28, 39: 25, 40: 26, - 41: 23, 42: 24, 43: 21, 44: 22} - score: '0.716' - edge_lig_8a_lig_5k: - ligand_a: lig_8a - ligand_b: lig_5k - atom mapping: {0: 15, 1: 14, 2: 12, 4: 11, 5: 20, 6: 18, 7: 19, 8: 16, 9: 17, - 10: 21, 11: 22, 12: 23, 13: 24, 14: 9, 15: 8, 16: 6, 17: 7, 18: 4, 19: 5, 20: 3, - 39: 27, 40: 28, 41: 25, 42: 26, 43: 10} - score: '0.736' - edge_lig_8e_lig_1a: - ligand_a: lig_8e - ligand_b: lig_1a - atom mapping: {0: 13, 1: 12, 2: 14, 4: 16, 5: 17, 6: 18, 7: 9, 8: 10, 10: 8, 11: 7, - 12: 6, 13: 4, 14: 5, 15: 2, 16: 3, 17: 1, 37: 25, 38: 26, 39: 23, 40: 24, 41: 21, - 42: 22, 43: 19, 44: 20} - score: '0.830' - edge_lig_8e_lig_5a: - ligand_a: lig_8e - ligand_b: lig_5a - atom mapping: {0: 15, 1: 14, 2: 16, 4: 18, 5: 19, 6: 20, 7: 11, 8: 12, 10: 10, - 11: 9, 12: 8, 13: 6, 14: 7, 15: 4, 16: 5, 17: 3, 37: 27, 38: 28, 39: 25, 40: 26, - 41: 23, 42: 24, 43: 21, 44: 22} - score: '0.709' - edge_lig_8e_lig_7: - ligand_a: lig_8e - ligand_b: lig_7 - atom mapping: {0: 14, 1: 13, 2: 15, 3: 16, 4: 17, 5: 18, 6: 19, 7: 10, 8: 11, - 10: 9, 11: 8, 12: 7, 13: 23, 14: 24, 15: 25, 16: 26, 17: 3, 37: 4, 38: 5, 39: 6, - 41: 22, 43: 20, 44: 21} - score: '0.723' - edge_lig_8b_lig_5p: - ligand_a: lig_8b - ligand_b: lig_5p - atom mapping: {0: 17, 1: 16, 2: 18, 3: 19, 4: 20, 23: 42, 24: 43, 25: 44, 26: 45, - 27: 15, 28: 14, 29: 46, 30: 4, 31: 5, 32: 6, 33: 7, 34: 8, 35: 9, 36: 1, 37: 0, - 38: 2, 43: 10, 44: 11, 45: 12, 46: 13} - score: '0.638' - edge_lig_8e_lig_5d: - ligand_a: lig_8e - ligand_b: lig_5d - atom mapping: {0: 15, 1: 14, 2: 16, 3: 17, 4: 18, 5: 19, 6: 20, 7: 11, 8: 12, - 10: 10, 11: 9, 12: 8, 13: 6, 14: 7, 15: 4, 16: 5, 17: 3, 37: 27, 38: 28, 39: 25, - 40: 26, 41: 23, 42: 24, 43: 21, 44: 22} - score: '0.731' - edge_lig_8f_lig_5p: - ligand_a: lig_8f - ligand_b: lig_5p - atom mapping: {0: 17, 1: 16, 2: 18, 3: 19, 4: 20, 24: 42, 25: 43, 26: 44, 27: 45, - 28: 15, 29: 14, 30: 46, 31: 4, 32: 5, 33: 6, 34: 7, 35: 8, 36: 9, 37: 1, 38: 0, - 39: 2, 44: 10, 45: 11, 46: 12, 47: 13} - score: '0.638' - edge_lig_5o_lig_8a: - ligand_a: lig_5o - ligand_b: lig_8a - atom mapping: {10: 20, 11: 18, 12: 19, 13: 16, 14: 17, 15: 15, 16: 14, 17: 43, - 18: 4, 19: 5, 20: 6, 21: 7, 22: 8, 23: 9, 24: 1, 25: 0, 26: 2, 31: 10, 32: 11, - 33: 12, 34: 13, 35: 41, 36: 42, 37: 39, 38: 40} - score: '0.654' - edge_lig_5o_lig_8e: - ligand_a: lig_5o - ligand_b: lig_8e - atom mapping: {10: 17, 11: 15, 12: 16, 13: 13, 14: 14, 15: 12, 16: 11, 17: 10, - 18: 7, 19: 6, 20: 4, 21: 5, 22: 2, 23: 3, 24: 1, 25: 0, 26: 8, 27: 9, 31: 43, - 32: 44, 33: 41, 34: 42, 35: 39, 36: 40, 37: 37, 38: 38} - score: '0.665' - edge_lig_8a_lig_5h: - ligand_a: lig_8a - ligand_b: lig_5h - atom mapping: {0: 19, 1: 18, 2: 12, 4: 11, 5: 24, 6: 22, 7: 23, 8: 20, 10: 25, - 11: 26, 12: 27, 13: 28, 14: 9, 15: 8, 16: 6, 17: 7, 18: 4, 19: 5, 20: 3, 39: 31, - 40: 32, 41: 29, 42: 30, 43: 10} - score: '0.675' - edge_lig_5i_lig_8a: - ligand_a: lig_5i - ligand_b: lig_8a - atom mapping: {3: 20, 4: 18, 5: 19, 6: 16, 7: 17, 8: 15, 9: 14, 10: 43, 11: 4, - 12: 5, 13: 6, 14: 7, 15: 8, 17: 1, 18: 0, 19: 2, 24: 10, 25: 11, 26: 12, 27: 13, - 28: 41, 29: 42, 30: 39, 31: 40} - score: '0.684' - edge_lig_8e_lig_5e: - ligand_a: lig_8e - ligand_b: lig_5e - atom mapping: {0: 15, 1: 14, 2: 16, 3: 17, 4: 18, 5: 19, 6: 20, 7: 11, 8: 12, - 10: 10, 11: 9, 12: 8, 13: 6, 14: 7, 15: 4, 16: 5, 17: 3, 37: 27, 38: 28, 39: 25, - 40: 26, 41: 23, 42: 24, 43: 21, 44: 22} - score: '0.731' - edge_lig_8c_lig_5p: - ligand_a: lig_8c - ligand_b: lig_5p - atom mapping: {0: 0, 1: 1, 2: 8, 3: 9, 4: 6, 5: 7, 6: 5, 7: 4, 8: 2, 10: 46, 11: 14, - 12: 15, 13: 44, 14: 45, 15: 42, 16: 43, 17: 20, 34: 18, 35: 19, 36: 16, 37: 17, - 38: 12, 39: 13, 40: 10, 41: 11} - score: '0.672' - edge_lig_8e_lig_5p: - ligand_a: lig_8e - ligand_b: lig_5p - atom mapping: {0: 0, 1: 1, 2: 8, 3: 9, 4: 6, 5: 7, 6: 5, 7: 4, 8: 2, 10: 46, 11: 14, - 12: 15, 13: 44, 14: 45, 15: 42, 16: 43, 17: 20, 37: 18, 38: 19, 39: 16, 40: 17, - 41: 12, 42: 13, 43: 10, 44: 11} - score: '0.646' - edge_lig_8e_lig_5n: - ligand_a: lig_8e - ligand_b: lig_5n - atom mapping: {0: 22, 1: 21, 2: 23, 3: 24, 4: 25, 5: 26, 6: 27, 7: 18, 8: 19, - 10: 17, 11: 16, 12: 15, 13: 13, 14: 14, 15: 11, 16: 12, 17: 10, 37: 34, 38: 35, - 39: 32, 40: 33, 41: 30, 42: 31, 43: 28, 44: 29} - score: '0.663' - edge_lig_8e_lig_1b: - ligand_a: lig_8e - ligand_b: lig_1b - atom mapping: {0: 0, 1: 1, 2: 2, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 10: 10, 11: 11, - 12: 12, 13: 25, 14: 26, 15: 23, 16: 24, 17: 17, 37: 15, 38: 16, 39: 13, 40: 14, - 41: 27, 42: 28, 43: 29, 44: 30} - score: '0.777' - edge_lig_8a_lig_5l: - ligand_a: lig_8a - ligand_b: lig_5l - atom mapping: {0: 15, 1: 14, 2: 12, 4: 11, 5: 20, 6: 18, 8: 16, 10: 21, 11: 22, - 12: 23, 13: 24, 14: 9, 15: 8, 16: 6, 17: 7, 18: 4, 19: 5, 20: 3, 39: 27, 40: 28, - 41: 25, 42: 26, 43: 10} - score: '0.700' - edge_lig_8e_lig_3a: - ligand_a: lig_8e - ligand_b: lig_3a - atom mapping: {0: 0, 1: 1, 2: 2, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 10: 10, 11: 11, - 12: 12, 13: 33, 14: 34, 15: 31, 16: 32, 17: 17, 37: 15, 38: 16, 39: 13, 40: 14, - 41: 35, 42: 36, 43: 37, 44: 38} - score: '0.689' - edge_lig_8e_lig_5b: - ligand_a: lig_8e - ligand_b: lig_5b - atom mapping: {0: 15, 1: 14, 2: 16, 4: 18, 6: 20, 7: 11, 8: 12, 10: 10, 11: 9, - 12: 8, 13: 6, 14: 7, 15: 4, 16: 5, 17: 3, 37: 27, 38: 28, 39: 25, 40: 26, 41: 23, - 42: 24, 43: 21, 44: 22} - score: '0.694' - edge_lig_8e_lig_3b: - ligand_a: lig_8e - ligand_b: lig_3b - atom mapping: {0: 0, 1: 1, 2: 8, 3: 9, 4: 6, 5: 7, 6: 5, 7: 4, 8: 2, 10: 38, 11: 14, - 12: 15, 13: 36, 14: 37, 15: 34, 16: 35, 17: 20, 37: 18, 38: 19, 39: 16, 40: 17, - 41: 12, 42: 13, 43: 10, 44: 11} - score: '0.710' - edge_lig_8d_lig_5p: - ligand_a: lig_8d - ligand_b: lig_5p - atom mapping: {0: 17, 1: 16, 2: 18, 3: 19, 4: 20, 21: 42, 22: 43, 23: 44, 24: 45, - 25: 15, 26: 14, 27: 46, 28: 4, 29: 5, 30: 6, 31: 7, 32: 8, 33: 9, 34: 1, 35: 0, - 36: 2, 41: 10, 42: 11, 43: 12, 44: 13} - score: '0.646' - edge_lig_8e_lig_5c: - ligand_a: lig_8e - ligand_b: lig_5c - atom mapping: {0: 15, 1: 14, 2: 16, 4: 18, 6: 20, 7: 11, 8: 12, 10: 10, 11: 9, - 12: 8, 13: 6, 14: 7, 15: 4, 16: 5, 17: 3, 37: 27, 38: 28, 39: 25, 40: 26, 41: 23, - 42: 24, 43: 21, 44: 22} - score: '0.694' diff --git a/data/tyk2/03_edges/01_perses_openfe.yml b/data/tyk2/03_edges/01_perses_openfe.yml deleted file mode 100644 index f86683f32..000000000 --- a/data/tyk2/03_edges/01_perses_openfe.yml +++ /dev/null @@ -1,88 +0,0 @@ -mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, - coordinate_tolerance=0.2), default non geometric scorer -planner: openfe v0.5 minimal_spanning_graph -edges: - edge_lig_ejm_55_lig_ejm_48: - ligand_a: lig_ejm_55 - ligand_b: lig_ejm_48 - atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 29: 38, 30: 39, 31: 8, 32: 7} - score: '0.847' - edge_lig_jmc_27_lig_ejm_48: - ligand_a: lig_jmc_27 - ligand_b: lig_ejm_48 - atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 32: 38, 33: 39, 34: 40, 35: 41} - score: '0.807' - edge_lig_ejm_46_lig_ejm_48: - ligand_a: lig_ejm_46 - ligand_b: lig_ejm_48 - atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 32: 38, 33: 39, 34: 8, 35: 7} - score: '0.807' - edge_lig_ejm_31_lig_ejm_48: - ligand_a: lig_ejm_31 - ligand_b: lig_ejm_48 - atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 28: 38, 29: 39, 30: 8, 31: 7} - score: '0.860' - edge_lig_jmc_28_lig_ejm_48: - ligand_a: lig_jmc_28 - ligand_b: lig_ejm_48 - atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 35: 38, 36: 39, 37: 8, 38: 7} - score: '0.772' - edge_lig_ejm_43_lig_ejm_48: - ligand_a: lig_ejm_43 - ligand_b: lig_ejm_48 - atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 34: 38, 35: 39, 36: 8, 37: 7} - score: '0.783' - edge_lig_ejm_50_lig_ejm_48: - ligand_a: lig_ejm_50 - ligand_b: lig_ejm_48 - atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 29: 38, 30: 39, 31: 8, 32: 7} - score: '0.847' - edge_lig_ejm_45_lig_ejm_48: - ligand_a: lig_ejm_45 - ligand_b: lig_ejm_48 - atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 35: 38, 36: 39, 37: 8, 38: 7} - score: '0.772' - edge_lig_ejm_54_lig_ejm_48: - ligand_a: lig_ejm_54 - ligand_b: lig_ejm_48 - atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 33: 38, 34: 39, 35: 8, 36: 7} - score: '0.795' - edge_lig_jmc_23_lig_ejm_48: - ligand_a: lig_jmc_23 - ligand_b: lig_ejm_48 - atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 32: 38, 33: 39, 34: 8, 35: 7} - score: '0.807' - edge_lig_ejm_42_lig_ejm_48: - ligand_a: lig_ejm_42 - ligand_b: lig_ejm_48 - atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 31: 38, 32: 39, 33: 8, 34: 7} - score: '0.820' - edge_lig_ejm_47_lig_ejm_48: - ligand_a: lig_ejm_47 - ligand_b: lig_ejm_48 - atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, - 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, - 21: 21, 22: 22, 23: 23, 35: 38, 36: 39, 37: 8, 38: 7} - score: '0.772' From d2f51acb14526fb75555a10265da288e7bef006f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Iv=C3=A1n=20Pulido?= <2949729+ijpulidos@users.noreply.github.com> Date: Mon, 5 Jun 2023 13:09:44 -0400 Subject: [PATCH 6/6] Revert "Removing current edges file to merge to main." This reverts commit b18c0b1bda9ff4a96410e91dbb0a3364ead3bd8d. --- data/cdk2/03_edges/01_perses_openfe.yml | 85 ++++++ data/cdk8/03_edges/01_perses_openfe.yml | 184 ++++++++++++ data/cmet/03_edges/01_perses_openfe.yml | 36 +++ data/eg5/03_edges/01_perses_openfe.yml | 204 +++++++++++++ data/hif2a/03_edges/01_perses_openfe.yml | 210 ++++++++++++++ data/mcl1/03_edges/01_perses_openfe.yml | 172 +++++++++++ data/p38/03_edges/01_perses_openfe.yml | 201 +++++++++++++ data/pde2/03_edges/01_perses_openfe.yml | 184 ++++++++++++ data/pfkfb3/03_edges/01_perses_openfe.yml | 229 +++++++++++++++ data/ptp1b/03_edges/01_perses_openfe.yml | 151 ++++++++++ data/shp2/03_edges/01_perses_openfe.yml | 145 ++++++++++ data/syk/03_edges/01_perses_openfe.yml | 305 ++++++++++++++++++++ data/thrombin/03_edges/01_perses_openfe.yml | 180 ++++++++++++ data/tnks2/03_edges/01_perses_openfe.yml | 186 ++++++++++++ data/tyk2/03_edges/01_perses_openfe.yml | 88 ++++++ 15 files changed, 2560 insertions(+) create mode 100644 data/cdk2/03_edges/01_perses_openfe.yml create mode 100644 data/cdk8/03_edges/01_perses_openfe.yml create mode 100644 data/cmet/03_edges/01_perses_openfe.yml create mode 100644 data/eg5/03_edges/01_perses_openfe.yml create mode 100644 data/hif2a/03_edges/01_perses_openfe.yml create mode 100644 data/mcl1/03_edges/01_perses_openfe.yml create mode 100644 data/p38/03_edges/01_perses_openfe.yml create mode 100644 data/pde2/03_edges/01_perses_openfe.yml create mode 100644 data/pfkfb3/03_edges/01_perses_openfe.yml create mode 100644 data/ptp1b/03_edges/01_perses_openfe.yml create mode 100644 data/shp2/03_edges/01_perses_openfe.yml create mode 100644 data/syk/03_edges/01_perses_openfe.yml create mode 100644 data/thrombin/03_edges/01_perses_openfe.yml create mode 100644 data/tnks2/03_edges/01_perses_openfe.yml create mode 100644 data/tyk2/03_edges/01_perses_openfe.yml diff --git a/data/cdk2/03_edges/01_perses_openfe.yml b/data/cdk2/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..e4edf0035 --- /dev/null +++ b/data/cdk2/03_edges/01_perses_openfe.yml @@ -0,0 +1,85 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.5 minimal_spanning_graph +edges: + edge_lig_22_lig_1oiy: + ligand_a: lig_22 + ligand_b: lig_1oiy + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, + 31: 43, 32: 44, 33: 41, 34: 42, 35: 35, 37: 33, 43: 31, 44: 32, 45: 45, 46: 46, + 47: 47, 48: 48} + score: '0.907' + edge_lig_20_lig_1oiy: + ligand_a: lig_20 + ligand_b: lig_1oiy + atom mapping: {5: 33, 6: 35, 8: 41, 9: 42, 10: 43, 11: 44, 12: 30, 13: 28, 14: 29, + 15: 27, 16: 26, 17: 4, 18: 5, 19: 6, 20: 8, 21: 7, 22: 9, 23: 10, 24: 23, 25: 24, + 26: 25, 27: 20, 28: 21, 29: 22, 30: 17, 31: 19, 32: 18, 33: 14, 34: 16, 35: 15, + 36: 11, 37: 12, 38: 13, 39: 3, 40: 2, 41: 1, 42: 0, 43: 47, 44: 48, 45: 46, + 46: 45, 47: 31, 48: 32} + score: '0.907' + edge_lig_17_lig_1oiy: + ligand_a: lig_17 + ligand_b: lig_1oiy + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, + 31: 43, 32: 44, 33: 41, 34: 42, 35: 35, 37: 33, 39: 31, 40: 32, 41: 45, 42: 46, + 43: 47, 44: 48} + score: '0.954' + edge_lig_21_lig_1oiy: + ligand_a: lig_21 + ligand_b: lig_1oiy + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, + 31: 43, 32: 44, 33: 41, 34: 42, 35: 35, 37: 33, 43: 31, 44: 32, 45: 45, 46: 46, + 47: 47, 48: 48} + score: '0.907' + edge_lig_1oiu_lig_1h1r: + ligand_a: lig_1oiu + ligand_b: lig_1h1r + atom mapping: {0: 43, 1: 40, 2: 39, 3: 15, 4: 16, 5: 18, 6: 19, 7: 20, 8: 21, + 9: 22, 10: 38, 11: 23, 12: 37, 13: 36, 14: 24, 15: 35, 16: 34, 17: 25, 18: 32, + 19: 33, 20: 26, 21: 30, 22: 31, 23: 27, 24: 29, 25: 28, 26: 17, 27: 12, 28: 10, + 29: 11, 30: 3, 31: 2, 32: 44, 33: 1, 40: 6, 41: 7, 42: 5, 44: 4, 45: 9, 46: 13, + 47: 14, 48: 41, 49: 42} + score: '0.948' + edge_lig_1oiu_lig_1oiy: + ligand_a: lig_1oiu + ligand_b: lig_1oiy + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, + 31: 43, 32: 44, 33: 41, 40: 35, 42: 33, 43: 34, 44: 31, 45: 32, 46: 45, 47: 46, + 48: 47, 49: 48} + score: '0.901' + edge_lig_1oiu_lig_1h1q: + ligand_a: lig_1oiu + ligand_b: lig_1h1q + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, + 31: 39, 32: 40, 33: 37, 40: 35, 41: 36, 42: 33, 43: 34, 44: 31, 45: 32, 46: 41, + 47: 42, 48: 43, 49: 44} + score: '0.961' + edge_lig_1oi9_lig_1oiu: + ligand_a: lig_1oi9 + ligand_b: lig_1oiu + atom mapping: {2: 40, 3: 33, 5: 31, 6: 32, 7: 30, 8: 28, 9: 29, 10: 27, 11: 26, + 12: 4, 13: 5, 14: 6, 15: 7, 16: 8, 17: 9, 18: 10, 19: 11, 20: 12, 21: 13, 22: 14, + 23: 16, 24: 15, 25: 17, 26: 18, 27: 19, 28: 20, 29: 22, 30: 21, 31: 23, 32: 24, + 33: 25, 34: 3, 35: 2, 36: 1, 37: 0, 38: 48, 39: 49, 40: 47, 41: 46, 42: 44, + 43: 45, 44: 42, 45: 43} + score: '0.936' + edge_lig_26_lig_1oiu: + ligand_a: lig_26 + ligand_b: lig_1oiu + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 13, 13: 12, 14: 14, 15: 16, 16: 15, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 25, 25: 24, 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, + 31: 44, 32: 45, 33: 42, 34: 43, 35: 40, 41: 33, 43: 31, 44: 32, 45: 46, 46: 47, + 47: 48, 48: 49} + score: '0.901' diff --git a/data/cdk8/03_edges/01_perses_openfe.yml b/data/cdk8/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..2ee334fc2 --- /dev/null +++ b/data/cdk8/03_edges/01_perses_openfe.yml @@ -0,0 +1,184 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.5 minimal_spanning_graph +edges: + edge_lig_22_lig_43: + ligand_a: lig_22 + ligand_b: lig_43 + atom mapping: {17: 13, 18: 14, 19: 15, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 40: 40, 41: 41, 42: 42, 43: 43} + score: '0.358' + edge_lig_33_lig_45: + ligand_a: lig_33 + ligand_b: lig_45 + atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 41: 41, 42: 42, 43: 43, 44: 44} + score: '0.396' + edge_lig_40_lig_45: + ligand_a: lig_40 + ligand_b: lig_45 + atom mapping: {17: 13, 18: 14, 19: 15, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 46: 41, 47: 42, 48: 43, 49: 44} + score: '0.386' + edge_lig_42_lig_20: + ligand_a: lig_42 + ligand_b: lig_20 + atom mapping: {8: 37, 9: 38, 10: 36, 11: 34, 12: 35, 13: 33, 14: 32, 15: 47, 16: 48, + 17: 45, 18: 46, 19: 30, 20: 31, 21: 29, 22: 28, 23: 25, 24: 27, 25: 26} + score: '0.391' + edge_lig_43_lig_32: + ligand_a: lig_43 + ligand_b: lig_32 + atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, + 21: 25, 22: 26, 23: 27, 24: 28, 25: 29, 26: 30, 40: 34, 41: 35, 42: 36, 43: 37} + score: '0.430' + edge_lig_39_lig_45: + ligand_a: lig_39 + ligand_b: lig_45 + atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 45: 41, 46: 42, 47: 43, 48: 44} + score: '0.386' + edge_lig_38_lig_45: + ligand_a: lig_38 + ligand_b: lig_45 + atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 44: 41, 45: 42, 46: 43, 47: 44} + score: '0.385' + edge_lig_28_lig_17: + ligand_a: lig_28 + ligand_b: lig_17 + atom mapping: {17: 15, 18: 17, 19: 16, 20: 18, 21: 19, 22: 20, 23: 21, 24: 22, + 25: 23, 26: 24, 27: 25, 28: 26, 43: 35, 44: 36, 45: 37, 46: 38} + score: '0.392' + edge_lig_21_lig_43: + ligand_a: lig_21 + ligand_b: lig_43 + atom mapping: {17: 13, 18: 14, 19: 15, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 40: 40, 41: 41, 42: 42, 43: 43} + score: '0.358' + edge_lig_28_lig_14: + ligand_a: lig_28 + ligand_b: lig_14 + atom mapping: {17: 7, 18: 9, 20: 6, 21: 20, 22: 21, 23: 22, 24: 4, 25: 5, 26: 23, + 27: 24, 28: 25, 43: 1, 44: 0, 45: 2, 46: 3} + score: '0.418' + edge_lig_41_lig_45: + ligand_a: lig_41 + ligand_b: lig_45 + atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 47: 41, 48: 42, 49: 43, 50: 44} + score: '0.386' + edge_lig_30_lig_45: + ligand_a: lig_30 + ligand_b: lig_45 + atom mapping: {8: 25, 9: 26, 10: 24, 11: 22, 12: 23, 13: 21, 14: 20, 15: 43, 16: 44, + 17: 41, 18: 42, 19: 18, 20: 19, 21: 17, 22: 16, 23: 13, 24: 15, 25: 14} + score: '0.388' + edge_lig_26_lig_45: + ligand_a: lig_26 + ligand_b: lig_45 + atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 41: 41, 42: 42, 43: 43, 44: 44} + score: '0.356' + edge_lig_13_lig_45: + ligand_a: lig_13 + ligand_b: lig_45 + atom mapping: {2: 41, 3: 24, 4: 25, 5: 26, 20: 22, 21: 23, 22: 21, 23: 16, 24: 13, + 25: 15, 26: 14, 41: 17, 42: 18, 43: 19, 44: 20, 45: 43, 46: 44} + score: '0.395' + edge_lig_43_lig_15: + ligand_a: lig_43 + ligand_b: lig_15 + atom mapping: {13: 5, 14: 6, 15: 7, 16: 8, 17: 9, 18: 10, 19: 11, 20: 12, 21: 13, + 22: 14, 23: 15, 24: 16, 25: 17, 26: 18, 40: 25, 41: 26, 42: 27, 43: 28} + score: '0.425' + edge_lig_28_lig_18: + ligand_a: lig_28 + ligand_b: lig_18 + atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 43: 33, 44: 34, 45: 35, 46: 36} + score: '0.392' + edge_lig_28_lig_44: + ligand_a: lig_28 + ligand_b: lig_44 + atom mapping: {17: 23, 18: 25, 19: 24, 20: 22, 21: 21, 22: 19, 23: 20, 24: 14, + 25: 13, 26: 11, 27: 12, 28: 10, 43: 17, 44: 18, 45: 15, 46: 16} + score: '0.368' + edge_lig_42_lig_36: + ligand_a: lig_42 + ligand_b: lig_36 + atom mapping: {8: 29, 9: 30, 10: 28, 11: 26, 12: 27, 13: 25, 14: 24, 15: 47, 16: 48, + 17: 45, 18: 46, 19: 22, 20: 23, 21: 21, 22: 20, 23: 17, 24: 19, 25: 18} + score: '0.389' + edge_lig_37_lig_45: + ligand_a: lig_37 + ligand_b: lig_45 + atom mapping: {17: 13, 18: 14, 19: 15, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 30: 26, 44: 41, 45: 42, 46: 43, 47: 44} + score: '0.390' + edge_lig_43_lig_24: + ligand_a: lig_43 + ligand_b: lig_24 + atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, + 21: 25, 22: 26, 23: 27, 24: 28, 25: 29, 40: 37, 41: 38, 42: 39, 43: 40} + score: '0.395' + edge_lig_43_lig_28: + ligand_a: lig_43 + ligand_b: lig_28 + atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, + 21: 25, 22: 26, 23: 27, 24: 28, 40: 43, 41: 44, 42: 45, 43: 46} + score: '0.356' + edge_lig_42_lig_27: + ligand_a: lig_42 + ligand_b: lig_27 + atom mapping: {8: 29, 10: 28, 11: 26, 12: 27, 13: 25, 14: 24, 15: 47, 16: 48, + 17: 45, 18: 46, 19: 22, 20: 23, 21: 21, 22: 20, 23: 17, 24: 19, 25: 18} + score: '0.375' + edge_lig_43_lig_16: + ligand_a: lig_43 + ligand_b: lig_16 + atom mapping: {13: 5, 14: 6, 15: 7, 16: 8, 17: 9, 18: 10, 19: 11, 20: 12, 21: 13, + 22: 14, 23: 15, 24: 16, 25: 17, 26: 18, 40: 25, 41: 26, 42: 27, 43: 28} + score: '0.454' + edge_lig_29_lig_45: + ligand_a: lig_29 + ligand_b: lig_45 + atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 29: 25, 31: 26, 42: 41, 43: 42, 44: 43, 45: 44} + score: '0.394' + edge_lig_42_lig_34: + ligand_a: lig_42 + ligand_b: lig_34 + atom mapping: {8: 29, 9: 30, 10: 28, 11: 26, 12: 27, 13: 25, 14: 24, 15: 43, 16: 44, + 17: 41, 18: 42, 19: 22, 20: 23, 21: 21, 22: 20, 23: 17, 24: 19, 25: 18} + score: '0.389' + edge_lig_42_lig_35: + ligand_a: lig_42 + ligand_b: lig_35 + atom mapping: {8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, + 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, 22: 22, 23: 23, 24: 25, 25: 24} + score: '0.392' + edge_lig_43_lig_25: + ligand_a: lig_43 + ligand_b: lig_25 + atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, + 21: 25, 22: 26, 23: 27, 24: 28, 25: 29, 40: 38, 41: 39, 42: 40, 43: 41} + score: '0.390' + edge_lig_28_lig_45: + ligand_a: lig_28 + ligand_b: lig_45 + atom mapping: {17: 13, 18: 15, 19: 14, 20: 16, 21: 17, 22: 18, 23: 19, 24: 20, + 25: 21, 26: 22, 27: 23, 28: 24, 43: 41, 44: 42, 45: 43, 46: 44} + score: '0.354' + edge_lig_43_lig_19: + ligand_a: lig_43 + ligand_b: lig_19 + atom mapping: {13: 17, 14: 19, 15: 18, 16: 20, 17: 21, 18: 22, 19: 23, 20: 24, + 21: 25, 22: 26, 23: 27, 24: 28, 25: 29, 26: 30, 40: 37, 41: 38, 42: 39, 43: 40} + score: '0.414' + edge_lig_42_lig_28: + ligand_a: lig_42 + ligand_b: lig_28 + atom mapping: {10: 28, 11: 26, 12: 27, 13: 25, 14: 24, 15: 45, 16: 46, 17: 43, + 18: 44, 19: 22, 20: 23, 21: 21, 22: 20, 23: 17, 24: 19, 25: 18} + score: '0.354' diff --git a/data/cmet/03_edges/01_perses_openfe.yml b/data/cmet/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..129f22a94 --- /dev/null +++ b/data/cmet/03_edges/01_perses_openfe.yml @@ -0,0 +1,36 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.5 minimal_spanning_graph +edges: + edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402754_40_14: + ligand_a: lig_CHEMBL3402745_200_5 + ligand_b: lig_CHEMBL3402754_40_14 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 14, 7: 15, 8: 12, 9: 13, + 10: 10, 11: 11, 12: 8, 13: 9, 14: 6, 15: 7, 16: 16, 17: 17, 18: 18, 19: 19, + 20: 20, 21: 21, 22: 41, 23: 42, 24: 28, 26: 26, 27: 27, 28: 24, 41: 22, 42: 23, + 43: 43, 44: 44} + score: '0.716' + edge_lig_CHEMBL3402761_1_21_lig_CHEMBL3402749_500_9: + ligand_a: lig_CHEMBL3402761_1_21 + ligand_b: lig_CHEMBL3402749_500_9 + atom mapping: {0: 37, 1: 36, 2: 34, 3: 35, 4: 22, 5: 23, 6: 32, 7: 33, 8: 30, + 10: 28, 11: 29, 12: 26, 13: 27, 15: 24, 16: 25, 17: 21, 18: 20, 19: 17, 20: 18, + 21: 19, 22: 16, 23: 14, 24: 15, 25: 12, 26: 13, 27: 10, 28: 11, 29: 9, 59: 40, + 60: 41, 61: 38, 62: 39} + score: '0.675' + edge_lig_CHEMBL3402744_300_4_lig_CHEMBL3402761_1_21: + ligand_a: lig_CHEMBL3402744_300_4 + ligand_b: lig_CHEMBL3402761_1_21 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 15, 7: 16, 8: 12, 9: 13, + 10: 10, 11: 11, 12: 8, 14: 6, 15: 7, 16: 17, 17: 18, 18: 19, 19: 20, 20: 21, + 21: 22, 22: 59, 23: 60, 24: 29, 26: 27, 27: 28, 28: 25, 38: 23, 39: 24, 40: 61, + 41: 62} + score: '0.671' + edge_lig_CHEMBL3402745_200_5_lig_CHEMBL3402761_1_21: + ligand_a: lig_CHEMBL3402745_200_5 + ligand_b: lig_CHEMBL3402761_1_21 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 15, 7: 16, 8: 12, 9: 13, + 10: 10, 11: 11, 12: 8, 14: 6, 15: 7, 16: 17, 17: 18, 18: 19, 19: 20, 20: 21, + 21: 22, 22: 59, 23: 60, 24: 29, 26: 27, 27: 28, 28: 25, 41: 23, 42: 24, 43: 61, + 44: 62} + score: '0.648' diff --git a/data/eg5/03_edges/01_perses_openfe.yml b/data/eg5/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..fd212f12f --- /dev/null +++ b/data/eg5/03_edges/01_perses_openfe.yml @@ -0,0 +1,204 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.5 minimal_spanning_graph +edges: + edge_lig_CHEMBL1084676_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1084676 + ligand_b: lig_CHEMBL1078998 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 17: 17, 18: 18, 19: 22, 20: 26, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, + 26: 35, 27: 36, 28: 38, 52: 39, 53: 40, 54: 41, 55: 42, 56: 43, 57: 44, 58: 45, + 59: 46} + score: '0.598' + edge_lig_CHEMBL1084678_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1084678 + ligand_b: lig_CHEMBL1078998 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 17: 17, 18: 18, 19: 22, 20: 26, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, + 26: 35, 27: 36, 28: 38, 52: 39, 53: 40, 54: 41, 55: 42, 56: 43, 57: 44, 58: 45, + 59: 46} + score: '0.598' + edge_lig_CHEMBL1078998_lig_CHEMBL1083836: + ligand_a: lig_CHEMBL1078998 + ligand_b: lig_CHEMBL1083836 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 30: 25, 31: 26, 32: 27, 33: 28, 34: 29, 35: 30, 36: 31, 37: 32, 39: 42, + 40: 43, 41: 44, 42: 45, 43: 46, 44: 47, 45: 48, 46: 49} + score: '0.544' + edge_lig_CHEMBL1085895_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1085895 + ligand_b: lig_CHEMBL1078998 + atom mapping: {20: 36, 21: 38, 22: 35, 23: 33, 24: 34, 25: 32, 26: 30, 27: 31, + 28: 16, 29: 17, 30: 26, 31: 22, 32: 18, 33: 14, 34: 15, 35: 12, 36: 13, 37: 11, + 38: 9, 39: 10, 40: 7, 41: 8, 53: 45, 54: 46, 55: 42, 56: 44, 57: 43, 58: 39, + 59: 41, 60: 40} + score: '0.602' + edge_lig_CHEMBL1084143_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1084143 + ligand_b: lig_CHEMBL1078998 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 17: 17, 19: 26, 20: 27, 21: 28, 22: 29, 23: 18, 24: 19, 25: 20, 26: 21, + 27: 30, 28: 31, 29: 32, 30: 33, 31: 34, 32: 35, 33: 36, 34: 37, 61: 39, 62: 41, + 63: 40, 64: 42, 65: 44, 66: 43, 67: 45, 68: 46} + score: '0.653' + edge_lig_CHEMBL1085666_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1085666 + ligand_b: lig_CHEMBL1078998 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 17: 17, 18: 26, 19: 22, 20: 18, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, + 26: 35, 27: 36, 28: 37, 35: 39, 36: 41, 37: 40, 38: 42, 39: 44, 40: 43, 41: 45, + 42: 46} + score: '0.628' + edge_lig_CHEMBL1084677_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1084677 + ligand_b: lig_CHEMBL1078998 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 17: 17, 18: 26, 19: 22, 20: 18, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, + 26: 35, 27: 36, 28: 37, 49: 39, 50: 41, 51: 40, 52: 42, 53: 44, 54: 43, 55: 45, + 56: 46} + score: '0.602' + edge_lig_CHEMBL1077204_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1077204 + ligand_b: lig_CHEMBL1078998 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 17: 17, 18: 26, 19: 22, 20: 18, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, + 26: 35, 27: 36, 28: 37, 53: 39, 54: 41, 55: 40, 56: 42, 57: 44, 58: 43, 59: 45, + 60: 46} + score: '0.598' + edge_lig_CHEMBL1084935_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1084935 + ligand_b: lig_CHEMBL1078998 + atom mapping: {19: 36, 20: 38, 21: 35, 22: 33, 23: 34, 24: 32, 25: 30, 26: 31, + 27: 16, 28: 17, 29: 18, 30: 19, 31: 20, 32: 21, 33: 22, 34: 25, 35: 24, 36: 23, + 37: 26, 38: 27, 39: 28, 40: 29, 41: 14, 42: 15, 43: 12, 44: 13, 45: 11, 46: 9, + 47: 10, 48: 7, 49: 8, 61: 45, 62: 46, 63: 42, 64: 44, 65: 43, 66: 39, 67: 41, + 68: 40} + score: '0.720' + edge_lig_CHEMBL1078691_lig_CHEMBL1077227: + ligand_a: lig_CHEMBL1078691 + ligand_b: lig_CHEMBL1077227 + atom mapping: {8: 7, 9: 8, 10: 9, 11: 10, 12: 11, 13: 12, 14: 13, 15: 14, 16: 15, + 17: 16, 18: 17, 19: 26, 20: 27, 21: 28, 22: 29, 23: 22, 24: 25, 25: 24, 26: 23, + 27: 18, 28: 19, 29: 20, 30: 21, 31: 30, 32: 31, 33: 32, 34: 33, 35: 34, 36: 35, + 37: 36, 38: 37, 40: 47, 41: 48, 42: 49, 43: 50, 44: 51, 45: 52, 46: 53, 47: 54} + score: '0.707' + edge_lig_CHEMBL1078774_lig_CHEMBL1077227: + ligand_a: lig_CHEMBL1078774 + ligand_b: lig_CHEMBL1077227 + atom mapping: {8: 7, 9: 8, 10: 9, 11: 10, 12: 11, 13: 12, 14: 13, 15: 14, 16: 15, + 17: 16, 18: 17, 19: 26, 20: 27, 21: 28, 22: 29, 23: 22, 24: 25, 25: 24, 26: 23, + 27: 18, 28: 19, 29: 20, 30: 21, 31: 30, 32: 31, 33: 32, 34: 33, 35: 34, 36: 35, + 37: 36, 38: 37, 40: 47, 41: 48, 42: 49, 43: 50, 44: 51, 45: 52, 46: 53, 47: 54} + score: '0.707' + edge_lig_CHEMBL1089056_lig_CHEMBL1077227: + ligand_a: lig_CHEMBL1089056 + ligand_b: lig_CHEMBL1077227 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, + 26: 26, 27: 27, 28: 28, 29: 29, 30: 30, 31: 31, 32: 32, 33: 33, 34: 34, 35: 35, + 36: 36, 38: 37, 39: 47, 40: 48, 41: 49, 42: 50, 43: 51, 44: 52, 45: 53, 46: 54} + score: '0.716' + edge_lig_CHEMBL1078998_lig_CHEMBL1082248: + ligand_a: lig_CHEMBL1078998 + ligand_b: lig_CHEMBL1082248 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 14: 14, 15: 15, 16: 16, + 17: 17, 30: 18, 31: 19, 32: 20, 33: 21, 34: 22, 35: 23, 36: 24, 37: 25, 39: 35, + 40: 36, 41: 37, 42: 38, 43: 39, 44: 40, 45: 41, 46: 42} + score: '0.562' + edge_lig_CHEMBL1078998_lig_CHEMBL1085692: + ligand_a: lig_CHEMBL1078998 + ligand_b: lig_CHEMBL1085692 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 14: 14, 15: 15, 16: 16, + 17: 17, 30: 18, 31: 19, 32: 20, 33: 21, 34: 22, 35: 23, 36: 24, 37: 25, 39: 51, + 40: 52, 41: 53, 42: 54, 43: 55, 44: 56, 45: 57, 46: 58} + score: '0.538' + edge_lig_CHEMBL1089393_lig_CHEMBL1077227: + ligand_a: lig_CHEMBL1089393 + ligand_b: lig_CHEMBL1077227 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 17: 17, 18: 30, 19: 31, 20: 32, 21: 33, 22: 34, 23: 35, 24: 36, 26: 37, + 27: 47, 28: 48, 29: 49, 30: 50, 31: 51, 32: 52, 33: 53, 34: 54} + score: '0.645' + edge_lig_CHEMBL1088740_lig_CHEMBL1077227: + ligand_a: lig_CHEMBL1088740 + ligand_b: lig_CHEMBL1077227 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 17: 17, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, 26: 35, 27: 36, 28: 37, + 30: 47, 31: 49, 32: 48, 33: 50, 34: 52, 35: 51, 36: 53, 37: 54} + score: '0.618' + edge_lig_CHEMBL1093088_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1093088 + ligand_b: lig_CHEMBL1078998 + atom mapping: {7: 36, 8: 37, 9: 35, 10: 33, 11: 34, 12: 32, 13: 30, 14: 31, 15: 16, + 16: 17, 17: 26, 18: 22, 19: 18, 20: 14, 21: 15, 22: 12, 23: 13, 24: 11, 25: 9, + 26: 10, 27: 7, 28: 8, 40: 45, 41: 46, 42: 42, 43: 44, 44: 43, 45: 39, 46: 41, + 47: 40} + score: '0.598' + edge_lig_CHEMBL1083517_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1083517 + ligand_b: lig_CHEMBL1078998 + atom mapping: {8: 7, 9: 8, 10: 9, 11: 10, 12: 11, 13: 12, 14: 13, 15: 14, 16: 15, + 17: 16, 18: 17, 19: 18, 20: 22, 21: 26, 22: 30, 23: 31, 24: 32, 25: 33, 26: 34, + 27: 35, 28: 36, 29: 37, 39: 39, 40: 40, 41: 41, 42: 42, 43: 43, 44: 44, 45: 45, + 46: 46} + score: '0.621' + edge_lig_CHEMBL1084115_lig_CHEMBL1085692: + ligand_a: lig_CHEMBL1084115 + ligand_b: lig_CHEMBL1085692 + atom mapping: {5: 7, 6: 8, 7: 9, 8: 10, 9: 11, 10: 12, 12: 14, 13: 15, 14: 16, + 15: 17, 28: 18, 29: 19, 30: 20, 31: 21, 32: 22, 33: 23, 34: 24, 36: 25, 37: 51, + 38: 53, 39: 52, 40: 54, 41: 55, 42: 56, 43: 57, 44: 58} + score: '0.538' + edge_lig_CHEMBL1096003_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1096003 + ligand_b: lig_CHEMBL1078998 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 14: 14, 15: 15, 16: 16, + 17: 17, 18: 30, 19: 31, 20: 32, 21: 33, 22: 34, 23: 35, 24: 36, 25: 37, 49: 39, + 50: 41, 51: 40, 52: 42, 53: 44, 54: 43, 55: 45, 56: 46} + score: '0.538' + edge_lig_CHEMBL1078998_lig_CHEMBL1096002: + ligand_a: lig_CHEMBL1078998 + ligand_b: lig_CHEMBL1096002 + atom mapping: {7: 30, 8: 31, 9: 28, 10: 29, 11: 27, 12: 25, 14: 23, 15: 24, 16: 21, + 17: 22, 30: 19, 31: 20, 32: 18, 33: 16, 34: 17, 35: 15, 36: 13, 38: 14, 39: 48, + 40: 49, 41: 50, 42: 45, 43: 46, 44: 47, 45: 43, 46: 44} + score: '0.555' + edge_lig_CHEMBL1078998_lig_CHEMBL1082249: + ligand_a: lig_CHEMBL1078998 + ligand_b: lig_CHEMBL1082249 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 14: 14, 15: 15, 16: 16, + 17: 17, 30: 18, 31: 19, 32: 20, 33: 21, 34: 22, 35: 23, 36: 24, 37: 25, 39: 45, + 40: 46, 41: 47, 42: 48, 43: 49, 44: 50, 45: 51, 46: 52} + score: '0.545' + edge_lig_CHEMBL1086409_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1086409 + ligand_b: lig_CHEMBL1078998 + atom mapping: {5: 7, 6: 8, 7: 9, 8: 10, 9: 11, 10: 12, 11: 13, 12: 14, 13: 15, + 14: 16, 15: 17, 16: 18, 17: 22, 18: 26, 19: 30, 20: 31, 21: 32, 22: 33, 23: 34, + 24: 35, 25: 36, 26: 38, 36: 39, 37: 41, 38: 40, 39: 42, 40: 44, 41: 43, 42: 45, + 43: 46} + score: '0.621' + edge_lig_CHEMBL1077227_lig_CHEMBL1085692: + ligand_a: lig_CHEMBL1077227 + ligand_b: lig_CHEMBL1085692 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 14: 14, 15: 15, 16: 16, + 17: 17, 30: 18, 31: 19, 32: 20, 33: 21, 34: 22, 35: 23, 36: 24, 37: 25, 38: 26, + 39: 28, 40: 27, 41: 29, 42: 30, 43: 31, 47: 51, 48: 53, 49: 52, 50: 54, 51: 56, + 52: 55, 53: 57, 54: 58} + score: '0.567' + edge_lig_CHEMBL1093087_lig_CHEMBL1084115: + ligand_a: lig_CHEMBL1093087 + ligand_b: lig_CHEMBL1084115 + atom mapping: {20: 34, 21: 36, 22: 33, 23: 31, 24: 32, 25: 30, 26: 28, 27: 29, + 28: 14, 29: 15, 30: 16, 31: 20, 32: 24, 33: 12, 34: 13, 35: 10, 36: 11, 37: 9, + 38: 7, 39: 8, 40: 5, 41: 6, 53: 43, 54: 44, 55: 40, 56: 41, 57: 42, 58: 37, + 59: 39, 60: 38} + score: '0.547' + edge_lig_CHEMBL1086410_lig_CHEMBL1078998: + ligand_a: lig_CHEMBL1086410 + ligand_b: lig_CHEMBL1078998 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, + 16: 16, 17: 17, 18: 26, 19: 29, 20: 28, 21: 27, 22: 22, 23: 25, 24: 24, 25: 23, + 26: 18, 27: 21, 28: 20, 29: 19, 30: 30, 31: 31, 32: 32, 33: 33, 34: 34, 35: 35, + 36: 36, 37: 37, 47: 39, 48: 41, 49: 40, 50: 42, 51: 44, 52: 43, 53: 45, 54: 46} + score: '0.738' diff --git a/data/hif2a/03_edges/01_perses_openfe.yml b/data/hif2a/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..1070dce53 --- /dev/null +++ b/data/hif2a/03_edges/01_perses_openfe.yml @@ -0,0 +1,210 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.5 minimal_spanning_graph +edges: + edge_lig_165_lig_54: + ligand_a: lig_165 + ligand_b: lig_54 + atom mapping: {0: 19, 1: 18, 2: 16, 3: 17, 4: 14, 5: 15, 6: 13, 7: 12, 34: 22, + 35: 23, 36: 20, 37: 21} + score: '0.367' + edge_lig_43_lig_84: + ligand_a: lig_43 + ligand_b: lig_84 + atom mapping: {9: 7, 10: 6, 11: 4, 12: 5, 13: 2, 15: 1, 16: 0, 17: 31, 18: 32, + 20: 29, 21: 30} + score: '0.363' + edge_lig_124_lig_224: + ligand_a: lig_124 + ligand_b: lig_224 + atom mapping: {14: 24, 15: 26, 16: 25, 17: 27, 18: 28, 19: 29, 20: 30} + score: '0.174' + edge_lig_1_lig_43: + ligand_a: lig_1 + ligand_b: lig_43 + atom mapping: {7: 9, 8: 10, 9: 20, 10: 21, 11: 17, 12: 18, 13: 15, 14: 16, 15: 13, + 17: 11, 18: 12} + score: '0.357' + edge_lig_156_lig_54: + ligand_a: lig_156 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 13: 18, 14: 19, 15: 16, 16: 17, + 18: 14, 19: 15} + score: '0.346' + edge_lig_57_lig_54: + ligand_a: lig_57 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.364' + edge_lig_30_lig_224: + ligand_a: lig_30 + ligand_b: lig_224 + atom mapping: {14: 24, 15: 26, 16: 25, 17: 27, 19: 29, 20: 28} + score: '0.152' + edge_lig_206_lig_54: + ligand_a: lig_206 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.364' + edge_lig_54_lig_224: + ligand_a: lig_54 + ligand_b: lig_224 + atom mapping: {29: 24, 30: 26, 31: 25, 32: 27} + score: '0.093' + edge_lig_67_lig_124: + ligand_a: lig_67 + ligand_b: lig_124 + atom mapping: {7: 7, 8: 8, 9: 9, 10: 10, 11: 11, 13: 13, 15: 21, 17: 23} + score: '0.311' + edge_lig_35_lig_224: + ligand_a: lig_35 + ligand_b: lig_224 + atom mapping: {27: 24, 28: 26, 29: 25, 30: 27, 32: 29, 33: 28} + score: '0.145' + edge_lig_227_lig_54: + ligand_a: lig_227 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.361' + edge_lig_31_lig_224: + ligand_a: lig_31 + ligand_b: lig_224 + atom mapping: {17: 24, 18: 26, 19: 25, 20: 27, 22: 29, 23: 28} + score: '0.145' + edge_lig_338_lig_54: + ligand_a: lig_338 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 14, 10: 15, 11: 16, 12: 17, 13: 18, 14: 19, 15: 20, + 16: 21, 18: 22, 19: 23} + score: '0.364' + edge_lig_336_lig_54: + ligand_a: lig_336 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 14, 10: 15, 11: 16, 12: 17, 13: 18, 14: 19, 15: 20, + 16: 21, 18: 22, 19: 23} + score: '0.367' + edge_lig_50_lig_224: + ligand_a: lig_50 + ligand_b: lig_224 + atom mapping: {14: 24, 15: 25, 16: 26, 17: 27} + score: '0.098' + edge_lig_231_lig_54: + ligand_a: lig_231 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.370' + edge_lig_290_lig_54: + ligand_a: lig_290 + ligand_b: lig_54 + atom mapping: {0: 19, 1: 18, 2: 16, 3: 17, 4: 14, 5: 15, 6: 13, 7: 12, 34: 22, + 35: 23, 36: 20, 37: 21} + score: '0.359' + edge_lig_163_lig_54: + ligand_a: lig_163 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.367' + edge_lig_42_lig_224: + ligand_a: lig_42 + ligand_b: lig_224 + atom mapping: {27: 24, 28: 26, 29: 25, 30: 27, 32: 29, 33: 30} + score: '0.145' + edge_lig_215_lig_54: + ligand_a: lig_215 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.364' + edge_lig_61_lig_43: + ligand_a: lig_61 + ligand_b: lig_43 + atom mapping: {7: 9, 8: 10, 9: 20, 10: 21, 11: 17, 12: 18, 13: 15, 14: 16, 15: 13, + 17: 11, 18: 12} + score: '0.360' + edge_lig_41_lig_224: + ligand_a: lig_41 + ligand_b: lig_224 + atom mapping: {26: 24, 27: 25, 28: 26, 29: 27, 31: 29, 32: 30} + score: '0.147' + edge_lig_43_lig_224: + ligand_a: lig_43 + ligand_b: lig_224 + atom mapping: {27: 24, 28: 25, 29: 26, 30: 27, 32: 29, 33: 30} + score: '0.145' + edge_lig_251_lig_43: + ligand_a: lig_251 + ligand_b: lig_43 + atom mapping: {7: 9, 8: 10, 9: 11, 10: 12, 11: 13, 13: 15, 14: 16, 15: 17, 16: 18, + 17: 20, 18: 21} + score: '0.355' + edge_lig_234_lig_54: + ligand_a: lig_234 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.367' + edge_lig_235_lig_54: + ligand_a: lig_235 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 18, 13: 19, 14: 16, 15: 17, + 17: 14, 18: 15} + score: '0.338' + edge_lig_15_lig_54: + ligand_a: lig_15 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.361' + edge_lig_155_lig_54: + ligand_a: lig_155 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.367' + edge_lig_289_lig_54: + ligand_a: lig_289 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.367' + edge_lig_254_lig_54: + ligand_a: lig_254 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 14, 10: 15, 11: 16, 12: 17, 13: 18, 14: 19, 15: 20, + 16: 21, 18: 22, 19: 23} + score: '0.364' + edge_lig_252_lig_54: + ligand_a: lig_252 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 14, 10: 15, 11: 16, 12: 17, 13: 18, 14: 19, 15: 20, + 16: 21, 18: 22, 19: 23} + score: '0.367' + edge_lig_167_lig_54: + ligand_a: lig_167 + ligand_b: lig_54 + atom mapping: {7: 12, 8: 13, 9: 22, 10: 23, 11: 20, 12: 21, 13: 18, 14: 19, 15: 16, + 16: 17, 18: 14, 19: 15} + score: '0.364' + edge_lig_256_lig_43: + ligand_a: lig_256 + ligand_b: lig_43 + atom mapping: {7: 9, 8: 10, 9: 11, 10: 12, 11: 13, 13: 15, 14: 16, 15: 17, 16: 18, + 17: 20, 18: 21} + score: '0.357' + edge_lig_23_lig_43: + ligand_a: lig_23 + ligand_b: lig_43 + atom mapping: {7: 9, 8: 10, 9: 20, 10: 21, 11: 17, 12: 18, 13: 15, 14: 16, 15: 13, + 17: 11, 18: 12} + score: '0.355' + edge_lig_25_lig_43: + ligand_a: lig_25 + ligand_b: lig_43 + atom mapping: {7: 9, 8: 10, 9: 11, 10: 12, 11: 13, 13: 15, 14: 16, 15: 17, 16: 20, + 17: 21} + score: '0.331' diff --git a/data/mcl1/03_edges/01_perses_openfe.yml b/data/mcl1/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..403c2050f --- /dev/null +++ b/data/mcl1/03_edges/01_perses_openfe.yml @@ -0,0 +1,172 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.5 minimal_spanning_graph +edges: + edge_lig_47_lig_34: + ligand_a: lig_47 + ligand_b: lig_34 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 23, 23: 22, 24: 24, 41: 39, 42: 40} + score: '0.583' + edge_lig_47_lig_52: + ligand_a: lig_47 + ligand_b: lig_52 + atom mapping: {0: 40, 1: 2, 2: 3, 3: 4, 4: 5, 5: 6, 6: 1, 7: 0, 8: 7, 9: 8, 10: 9, + 11: 10, 12: 11, 13: 12, 14: 13, 15: 14, 16: 16, 17: 15, 18: 17, 19: 18, 20: 19, + 21: 20, 22: 22, 23: 21, 24: 23, 41: 38} + score: '0.570' + edge_lig_47_lig_27: + ligand_a: lig_47 + ligand_b: lig_27 + atom mapping: {0: 30, 1: 25, 2: 26, 3: 27, 4: 22, 5: 23, 6: 24, 7: 31, 8: 19, + 9: 20, 10: 21, 11: 32, 12: 33, 13: 34, 14: 35, 15: 16, 16: 18, 17: 17, 18: 13, + 19: 14, 20: 15, 21: 10, 22: 12, 23: 11, 24: 9, 41: 28, 42: 29} + score: '0.608' + edge_lig_47_lig_61: + ligand_a: lig_47 + ligand_b: lig_61 + atom mapping: {0: 7, 1: 6, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 8: 9, 9: 10, 10: 11, + 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, 21: 21, + 22: 23, 23: 22, 24: 24, 41: 42, 42: 0} + score: '0.542' + edge_lig_43_lig_56: + ligand_a: lig_43 + ligand_b: lig_56 + atom mapping: {14: 27, 15: 24, 16: 25, 17: 26, 18: 21, 19: 23, 20: 22, 21: 18, + 22: 20, 23: 19, 24: 8, 25: 9, 26: 10, 27: 4, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, + 33: 45, 34: 46, 35: 0, 36: 7, 38: 15, 39: 16, 40: 17} + score: '0.548' + edge_lig_47_lig_63: + ligand_a: lig_47 + ligand_b: lig_63 + atom mapping: {0: 42, 1: 2, 2: 3, 3: 4, 4: 5, 5: 6, 6: 1, 7: 0, 8: 7, 9: 8, 10: 9, + 12: 10, 13: 11, 14: 12, 15: 13, 16: 15, 17: 14, 18: 16, 19: 17, 20: 18, 21: 19, + 22: 21, 23: 20, 24: 22, 41: 40} + score: '0.542' + edge_lig_43_lig_36: + ligand_a: lig_43 + ligand_b: lig_36 + atom mapping: {14: 24, 15: 21, 16: 22, 17: 23, 18: 18, 19: 20, 20: 19, 21: 15, + 22: 17, 23: 16, 24: 8, 25: 9, 26: 10, 27: 4, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, + 33: 42, 34: 43, 35: 0, 36: 7, 37: 11, 38: 12, 39: 13, 40: 14} + score: '0.561' + edge_lig_46_lig_58: + ligand_a: lig_46 + ligand_b: lig_58 + atom mapping: {0: 46, 1: 2, 2: 3, 3: 4, 4: 5, 5: 6, 6: 1, 7: 0, 8: 7, 9: 8, 10: 9, + 12: 14, 13: 15, 14: 16, 15: 17, 16: 19, 17: 18, 18: 20, 19: 21, 20: 22, 21: 23, + 22: 25, 23: 24, 24: 26, 43: 44} + score: '0.550' + edge_lig_47_lig_30: + ligand_a: lig_47 + ligand_b: lig_30 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 23, 23: 22, 24: 24, 41: 39, 42: 40} + score: '0.583' + edge_lig_43_lig_37: + ligand_a: lig_43 + ligand_b: lig_37 + atom mapping: {14: 24, 15: 21, 16: 22, 17: 23, 18: 18, 19: 20, 20: 19, 21: 15, + 22: 17, 23: 16, 24: 8, 25: 9, 26: 10, 27: 4, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, + 33: 42, 34: 43, 35: 0, 36: 7, 37: 11, 38: 12, 39: 13, 40: 14} + score: '0.561' + edge_lig_43_lig_50: + ligand_a: lig_43 + ligand_b: lig_50 + atom mapping: {14: 25, 15: 22, 16: 23, 17: 24, 18: 19, 19: 21, 20: 20, 21: 16, + 22: 18, 23: 17, 24: 9, 25: 10, 26: 11, 27: 3, 28: 4, 29: 5, 30: 6, 31: 1, 32: 2, + 33: 43, 34: 0, 35: 7, 37: 12, 38: 13, 39: 14, 40: 15} + score: '0.548' + edge_lig_47_lig_31: + ligand_a: lig_47 + ligand_b: lig_31 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 23, 23: 22, 24: 24, 41: 39, 42: 40} + score: '0.583' + edge_lig_43_lig_53: + ligand_a: lig_43 + ligand_b: lig_53 + atom mapping: {14: 23, 15: 20, 16: 21, 17: 22, 18: 17, 19: 19, 20: 18, 21: 14, + 22: 16, 23: 15, 24: 7, 25: 8, 26: 9, 27: 5, 28: 6, 29: 1, 30: 2, 31: 3, 32: 4, + 33: 41, 35: 43, 36: 0, 37: 10, 38: 11, 39: 12, 40: 13} + score: '0.548' + edge_lig_47_lig_67: + ligand_a: lig_47 + ligand_b: lig_67 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 12: 11, 13: 12, 14: 13, 15: 14, 16: 16, 17: 15, 18: 17, 19: 18, 20: 19, 21: 20, + 22: 22, 23: 21, 24: 23, 41: 41, 42: 42} + score: '0.555' + edge_lig_47_lig_33: + ligand_a: lig_47 + ligand_b: lig_33 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 23, 23: 22, 24: 24, 41: 36, 42: 37} + score: '0.608' + edge_lig_43_lig_58: + ligand_a: lig_43 + ligand_b: lig_58 + atom mapping: {14: 26, 15: 23, 16: 24, 17: 25, 18: 20, 19: 22, 20: 21, 21: 17, + 22: 19, 23: 18, 24: 7, 25: 8, 26: 9, 27: 5, 28: 6, 29: 1, 30: 2, 31: 3, 32: 4, + 33: 44, 35: 46, 36: 0, 38: 14, 39: 15, 40: 16} + score: '0.531' + edge_lig_58_lig_48: + ligand_a: lig_58 + ligand_b: lig_48 + atom mapping: {0: 7, 1: 6, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 7: 8, 8: 9, 9: 10, 14: 12, + 15: 13, 16: 14, 17: 15, 18: 17, 19: 16, 20: 18, 21: 20, 22: 19, 23: 21, 24: 23, + 25: 22, 26: 24, 44: 40, 46: 0} + score: '0.573' + edge_lig_47_lig_35: + ligand_a: lig_47 + ligand_b: lig_35 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 23, 23: 22, 24: 24, 41: 39, 42: 40} + score: '0.583' + edge_lig_47_lig_58: + ligand_a: lig_47 + ligand_b: lig_58 + atom mapping: {0: 46, 1: 2, 2: 3, 3: 4, 4: 5, 5: 6, 6: 1, 7: 0, 8: 7, 9: 8, 10: 9, + 12: 14, 13: 15, 14: 16, 15: 17, 16: 19, 17: 18, 18: 20, 19: 21, 20: 22, 21: 23, + 22: 25, 23: 24, 24: 26, 41: 44} + score: '0.538' + edge_lig_47_lig_49: + ligand_a: lig_47 + ligand_b: lig_49 + atom mapping: {0: 7, 1: 6, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 8: 9, 9: 10, 10: 11, + 11: 12, 12: 13, 13: 14, 14: 15, 15: 16, 16: 18, 17: 17, 18: 19, 19: 20, 20: 21, + 21: 22, 22: 24, 23: 23, 24: 25, 41: 40, 42: 0} + score: '0.570' + edge_lig_47_lig_28: + ligand_a: lig_47 + ligand_b: lig_28 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 23, 23: 22, 24: 24, 41: 39, 42: 40} + score: '0.583' + edge_lig_47_lig_65: + ligand_a: lig_47 + ligand_b: lig_65 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 42, 8: 11, 9: 10, + 10: 9, 12: 39, 13: 40, 14: 41, 15: 12, 16: 14, 17: 13, 18: 15, 19: 16, 20: 17, + 21: 18, 22: 20, 23: 19, 24: 21, 42: 7} + score: '0.542' + edge_lig_47_lig_32: + ligand_a: lig_47 + ligand_b: lig_32 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 17, 17: 16, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 23, 23: 22, 24: 24, 41: 39, 42: 40} + score: '0.583' + edge_lig_47_lig_60: + ligand_a: lig_47 + ligand_b: lig_60 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 12: 11, 13: 12, 14: 13, 15: 14, 16: 16, 17: 15, 18: 17, 19: 18, 20: 19, 21: 20, + 22: 22, 23: 21, 24: 23, 41: 41, 42: 42} + score: '0.555' diff --git a/data/p38/03_edges/01_perses_openfe.yml b/data/p38/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..5698988bd --- /dev/null +++ b/data/p38/03_edges/01_perses_openfe.yml @@ -0,0 +1,201 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.5 minimal_spanning_graph +edges: + edge_lig_p38a_3flw_lig_p38a_2m: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2m + atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, 19: 41, + 24: 39, 25: 40, 26: 26, 27: 27, 28: 28, 29: 37, 31: 35, 32: 36, 33: 33, 34: 34, + 35: 31, 36: 32, 37: 29, 39: 24, 40: 25} + score: '0.598' + edge_lig_p38a_2y_lig_p38a_2m: + ligand_a: lig_p38a_2y + ligand_b: lig_p38a_2m + atom mapping: {14: 4, 15: 5, 16: 3, 17: 21, 18: 22, 19: 23, 20: 1, 21: 0, 22: 2, + 23: 24, 24: 25, 25: 26, 26: 27, 27: 28, 28: 37, 30: 35, 31: 36, 32: 33, 33: 34, + 34: 31, 35: 32, 36: 29, 38: 39, 39: 40, 40: 41} + score: '0.641' + edge_lig_p38a_2s_lig_p38a_3flw: + ligand_a: lig_p38a_2s + ligand_b: lig_p38a_3flw + atom mapping: {9: 20, 10: 23, 11: 22, 12: 19, 13: 24, 14: 25, 15: 26, 16: 27, + 17: 28, 18: 29, 20: 31, 21: 32, 22: 33, 23: 34, 24: 35, 25: 36, 26: 37, 28: 39, + 29: 40, 30: 16, 31: 17, 32: 18, 33: 12, 34: 10, 51: 13, 52: 14, 53: 15} + score: '0.641' + edge_lig_p38a_3flw_lig_p38a_2o: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2o + atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, 19: 41, + 20: 42, 22: 44, 23: 43, 24: 39, 25: 40, 26: 26, 27: 27, 28: 28, 29: 37, 31: 35, + 32: 36, 33: 33, 34: 34, 35: 31, 36: 32, 37: 29, 39: 24, 40: 25} + score: '0.638' + edge_lig_p38a_3fmh_lig_p38a_2f: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_2f + atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, + 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, + 30: 35, 32: 33, 34: 31, 35: 32, 36: 29, 37: 30, 38: 24, 39: 25} + score: '0.668' + edge_lig_p38a_3flw_lig_p38a_2i: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2i + atom mapping: {10: 4, 11: 5, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, + 19: 43, 20: 44, 21: 45, 22: 46, 23: 47, 24: 41, 25: 42, 26: 26, 27: 27, 28: 30, + 29: 31, 31: 33, 32: 34, 33: 35, 35: 37, 36: 38, 37: 39, 39: 24, 40: 25} + score: '0.667' + edge_lig_p38a_3fly_lig_p38a_2m: + ligand_a: lig_p38a_3fly + ligand_b: lig_p38a_2m + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 16: 21, 17: 22, 18: 23, 19: 24, 20: 25, + 21: 26, 22: 27, 23: 28, 24: 37, 26: 35, 27: 36, 28: 33, 29: 34, 30: 31, 31: 32, + 32: 29, 34: 39, 35: 40, 36: 41} + score: '0.661' + edge_lig_p38a_3fmh_lig_p38a_2m: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_2m + atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, + 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, 30: 35, 31: 36, 32: 33, 33: 34, + 34: 31, 35: 32, 36: 29, 38: 24, 39: 25} + score: '0.620' + edge_lig_p38a_3fmh_lig_p38a_2e: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_2e + atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, + 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, + 30: 35, 31: 36, 32: 33, 33: 34, 34: 31, 35: 32, 36: 29, 37: 30, 38: 24, 39: 25} + score: '0.699' + edge_lig_p38a_3fmh_lig_p38a_2h: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_2h + atom mapping: {9: 4, 10: 5, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, + 18: 41, 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, + 28: 29, 30: 31, 31: 32, 32: 33, 34: 35, 35: 36, 36: 37, 38: 24, 39: 25} + score: '0.680' + edge_lig_p38a_2x_lig_p38a_2m: + ligand_a: lig_p38a_2x + ligand_b: lig_p38a_2m + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 18: 21, 19: 22, 20: 23, 21: 24, + 22: 25, 23: 26, 24: 27, 25: 28, 26: 37, 28: 35, 29: 36, 30: 33, 31: 34, 32: 31, + 33: 32, 34: 29, 36: 39, 37: 40, 38: 41} + score: '0.657' + edge_lig_p38a_3flw_lig_p38a_2ee: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2ee + atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 29, 17: 28, 18: 27, 19: 47, + 20: 48, 21: 51, 22: 50, 23: 49, 24: 45, 25: 46, 26: 32, 27: 33, 28: 34, 29: 43, + 31: 41, 32: 42, 33: 39, 34: 40, 35: 37, 36: 38, 37: 35, 39: 30, 40: 31} + score: '0.657' + edge_lig_p38a_2bb_lig_p38a_2m: + ligand_a: lig_p38a_2bb + ligand_b: lig_p38a_2m + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 19: 21, 20: 22, 21: 23, 22: 24, 23: 25, + 24: 26, 25: 27, 26: 28, 27: 37, 29: 35, 30: 36, 31: 33, 32: 34, 33: 31, 34: 32, + 35: 29, 37: 39, 38: 40, 39: 41} + score: '0.636' + edge_lig_p38a_3fmh_lig_p38a_3fln: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_3fln + atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, + 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, + 30: 35, 31: 36, 32: 33, 33: 34, 34: 31, 35: 32, 36: 29, 38: 24, 39: 25} + score: '0.686' + edge_lig_p38a_3flw_lig_p38a_2l: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2l + atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, 19: 41, + 20: 42, 22: 44, 23: 43, 24: 39, 25: 40, 26: 26, 27: 27, 28: 28, 29: 37, 31: 35, + 32: 36, 33: 33, 34: 34, 35: 31, 36: 32, 37: 29, 39: 24, 40: 25} + score: '0.653' + edge_lig_p38a_3fmh_lig_p38a_2g: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_2g + atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, + 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, + 30: 35, 31: 36, 32: 33, 34: 31, 35: 32, 36: 29, 38: 24, 39: 25} + score: '0.668' + edge_lig_p38a_2z_lig_p38a_2m: + ligand_a: lig_p38a_2z + ligand_b: lig_p38a_2m + atom mapping: {6: 4, 7: 5, 8: 3, 9: 21, 10: 22, 11: 23, 12: 1, 13: 0, 14: 2, 15: 24, + 16: 25, 17: 26, 18: 27, 19: 28, 20: 37, 22: 35, 23: 36, 24: 33, 25: 34, 26: 31, + 27: 32, 28: 29, 30: 39, 31: 40, 32: 41} + score: '0.641' + edge_lig_p38a_3flw_lig_p38a_2gg: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2gg + atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 25, 17: 24, 18: 23, 19: 43, + 20: 44, 21: 47, 22: 46, 23: 45, 24: 41, 25: 42, 26: 28, 27: 29, 28: 30, 29: 39, + 31: 37, 32: 38, 33: 35, 34: 36, 35: 33, 36: 34, 37: 31, 39: 26, 40: 27} + score: '0.670' + edge_lig_p38a_3flw_lig_p38a_2j: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2j + atom mapping: {10: 4, 11: 5, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, + 19: 43, 20: 44, 21: 45, 22: 46, 23: 47, 24: 41, 25: 42, 26: 26, 27: 27, 28: 30, + 29: 31, 31: 33, 32: 34, 33: 35, 34: 36, 35: 37, 36: 38, 37: 39, 39: 24, 40: 25} + score: '0.686' + edge_lig_p38a_3fmh_lig_p38a_2k: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_2k + atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, + 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, 30: 35, 31: 36, 32: 33, 33: 34, + 34: 31, 35: 32, 36: 29, 38: 24, 39: 25} + score: '0.654' + edge_lig_p38a_3flw_lig_p38a_2ff: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2ff + atom mapping: {10: 12, 12: 14, 13: 20, 14: 18, 15: 19, 16: 17, 17: 16, 18: 15, + 19: 38, 20: 39, 21: 42, 22: 41, 23: 40, 24: 36, 25: 37, 26: 23, 27: 24, 28: 25, + 29: 34, 31: 32, 32: 33, 33: 30, 34: 31, 35: 28, 36: 29, 37: 26, 39: 21, 40: 22} + score: '0.665' + edge_lig_p38a_3fmh_lig_p38a_3flz: + ligand_a: lig_p38a_3fmh + ligand_b: lig_p38a_3flz + atom mapping: {9: 4, 11: 3, 12: 2, 13: 1, 14: 0, 15: 23, 16: 22, 17: 21, 18: 41, + 19: 42, 20: 43, 21: 44, 22: 45, 23: 39, 24: 40, 25: 26, 26: 27, 27: 28, 28: 37, + 30: 35, 31: 36, 32: 33, 34: 31, 35: 32, 36: 29, 37: 30, 38: 24, 39: 25} + score: '0.680' + edge_lig_p38a_3flw_lig_p38a_2n: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2n + atom mapping: {10: 33, 11: 34, 12: 32, 13: 50, 14: 51, 15: 52, 16: 29, 17: 30, + 18: 31, 19: 11, 20: 8, 22: 9, 23: 10, 24: 12, 25: 13, 26: 14, 27: 15, 28: 16, + 29: 17, 31: 19, 32: 20, 33: 21, 34: 22, 35: 23, 36: 24, 37: 25, 39: 27, 40: 28} + score: '0.657' + edge_lig_p38a_3flw_lig_p38a_2p: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2p + atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, 19: 41, + 20: 42, 22: 44, 23: 43, 24: 39, 25: 40, 26: 26, 27: 27, 28: 28, 29: 37, 31: 35, + 32: 36, 33: 33, 34: 34, 35: 31, 36: 32, 37: 29, 39: 24, 40: 25} + score: '0.634' + edge_lig_p38a_3flw_lig_p38a_2t: + ligand_a: lig_p38a_3flw + ligand_b: lig_p38a_2t + atom mapping: {10: 4, 12: 3, 13: 2, 14: 1, 15: 0, 16: 23, 17: 22, 18: 21, 19: 41, + 20: 42, 22: 44, 23: 43, 24: 39, 25: 40, 26: 26, 27: 27, 28: 28, 29: 37, 31: 35, + 32: 36, 33: 33, 34: 34, 35: 31, 36: 32, 37: 29, 39: 24, 40: 25} + score: '0.665' + edge_lig_p38a_2aa_lig_p38a_2m: + ligand_a: lig_p38a_2aa + ligand_b: lig_p38a_2m + atom mapping: {7: 4, 9: 3, 10: 21, 11: 22, 12: 23, 13: 1, 14: 0, 15: 2, 16: 24, + 17: 25, 18: 26, 19: 27, 20: 28, 21: 37, 23: 35, 24: 36, 25: 33, 26: 34, 27: 31, + 28: 32, 29: 29, 31: 39, 32: 40, 33: 41} + score: '0.644' + edge_lig_p38a_2m_lig_p38a_2v: + ligand_a: lig_p38a_2m + ligand_b: lig_p38a_2v + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 21: 10, 22: 11, 23: 12, 24: 13, 25: 14, + 26: 15, 27: 16, 28: 17, 29: 26, 31: 24, 32: 25, 33: 22, 34: 23, 35: 20, 36: 21, + 37: 18, 39: 28, 40: 29, 41: 30} + score: '0.718' + edge_lig_p38a_2r_lig_p38a_3flw: + ligand_a: lig_p38a_2r + ligand_b: lig_p38a_3flw + atom mapping: {11: 20, 12: 23, 13: 22, 14: 19, 15: 24, 16: 25, 17: 26, 18: 27, + 19: 28, 20: 29, 21: 30, 22: 31, 23: 32, 24: 33, 25: 34, 26: 35, 27: 36, 28: 37, + 29: 38, 30: 39, 31: 40, 32: 16, 33: 17, 34: 18, 35: 12, 36: 10, 53: 13, 54: 14, + 55: 15} + score: '0.671' diff --git a/data/pde2/03_edges/01_perses_openfe.yml b/data/pde2/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..2a87e6097 --- /dev/null +++ b/data/pde2/03_edges/01_perses_openfe.yml @@ -0,0 +1,184 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.5 minimal_spanning_graph +edges: + edge_lig_49582390_lig_49585367: + ligand_a: lig_49582390 + ligand_b: lig_49585367 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 32, 33: 33, + 34: 34, 35: 35, 36: 36, 37: 37, 38: 39, 39: 38, 40: 40, 41: 41, 42: 43, 43: 42, + 44: 44, 45: 45, 46: 47, 47: 46, 48: 48, 49: 49, 50: 50, 52: 52} + score: '0.877' + edge_lig_49175789_lig_49582390: + ligand_a: lig_49175789 + ligand_b: lig_49582390 + atom mapping: {3: 28, 4: 27, 5: 23, 6: 24, 7: 25, 8: 26, 9: 21, 10: 22, 11: 5, + 12: 4, 13: 3, 14: 2, 15: 6, 16: 7, 17: 8, 18: 9, 19: 10, 20: 11, 21: 12, 22: 13, + 23: 1, 24: 0, 25: 14, 26: 15, 27: 20, 28: 19, 29: 18, 30: 17, 31: 16, 40: 52, + 42: 49, 44: 48, 45: 35, 46: 36, 47: 37, 48: 32, 49: 33, 50: 34, 51: 39, 52: 38, + 53: 46, 54: 47, 55: 44, 56: 45, 57: 42, 58: 43, 59: 40, 60: 41} + score: '0.861' + edge_lig_49582390_lig_49582468: + ligand_a: lig_49582390 + ligand_b: lig_49582468 + atom mapping: {0: 23, 1: 22, 2: 13, 3: 12, 4: 11, 5: 10, 6: 14, 7: 15, 8: 16, + 9: 17, 10: 18, 11: 19, 12: 20, 13: 21, 14: 24, 15: 25, 16: 26, 17: 27, 18: 28, + 19: 29, 20: 30, 21: 6, 22: 5, 23: 4, 24: 9, 25: 8, 26: 7, 27: 3, 28: 2, 32: 46, + 33: 45, 34: 44, 35: 41, 36: 42, 37: 43, 38: 47, 39: 48, 40: 49, 41: 50, 42: 52, + 43: 51, 44: 53, 45: 54, 46: 56, 47: 55, 48: 38, 49: 40, 50: 39} + score: '0.875' + edge_lig_49582390_lig_49072088: + ligand_a: lig_49582390 + ligand_b: lig_49072088 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 31, 33: 32, + 34: 33, 35: 34, 36: 35, 37: 36, 38: 38, 39: 37, 40: 39, 41: 40, 42: 42, 43: 41, + 44: 43, 45: 44, 46: 46, 47: 45, 48: 47, 49: 48, 50: 49} + score: '0.875' + edge_lig_50181001_lig_43249674: + ligand_a: lig_50181001 + ligand_b: lig_43249674 + atom mapping: {5: 25, 6: 26, 7: 21, 8: 22, 9: 23, 10: 24, 12: 5, 13: 4, 14: 3, + 15: 2, 16: 6, 17: 7, 18: 8, 19: 9, 20: 10, 21: 11, 22: 12, 23: 13, 24: 1, 25: 0, + 26: 14, 27: 15, 28: 20, 29: 19, 30: 18, 31: 17, 32: 16, 43: 44, 44: 31, 45: 32, + 46: 33, 47: 28, 48: 29, 49: 30, 50: 34, 51: 35, 52: 43, 53: 42, 54: 41, 55: 40, + 56: 38, 57: 39, 58: 36, 59: 37} + score: '0.917' + edge_lig_49582390_lig_50107616: + ligand_a: lig_49582390 + ligand_b: lig_50107616 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 32, 33: 33, + 34: 34, 35: 35, 36: 36, 37: 37, 38: 39, 39: 38, 40: 40, 41: 41, 42: 43, 43: 42, + 44: 44, 45: 45, 46: 47, 47: 46, 48: 48, 49: 49, 50: 50, 52: 53} + score: '0.877' + edge_lig_49582390_lig_49580115: + ligand_a: lig_49582390 + ligand_b: lig_49580115 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 31, 33: 32, + 34: 33, 35: 34, 36: 35, 37: 36, 38: 38, 39: 37, 40: 39, 41: 40, 42: 42, 43: 41, + 44: 43, 45: 44, 46: 46, 47: 45, 48: 47, 49: 48, 50: 49, 52: 50} + score: '0.915' + edge_lig_49582390_lig_49175828: + ligand_a: lig_49582390 + ligand_b: lig_49175828 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 28, 28: 29, 32: 32, 33: 33, + 34: 34, 35: 35, 36: 36, 37: 37, 38: 39, 39: 38, 40: 40, 41: 41, 42: 43, 43: 42, + 44: 44, 45: 45, 46: 47, 47: 46, 48: 48, 49: 49} + score: '0.855' + edge_lig_49582390_lig_49932129: + ligand_a: lig_49582390 + ligand_b: lig_49932129 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 31, 33: 32, + 34: 33, 35: 34, 36: 35, 37: 36, 38: 38, 39: 37, 40: 39, 41: 40, 42: 42, 43: 41, + 44: 43, 45: 44, 46: 46, 47: 45, 48: 47, 49: 48, 50: 49, 52: 53} + score: '0.886' + edge_lig_48168913_lig_49137374: + ligand_a: lig_48168913 + ligand_b: lig_49137374 + atom mapping: {1: 22, 2: 21, 3: 26, 4: 25, 5: 24, 6: 23, 7: 5, 8: 4, 9: 3, 10: 2, + 11: 6, 12: 7, 13: 8, 14: 9, 15: 10, 16: 11, 17: 12, 18: 13, 19: 1, 20: 0, 21: 14, + 22: 15, 23: 16, 24: 17, 25: 18, 26: 19, 27: 20, 32: 48, 33: 47, 34: 33, 35: 34, + 36: 35, 37: 30, 38: 31, 39: 32, 40: 37, 41: 36, 42: 38, 43: 39, 44: 40, 45: 41, + 46: 43, 47: 42, 48: 45, 49: 44} + score: '0.923' + edge_lig_49582390_lig_48009208: + ligand_a: lig_49582390 + ligand_b: lig_48009208 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 26, 23: 25, 24: 24, 25: 23, 26: 22, 32: 29, 33: 30, 34: 31, 35: 32, + 36: 33, 37: 34, 38: 36, 39: 35, 40: 37, 41: 38, 42: 40, 43: 39, 44: 41, 45: 42, + 46: 44, 47: 43, 50: 45} + score: '0.909' + edge_lig_48168913_lig_50181001: + ligand_a: lig_48168913 + ligand_b: lig_50181001 + atom mapping: {1: 8, 2: 7, 3: 6, 4: 5, 5: 10, 6: 9, 7: 12, 8: 13, 9: 14, 10: 15, + 11: 16, 12: 17, 13: 18, 14: 19, 15: 20, 16: 21, 17: 22, 18: 23, 19: 24, 20: 25, + 21: 26, 22: 27, 23: 28, 24: 29, 25: 30, 26: 31, 27: 32, 31: 42, 34: 44, 35: 45, + 36: 46, 37: 47, 38: 48, 39: 49, 40: 51, 41: 50, 42: 52, 43: 53, 44: 54, 45: 55, + 46: 57, 47: 56, 48: 59, 49: 58} + score: '0.895' + edge_lig_50181001_lig_48022468: + ligand_a: lig_50181001 + ligand_b: lig_48022468 + atom mapping: {5: 25, 6: 26, 7: 21, 8: 22, 9: 23, 10: 24, 12: 5, 13: 4, 14: 3, + 15: 2, 16: 6, 17: 7, 18: 8, 19: 9, 20: 10, 21: 11, 22: 12, 23: 13, 24: 1, 25: 0, + 26: 14, 27: 15, 28: 20, 29: 19, 30: 18, 31: 17, 32: 16, 44: 32, 45: 33, 46: 34, + 47: 29, 48: 30, 49: 31, 50: 35, 51: 36, 52: 44, 53: 43, 54: 42, 55: 41, 56: 39, + 57: 40, 58: 37, 59: 38} + score: '0.905' + edge_lig_49220392_lig_49582390: + ligand_a: lig_49220392 + ligand_b: lig_49582390 + atom mapping: {1: 28, 2: 27, 3: 23, 4: 24, 5: 25, 6: 26, 7: 21, 8: 22, 9: 5, 10: 4, + 11: 3, 12: 2, 13: 6, 14: 7, 15: 8, 16: 9, 17: 10, 18: 11, 19: 12, 20: 13, 21: 1, + 22: 0, 23: 14, 24: 15, 25: 16, 26: 17, 27: 18, 28: 19, 29: 20, 34: 52, 36: 49, + 38: 48, 39: 35, 40: 36, 41: 37, 42: 34, 43: 33, 44: 32, 45: 38, 46: 39, 47: 41, + 48: 40, 49: 43, 50: 42, 51: 45, 52: 44, 53: 47, 54: 46} + score: '0.894' + edge_lig_49220548_lig_49582390: + ligand_a: lig_49220548 + ligand_b: lig_49582390 + atom mapping: {2: 28, 3: 27, 4: 23, 5: 24, 6: 25, 7: 26, 8: 21, 9: 22, 10: 5, + 11: 4, 12: 3, 13: 2, 14: 6, 15: 7, 16: 8, 17: 9, 18: 10, 19: 11, 20: 12, 21: 13, + 22: 1, 23: 0, 24: 14, 25: 15, 26: 20, 27: 19, 28: 18, 29: 17, 30: 16, 37: 52, + 39: 49, 41: 48, 42: 35, 43: 36, 44: 37, 45: 32, 46: 33, 47: 34, 48: 39, 49: 38, + 50: 47, 51: 46, 52: 45, 53: 44, 54: 42, 55: 43, 56: 40, 57: 41} + score: '0.866' + edge_lig_48168913_lig_48271249: + ligand_a: lig_48168913 + ligand_b: lig_48271249 + atom mapping: {1: 26, 2: 21, 3: 22, 4: 23, 5: 24, 6: 25, 7: 5, 8: 4, 9: 3, 10: 2, + 11: 6, 12: 7, 13: 8, 14: 9, 15: 10, 16: 11, 17: 12, 18: 13, 19: 1, 20: 0, 21: 14, + 22: 15, 23: 16, 24: 17, 25: 18, 26: 19, 27: 20, 31: 45, 33: 46, 34: 32, 35: 33, + 36: 34, 37: 29, 38: 30, 39: 31, 40: 36, 41: 35, 42: 37, 43: 38, 44: 39, 45: 40, + 46: 42, 47: 41, 48: 44, 49: 43} + score: '0.929' + edge_lig_49582390_lig_49932714: + ligand_a: lig_49582390 + ligand_b: lig_49932714 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 24: 24, 25: 25, 26: 26, 27: 27, 28: 28, 32: 32, 33: 33, + 34: 34, 35: 35, 36: 36, 37: 37, 38: 39, 39: 38, 40: 40, 41: 41, 42: 43, 43: 42, + 44: 44, 45: 45, 46: 47, 47: 46, 48: 48, 49: 49, 50: 50, 52: 52} + score: '0.886' + edge_lig_49582390_lig_49137530: + ligand_a: lig_49582390 + ligand_b: lig_49137530 + atom mapping: {0: 24, 1: 23, 2: 14, 3: 13, 4: 12, 5: 11, 6: 15, 7: 16, 8: 17, + 9: 18, 10: 19, 11: 20, 12: 21, 13: 22, 14: 25, 15: 26, 16: 27, 17: 28, 18: 29, + 19: 30, 20: 31, 21: 7, 22: 6, 23: 5, 24: 10, 25: 9, 26: 8, 27: 4, 28: 3, 32: 47, + 33: 48, 34: 49, 35: 44, 36: 45, 37: 46, 38: 51, 39: 50, 40: 52, 41: 53, 42: 55, + 43: 54, 44: 56, 45: 57, 46: 59, 47: 58, 48: 41, 49: 43, 50: 42, 52: 39} + score: '0.877' + edge_lig_49582390_lig_49396360: + ligand_a: lig_49582390 + ligand_b: lig_49396360 + atom mapping: {0: 23, 1: 22, 2: 13, 3: 12, 4: 11, 5: 10, 6: 14, 7: 15, 8: 16, + 9: 17, 10: 18, 11: 19, 12: 20, 13: 21, 14: 24, 15: 25, 16: 26, 17: 27, 18: 28, + 19: 29, 20: 30, 21: 6, 22: 5, 23: 4, 24: 9, 25: 8, 26: 7, 27: 3, 28: 2, 32: 44, + 33: 45, 34: 46, 35: 41, 36: 42, 37: 43, 38: 48, 39: 47, 40: 49, 41: 50, 42: 52, + 43: 51, 44: 53, 45: 54, 46: 56, 47: 55, 48: 38, 49: 40, 50: 39, 52: 36} + score: '0.886' + edge_lig_50181001_lig_49582390: + ligand_a: lig_50181001 + ligand_b: lig_49582390 + atom mapping: {3: 28, 4: 27, 5: 23, 6: 22, 7: 21, 8: 26, 9: 25, 10: 24, 12: 5, + 13: 4, 14: 3, 15: 2, 16: 6, 17: 7, 18: 8, 19: 9, 20: 10, 21: 11, 22: 12, 23: 13, + 24: 1, 25: 0, 26: 14, 27: 15, 28: 20, 29: 19, 30: 18, 31: 17, 32: 16, 40: 52, + 42: 48, 43: 50, 44: 35, 45: 36, 46: 37, 47: 34, 48: 33, 49: 32, 50: 38, 51: 39, + 52: 47, 53: 46, 54: 45, 55: 44, 56: 43, 57: 42, 58: 41, 59: 40} + score: '0.861' diff --git a/data/pfkfb3/03_edges/01_perses_openfe.yml b/data/pfkfb3/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..6cc3d2211 --- /dev/null +++ b/data/pfkfb3/03_edges/01_perses_openfe.yml @@ -0,0 +1,229 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.5 minimal_spanning_graph +edges: + edge_lig_24_lig_69: + ligand_a: lig_24 + ligand_b: lig_69 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 26, 28: 27, + 29: 28, 30: 29, 31: 30, 32: 31, 33: 32, 35: 40, 36: 41, 37: 42, 38: 43, 39: 44, + 41: 45, 44: 47, 45: 48} + score: '0.580' + edge_lig_24_lig_63: + ligand_a: lig_24 + ligand_b: lig_63 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 21, 28: 22, + 29: 23, 30: 24, 31: 25, 32: 26, 33: 27, 35: 35, 36: 36, 37: 37, 38: 38, 39: 39, + 41: 40, 44: 42, 45: 43} + score: '0.597' + edge_lig_24_lig_70: + ligand_a: lig_24 + ligand_b: lig_70 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 26, 28: 27, + 29: 28, 30: 29, 31: 30, 32: 31, 33: 32, 35: 40, 36: 41, 37: 42, 38: 43, 39: 44, + 41: 45, 44: 47, 45: 48} + score: '0.580' + edge_lig_26_lig_59: + ligand_a: lig_26 + ligand_b: lig_59 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 26, 28: 27, + 29: 28, 30: 29, 31: 30, 32: 31, 33: 39, 34: 40, 35: 41, 36: 43, 39: 37, 40: 38, + 41: 35, 42: 36, 43: 34, 45: 32, 46: 33, 47: 47, 48: 48} + score: '0.618' + edge_lig_35_lig_38: + ligand_a: lig_35 + ligand_b: lig_38 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 49, 5: 50, 6: 30, 7: 31, 8: 32, 9: 33, + 10: 41, 11: 42, 12: 44, 13: 43, 14: 45, 15: 46, 16: 47, 17: 48, 18: 39, 19: 40, + 20: 37, 21: 38, 22: 36, 23: 34, 24: 35, 25: 28, 26: 29, 27: 8, 46: 4, 47: 5, + 48: 6, 49: 7} + score: '0.663' + edge_lig_55_lig_38: + ligand_a: lig_55 + ligand_b: lig_38 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 49, 5: 50, 6: 30, 7: 31, 8: 32, 9: 33, + 10: 34, 11: 35, 12: 36, 13: 37, 14: 38, 15: 39, 16: 40, 17: 41, 18: 42, 19: 44, + 20: 43, 21: 45, 22: 48, 23: 47, 24: 46, 25: 28, 26: 29, 27: 8, 46: 4, 47: 5, + 48: 6, 49: 7} + score: '0.659' + edge_lig_24_lig_39: + ligand_a: lig_24 + ligand_b: lig_39 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 22, 28: 23, + 29: 24, 30: 25, 31: 26, 32: 27, 33: 35, 35: 33, 36: 34, 37: 31, 38: 32, 39: 30, + 41: 28, 44: 43, 45: 44} + score: '0.594' + edge_lig_24_lig_38: + ligand_a: lig_24 + ligand_b: lig_38 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 28, 28: 29, + 29: 30, 30: 31, 31: 32, 32: 33, 33: 41, 35: 39, 36: 40, 37: 37, 38: 38, 39: 36, + 41: 34, 44: 49, 45: 50} + score: '0.584' + edge_lig_24_lig_47: + ligand_a: lig_24 + ligand_b: lig_47 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 45, 5: 46, 6: 47, 7: 48, 8: 27, 27: 25, + 28: 26, 29: 6, 30: 7, 31: 8, 32: 9, 33: 17, 35: 15, 36: 16, 37: 13, 38: 14, + 39: 12, 41: 10, 44: 4, 45: 5} + score: '0.587' + edge_lig_58_lig_59: + ligand_a: lig_58 + ligand_b: lig_59 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 25: 26, 26: 27, + 27: 28, 28: 29, 29: 30, 30: 31, 31: 32, 32: 33, 33: 34, 34: 35, 35: 36, 36: 37, + 37: 38, 38: 39, 39: 40, 40: 42, 41: 41, 42: 43, 43: 44, 44: 45, 45: 46, 46: 47, + 47: 48} + score: '0.674' + edge_lig_24_lig_41: + ligand_a: lig_24 + ligand_b: lig_41 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, + 29: 26, 30: 27, 31: 28, 32: 29, 33: 37, 35: 35, 36: 36, 37: 33, 38: 34, 39: 32, + 41: 30, 44: 45, 45: 46} + score: '0.577' + edge_lig_24_lig_44: + ligand_a: lig_24 + ligand_b: lig_44 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 20, 28: 21, + 29: 22, 30: 23, 31: 24, 32: 25, 33: 33, 35: 31, 36: 32, 37: 29, 38: 30, 39: 28, + 41: 26, 44: 41, 45: 42} + score: '0.608' + edge_lig_24_lig_62: + ligand_a: lig_24 + ligand_b: lig_62 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 21, 28: 22, + 29: 23, 30: 24, 31: 25, 32: 26, 33: 27, 35: 35, 36: 36, 37: 37, 38: 38, 39: 39, + 41: 40, 44: 42, 45: 43} + score: '0.597' + edge_lig_33_lig_41: + ligand_a: lig_33 + ligand_b: lig_41 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 45, 5: 46, 6: 26, 7: 27, 8: 28, 9: 29, + 10: 37, 11: 38, 13: 35, 14: 36, 15: 33, 16: 34, 17: 32, 18: 30, 19: 31, 20: 24, + 21: 25, 22: 8, 41: 4, 42: 5, 43: 6, 44: 7} + score: '0.612' + edge_lig_57_lig_38: + ligand_a: lig_57 + ligand_b: lig_38 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 28, 28: 29, + 29: 30, 30: 31, 31: 32, 32: 33, 33: 34, 34: 35, 35: 36, 36: 37, 37: 38, 38: 39, + 39: 40, 40: 41, 41: 42, 42: 44, 43: 43, 44: 45, 45: 48, 46: 47, 47: 46, 48: 49, + 49: 50} + score: '0.656' + edge_lig_37_lig_38: + ligand_a: lig_37 + ligand_b: lig_38 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 28, 28: 29, + 29: 30, 30: 31, 31: 32, 32: 33, 33: 34, 34: 35, 35: 36, 36: 37, 37: 38, 38: 39, + 39: 40, 40: 41, 41: 42, 42: 43, 43: 45, 60: 49, 61: 50} + score: '0.578' + edge_lig_24_lig_49: + ligand_a: lig_24 + ligand_b: lig_49 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 22, 28: 23, + 29: 24, 30: 25, 31: 26, 32: 27, 33: 35, 35: 33, 36: 34, 37: 31, 38: 32, 39: 30, + 41: 28, 44: 43, 45: 44} + score: '0.594' + edge_lig_24_lig_43: + ligand_a: lig_24 + ligand_b: lig_43 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 20, 28: 21, + 29: 22, 30: 23, 31: 24, 32: 25, 33: 33, 35: 31, 36: 32, 37: 29, 38: 30, 39: 28, + 41: 26, 44: 41, 45: 42} + score: '0.608' + edge_lig_29_lig_38: + ligand_a: lig_29 + ligand_b: lig_38 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 49, 5: 50, 6: 30, 7: 31, 8: 32, 9: 33, + 10: 41, 11: 42, 12: 44, 13: 43, 14: 45, 15: 46, 16: 47, 17: 48, 18: 39, 19: 40, + 20: 37, 21: 38, 22: 36, 24: 34, 25: 35, 26: 28, 27: 29, 28: 8, 47: 4, 48: 5, + 49: 6, 50: 7} + score: '0.656' + edge_lig_23_lig_41: + ligand_a: lig_23 + ligand_b: lig_41 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 45, 5: 46, 6: 26, 7: 27, 8: 28, 9: 29, + 10: 30, 11: 31, 12: 32, 13: 33, 14: 34, 15: 35, 16: 36, 17: 37, 19: 24, 20: 25, + 21: 8, 40: 4, 41: 5, 42: 6, 43: 7} + score: '0.602' + edge_lig_24_lig_42: + ligand_a: lig_24 + ligand_b: lig_42 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, + 29: 26, 30: 27, 31: 28, 32: 29, 33: 37, 35: 35, 36: 36, 37: 33, 38: 34, 39: 32, + 41: 30, 44: 45, 45: 46} + score: '0.587' + edge_lig_24_lig_65: + ligand_a: lig_24 + ligand_b: lig_65 + atom mapping: {0: 37, 1: 36, 2: 38, 3: 31, 4: 32, 5: 33, 6: 34, 7: 35, 8: 7, 27: 8, + 28: 9, 29: 10, 30: 11, 31: 12, 32: 13, 33: 21, 35: 19, 36: 20, 37: 17, 38: 18, + 39: 16, 41: 14, 44: 29, 45: 30} + score: '0.590' + edge_lig_52_lig_38: + ligand_a: lig_52 + ligand_b: lig_38 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 30: 28, 31: 29, + 32: 30, 33: 31, 34: 32, 35: 33, 36: 34, 37: 35, 38: 36, 39: 37, 40: 38, 41: 39, + 42: 40, 43: 41, 44: 42, 45: 44, 46: 43, 47: 45, 48: 48, 49: 47, 50: 46, 51: 49, + 52: 50} + score: '0.652' + edge_lig_34_lig_59: + ligand_a: lig_34 + ligand_b: lig_59 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 26, 28: 27, + 29: 28, 30: 29, 31: 30, 32: 31, 33: 39, 34: 40, 35: 41, 36: 43, 39: 37, 40: 38, + 41: 35, 42: 36, 43: 34, 44: 32, 45: 33, 46: 47, 47: 48} + score: '0.625' + edge_lig_24_lig_20: + ligand_a: lig_24 + ligand_b: lig_20 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, + 29: 26, 30: 27, 31: 28, 32: 29, 33: 37, 35: 35, 36: 36, 37: 33, 38: 34, 39: 32, + 41: 30, 44: 45, 45: 46} + score: '0.587' + edge_lig_64_lig_41: + ligand_a: lig_64 + ligand_b: lig_41 + atom mapping: {9: 8, 10: 24, 11: 25, 12: 26, 13: 27, 14: 28, 15: 29, 16: 37, 17: 38, + 18: 40, 19: 39, 20: 41, 21: 42, 22: 43, 23: 44, 24: 35, 25: 36, 26: 33, 27: 34, + 28: 32, 29: 30, 30: 31, 31: 45, 32: 46, 33: 3, 34: 4, 35: 5, 36: 6, 37: 7, 38: 1, + 39: 0, 40: 2} + score: '0.696' + edge_lig_56_lig_38: + ligand_a: lig_56 + ligand_b: lig_38 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 30: 28, 31: 29, + 32: 30, 33: 31, 34: 32, 35: 33, 36: 34, 37: 35, 38: 36, 39: 37, 40: 38, 41: 39, + 42: 40, 43: 41, 44: 42, 45: 43, 46: 44, 47: 45, 48: 46, 49: 47, 50: 48, 51: 49, + 52: 50} + score: '0.652' + edge_lig_19_lig_41: + ligand_a: lig_19 + ligand_b: lig_41 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 45, 5: 46, 6: 26, 7: 27, 8: 28, 9: 29, + 10: 30, 11: 31, 12: 32, 14: 33, 15: 34, 16: 35, 17: 36, 18: 37, 20: 24, 21: 25, + 22: 8, 41: 4, 42: 5, 43: 6, 44: 7} + score: '0.595' + edge_lig_59_lig_31: + ligand_a: lig_59 + ligand_b: lig_31 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 44, 5: 45, 6: 46, 7: 47, 8: 25, 26: 23, + 27: 24, 28: 6, 29: 7, 30: 8, 31: 9, 32: 10, 33: 11, 34: 12, 35: 13, 36: 14, + 37: 15, 38: 16, 39: 17, 40: 18, 43: 19, 44: 22, 45: 21, 46: 20, 47: 4, 48: 5} + score: '0.642' + edge_lig_24_lig_59: + ligand_a: lig_24 + ligand_b: lig_59 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 26, 28: 27, + 29: 28, 30: 29, 31: 30, 32: 31, 33: 39, 35: 37, 36: 38, 37: 35, 38: 36, 39: 34, + 41: 32, 44: 47, 45: 48} + score: '0.578' + edge_lig_24_lig_48: + ligand_a: lig_24 + ligand_b: lig_48 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, + 29: 26, 30: 27, 31: 28, 32: 29, 33: 37, 35: 35, 36: 36, 37: 33, 38: 34, 39: 32, + 41: 30, 44: 45, 45: 46} + score: '0.587' diff --git a/data/ptp1b/03_edges/01_perses_openfe.yml b/data/ptp1b/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..4720cb656 --- /dev/null +++ b/data/ptp1b/03_edges/01_perses_openfe.yml @@ -0,0 +1,151 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.5 minimal_spanning_graph +edges: + edge_lig_23485_lig_23480: + ligand_a: lig_23485 + ligand_b: lig_23480 + atom mapping: {0: 52, 1: 2, 2: 1, 3: 6, 4: 5, 5: 4, 6: 3, 8: 35, 9: 8, 12: 10, + 15: 13, 16: 18, 17: 17, 18: 16, 19: 15, 20: 14, 21: 33, 22: 32, 23: 31, 24: 30, + 26: 23, 57: 22, 58: 21, 59: 20, 60: 19, 61: 7, 62: 0} + score: '0.488' + edge_lig_23476_lig_23484: + ligand_a: lig_23476 + ligand_b: lig_23484 + atom mapping: {0: 52, 1: 30, 2: 31, 3: 32, 4: 33, 5: 28, 6: 29, 7: 53, 8: 26, + 9: 27, 30: 34, 31: 35, 32: 36, 33: 37, 34: 38, 35: 39, 36: 40, 37: 41, 38: 42, + 39: 43, 40: 44, 41: 45, 42: 46, 43: 47, 44: 48, 45: 49, 47: 51} + score: '0.545' + edge_lig_23484_lig_20669_2qbr: + ligand_a: lig_23484 + ligand_b: lig_20669_2qbr + atom mapping: {26: 12, 28: 14, 29: 15, 30: 16, 31: 17, 32: 18, 33: 19, 34: 20, + 35: 21, 36: 22, 37: 23, 38: 24, 39: 25, 40: 26, 41: 27, 42: 28, 43: 29, 44: 30, + 45: 32, 46: 31, 47: 33, 48: 34, 49: 35, 51: 37, 52: 38, 53: 39} + score: '0.574' + edge_lig_20667_2qbp_lig_23480: + ligand_a: lig_20667_2qbp + ligand_b: lig_23480 + atom mapping: {0: 52, 1: 2, 2: 3, 3: 4, 4: 5, 5: 6, 6: 1, 7: 0, 8: 7, 9: 8, 12: 10, + 15: 13, 16: 14, 17: 15, 18: 16, 19: 17, 20: 18, 21: 20, 22: 19, 23: 22, 24: 21, + 26: 23, 54: 30, 55: 31, 56: 32, 57: 33, 58: 35} + score: '0.488' + edge_lig_23484_lig_23468: + ligand_a: lig_23484 + ligand_b: lig_23468 + atom mapping: {26: 8, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, 33: 4, 34: 19, 35: 20, + 36: 21, 37: 22, 38: 23, 39: 24, 40: 25, 41: 26, 42: 27, 43: 28, 44: 29, 45: 31, + 46: 30, 47: 32, 48: 33, 49: 34, 51: 36, 52: 0, 53: 7} + score: '0.612' + edge_lig_23480_lig_23484: + ligand_a: lig_23480 + ligand_b: lig_23484 + atom mapping: {0: 7, 1: 6, 2: 1, 3: 2, 4: 3, 5: 4, 6: 5, 7: 8, 8: 9, 10: 12, 13: 15, + 14: 20, 15: 19, 16: 18, 17: 17, 18: 16, 19: 56, 20: 57, 21: 55, 22: 54, 23: 26, + 30: 23, 31: 24, 32: 22, 33: 21, 35: 58, 52: 0} + score: '0.491' + edge_lig_23480_lig_23479: + ligand_a: lig_23480 + ligand_b: lig_23479 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 35: 31, 36: 32, + 37: 33, 38: 34, 39: 35, 40: 36, 41: 37, 42: 38, 43: 39, 44: 40, 45: 41, 46: 43, + 47: 42, 48: 44, 49: 45, 50: 46, 51: 47, 52: 48} + score: '0.610' + edge_lig_23477_lig_23472: + ligand_a: lig_23477 + ligand_b: lig_23472 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 25: 24, 26: 25, + 27: 26, 28: 27, 29: 28, 30: 29, 31: 30, 32: 31, 33: 32, 34: 33, 35: 34, 36: 35, + 37: 36, 38: 37, 39: 38, 40: 39, 41: 40, 42: 41} + score: '0.632' + edge_lig_23480_lig_23482: + ligand_a: lig_23480 + ligand_b: lig_23482 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 35: 32, 36: 33, + 37: 34, 38: 35, 39: 36, 40: 37, 41: 38, 42: 39, 43: 40, 44: 41, 45: 42, 46: 44, + 47: 43, 48: 45, 49: 46, 50: 47, 51: 48, 52: 49} + score: '0.602' + edge_lig_23484_lig_23472: + ligand_a: lig_23484 + ligand_b: lig_23472 + atom mapping: {26: 8, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, 33: 4, 34: 24, 35: 25, + 36: 26, 37: 27, 38: 28, 39: 29, 40: 30, 41: 31, 42: 32, 43: 33, 44: 34, 45: 36, + 46: 35, 47: 37, 48: 38, 49: 39, 51: 41, 52: 0, 53: 7} + score: '0.574' + edge_lig_23466_lig_23472: + ligand_a: lig_23466 + ligand_b: lig_23472 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 11: 24, + 12: 25, 13: 26, 14: 27, 15: 28, 16: 29, 17: 30, 18: 31, 19: 32, 20: 33, 21: 34, + 22: 36, 23: 35, 24: 37, 25: 38, 26: 39, 27: 40, 28: 41} + score: '0.783' + edge_lig_20670_2qbs_lig_23472: + ligand_a: lig_20670_2qbs + ligand_b: lig_23472 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 27: 24, 28: 25, + 29: 26, 30: 27, 31: 28, 32: 29, 33: 30, 34: 31, 35: 32, 36: 33, 37: 34, 38: 35, + 39: 36, 40: 37, 41: 38, 42: 39, 43: 40, 44: 41} + score: '0.632' + edge_lig_23485_lig_23474: + ligand_a: lig_23485 + ligand_b: lig_23474 + atom mapping: {0: 47, 1: 2, 2: 1, 3: 6, 4: 5, 5: 4, 6: 3, 8: 30, 9: 8, 12: 10, + 15: 13, 16: 18, 17: 17, 18: 16, 19: 15, 20: 14, 21: 28, 22: 27, 23: 26, 24: 25, + 25: 24, 57: 21, 58: 22, 59: 19, 60: 20, 61: 7, 62: 0} + score: '0.511' + edge_lig_23467_lig_23472: + ligand_a: lig_23467 + ligand_b: lig_23472 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 13: 24, 14: 25, + 15: 26, 16: 27, 17: 28, 18: 29, 19: 30, 20: 31, 21: 32, 22: 33, 23: 34, 24: 36, + 25: 35, 26: 37, 27: 38, 28: 39, 29: 40, 30: 41} + score: '0.742' + edge_lig_23484_lig_23471: + ligand_a: lig_23484 + ligand_b: lig_23471 + atom mapping: {26: 8, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, 33: 4, 34: 17, 35: 18, + 36: 19, 37: 20, 38: 21, 39: 22, 40: 23, 41: 24, 42: 25, 43: 26, 44: 27, 45: 29, + 46: 28, 47: 30, 48: 31, 49: 32, 51: 34, 52: 0, 53: 7} + score: '0.682' + edge_lig_23484_lig_23473: + ligand_a: lig_23484 + ligand_b: lig_23473 + atom mapping: {26: 12, 28: 13, 29: 14, 30: 15, 31: 16, 32: 17, 33: 18, 34: 19, + 35: 20, 36: 21, 37: 22, 38: 23, 39: 24, 40: 25, 41: 26, 42: 27, 43: 28, 44: 29, + 45: 31, 46: 30, 47: 32, 48: 33, 49: 34, 51: 36, 52: 37, 53: 38} + score: '0.581' + edge_lig_23480_lig_23483: + ligand_a: lig_23480 + ligand_b: lig_23483 + atom mapping: {0: 49, 1: 27, 2: 28, 3: 29, 4: 30, 5: 25, 6: 26, 7: 50, 8: 23, + 35: 31, 36: 32, 37: 33, 38: 34, 39: 35, 40: 36, 41: 37, 42: 38, 43: 39, 44: 40, + 45: 41, 46: 43, 47: 42, 48: 44, 49: 45, 50: 46, 51: 47, 52: 48} + score: '0.520' + edge_lig_23484_lig_23469: + ligand_a: lig_23484 + ligand_b: lig_23469 + atom mapping: {26: 11, 28: 13, 29: 14, 30: 15, 31: 16, 32: 17, 33: 18, 34: 19, + 35: 20, 36: 21, 37: 22, 38: 23, 39: 24, 40: 25, 41: 26, 42: 27, 43: 28, 44: 29, + 45: 31, 46: 30, 47: 32, 48: 33, 49: 34, 51: 36, 52: 37, 53: 38} + score: '0.581' + edge_lig_23484_lig_23475: + ligand_a: lig_23484 + ligand_b: lig_23475 + atom mapping: {26: 8, 27: 9, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, 33: 4, 34: 24, + 35: 25, 36: 26, 37: 27, 38: 28, 39: 29, 40: 30, 41: 31, 42: 32, 43: 33, 44: 34, + 45: 36, 46: 35, 47: 37, 48: 38, 49: 39, 51: 41, 52: 0, 53: 7} + score: '0.586' + edge_lig_23484_lig_23470: + ligand_a: lig_23484 + ligand_b: lig_23470 + atom mapping: {26: 8, 28: 5, 29: 6, 30: 1, 31: 2, 32: 3, 33: 4, 34: 24, 35: 25, + 36: 26, 37: 27, 38: 28, 39: 29, 40: 30, 41: 31, 42: 32, 43: 33, 44: 34, 45: 36, + 46: 35, 47: 37, 48: 38, 49: 39, 51: 41, 52: 0, 53: 7} + score: '0.574' + edge_lig_23480_lig_23486: + ligand_a: lig_23480 + ligand_b: lig_23486 + atom mapping: {0: 59, 1: 2, 2: 1, 3: 6, 4: 5, 5: 4, 6: 3, 7: 58, 8: 9, 10: 12, + 13: 15, 14: 20, 15: 19, 16: 18, 17: 17, 18: 16, 19: 56, 20: 57, 21: 55, 22: 54, + 23: 26, 30: 23, 31: 24, 32: 22, 33: 21, 35: 8, 52: 0} + score: '0.488' diff --git a/data/shp2/03_edges/01_perses_openfe.yml b/data/shp2/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..3831570c5 --- /dev/null +++ b/data/shp2/03_edges/01_perses_openfe.yml @@ -0,0 +1,145 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.5 minimal_spanning_graph +edges: + edge_lig_E14_lig_10: + ligand_a: lig_E14 + ligand_b: lig_10 + atom mapping: {0: 26, 1: 25, 2: 27, 3: 28, 4: 29, 5: 38, 7: 36, 9: 34, 10: 35, + 11: 32, 13: 30, 15: 1, 19: 2, 20: 3} + score: '0.507' + edge_lig_E14_lig_E30: + ligand_a: lig_E14 + ligand_b: lig_E30 + atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 39, + 15: 35, 16: 36, 17: 38, 18: 37, 19: 34, 20: 12} + score: '0.540' + edge_lig_E14_lig_SHP099-1: + ligand_a: lig_E14 + ligand_b: lig_SHP099-1 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 13, 7: 11, 9: 9, 10: 10, 11: 7, + 13: 5, 15: 15, 16: 16, 17: 18, 18: 17, 19: 19, 20: 20} + score: '0.555' + edge_lig_E3_lig_E14: + ligand_a: lig_E3 + ligand_b: lig_E14 + atom mapping: {6: 3, 7: 2, 9: 1, 10: 20, 32: 19, 33: 15, 34: 16, 35: 17, 36: 18} + score: '0.292' + edge_lig_E28_lig_7: + ligand_a: lig_E28 + ligand_b: lig_7 + atom mapping: {15: 33, 16: 1, 17: 2, 19: 3, 20: 4, 21: 5, 22: 6, 23: 7, 24: 8, + 25: 9, 26: 10, 27: 11, 28: 13, 35: 22, 36: 24, 37: 23, 38: 25, 39: 27, 40: 26, + 41: 28, 42: 29, 43: 30, 44: 32, 45: 31} + score: '0.534' + edge_lig_6_lig_E14: + ligand_a: lig_6 + ligand_b: lig_E14 + atom mapping: {1: 2, 2: 1, 3: 20, 22: 19, 23: 15, 24: 16, 25: 18, 26: 17, 27: 3, + 28: 4, 29: 13, 31: 11, 33: 9, 34: 10, 35: 7, 37: 5} + score: '0.544' + edge_lig_E8_lig_E14: + ligand_a: lig_E8 + ligand_b: lig_E14 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 13, 7: 11, 9: 9, 10: 10, 11: 7, + 13: 5, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20} + score: '0.551' + edge_lig_E14_lig_E2: + ligand_a: lig_E14 + ligand_b: lig_E2 + atom mapping: {1: 2, 2: 1, 3: 30, 4: 31, 5: 43, 7: 38, 9: 36, 10: 37, 11: 34, + 13: 32, 15: 26, 16: 27, 17: 29, 18: 28, 19: 25, 20: 3} + score: '0.540' + edge_lig_E14_lig_E22: + ligand_a: lig_E14 + ligand_b: lig_E22 + atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 40, + 15: 36, 16: 37, 17: 39, 18: 38, 19: 35, 20: 13} + score: '0.536' + edge_lig_E14_lig_E28: + ligand_a: lig_E14 + ligand_b: lig_E28 + atom mapping: {0: 18, 1: 17, 2: 16, 3: 15, 15: 42, 16: 43, 17: 44, 18: 45, 19: 41, + 20: 19} + score: '0.296' + edge_lig_E4_lig_E27: + ligand_a: lig_E4 + ligand_b: lig_E27 + atom mapping: {3: 3, 4: 2, 6: 1, 7: 20, 8: 21, 9: 39, 10: 41, 11: 40, 12: 33, + 14: 34, 15: 31, 23: 25, 25: 26, 26: 22, 27: 24, 28: 23, 29: 19, 30: 15, 31: 16, + 32: 18, 33: 17} + score: '0.520' + edge_lig_E14_lig_E6: + ligand_a: lig_E14 + ligand_b: lig_E6 + atom mapping: {1: 13, 2: 11, 3: 10, 4: 9, 5: 7, 7: 5, 9: 3, 10: 4, 11: 2, 12: 1, + 13: 41, 15: 37, 16: 38, 17: 40, 18: 39, 19: 36, 20: 14} + score: '0.558' + edge_lig_SHP836-2_lig_E28: + ligand_a: lig_SHP836-2 + ligand_b: lig_E28 + atom mapping: {1: 16, 2: 17, 3: 19, 4: 20, 5: 38, 6: 40, 7: 39, 8: 35, 9: 36, + 14: 27, 16: 24, 17: 25, 22: 21, 23: 23, 24: 22, 25: 41, 26: 42, 27: 43, 28: 45, + 29: 44, 30: 15} + score: '0.508' + edge_lig_E14_lig_E25: + ligand_a: lig_E14 + ligand_b: lig_E25 + atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 41, + 15: 37, 16: 38, 17: 40, 18: 39, 19: 36, 20: 14} + score: '0.532' + edge_lig_3_lig_E28: + ligand_a: lig_3 + ligand_b: lig_E28 + atom mapping: {1: 16, 2: 17, 3: 19, 4: 20, 5: 38, 6: 40, 7: 39, 8: 35, 9: 36, + 14: 27, 16: 24, 17: 25, 22: 21, 23: 23, 24: 22, 25: 41, 26: 42, 27: 43, 28: 45, + 29: 44, 30: 15} + score: '0.508' + edge_lig_E14_lig_E23: + ligand_a: lig_E14 + ligand_b: lig_E23 + atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 40, + 15: 36, 16: 37, 17: 39, 18: 38, 19: 35, 20: 13} + score: '0.536' + edge_lig_E14_lig_E24: + ligand_a: lig_E14 + ligand_b: lig_E24 + atom mapping: {1: 11, 2: 10, 3: 9, 4: 8, 5: 6, 7: 4, 9: 2, 10: 3, 11: 1, 13: 43, + 15: 39, 16: 40, 17: 42, 18: 41, 19: 38, 20: 16} + score: '0.536' + edge_lig_E9_lig_E14: + ligand_a: lig_E9 + ligand_b: lig_E14 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 13, 7: 11, 9: 9, 10: 10, 11: 7, + 13: 5, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20} + score: '0.555' + edge_lig_E14_lig_11: + ligand_a: lig_E14 + ligand_b: lig_11 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 13, 7: 11, 9: 9, 10: 10, 11: 7, + 13: 5, 15: 15, 16: 16, 18: 17, 19: 22, 20: 23} + score: '0.536' + edge_lig_E14_lig_E29: + ligand_a: lig_E14 + ligand_b: lig_E29 + atom mapping: {0: 6, 1: 5, 2: 4, 3: 3, 15: 30, 16: 31, 17: 32, 18: 33, 19: 29, + 20: 7} + score: '0.305' + edge_lig_E28_lig_E5: + ligand_a: lig_E28 + ligand_b: lig_E5 + atom mapping: {15: 30, 16: 1, 17: 2, 19: 3, 20: 4, 21: 5, 22: 6, 23: 7, 24: 8, + 25: 9, 26: 10, 27: 11, 28: 16, 32: 12, 35: 19, 36: 21, 37: 20, 38: 22, 39: 24, + 40: 23, 41: 25, 42: 26, 43: 27, 44: 29, 45: 28} + score: '0.543' + edge_lig_E4_lig_E14: + ligand_a: lig_E4 + ligand_b: lig_E14 + atom mapping: {3: 3, 4: 2, 6: 1, 7: 20, 29: 19, 30: 15, 31: 16, 32: 17, 33: 18} + score: '0.292' + edge_lig_E1_lig_E14: + ligand_a: lig_E1 + ligand_b: lig_E14 + atom mapping: {1: 2, 2: 1, 3: 20, 25: 19, 26: 15, 27: 16, 28: 17, 29: 18, 30: 3, + 31: 4, 32: 13, 34: 11, 36: 9, 37: 10, 38: 7, 40: 5} + score: '0.540' diff --git a/data/syk/03_edges/01_perses_openfe.yml b/data/syk/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..2a7975a12 --- /dev/null +++ b/data/syk/03_edges/01_perses_openfe.yml @@ -0,0 +1,305 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.5 minimal_spanning_graph +edges: + edge_lig_CHEMBL3264994_lig_CHEMBL3265022: + ligand_a: lig_CHEMBL3264994 + ligand_b: lig_CHEMBL3265022 + atom mapping: {0: 19, 1: 18, 2: 20, 3: 21, 4: 15, 5: 16, 6: 17, 7: 22, 8: 23, + 9: 24, 10: 25, 11: 42, 12: 43, 13: 36, 15: 30, 16: 31, 21: 32, 22: 33, 23: 34, + 24: 35, 29: 28, 30: 29, 31: 26, 32: 27, 33: 44, 34: 12, 62: 13, 63: 14} + score: '0.507' + edge_lig_CHEMBL3265002_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265002 + ligand_b: lig_CHEMBL3265031 + atom mapping: {25: 24, 26: 39, 27: 40, 28: 41, 29: 42, 30: 43, 31: 44, 32: 45, + 33: 46, 34: 47, 35: 22, 36: 20, 37: 21, 38: 19, 39: 48, 40: 49, 41: 50, 42: 51, + 43: 14, 49: 15, 55: 17, 56: 18, 57: 23} + score: '0.397' + edge_lig_CHEMBL3265003_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265003 + ligand_b: lig_CHEMBL3265031 + atom mapping: {24: 24, 25: 39, 26: 40, 27: 41, 28: 42, 29: 43, 30: 44, 31: 45, + 32: 46, 33: 47, 34: 22, 35: 20, 36: 21, 37: 19, 38: 17, 39: 18, 40: 15, 41: 16, + 42: 14, 48: 50, 54: 48, 55: 49, 56: 23} + score: '0.397' + edge_lig_CHEMBL3264998_lig_CHEMBL3265027: + ligand_a: lig_CHEMBL3264998 + ligand_b: lig_CHEMBL3265027 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 29, 27: 31, 28: 32, + 29: 33, 30: 9, 61: 10, 62: 11} + score: '0.499' + edge_lig_CHEMBL3264994_lig_CHEMBL3265019: + ligand_a: lig_CHEMBL3264994 + ligand_b: lig_CHEMBL3265019 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 25: 17, 26: 18, 27: 19, 28: 20, + 29: 21, 31: 27, 32: 28, 33: 29, 34: 30, 62: 44, 63: 45} + score: '0.530' + edge_lig_CHEMBL3265033_lig_CHEMBL3265024: + ligand_a: lig_CHEMBL3265033 + ligand_b: lig_CHEMBL3265024 + atom mapping: {9: 30, 10: 48, 11: 49, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, + 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, + 44: 21, 46: 27, 47: 28, 48: 29} + score: '0.474' + edge_lig_CHEMBL3265012_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265012 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 46: 39, 47: 40} + score: '0.485' + edge_lig_CHEMBL3265001_lig_CHEMBL3265030_n: + ligand_a: lig_CHEMBL3265001 + ligand_b: lig_CHEMBL3265030_n + atom mapping: {0: 42, 1: 41, 2: 43, 3: 44, 4: 38, 5: 39, 6: 40, 7: 19, 8: 17, + 9: 18, 10: 16, 11: 45, 12: 46, 13: 47, 14: 48, 15: 11, 21: 12, 27: 14, 28: 15, + 29: 20, 30: 21, 60: 36, 61: 37} + score: '0.417' + edge_lig_CHEMBL3264995_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3264995 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 58: 39, 59: 40} + score: '0.404' + edge_lig_CHEMBL3265000_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265000 + ligand_b: lig_CHEMBL3265033 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 44, 27: 46, 28: 47, + 29: 48, 30: 9, 65: 10, 66: 11} + score: '0.412' + edge_lig_CHEMBL3264999_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3264999 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 60: 39, 61: 40} + score: '0.404' + edge_lig_CHEMBL3265001_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265001 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 60: 39, 61: 40} + score: '0.397' + edge_lig_CHEMBL3264998_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3264998 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 61: 39, 62: 40} + score: '0.402' + edge_lig_CHEMBL3265006_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265006 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 49: 39, 50: 40} + score: '0.469' + edge_lig_CHEMBL3265000_lig_CHEMBL3265036: + ligand_a: lig_CHEMBL3265000 + ligand_b: lig_CHEMBL3265036 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 45, 27: 47, 28: 48, + 29: 49, 30: 9, 65: 10, 66: 11} + score: '0.407' + edge_lig_CHEMBL3264994_lig_CHEMBL3265018: + ligand_a: lig_CHEMBL3264994 + ligand_b: lig_CHEMBL3265018 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 16: 28, 25: 29, 26: 30, + 27: 31, 28: 32, 29: 33, 31: 39, 32: 40, 33: 41, 34: 9, 62: 10, 63: 11} + score: '0.524' + edge_lig_CHEMBL3265001_lig_CHEMBL3265029: + ligand_a: lig_CHEMBL3265001 + ligand_b: lig_CHEMBL3265029 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 16: 28, 17: 29, 18: 32, + 19: 31, 20: 30, 21: 33, 27: 35, 28: 36, 29: 37, 30: 9, 60: 10, 61: 11} + score: '0.530' + edge_lig_CHEMBL3265009_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265009 + ligand_b: lig_CHEMBL3265033 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 44, 27: 46, 28: 47, + 29: 48, 30: 9, 49: 10, 50: 11} + score: '0.469' + edge_lig_CHEMBL3265004_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265004 + ligand_b: lig_CHEMBL3265031 + atom mapping: {26: 24, 27: 39, 28: 40, 29: 41, 30: 42, 31: 43, 32: 44, 33: 45, + 34: 46, 35: 47, 36: 22, 37: 20, 38: 21, 39: 19, 40: 17, 41: 18, 42: 15, 43: 16, + 44: 14, 50: 50, 56: 48, 57: 49, 58: 23} + score: '0.397' + edge_lig_CHEMBL3265001_lig_CHEMBL3265035: + ligand_a: lig_CHEMBL3265001 + ligand_b: lig_CHEMBL3265035 + atom mapping: {0: 40, 1: 39, 2: 41, 3: 42, 4: 36, 5: 37, 6: 38, 7: 17, 8: 15, + 9: 16, 10: 14, 11: 43, 12: 44, 13: 45, 14: 46, 15: 9, 16: 8, 17: 5, 18: 7, 19: 6, + 21: 10, 27: 12, 28: 13, 29: 18, 30: 19, 60: 34, 61: 35} + score: '0.472' + edge_lig_CHEMBL3265033_lig_CHEMBL3265025: + ligand_a: lig_CHEMBL3265033 + ligand_b: lig_CHEMBL3265025 + atom mapping: {9: 30, 10: 48, 11: 49, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, + 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, + 44: 21, 46: 27, 47: 28, 48: 29} + score: '0.474' + edge_lig_CHEMBL3265023_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265023 + ligand_b: lig_CHEMBL3265031 + atom mapping: {14: 24, 15: 39, 16: 40, 17: 41, 18: 42, 19: 43, 20: 44, 21: 45, + 22: 46, 23: 47, 24: 22, 25: 20, 26: 21, 27: 19, 28: 48, 29: 49, 30: 50, 31: 51, + 32: 14, 38: 15, 44: 17, 45: 18, 46: 23} + score: '0.474' + edge_lig_CHEMBL3265033_lig_CHEMBL3265026: + ligand_a: lig_CHEMBL3265033 + ligand_b: lig_CHEMBL3265026 + atom mapping: {9: 30, 10: 49, 11: 50, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, + 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, + 44: 21, 46: 27, 47: 28, 48: 29} + score: '0.469' + edge_lig_CHEMBL3265000_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3265000 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 65: 39, 66: 40} + score: '0.397' + edge_lig_CHEMBL3265033_lig_CHEMBL3265020: + ligand_a: lig_CHEMBL3265033 + ligand_b: lig_CHEMBL3265020 + atom mapping: {9: 30, 10: 46, 11: 47, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, + 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, + 44: 21, 46: 27, 47: 28, 48: 29} + score: '0.485' + edge_lig_CHEMBL3265000_lig_CHEMBL3265034: + ligand_a: lig_CHEMBL3265000 + ligand_b: lig_CHEMBL3265034 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 43, 27: 45, 28: 46, + 29: 47, 30: 9, 65: 10, 66: 11} + score: '0.416' + edge_lig_CHEMBL3265033_lig_CHEMBL3265021: + ligand_a: lig_CHEMBL3265033 + ligand_b: lig_CHEMBL3265021 + atom mapping: {9: 11, 10: 12, 11: 13, 12: 14, 13: 15, 14: 16, 15: 17, 16: 18, + 17: 19, 18: 20, 19: 21, 20: 22, 21: 23, 22: 24, 23: 25, 24: 26, 25: 27, 26: 28, + 27: 29, 44: 35, 46: 41, 47: 42, 48: 43} + score: '0.491' + edge_lig_CHEMBL3265011_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265011 + ligand_b: lig_CHEMBL3265033 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 44, 27: 46, 28: 47, + 29: 48, 30: 9, 49: 10, 50: 11} + score: '0.469' + edge_lig_CHEMBL3264994_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3264994 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 29: 15, 30: 16, 31: 17, + 32: 18, 33: 23, 34: 24, 62: 39, 63: 40} + score: '0.414' + edge_lig_CHEMBL3265033_lig_CHEMBL3265013: + ligand_a: lig_CHEMBL3265033 + ligand_b: lig_CHEMBL3265013 + atom mapping: {9: 30, 10: 49, 11: 50, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, + 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, + 44: 21, 46: 27, 47: 28, 48: 29} + score: '0.469' + edge_lig_CHEMBL3265010_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265010 + ligand_b: lig_CHEMBL3265033 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 44, 27: 46, 28: 47, + 29: 48, 30: 9, 50: 10, 51: 11} + score: '0.464' + edge_lig_CHEMBL3264994_lig_CHEMBL3265028: + ligand_a: lig_CHEMBL3264994 + ligand_b: lig_CHEMBL3265028 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 29: 29, 31: 35, 32: 36, + 33: 37, 34: 9, 62: 10, 63: 11} + score: '0.479' + edge_lig_CHEMBL3264994_lig_CHEMBL3265016: + ligand_a: lig_CHEMBL3264994 + ligand_b: lig_CHEMBL3265016 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 27, 12: 28, 13: 21, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, 29: 13, + 30: 14, 31: 11, 32: 12, 33: 29, 34: 30, 62: 46, 63: 47} + score: '0.518' + edge_lig_CHEMBL3265005_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265005 + ligand_b: lig_CHEMBL3265033 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 44, 27: 46, 28: 47, + 29: 48, 30: 9, 46: 10, 47: 11} + score: '0.485' + edge_lig_CHEMBL3264996_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3264996 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 62: 39, 63: 40} + score: '0.402' + edge_lig_CHEMBL3264997_lig_CHEMBL3265031: + ligand_a: lig_CHEMBL3264997 + ligand_b: lig_CHEMBL3265031 + atom mapping: {0: 45, 1: 44, 2: 46, 3: 47, 4: 41, 5: 42, 6: 43, 7: 22, 8: 20, + 9: 21, 10: 19, 11: 48, 12: 49, 13: 50, 14: 51, 15: 14, 21: 15, 27: 17, 28: 18, + 29: 23, 30: 24, 58: 39, 59: 40} + score: '0.404' + edge_lig_CHEMBL3264994_lig_CHEMBL3265017: + ligand_a: lig_CHEMBL3264994 + ligand_b: lig_CHEMBL3265017 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 39, 12: 40, 13: 33, 15: 27, 16: 28, 21: 29, 22: 30, 23: 31, + 24: 32, 29: 25, 30: 26, 31: 23, 32: 24, 33: 41, 34: 9, 62: 10, 63: 11} + score: '0.524' + edge_lig_CHEMBL3265000_lig_CHEMBL3265032: + ligand_a: lig_CHEMBL3265000 + ligand_b: lig_CHEMBL3265032 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 42, 27: 44, 28: 45, + 29: 46, 30: 9, 65: 10, 66: 11} + score: '0.421' + edge_lig_CHEMBL3264994_lig_CHEMBL3265037: + ligand_a: lig_CHEMBL3264994 + ligand_b: lig_CHEMBL3265037 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 29: 42, 31: 48, 32: 49, + 33: 50, 34: 9, 62: 10, 63: 11} + score: '0.412' + edge_lig_CHEMBL3265008_lig_CHEMBL3265033: + ligand_a: lig_CHEMBL3265008 + ligand_b: lig_CHEMBL3265033 + atom mapping: {0: 16, 1: 15, 2: 17, 3: 18, 4: 12, 5: 13, 6: 14, 7: 19, 8: 20, + 9: 21, 10: 22, 11: 23, 12: 24, 13: 25, 14: 26, 15: 27, 21: 44, 27: 46, 28: 47, + 29: 48, 30: 9, 46: 10, 47: 11} + score: '0.485' + edge_lig_CHEMBL3265033_lig_CHEMBL3265014: + ligand_a: lig_CHEMBL3265033 + ligand_b: lig_CHEMBL3265014 + atom mapping: {9: 30, 10: 50, 11: 51, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, + 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, + 44: 21, 46: 27, 47: 28, 48: 29} + score: '0.464' + edge_lig_CHEMBL3265033_lig_CHEMBL3265015: + ligand_a: lig_CHEMBL3265033 + ligand_b: lig_CHEMBL3265015 + atom mapping: {9: 30, 10: 49, 11: 50, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, + 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, + 44: 21, 46: 27, 47: 28, 48: 29} + score: '0.469' + edge_lig_CHEMBL3265033_lig_CHEMBL3259820: + ligand_a: lig_CHEMBL3265033 + ligand_b: lig_CHEMBL3259820 + atom mapping: {9: 30, 10: 46, 11: 47, 12: 4, 13: 5, 14: 6, 15: 1, 16: 0, 17: 2, + 18: 3, 19: 7, 20: 8, 21: 9, 22: 10, 23: 11, 24: 12, 25: 13, 26: 14, 27: 15, + 44: 21, 46: 27, 47: 28, 48: 29} + score: '0.485' diff --git a/data/thrombin/03_edges/01_perses_openfe.yml b/data/thrombin/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..58b7f6625 --- /dev/null +++ b/data/thrombin/03_edges/01_perses_openfe.yml @@ -0,0 +1,180 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.5 minimal_spanning_graph +edges: + edge_lig_7e_lig_7d: + ligand_a: lig_7e + ligand_b: lig_7d + atom mapping: {0: 17, 1: 7, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 1, 8: 18, 9: 19, + 10: 20, 11: 21, 12: 26, 13: 25, 14: 24, 15: 23, 16: 22, 17: 0, 18: 8, 19: 9, + 28: 27, 29: 28, 30: 29, 31: 30, 32: 35, 33: 36, 34: 33, 35: 34, 36: 31, 37: 32, + 38: 53, 39: 52, 40: 58, 41: 57, 42: 56, 43: 55, 44: 54, 45: 37, 46: 38, 47: 39} + score: '0.693' + edge_lig_2e_lig_7d: + ligand_a: lig_2e + ligand_b: lig_7d + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 19: 17, + 20: 18, 21: 19, 22: 20, 23: 21, 24: 26, 25: 25, 26: 24, 27: 23, 28: 22, 29: 27, + 30: 28, 31: 30, 32: 29, 33: 32, 34: 31, 35: 33, 36: 34, 37: 36, 38: 35, 39: 37, + 40: 39, 41: 38, 46: 52, 47: 53, 48: 58, 49: 57, 50: 56, 51: 55, 52: 54} + score: '0.706' + edge_lig_6b_lig_7d: + ligand_a: lig_6b + ligand_b: lig_7d + atom mapping: {7: 9, 8: 8, 9: 7, 10: 17, 11: 6, 12: 5, 13: 4, 14: 3, 15: 2, 16: 1, + 17: 0, 18: 18, 19: 20, 20: 21, 21: 22, 22: 23, 23: 24, 24: 25, 25: 26, 26: 19, + 28: 27, 29: 28, 30: 29, 31: 30, 38: 39, 39: 38, 40: 37, 41: 36, 42: 35, 43: 34, + 44: 33, 45: 32, 46: 31, 47: 52, 48: 53, 49: 54, 50: 55, 51: 56, 52: 57, 53: 58} + score: '0.701' + edge_lig_6a_lig_7d: + ligand_a: lig_6a + ligand_b: lig_7d + atom mapping: {0: 24, 1: 25, 2: 26, 3: 21, 4: 22, 5: 23, 6: 20, 7: 18, 8: 1, 9: 0, + 10: 2, 11: 3, 12: 4, 13: 5, 14: 6, 15: 7, 16: 17, 17: 8, 18: 9, 27: 19, 28: 28, + 29: 27, 30: 30, 31: 29, 32: 56, 33: 57, 34: 58, 35: 54, 36: 55, 37: 53, 38: 52, + 39: 31, 40: 32, 41: 33, 42: 34, 43: 36, 44: 35, 45: 37, 46: 38, 47: 39} + score: '0.727' + edge_lig_2b_lig_7d: + ligand_a: lig_2b + ligand_b: lig_7d + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 18: 17, + 19: 18, 20: 19, 21: 20, 22: 21, 23: 26, 24: 25, 25: 24, 26: 23, 27: 22, 28: 27, + 29: 28, 30: 30, 31: 29, 32: 32, 33: 31, 34: 33, 35: 34, 36: 36, 37: 35, 38: 37, + 39: 39, 40: 38, 48: 52, 49: 53, 50: 58, 51: 57, 52: 56, 53: 55, 54: 54} + score: '0.693' + edge_lig_2d_lig_7d: + ligand_a: lig_2d + ligand_b: lig_7d + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 17: 17, + 18: 18, 19: 19, 20: 20, 21: 21, 22: 26, 23: 25, 24: 24, 25: 23, 26: 22, 27: 27, + 28: 28, 29: 30, 30: 29, 31: 32, 32: 31, 33: 33, 34: 34, 35: 36, 36: 35, 37: 37, + 38: 39, 39: 38, 46: 52, 47: 53, 48: 58, 49: 57, 50: 56, 51: 55, 52: 54} + score: '0.714' + edge_lig_7d_lig_7b: + ligand_a: lig_7d + ligand_b: lig_7b + atom mapping: {0: 17, 1: 7, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 1, 8: 18, 9: 19, + 17: 0, 18: 8, 19: 9, 20: 10, 21: 11, 22: 16, 23: 15, 24: 14, 25: 13, 26: 12, + 27: 27, 28: 28, 29: 30, 30: 29, 31: 36, 32: 35, 33: 33, 34: 34, 35: 32, 36: 31, + 37: 44, 38: 46, 39: 45, 52: 37, 53: 38, 54: 43, 55: 42, 56: 41, 57: 40, 58: 39} + score: '0.732' + edge_lig_1c_lig_7d: + ligand_a: lig_1c + ligand_b: lig_7d + atom mapping: {0: 24, 1: 25, 2: 26, 3: 21, 4: 22, 5: 23, 6: 20, 7: 18, 8: 1, 9: 0, + 10: 2, 11: 3, 12: 4, 13: 5, 14: 6, 15: 7, 16: 17, 17: 8, 18: 9, 26: 19, 27: 28, + 28: 27, 29: 30, 30: 29, 31: 56, 32: 57, 33: 58, 34: 54, 35: 55, 36: 53, 37: 52, + 38: 31, 39: 32, 40: 33, 41: 34, 42: 36, 43: 35, 44: 37, 45: 38, 46: 39} + score: '0.732' + edge_lig_6c_lig_7d: + ligand_a: lig_6c + ligand_b: lig_7d + atom mapping: {0: 17, 1: 7, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 1, 8: 18, 9: 19, + 10: 20, 11: 21, 12: 22, 13: 23, 14: 24, 15: 25, 16: 26, 17: 0, 18: 8, 19: 9, + 29: 27, 30: 28, 31: 29, 32: 30, 33: 35, 34: 36, 35: 33, 36: 34, 37: 31, 38: 32, + 39: 53, 40: 52, 41: 54, 42: 55, 43: 56, 44: 57, 45: 58, 46: 37, 47: 38, 48: 39} + score: '0.689' + edge_lig_7d_lig_5: + ligand_a: lig_7d + ligand_b: lig_5 + atom mapping: {0: 9, 1: 8, 2: 10, 3: 11, 4: 12, 5: 13, 6: 14, 7: 15, 8: 17, 9: 18, + 17: 16, 18: 7, 19: 25, 20: 6, 21: 3, 22: 2, 23: 1, 24: 0, 25: 5, 26: 4, 27: 27, + 28: 26, 29: 29, 30: 28, 31: 38, 32: 37, 33: 39, 34: 40, 35: 42, 36: 41, 37: 43, + 38: 45, 39: 44, 52: 35, 53: 36, 54: 32, 55: 31, 56: 30, 57: 34, 58: 33} + score: '0.732' + edge_lig_4_lig_7d: + ligand_a: lig_4 + ligand_b: lig_7d + atom mapping: {0: 17, 1: 7, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 1, 8: 18, 9: 19, + 10: 20, 11: 21, 12: 26, 13: 25, 14: 24, 15: 23, 16: 22, 17: 0, 18: 8, 19: 9, + 29: 27, 30: 28, 31: 29, 32: 30, 33: 35, 34: 36, 35: 33, 36: 34, 37: 31, 38: 32, + 39: 53, 40: 52, 41: 58, 42: 57, 43: 56, 44: 55, 45: 54, 46: 37, 47: 38, 48: 39} + score: '0.673' + edge_lig_3a_lig_7d: + ligand_a: lig_3a + ligand_b: lig_7d + atom mapping: {7: 9, 8: 8, 9: 7, 10: 17, 11: 6, 12: 5, 13: 4, 14: 3, 15: 2, 16: 1, + 17: 0, 18: 18, 19: 20, 20: 21, 21: 22, 22: 23, 23: 24, 24: 25, 25: 26, 26: 19, + 27: 27, 28: 28, 29: 29, 30: 30, 38: 39, 39: 38, 40: 37, 41: 36, 42: 35, 43: 33, + 44: 34, 45: 32, 46: 31, 47: 52, 48: 53, 49: 54, 50: 55, 51: 56, 52: 57, 53: 58} + score: '0.706' + edge_lig_7d_lig_2a: + ligand_a: lig_7d + ligand_b: lig_2a + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 17: 20, + 18: 21, 19: 22, 20: 23, 21: 24, 22: 29, 23: 28, 24: 27, 25: 26, 26: 25, 27: 30, + 28: 31, 29: 33, 30: 32, 31: 35, 32: 34, 33: 36, 34: 37, 35: 39, 36: 38, 37: 40, + 38: 42, 39: 41, 52: 47, 53: 48, 54: 53, 55: 52, 56: 51, 57: 50, 58: 49} + score: '0.693' + edge_lig_6d_lig_7d: + ligand_a: lig_6d + ligand_b: lig_7d + atom mapping: {3: 9, 4: 8, 5: 7, 6: 6, 7: 5, 8: 4, 9: 3, 10: 2, 11: 1, 12: 18, + 13: 19, 14: 20, 15: 21, 16: 22, 17: 23, 18: 24, 19: 25, 20: 26, 21: 0, 22: 17, + 28: 27, 29: 28, 30: 29, 31: 30, 33: 38, 34: 39, 35: 37, 36: 36, 37: 35, 38: 33, + 39: 34, 40: 32, 41: 31, 42: 52, 43: 53, 44: 54, 45: 55, 46: 56, 47: 57, 48: 58} + score: '0.718' + edge_lig_1b_lig_7d: + ligand_a: lig_1b + ligand_b: lig_7d + atom mapping: {0: 24, 1: 25, 2: 26, 3: 21, 4: 22, 5: 23, 6: 20, 7: 18, 8: 1, 9: 0, + 10: 2, 11: 3, 12: 4, 13: 5, 14: 6, 15: 7, 16: 17, 17: 8, 18: 9, 26: 19, 27: 28, + 28: 27, 29: 30, 30: 29, 31: 56, 32: 57, 33: 58, 34: 54, 35: 55, 36: 53, 37: 52, + 38: 31, 39: 32, 40: 33, 41: 34, 42: 36, 43: 35, 44: 37, 45: 38, 46: 39} + score: '0.732' + edge_lig_2c_lig_7d: + ligand_a: lig_2c + ligand_b: lig_7d + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 17: 17, + 18: 18, 19: 19, 20: 20, 21: 21, 22: 26, 23: 25, 24: 24, 25: 23, 26: 22, 27: 27, + 28: 28, 29: 30, 30: 29, 31: 32, 32: 31, 33: 33, 34: 34, 35: 36, 36: 35, 37: 37, + 38: 39, 39: 38, 45: 52, 46: 53, 47: 58, 48: 57, 49: 56, 50: 55, 51: 54} + score: '0.723' + edge_lig_7d_lig_3b: + ligand_a: lig_7d + ligand_b: lig_3b + atom mapping: {0: 18, 1: 17, 2: 16, 3: 15, 4: 14, 5: 13, 6: 12, 7: 10, 8: 9, 9: 8, + 17: 11, 18: 19, 19: 27, 20: 20, 21: 21, 22: 26, 23: 25, 24: 24, 25: 23, 26: 22, + 27: 28, 28: 29, 29: 31, 30: 30, 31: 49, 32: 48, 33: 46, 34: 47, 35: 45, 36: 44, + 37: 43, 38: 42, 39: 41, 52: 50, 53: 51, 54: 56, 55: 55, 56: 54, 57: 53, 58: 52} + score: '0.677' + edge_lig_7f_lig_7d: + ligand_a: lig_7f + ligand_b: lig_7d + atom mapping: {0: 17, 1: 7, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 1, 8: 18, 9: 19, + 10: 20, 11: 21, 12: 26, 13: 25, 14: 24, 15: 23, 16: 22, 17: 0, 18: 8, 19: 9, + 28: 27, 29: 28, 30: 29, 31: 30, 32: 35, 33: 36, 34: 33, 35: 34, 36: 31, 37: 32, + 38: 53, 39: 52, 40: 58, 41: 57, 42: 56, 43: 55, 44: 54, 45: 37, 46: 38, 47: 39} + score: '0.693' + edge_lig_1d_lig_7d: + ligand_a: lig_1d + ligand_b: lig_7d + atom mapping: {0: 24, 1: 25, 2: 26, 3: 21, 4: 22, 5: 23, 6: 20, 7: 18, 8: 1, 9: 0, + 10: 2, 11: 3, 12: 4, 13: 5, 14: 6, 15: 7, 16: 17, 17: 8, 18: 9, 26: 19, 27: 28, + 28: 27, 29: 30, 30: 29, 31: 56, 32: 57, 33: 58, 34: 54, 35: 55, 36: 53, 37: 52, + 38: 31, 39: 32, 40: 33, 41: 34, 42: 36, 43: 35, 44: 37, 45: 38, 46: 39} + score: '0.732' + edge_lig_6e_lig_7d: + ligand_a: lig_6e + ligand_b: lig_7d + atom mapping: {0: 24, 1: 25, 2: 26, 3: 21, 4: 22, 5: 23, 6: 20, 7: 18, 8: 1, 9: 0, + 10: 2, 11: 3, 12: 4, 13: 5, 14: 6, 15: 7, 16: 17, 17: 8, 18: 9, 27: 19, 28: 28, + 29: 27, 30: 30, 31: 29, 32: 56, 33: 57, 34: 58, 35: 54, 36: 55, 37: 53, 38: 52, + 39: 31, 40: 32, 41: 33, 42: 34, 43: 36, 44: 35, 45: 37, 46: 38, 47: 39} + score: '0.727' + edge_lig_7c_lig_7d: + ligand_a: lig_7c + ligand_b: lig_7d + atom mapping: {0: 17, 1: 7, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 1, 8: 18, 9: 19, + 10: 20, 11: 21, 12: 26, 13: 25, 14: 24, 15: 23, 16: 22, 17: 0, 18: 8, 19: 9, + 27: 27, 28: 28, 29: 29, 30: 30, 31: 35, 32: 36, 33: 33, 34: 34, 35: 31, 36: 32, + 37: 53, 38: 52, 39: 58, 40: 57, 41: 56, 42: 55, 43: 54, 44: 37, 45: 38, 46: 39} + score: '0.732' + edge_lig_1a_lig_7d: + ligand_a: lig_1a + ligand_b: lig_7d + atom mapping: {0: 24, 1: 25, 2: 26, 3: 21, 4: 22, 5: 23, 6: 20, 7: 18, 8: 1, 9: 0, + 10: 2, 11: 3, 12: 4, 13: 5, 14: 6, 15: 7, 16: 17, 17: 8, 18: 9, 26: 19, 27: 28, + 28: 27, 29: 30, 30: 29, 31: 56, 32: 57, 33: 58, 34: 54, 35: 55, 36: 53, 37: 52, + 38: 31, 39: 32, 40: 33, 41: 34, 42: 36, 43: 35, 44: 37, 45: 38, 46: 39} + score: '0.732' diff --git a/data/tnks2/03_edges/01_perses_openfe.yml b/data/tnks2/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..02e60b372 --- /dev/null +++ b/data/tnks2/03_edges/01_perses_openfe.yml @@ -0,0 +1,186 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.5 minimal_spanning_graph +edges: + edge_lig_8a_lig_5m: + ligand_a: lig_8a + ligand_b: lig_5m + atom mapping: {0: 18, 1: 17, 2: 19, 4: 11, 5: 12, 6: 13, 7: 14, 8: 15, 9: 16, + 10: 24, 11: 25, 12: 26, 13: 27, 14: 9, 15: 8, 16: 6, 17: 7, 18: 4, 19: 5, 20: 3, + 39: 30, 40: 31, 41: 28, 42: 29, 43: 10} + score: '0.705' + edge_lig_5g_lig_8a: + ligand_a: lig_5g + ligand_b: lig_8a + atom mapping: {3: 20, 4: 18, 5: 19, 6: 16, 7: 17, 8: 15, 9: 14, 10: 43, 11: 4, + 12: 2, 14: 1, 15: 0, 16: 8, 18: 6, 19: 7, 20: 5, 21: 10, 22: 11, 23: 12, 24: 13, + 25: 41, 26: 42, 27: 39, 28: 40} + score: '0.714' + edge_lig_5f_lig_8a: + ligand_a: lig_5f + ligand_b: lig_8a + atom mapping: {3: 20, 4: 18, 5: 19, 6: 16, 7: 17, 8: 15, 9: 14, 10: 43, 11: 4, + 12: 2, 14: 1, 15: 0, 16: 8, 18: 6, 19: 7, 20: 5, 21: 10, 22: 11, 23: 12, 24: 13, + 25: 41, 26: 42, 27: 39, 28: 40} + score: '0.714' + edge_lig_8e_lig_5j: + ligand_a: lig_8e + ligand_b: lig_5j + atom mapping: {0: 15, 1: 14, 2: 16, 3: 17, 4: 18, 6: 20, 7: 11, 8: 12, 10: 10, + 11: 9, 12: 8, 13: 6, 14: 7, 15: 4, 16: 5, 17: 3, 37: 27, 38: 28, 39: 25, 40: 26, + 41: 23, 42: 24, 43: 21, 44: 22} + score: '0.716' + edge_lig_8a_lig_5k: + ligand_a: lig_8a + ligand_b: lig_5k + atom mapping: {0: 15, 1: 14, 2: 12, 4: 11, 5: 20, 6: 18, 7: 19, 8: 16, 9: 17, + 10: 21, 11: 22, 12: 23, 13: 24, 14: 9, 15: 8, 16: 6, 17: 7, 18: 4, 19: 5, 20: 3, + 39: 27, 40: 28, 41: 25, 42: 26, 43: 10} + score: '0.736' + edge_lig_8e_lig_1a: + ligand_a: lig_8e + ligand_b: lig_1a + atom mapping: {0: 13, 1: 12, 2: 14, 4: 16, 5: 17, 6: 18, 7: 9, 8: 10, 10: 8, 11: 7, + 12: 6, 13: 4, 14: 5, 15: 2, 16: 3, 17: 1, 37: 25, 38: 26, 39: 23, 40: 24, 41: 21, + 42: 22, 43: 19, 44: 20} + score: '0.830' + edge_lig_8e_lig_5a: + ligand_a: lig_8e + ligand_b: lig_5a + atom mapping: {0: 15, 1: 14, 2: 16, 4: 18, 5: 19, 6: 20, 7: 11, 8: 12, 10: 10, + 11: 9, 12: 8, 13: 6, 14: 7, 15: 4, 16: 5, 17: 3, 37: 27, 38: 28, 39: 25, 40: 26, + 41: 23, 42: 24, 43: 21, 44: 22} + score: '0.709' + edge_lig_8e_lig_7: + ligand_a: lig_8e + ligand_b: lig_7 + atom mapping: {0: 14, 1: 13, 2: 15, 3: 16, 4: 17, 5: 18, 6: 19, 7: 10, 8: 11, + 10: 9, 11: 8, 12: 7, 13: 23, 14: 24, 15: 25, 16: 26, 17: 3, 37: 4, 38: 5, 39: 6, + 41: 22, 43: 20, 44: 21} + score: '0.723' + edge_lig_8b_lig_5p: + ligand_a: lig_8b + ligand_b: lig_5p + atom mapping: {0: 17, 1: 16, 2: 18, 3: 19, 4: 20, 23: 42, 24: 43, 25: 44, 26: 45, + 27: 15, 28: 14, 29: 46, 30: 4, 31: 5, 32: 6, 33: 7, 34: 8, 35: 9, 36: 1, 37: 0, + 38: 2, 43: 10, 44: 11, 45: 12, 46: 13} + score: '0.638' + edge_lig_8e_lig_5d: + ligand_a: lig_8e + ligand_b: lig_5d + atom mapping: {0: 15, 1: 14, 2: 16, 3: 17, 4: 18, 5: 19, 6: 20, 7: 11, 8: 12, + 10: 10, 11: 9, 12: 8, 13: 6, 14: 7, 15: 4, 16: 5, 17: 3, 37: 27, 38: 28, 39: 25, + 40: 26, 41: 23, 42: 24, 43: 21, 44: 22} + score: '0.731' + edge_lig_8f_lig_5p: + ligand_a: lig_8f + ligand_b: lig_5p + atom mapping: {0: 17, 1: 16, 2: 18, 3: 19, 4: 20, 24: 42, 25: 43, 26: 44, 27: 45, + 28: 15, 29: 14, 30: 46, 31: 4, 32: 5, 33: 6, 34: 7, 35: 8, 36: 9, 37: 1, 38: 0, + 39: 2, 44: 10, 45: 11, 46: 12, 47: 13} + score: '0.638' + edge_lig_5o_lig_8a: + ligand_a: lig_5o + ligand_b: lig_8a + atom mapping: {10: 20, 11: 18, 12: 19, 13: 16, 14: 17, 15: 15, 16: 14, 17: 43, + 18: 4, 19: 5, 20: 6, 21: 7, 22: 8, 23: 9, 24: 1, 25: 0, 26: 2, 31: 10, 32: 11, + 33: 12, 34: 13, 35: 41, 36: 42, 37: 39, 38: 40} + score: '0.654' + edge_lig_5o_lig_8e: + ligand_a: lig_5o + ligand_b: lig_8e + atom mapping: {10: 17, 11: 15, 12: 16, 13: 13, 14: 14, 15: 12, 16: 11, 17: 10, + 18: 7, 19: 6, 20: 4, 21: 5, 22: 2, 23: 3, 24: 1, 25: 0, 26: 8, 27: 9, 31: 43, + 32: 44, 33: 41, 34: 42, 35: 39, 36: 40, 37: 37, 38: 38} + score: '0.665' + edge_lig_8a_lig_5h: + ligand_a: lig_8a + ligand_b: lig_5h + atom mapping: {0: 19, 1: 18, 2: 12, 4: 11, 5: 24, 6: 22, 7: 23, 8: 20, 10: 25, + 11: 26, 12: 27, 13: 28, 14: 9, 15: 8, 16: 6, 17: 7, 18: 4, 19: 5, 20: 3, 39: 31, + 40: 32, 41: 29, 42: 30, 43: 10} + score: '0.675' + edge_lig_5i_lig_8a: + ligand_a: lig_5i + ligand_b: lig_8a + atom mapping: {3: 20, 4: 18, 5: 19, 6: 16, 7: 17, 8: 15, 9: 14, 10: 43, 11: 4, + 12: 5, 13: 6, 14: 7, 15: 8, 17: 1, 18: 0, 19: 2, 24: 10, 25: 11, 26: 12, 27: 13, + 28: 41, 29: 42, 30: 39, 31: 40} + score: '0.684' + edge_lig_8e_lig_5e: + ligand_a: lig_8e + ligand_b: lig_5e + atom mapping: {0: 15, 1: 14, 2: 16, 3: 17, 4: 18, 5: 19, 6: 20, 7: 11, 8: 12, + 10: 10, 11: 9, 12: 8, 13: 6, 14: 7, 15: 4, 16: 5, 17: 3, 37: 27, 38: 28, 39: 25, + 40: 26, 41: 23, 42: 24, 43: 21, 44: 22} + score: '0.731' + edge_lig_8c_lig_5p: + ligand_a: lig_8c + ligand_b: lig_5p + atom mapping: {0: 0, 1: 1, 2: 8, 3: 9, 4: 6, 5: 7, 6: 5, 7: 4, 8: 2, 10: 46, 11: 14, + 12: 15, 13: 44, 14: 45, 15: 42, 16: 43, 17: 20, 34: 18, 35: 19, 36: 16, 37: 17, + 38: 12, 39: 13, 40: 10, 41: 11} + score: '0.672' + edge_lig_8e_lig_5p: + ligand_a: lig_8e + ligand_b: lig_5p + atom mapping: {0: 0, 1: 1, 2: 8, 3: 9, 4: 6, 5: 7, 6: 5, 7: 4, 8: 2, 10: 46, 11: 14, + 12: 15, 13: 44, 14: 45, 15: 42, 16: 43, 17: 20, 37: 18, 38: 19, 39: 16, 40: 17, + 41: 12, 42: 13, 43: 10, 44: 11} + score: '0.646' + edge_lig_8e_lig_5n: + ligand_a: lig_8e + ligand_b: lig_5n + atom mapping: {0: 22, 1: 21, 2: 23, 3: 24, 4: 25, 5: 26, 6: 27, 7: 18, 8: 19, + 10: 17, 11: 16, 12: 15, 13: 13, 14: 14, 15: 11, 16: 12, 17: 10, 37: 34, 38: 35, + 39: 32, 40: 33, 41: 30, 42: 31, 43: 28, 44: 29} + score: '0.663' + edge_lig_8e_lig_1b: + ligand_a: lig_8e + ligand_b: lig_1b + atom mapping: {0: 0, 1: 1, 2: 2, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 10: 10, 11: 11, + 12: 12, 13: 25, 14: 26, 15: 23, 16: 24, 17: 17, 37: 15, 38: 16, 39: 13, 40: 14, + 41: 27, 42: 28, 43: 29, 44: 30} + score: '0.777' + edge_lig_8a_lig_5l: + ligand_a: lig_8a + ligand_b: lig_5l + atom mapping: {0: 15, 1: 14, 2: 12, 4: 11, 5: 20, 6: 18, 8: 16, 10: 21, 11: 22, + 12: 23, 13: 24, 14: 9, 15: 8, 16: 6, 17: 7, 18: 4, 19: 5, 20: 3, 39: 27, 40: 28, + 41: 25, 42: 26, 43: 10} + score: '0.700' + edge_lig_8e_lig_3a: + ligand_a: lig_8e + ligand_b: lig_3a + atom mapping: {0: 0, 1: 1, 2: 2, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 10: 10, 11: 11, + 12: 12, 13: 33, 14: 34, 15: 31, 16: 32, 17: 17, 37: 15, 38: 16, 39: 13, 40: 14, + 41: 35, 42: 36, 43: 37, 44: 38} + score: '0.689' + edge_lig_8e_lig_5b: + ligand_a: lig_8e + ligand_b: lig_5b + atom mapping: {0: 15, 1: 14, 2: 16, 4: 18, 6: 20, 7: 11, 8: 12, 10: 10, 11: 9, + 12: 8, 13: 6, 14: 7, 15: 4, 16: 5, 17: 3, 37: 27, 38: 28, 39: 25, 40: 26, 41: 23, + 42: 24, 43: 21, 44: 22} + score: '0.694' + edge_lig_8e_lig_3b: + ligand_a: lig_8e + ligand_b: lig_3b + atom mapping: {0: 0, 1: 1, 2: 8, 3: 9, 4: 6, 5: 7, 6: 5, 7: 4, 8: 2, 10: 38, 11: 14, + 12: 15, 13: 36, 14: 37, 15: 34, 16: 35, 17: 20, 37: 18, 38: 19, 39: 16, 40: 17, + 41: 12, 42: 13, 43: 10, 44: 11} + score: '0.710' + edge_lig_8d_lig_5p: + ligand_a: lig_8d + ligand_b: lig_5p + atom mapping: {0: 17, 1: 16, 2: 18, 3: 19, 4: 20, 21: 42, 22: 43, 23: 44, 24: 45, + 25: 15, 26: 14, 27: 46, 28: 4, 29: 5, 30: 6, 31: 7, 32: 8, 33: 9, 34: 1, 35: 0, + 36: 2, 41: 10, 42: 11, 43: 12, 44: 13} + score: '0.646' + edge_lig_8e_lig_5c: + ligand_a: lig_8e + ligand_b: lig_5c + atom mapping: {0: 15, 1: 14, 2: 16, 4: 18, 6: 20, 7: 11, 8: 12, 10: 10, 11: 9, + 12: 8, 13: 6, 14: 7, 15: 4, 16: 5, 17: 3, 37: 27, 38: 28, 39: 25, 40: 26, 41: 23, + 42: 24, 43: 21, 44: 22} + score: '0.694' diff --git a/data/tyk2/03_edges/01_perses_openfe.yml b/data/tyk2/03_edges/01_perses_openfe.yml new file mode 100644 index 000000000..f86683f32 --- /dev/null +++ b/data/tyk2/03_edges/01_perses_openfe.yml @@ -0,0 +1,88 @@ +mapper: Perses 0.10.1 (allow_ring_breaking=False, preserve_chirality=True, use_positions=True, + coordinate_tolerance=0.2), default non geometric scorer +planner: openfe v0.5 minimal_spanning_graph +edges: + edge_lig_ejm_55_lig_ejm_48: + ligand_a: lig_ejm_55 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 29: 38, 30: 39, 31: 8, 32: 7} + score: '0.847' + edge_lig_jmc_27_lig_ejm_48: + ligand_a: lig_jmc_27 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 7: 7, 8: 8, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 32: 38, 33: 39, 34: 40, 35: 41} + score: '0.807' + edge_lig_ejm_46_lig_ejm_48: + ligand_a: lig_ejm_46 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 32: 38, 33: 39, 34: 8, 35: 7} + score: '0.807' + edge_lig_ejm_31_lig_ejm_48: + ligand_a: lig_ejm_31 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 28: 38, 29: 39, 30: 8, 31: 7} + score: '0.860' + edge_lig_jmc_28_lig_ejm_48: + ligand_a: lig_jmc_28 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 35: 38, 36: 39, 37: 8, 38: 7} + score: '0.772' + edge_lig_ejm_43_lig_ejm_48: + ligand_a: lig_ejm_43 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 34: 38, 35: 39, 36: 8, 37: 7} + score: '0.783' + edge_lig_ejm_50_lig_ejm_48: + ligand_a: lig_ejm_50 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 29: 38, 30: 39, 31: 8, 32: 7} + score: '0.847' + edge_lig_ejm_45_lig_ejm_48: + ligand_a: lig_ejm_45 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 35: 38, 36: 39, 37: 8, 38: 7} + score: '0.772' + edge_lig_ejm_54_lig_ejm_48: + ligand_a: lig_ejm_54 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 33: 38, 34: 39, 35: 8, 36: 7} + score: '0.795' + edge_lig_jmc_23_lig_ejm_48: + ligand_a: lig_jmc_23 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 32: 38, 33: 39, 34: 8, 35: 7} + score: '0.807' + edge_lig_ejm_42_lig_ejm_48: + ligand_a: lig_ejm_42 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 31: 38, 32: 39, 33: 8, 34: 7} + score: '0.820' + edge_lig_ejm_47_lig_ejm_48: + ligand_a: lig_ejm_47 + ligand_b: lig_ejm_48 + atom mapping: {0: 0, 1: 1, 2: 6, 3: 5, 4: 4, 5: 3, 6: 2, 7: 41, 8: 40, 9: 9, 10: 10, + 11: 11, 12: 12, 13: 13, 14: 14, 15: 15, 16: 16, 17: 17, 18: 18, 19: 19, 20: 20, + 21: 21, 22: 22, 23: 23, 35: 38, 36: 39, 37: 8, 38: 7} + score: '0.772'