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.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/cdk8/00_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.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/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.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/eg5/00_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/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/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.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/mcl1/00_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.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/p38/00_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.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/pde2/00_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.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/pfkfb3/00_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.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/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.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/shp2/00_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.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/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.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/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.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/tnks2/00_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.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/tyk2/00_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.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' diff --git a/preparation/mappers/perses-mapper.py b/preparation/mappers/perses-mapper.py new file mode 100644 index 000000000..3ace11377 --- /dev/null +++ b/preparation/mappers/perses-mapper.py @@ -0,0 +1,48 @@ +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 +from collections import OrderedDict + +# 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 v0.5 minimal_spanning_graph" + +edges_dict = dict() + +for edge in network.edges: + edge_name = f'edge_{edge.componentA.name}_{edge.componentB.name}' + 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': edge.componentA_to_componentB, + 'score': f"{edge.annotations['score']:.3f}",} + +output['edges'] = edges_dict + +with open('01_perses_openfe.yml', 'w') as yaml_file: + yaml.dump(output, yaml_file, default_flow_style=None, sort_keys=False)