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Revert "Removing current edges file to merge to main."
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This reverts commit b18c0b1.
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@ijpulidos
ijpulidos committed Jun 5, 2023
1 parent b18c0b1 commit d2f51ac
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85 changes: 85 additions & 0 deletions data/cdk2/03_edges/01_perses_openfe.yml
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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'
184 changes: 184 additions & 0 deletions data/cdk8/03_edges/01_perses_openfe.yml
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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'
36 changes: 36 additions & 0 deletions data/cmet/03_edges/01_perses_openfe.yml
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Original file line number Diff line number Diff line change
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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'
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