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Changes PLB from openfe (#106)
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* Remove lig_7d due to unspecified absolute configuration in experimental data

* syk: change protonation state lig_CHEMBL3265030_n and lig_CHEMBL3265035, remove dublicate

* tnks2: Change protonation state lig_7

* thrombin: Change protonation state of primary amine of all ligands

* eg5: lig_CHEMBL1084935: Keep the same isomer that was used in old PLB

* P38 lig_2ff: Remove on of the two ligand conformations

* remove perses MST networks since those had been generated using the reverse score

* Add Kartograf mapper, Lomap scorer, MST networks (allow element changes)

* Add Kartograf mapper, Lomap scorer, MST networks (NO element changes)

* Kartograf mapper, MST networks, updated

* Kartograf mapper, MST networks, no element change, updated

* Kartograf mapper, lomap network, allow element changes

* Kartograf mapper, lomap network, NO element changes

* Add Lomap mapper, MST networks, with element changes

* Fix SYK ligands

* Fix Lomap MST networks

* Fix SYK Kartograf mapper networks

* Add Lomap mapper MST networks, no element changes

* Add Lomap mapper, Lomap networks, allow element changes

* Add Lomap mapper, Lomap network, no element changes

* Fix SYK Lomap MST network

* Lomap mapper, MST network, max3d=1

* Lomap mapper, MST network, max3d=1, element_changes=False

* Lomap mapper, Lomap network, max3d=1, element_changes=False

* Lomap mapper, Lomap network, max3d=1, allow element changes

* fix cofactor

* Change orientation of Rgroup for 2 PDE2 ligands

* add radial networks, new networks new pde2 inputs

* fix pde2 ligands

* Change protonation state of POP cofactor

* fix pde2 lomap network

* fix pfkfp3 cofactor

* Rename kartograph_mapper_lomap_network.yml to kartograf_mapper_lomap_network.yml

* Rename kartograph to kartograf

* remove old map pde2

* add comments to the target.yaml files

* change lomap networks pde, max_atom_distance=1.0

* add empty line to cofactor pfkfb3

* Fix experimental data for ligand lig_CHEMBL3265032 in the SYK system

* Manually fix mappings edge 2gg -- 2ee

* Remove networks that we have not tested yet

* Remove lomap networks for charge changing systems

* Remove radial networks charge changing systems

* Add lomap networks charge transformations, add radial networks

* Add kartograf_mapper_lomap_network_no_element_changes networks

* Add kartograf_mapper_mst_network_no_element_changes networks

* Add kartograf_mapper_lomap_network_no_element_changes networks

* Add lomap networks, lomap mapper charge changing systems

* Add lomap mapper, mst networks

* Add lomap mapper, mst networks, no element changes

---------

Co-authored-by: IAlibay <[email protected]>
Co-authored-by: Irfan Alibay <[email protected]>
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@hannahbaumann @IAlibay
3 people authored Jul 29, 2024
1 parent a0b67b9 commit fd88824
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Showing 168 changed files with 43,594 additions and 9,803 deletions.
85 changes: 0 additions & 85 deletions data/cdk2/03_edges/01_perses_openfe.yml
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146 changes: 146 additions & 0 deletions data/cdk2/03_edges/kartograf_mapper_lomap_network.yml
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remarks: Kartograph mapper, Lomap scorer, Lomap network, allow element changes
planner: openfe v0.14 lomap network
edges:
edge_lig_1h1q_lig_1h1r:
ligand_a: lig_1h1q
ligand_b: lig_1h1r
atom mapping: {0: 43, 7: 20, 8: 21, 10: 38, 12: 36, 13: 37, 15: 34, 16: 35, 18: 32,
19: 33, 21: 30, 22: 31, 24: 28, 25: 29, 29: 11, 32: 9, 34: 8, 36: 7, 38: 0,
40: 44, 44: 42, 1: 40, 2: 39, 3: 15, 4: 16, 5: 18, 6: 19, 9: 22, 11: 23, 14: 24,
17: 25, 20: 26, 23: 27, 26: 17, 27: 12, 28: 10, 30: 3, 31: 4, 33: 5, 35: 6,
37: 1, 39: 2, 41: 13, 42: 14, 43: 41}
score: {value: '0.905', method: Lomap default scorer}
mapper: Kartograf (atom_map_hydrogens=True)
remarks: null
edge_lig_21_lig_22:
ligand_a: lig_21
ligand_b: lig_22
atom mapping: {0: 0, 7: 7, 8: 8, 10: 10, 12: 12, 13: 13, 15: 15, 16: 16, 18: 18,
19: 19, 21: 21, 22: 22, 24: 24, 25: 25, 29: 29, 32: 32, 34: 34, 36: 36, 40: 40,
41: 41, 44: 44, 48: 48, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 9: 9, 11: 11, 14: 14,
17: 17, 20: 20, 23: 23, 26: 26, 27: 27, 28: 28, 30: 30, 31: 31, 33: 33, 35: 35,
37: 37, 38: 38, 39: 39, 43: 43, 45: 45, 46: 46, 47: 47}
score: {value: '0.951', method: Lomap default scorer}
mapper: Kartograf (atom_map_hydrogens=True)
remarks: null
edge_lig_20_lig_1h1r:
ligand_a: lig_20
ligand_b: lig_1h1r
atom mapping: {7: 7, 9: 0, 11: 44, 14: 11, 20: 21, 21: 20, 23: 38, 25: 37, 26: 36,
28: 35, 29: 34, 31: 33, 32: 32, 34: 31, 35: 30, 37: 29, 38: 28, 42: 43, 44: 42,
48: 9, 2: 8, 5: 5, 6: 6, 8: 1, 10: 2, 12: 3, 13: 10, 15: 12, 16: 17, 17: 16,
18: 18, 19: 19, 22: 22, 24: 23, 27: 24, 30: 25, 33: 26, 36: 27, 39: 15, 40: 39,
41: 40, 43: 41, 45: 14, 46: 13, 47: 4}
score: {value: '0.861', method: Lomap default scorer}
mapper: Kartograf (atom_map_hydrogens=True)
remarks: null
edge_lig_1oi9_lig_1h1q:
ligand_a: lig_1oi9
ligand_b: lig_1h1q
atom mapping: {1: 36, 4: 38, 6: 40, 9: 29, 15: 7, 16: 8, 18: 10, 20: 12, 21: 13,
23: 15, 24: 16, 26: 18, 27: 19, 29: 21, 30: 22, 32: 24, 33: 25, 37: 0, 39: 44,
43: 32, 45: 34, 2: 35, 3: 37, 5: 39, 7: 30, 8: 28, 10: 27, 11: 26, 12: 4, 13: 5,
14: 6, 17: 9, 19: 11, 22: 14, 25: 17, 28: 20, 31: 23, 34: 3, 35: 2, 36: 1, 38: 43,
40: 42, 41: 41, 42: 31, 44: 33}
score: {value: '0.905', method: Lomap default scorer}
mapper: Kartograf (atom_map_hydrogens=True)
remarks: null
edge_lig_1oiu_lig_1h1q:
ligand_a: lig_1oiu
ligand_b: lig_1h1q
atom mapping: {0: 0, 7: 7, 8: 8, 10: 10, 12: 12, 13: 13, 15: 15, 16: 16, 18: 18,
19: 19, 21: 21, 22: 22, 24: 24, 25: 25, 29: 29, 32: 32, 34: 34, 41: 36, 43: 38,
45: 40, 49: 44, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 9: 9, 11: 11, 14: 14, 17: 17,
20: 20, 23: 23, 26: 26, 27: 27, 28: 28, 30: 30, 31: 31, 33: 33, 40: 35, 42: 37,
44: 39, 46: 41, 47: 42, 48: 43}
score: {value: '0.449', method: Lomap default scorer}
mapper: Kartograf (atom_map_hydrogens=True)
remarks: null
edge_lig_21_lig_17:
ligand_a: lig_21
ligand_b: lig_17
atom mapping: {0: 0, 7: 7, 8: 8, 10: 10, 12: 12, 13: 13, 15: 15, 16: 16, 18: 18,
19: 19, 21: 21, 22: 22, 24: 24, 25: 25, 29: 29, 32: 32, 34: 34, 36: 36, 44: 40,
48: 44, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 9: 9, 11: 11, 14: 14, 17: 17, 20: 20,
23: 23, 26: 26, 27: 27, 28: 28, 30: 30, 31: 31, 33: 33, 35: 35, 37: 37, 38: 38,
43: 39, 45: 41, 46: 42, 47: 43}
score: {value: '0.891', method: Lomap default scorer}
mapper: Kartograf (atom_map_hydrogens=True)
remarks: null
edge_lig_1oiu_lig_22:
ligand_a: lig_1oiu
ligand_b: lig_22
atom mapping: {0: 0, 7: 7, 8: 8, 10: 10, 12: 12, 13: 13, 15: 15, 16: 16, 18: 18,
19: 19, 21: 21, 22: 22, 24: 24, 25: 25, 29: 29, 32: 44, 41: 36, 43: 34, 45: 32,
49: 48, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 9: 9, 11: 11, 14: 14, 17: 17, 20: 20,
23: 23, 26: 26, 27: 27, 28: 28, 30: 30, 31: 43, 33: 37, 34: 38, 40: 35, 42: 33,
44: 31, 46: 45, 47: 46, 48: 47}
score: {value: '0.577', method: Lomap default scorer}
mapper: Kartograf (atom_map_hydrogens=True)
remarks: null
edge_lig_1h1q_lig_17:
ligand_a: lig_1h1q
ligand_b: lig_17
atom mapping: {0: 0, 7: 7, 8: 8, 10: 10, 12: 12, 13: 13, 15: 15, 16: 16, 18: 18,
19: 19, 21: 21, 22: 22, 24: 24, 25: 25, 29: 29, 32: 40, 34: 38, 36: 36, 38: 34,
40: 32, 44: 44, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 9: 9, 11: 11, 14: 14, 17: 17,
20: 20, 23: 23, 26: 26, 27: 27, 28: 28, 30: 30, 31: 39, 33: 37, 35: 35, 37: 33,
39: 31, 41: 41, 42: 42, 43: 43}
score: {value: '0.905', method: Lomap default scorer}
mapper: Kartograf (atom_map_hydrogens=True)
remarks: null
edge_lig_26_lig_1oiy:
ligand_a: lig_26
ligand_b: lig_1oiy
atom mapping: {0: 0, 7: 8, 8: 7, 10: 10, 12: 13, 13: 12, 15: 16, 16: 15, 18: 19,
19: 18, 21: 22, 22: 21, 24: 25, 25: 24, 29: 29, 32: 32, 34: 34, 38: 40, 40: 39,
42: 42, 44: 44, 48: 48, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 9: 9, 11: 11, 14: 14,
17: 17, 20: 20, 23: 23, 26: 26, 27: 27, 28: 28, 30: 30, 31: 31, 33: 33, 35: 35,
36: 36, 37: 38, 41: 41, 43: 43, 45: 45, 46: 46, 47: 47}
score: {value: '0.705', method: Lomap default scorer}
mapper: Kartograf (atom_map_hydrogens=True)
remarks: null
edge_lig_1h1q_lig_1oiy:
ligand_a: lig_1h1q
ligand_b: lig_1oiy
atom mapping: {0: 0, 7: 8, 8: 7, 10: 10, 12: 13, 13: 12, 15: 16, 16: 15, 18: 19,
19: 18, 21: 22, 22: 21, 24: 25, 25: 24, 29: 29, 32: 32, 34: 34, 36: 36, 38: 42,
40: 44, 44: 48, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 9: 9, 11: 11, 14: 14, 17: 17,
20: 20, 23: 23, 26: 26, 27: 27, 28: 28, 30: 30, 31: 31, 33: 33, 35: 35, 37: 41,
39: 43, 41: 45, 42: 46, 43: 47}
score: {value: '0.741', method: Lomap default scorer}
mapper: Kartograf (atom_map_hydrogens=True)
remarks: null
edge_lig_22_lig_17:
ligand_a: lig_22
ligand_b: lig_17
atom mapping: {0: 0, 7: 7, 8: 8, 10: 10, 12: 12, 13: 13, 15: 15, 16: 16, 18: 18,
19: 19, 21: 21, 22: 22, 24: 24, 25: 25, 29: 29, 32: 32, 34: 34, 36: 36, 44: 40,
48: 44, 1: 1, 2: 2, 3: 3, 4: 4, 5: 5, 6: 6, 9: 9, 11: 11, 14: 14, 17: 17, 20: 20,
23: 23, 26: 26, 27: 27, 28: 28, 30: 30, 31: 31, 33: 33, 35: 35, 37: 37, 38: 38,
43: 39, 45: 41, 46: 42, 47: 43}
score: {value: '0.861', method: Lomap default scorer}
mapper: Kartograf (atom_map_hydrogens=True)
remarks: null
edge_lig_20_lig_17:
ligand_a: lig_20
ligand_b: lig_17
atom mapping: {7: 36, 9: 34, 11: 32, 14: 29, 20: 8, 21: 7, 23: 10, 25: 13, 26: 12,
28: 16, 29: 15, 31: 19, 32: 18, 34: 22, 35: 21, 37: 25, 38: 24, 42: 0, 44: 44,
48: 40, 2: 38, 5: 37, 6: 35, 8: 33, 10: 31, 12: 30, 13: 28, 15: 27, 16: 26,
17: 4, 18: 5, 19: 6, 22: 9, 24: 11, 27: 14, 30: 17, 33: 20, 36: 23, 39: 3, 40: 2,
41: 1, 43: 43, 45: 42, 46: 41, 47: 39}
score: {value: '0.861', method: Lomap default scorer}
mapper: Kartograf (atom_map_hydrogens=True)
remarks: null
edge_lig_1oi9_lig_26:
ligand_a: lig_1oi9
ligand_b: lig_26
atom mapping: {4: 42, 6: 44, 9: 29, 15: 7, 16: 8, 18: 10, 20: 12, 21: 13, 23: 15,
24: 16, 26: 18, 27: 19, 29: 21, 30: 22, 32: 24, 33: 25, 37: 0, 39: 48, 43: 32,
45: 34, 1: 36, 2: 35, 3: 41, 5: 43, 7: 30, 8: 28, 10: 27, 11: 26, 12: 4, 13: 5,
14: 6, 17: 9, 19: 11, 22: 14, 25: 17, 28: 20, 31: 23, 34: 3, 35: 2, 36: 1, 38: 47,
40: 46, 41: 45, 42: 31, 44: 33}
score: {value: '0.905', method: Lomap default scorer}
mapper: Kartograf (atom_map_hydrogens=True)
remarks: null
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