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The number of PD conditions provided by posebusters_paper_results does not match the number I obtained using bust. #46

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liyue9129 opened this issue Oct 15, 2024 · 0 comments

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@liyue9129
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liyue9129 commented Oct 15, 2024

Hello. I am currently using posebuster to evaluate the rationality of molecules obtained from molecular docking methods, using the following code.
bust redocked_ligand.sdf -l crystal_ligand.sdf -p protein.pdb --outfmt csv
The number I obtained is as follows
'mol_pred_loaded', 'mol_true_loaded', 'mol_cond_loaded', 'sanitization', 'inchi_convertible', 'all_atoms_connected', 'molecular_formula', 'molecular_bonds', 'double_bond_stereochemistry', 'tetrahedral_chirality', 'bond_lengths,bond_angles', 'internal_steric_clash', 'aromatic_ring_flatness', 'double_bond_flatness', 'internal_energy', 'protein-ligand_maximum_distance', 'minimum_distance_to_protein', 'minimum_distance_to_organic_cofactors', 'minimum_distance_to_inorganic_cofactors', 'minimum_distance_to_waters', 'volume_overlap_with_protein', 'volume_overlap_with_organic_cofactors', 'volume_overlap_with_inorganic_cofactors', 'volume_overlap_with_waters', 'rmsd_≤_2å'

But the number of PD conditions provided by posebusters paper results are :
'molecule_passes_rdkit_sanity_check', 'molecular_formula_preserved', 'molecular_bonds_preserved', 'sp3_stereochemistry_preserved', 'double_bond_stereochemistry_preserved', 'bond_lengths_within_bounds', 'bond_angles_within_bounds', 'no_internal_clashes', 'aromatic_ring_flatness_passes', 'double_bond_flatness_passes', 'energy_ratio_within_threshold', 'no_clashes_with_protein', 'no_clashes_with_organic_cofactors', 'no_clashes_with_inorganic_cofactors', 'no_volume_clash_with_protein', 'no_volume_clash_with_organic_cofactors', 'no_volume_clash_with_inorganic_cofactors'

How can I convert the results I obtained to the number of PB conditions in the article?
Looking forward to hearing from you! Thanks.

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