User API examples

Setup python environment and install posebusters to run this notebook.

conda create -n posebusters python=3.10 jupyter notebook
conda activate posebusters
pip install posebusters --upgrade

from posebusters import PoseBusters
from pathlib import Path

pred_file = Path("inputs/generated_molecules.sdf") # predicted or generated molecules
true_file = Path("inputs/crystal_ligand.sdf") # "ground truth" molecules
cond_file = Path("inputs/protein.pdb") # conditioning molecule

PoseBusters default configs

redock

The `redock’ mode is for ligands docked into their cognate receptor crystal structures.

# by default only the binary test report columns are returned
buster = PoseBusters(config="redock")
df = buster.bust([pred_file], true_file, cond_file)
print(df.shape)
df

[20:53:44] WARNING:  Problems/mismatches: Mobile-H( Hydrogens: Number; Mobile-H groups: Falsely present, Attachment points; Charge(s): Do not match)

(3, 25)

		mol_pred_loaded	mol_true_loaded	mol_cond_loaded	sanitization	all_atoms_connected	molecular_formula	molecular_bonds	double_bond_stereochemistry	tetrahedral_chirality	bond_lengths	...	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
file	molecule
inputs/generated_molecules.sdf	molecule_1	True	True	True	True	True	False	False	True	False	False	...	False	True	True	True	True	True	True	True	True	False
	molecule_2	True	True	True	True	True	False	False	True	True	True	...	False	True	True	True	True	True	True	True	True	False
	molecule_3	True	True	True	True	True	False	False	True	True	True	...	False	True	True	True	True	True	True	True	True	False

3 rows × 25 columns

dock

The dock mode is for de-novo generated molecules for a given receptor or for ligands docked into a non-cognate receptor.

buster = PoseBusters(config="dock")
df = buster.bust([pred_file], true_file, cond_file)
print(df.shape)
df

(3, 19)

		mol_pred_loaded	mol_cond_loaded	sanitization	all_atoms_connected	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
file	molecule
inputs/generated_molecules.sdf	molecule_1	True	True	True	True	False	False	True	True	True	True	False	True	True	True	True	True	True	True	True
	molecule_2	True	True	True	True	True	True	True	True	True	True	False	True	True	True	True	True	True	True	True
	molecule_3	True	True	True	True	True	True	True	True	True	True	False	True	True	True	True	True	True	True	True

mol

The mol mode is for de-novo generated molecules or for generated molecular conformations.

buster = PoseBusters(config="mol")
df = buster.bust([pred_file], None, None)
print(df.shape)
df

(3, 9)

		mol_pred_loaded	sanitization	all_atoms_connected	bond_lengths	bond_angles	internal_steric_clash	aromatic_ring_flatness	double_bond_flatness	internal_energy
file	molecule
inputs/generated_molecules.sdf	molecule_1	True	True	True	False	False	True	True	True	True
	molecule_2	True	True	True	True	True	True	True	True	True
	molecule_3	True	True	True	True	True	True	True	True	True

Output formatting

full report

The full_report option of bust will return all columns of the test reports, not only the binary columns. This is useful for debugging and for further analysis of the results.

buster = PoseBusters(config="mol")
df = buster.bust([pred_file], None, None, full_report=True)
print(df.shape)
df

(3, 36)

		mol_pred_loaded	sanitization	all_atoms_connected	bond_lengths	bond_angles	internal_steric_clash	aromatic_ring_flatness	double_bond_flatness	internal_energy	mol_true_loaded	...	number_valid_noncov_pairs	number_aromatic_rings_checked	number_aromatic_rings_pass	aromatic_ring_maximum_distance_from_plane	number_double_bonds_checked	number_double_bonds_pass	double_bond_maximum_distance_from_plane	ensemble_avg_energy	mol_pred_energy	energy_ratio
file	molecule
inputs/generated_molecules.sdf	molecule_1	True	True	True	False	False	True	True	True	True	False	...	235	0	0	NaN	0	0	NaN	608.632249	1377.869730	2.263879
	molecule_2	True	True	True	True	True	True	True	True	True	False	...	260	1	1	0.078919	0	0	NaN	259.822517	253.508495	0.975699
	molecule_3	True	True	True	True	True	True	True	True	True	False	...	257	1	1	0.091866	0	0	NaN	301.579457	341.205292	1.131394

3 rows × 36 columns