MolecularDiffusion.runmodes.analyze.docking¶

AutoDock Vina scoring of generated ligands against a protein pocket.

Backs MolCraftDiff analyze metrics --metrics sbdd. Needs the [sbdd] extra (vina + meeko + gemmi); every import is deferred so the rest of the analysis commands keep working without it.

Protocol follows the SBDD literature (targetdiff / KGDiff / IPDiff / Apo2Mol):

the search box is centred on the ligand being scored, sized to its own extent plus a 5 A buffer – generated ligands already sit in the pocket frame, so their own bounding box defines the site;
three modes, increasing cost: score (in place), min (local minimisation), dock (full redock).

The pose matters, so molecules are perceived with OpenBabel, not xyz2mol: xyz2mol returns a topology with no conformer, which silently discards the coordinates the model generated.

Attributes¶

`BOX_BUFFER`
`DOCK_MODES`

Functions¶

`box_for`(mol[, buffer])	Search box centred on this molecule: (center, size), both length 3.
`ligand_pdbqt`(mol)	Sanitized, H-added mol -> PDBQT string (meeko 0.7 API).
`load_pose`(xyz_path)	Read one .xyz into a sanitized RDKit mol that still has its pose.
`prepare_receptor`(receptor_path[, out_dir])	Return a receptor PDBQT path, converting from PDB only if needed.
`score_pose`(mol, receptor_pdbqt[, mode, ...])	Vina affinities for one posed molecule.
`score_reference`(ref_ligand_sdf, receptor_pdbqt, **kwargs)	Score the reference (crystal) ligand -- the bar high_affinity uses.

Module Contents¶

MolecularDiffusion.runmodes.analyze.docking.box_for(mol, buffer=BOX_BUFFER)¶: Search box centred on this molecule: (center, size), both length 3.

MolecularDiffusion.runmodes.analyze.docking.ligand_pdbqt(mol)¶: Sanitized, H-added mol -> PDBQT string (meeko 0.7 API).

MolecularDiffusion.runmodes.analyze.docking.load_pose(xyz_path)¶

Read one .xyz into a sanitized RDKit mol that still has its pose.

Returns (smiles, mol); mol is None when the structure cannot be perceived, is multi-fragment, or lost its conformer.

MolecularDiffusion.runmodes.analyze.docking.prepare_receptor(receptor_path, out_dir=None)¶

Return a receptor PDBQT path, converting from PDB only if needed.

A .pdbqt is used as-is – CrossDocked-style test sets ship them, and reusing one keeps our numbers comparable with the upstream papers.

MolecularDiffusion.runmodes.analyze.docking.score_pose(mol, receptor_pdbqt, mode='dock', exhaustiveness=8, seed=42, buffer=BOX_BUFFER)¶

Vina affinities for one posed molecule.

Returns a dict with vina_score (always), plus vina_min for mode in {"min", "dock"} and vina_dock for mode == "dock".

MolecularDiffusion.runmodes.analyze.docking.score_reference(ref_ligand_sdf, receptor_pdbqt, **kwargs)¶: Score the reference (crystal) ligand – the bar high_affinity uses.

MolecularDiffusion.runmodes.analyze.docking.BOX_BUFFER = 5.0¶

MolecularDiffusion.runmodes.analyze.docking.DOCK_MODES = ('score', 'min', 'dock')¶