Ligand Preparation

class mockdock.ligand_prep.LigandPreparer(n_cpus=None, ph_low=6.4, ph_high=8.4, generate_isomers=True)

Bases: object

Prepare SMILES molecules as PDBQT files for docking.

Parameters:

• n_cpus (int | None)

• ph_low (float)

• ph_high (float)

• generate_isomers (bool)

prepare_batch(smiles_list, output_dir, batch_prefix='')

Prepare PDBQT files for a batch of SMILES. Returns a list of dictionaries: [{‘smiles’: str, ‘pdbqt_paths’: [Path]}] Preserves input order and duplicates.

Parameters:

• smiles_list (list[str])

• output_dir (Path)

• batch_prefix (str)

Return type:

list[dict]