Ligand preparation in Python

Creating a PDBQT string from an RDKit molecule

from meeko import MoleculePreparation
from meeko import PDBQTWriterLegacy
from rdkit import Chem

input_molecule_file = "example/BACE_macrocycle/BACE_4.sdf"

# there is one molecule in this SD file, this loop iterates just once
for mol in Chem.SDMolSupplier(input_molecule_file, removeHs=False):
    preparator = MoleculePreparation()
    mol_setups = preparator.prepare(mol)
    for setup in mol_setups:
        setup.show() # optional
        pdbqt_string = PDBQTWriterLegacy.write_string(setup)

At this point, pdbqt_string can be written to a file for docking with AutoDock-GPU or Vina, or passed directly to Vina within Python using set_ligand_from_string (pdbqt_string). For context, see the docs on using Vina from Python.

One advantage of this approach is that input PDBQT files are not written to the filesystem. The PDBQT format is lossy, because it lacks bond orders and non-polar hydrogens, making it a poor choice to store molecular information.

Another advantage is to write custom workflows entirely from Python without external calls to mk_prepare_ligand.py.