Exporting docking results in Python

from meeko import PDBQTMolecule
from meeko import RDKitMolCreate

fn = "autodock-gpu_results.dlg"
pdbqt_mol = PDBQTMolecule.from_file(fn, is_dlg=True, skip_typing=True)
rdkitmol_list = RDKitMolCreate.from_pdbqt_mol(pdbqt_mol)

The length of rdkitmol_list is one if there are no sidechains and only one ligand was docked. If multiple ligands and/or sidechains are docked simultaneously, each will be an individual RDKit molecule in rdkitmol_list. Sidechains are truncated at the C-alpha. Note that docking multiple ligands simultaneously is only available in Vina, and it differs from docking multiple ligands one after the other. Each failed creation of an RDKit molecule for a ligand or sidechain results in a None in rdkitmol_list.

For Vina’s output PDBQT files, omit is_dlg=True.

pdbqt_mol = PDBQTMolecule.from_file("vina_results.pdbqt", skip_typing=True)
rdkitmol_list = RDKitMolCreate.from_pdbqt_mol(pdbqt_mol)

When using Vina from Python, the output string can be passed directly. See the docs for context on the Vina object.

vina_output_string = v.poses()
pdbqt_mol = PDBQTMolecule(vina_output_string, is_dlg=True, skip_typing=True)
rdkitmol_list = RDKitMolCreate.from_pdbqt_mol(pdbqt_mol)