0163532bd311653fea70ab08474384e34027846a,oddt/docking/AutodockVina.py,autodock_vina,dock,#autodock_vina#Any#Any#Any#,256

Before Change

                    raise Exception("Autodock Vina failed. Command: "%s"" % " ".join(e.cmd))
            // HACK // overcome connectivity problems in obabel
            source_ligand = six.next(toolkit.readfile("pdbqt", ligand_file))
            del source_ligand.data["REMARK"]
            if (hasattr(oddt.toolkits, "ob") and
                    isinstance(self.protein, oddt.toolkits.ob.Molecule)):
                kwargs = {"opt": {"b": None}}
            else:

After Change

            else:
                kwargs = {"flexible": True}
                source_ligand = ligand  // rdkit perserves the order
            if "REMARK" in source_ligand.data:
                del source_ligand.data["REMARK"]
            for lig, scores in zip([lig for lig in toolkit.readfile("pdbqt", ligand_outfile, **kwargs)], vina):
                // HACK // copy data from source
                clone = source_ligand.clone
                clone.clone_coords(lig)

Instances