d637d972b42492ec8ca144e319611332d828fdb3,oddt/docking/AutodockVina.py,autodock_vina,dock,#autodock_vina#Any#Any#Any#,233

Before Change

            // write ligand to file
            ligand_file = ligand_dir + "/" + str(n) + "_" + re.sub("[^A-Za-z0-9]+", "_", ligand.title) + ".pdbqt"
            ligand_outfile = ligand_dir + "/" + str(n) + "_" + re.sub("[^A-Za-z0-9]+", "_", ligand.title) + "_out.pdbqt"
            ligand.write("pdbqt", ligand_file, overwrite=True, opt={"b": None})
            try:
                vina = parse_vina_docking_output(subprocess.check_output([self.executable,
                                                                          "--receptor",
                                                                          self.protein_file,

After Change

            // write ligand to file
            ligand_file = ligand_dir + "/" + str(n) + "_" + re.sub("[^A-Za-z0-9]+", "_", ligand.title) + ".pdbqt"
            ligand_outfile = ligand_dir + "/" + str(n) + "_" + re.sub("[^A-Za-z0-9]+", "_", ligand.title) + "_out.pdbqt"
            if (hasattr(oddt.toolkits, "ob") and
                    isinstance(self.protein, oddt.toolkits.ob.Molecule)):
                kwargs = {"opt": {"b": None}}
            else:
                kwargs = {"flexible": True}
            ligand.write("pdbqt", ligand_file, overwrite=True, **kwargs)
            try:
                vina = parse_vina_docking_output(subprocess.check_output([self.executable,
                                                                          "--receptor",

Instances