def _getSDFStream(f, mols): w = SDWriter(f) for m in mols: w.write(m) w.flush()
def _getSDFStream(f, mols): w = SDWriter(f) for m in mols: w.write(m) w.flush()
## Make directories for each transformation ## for pair in map_list: print('%s -> %s \n' % (pair[0], pair[1])) pair_dir = pair[0] + '_' + pair[1] os.mkdir(pair_dir) os.chdir(pair_dir) os.mkdir(dir_1_name) os.mkdir(dir_2_name) ## Write start ligand file, parameters ## os.chdir(dir_1_name) writer = SDWriter('for_parm.sdf') writer.write(ligands[ligands_name.index(pair[0])]) writer.flush() run_antechamber(ligands[ligands_name.index(pair[0])], 'for_parm.sdf', ff) os.chdir('../') ## Check and fix XYZ coords of transform ligand ## fix_mol = update_atom_position( ligands[ligands_name.index(pair[0])], ligands[ligands_name.index(pair[1])]) ## Write endpoint ligand file, parameters ## os.chdir(dir_2_name) writer = SDWriter('for_parm.sdf') writer.write(fix_mol) writer.flush() run_antechamber(ligands[ligands_name.index(pair[1])],