# -*- coding: utf-8; py-indent-offset: 2 -*- from __future__ import absolute_import, division, print_function from mmtbx.ions.environment import ChemicalEnvironment import mmtbx.ions.identify from mmtbx import ions import mmtbx.monomer_library.pdb_interpretation from mmtbx import monomer_library from mmtbx.ions.environment import chem_carboxy, chem_amide, chem_backbone, \ chem_water, chem_phosphate, \ chem_nitrogen_primary, chem_nitrogen_secondary, \ chem_chloride, chem_oxygen, chem_nitrogen, chem_sulfur import libtbx.load_env from collections import OrderedDict, Counter import os import sys from six.moves import zip from six.moves import range def exercise(): if not libtbx.env.has_module("phenix_regression"): print("Skipping {}".format(os.path.split(__file__)[1])) return models = OrderedDict([ ("2qng", [ Counter({chem_oxygen: 7, chem_carboxy: 2, chem_water: 2, chem_backbone: 3}), Counter({chem_oxygen: 6, chem_carboxy: 3, chem_water: 1, chem_backbone: 2}), ]), ("3rva", [ Counter({chem_oxygen: 6, chem_carboxy: 4, chem_water: 2}), Counter({chem_nitrogen: 1, chem_oxygen: 4, chem_nitrogen_secondary: 1, chem_carboxy: 3, chem_water: 1}), Counter({chem_nitrogen: 4, chem_nitrogen_primary: 1, chem_nitrogen_secondary: 3, chem_backbone: 3}), ]), ("1mjh", [ Counter({chem_oxygen: 6, chem_water: 3, chem_phosphate: 3}), Counter({chem_oxygen: 6, chem_water: 3, chem_phosphate: 3}), ]), ("4e1h", [ Counter({chem_oxygen: 6, chem_carboxy: 4}), Counter({chem_oxygen: 6, chem_carboxy: 3}), Counter({chem_oxygen: 6, chem_carboxy: 3}), ]), ("2xuz", [ Counter({chem_oxygen: 6}), ]), ("3zli", [ Counter({chem_nitrogen: 2, chem_oxygen: 4, chem_nitrogen_secondary: 2, chem_carboxy: 1, chem_water: 1}), Counter({chem_sulfur: 4}), Counter({chem_nitrogen: 2, chem_oxygen: 4, chem_nitrogen_secondary: 2, chem_carboxy: 1, chem_water: 1}), Counter({chem_sulfur: 4}), ]), ("3e0f", [ Counter({chem_nitrogen: 2, chem_oxygen: 4, chem_nitrogen_secondary: 2, chem_carboxy: 2, chem_phosphate: 2}), Counter({chem_nitrogen: 2, chem_oxygen: 2, chem_nitrogen_secondary: 2, chem_carboxy: 1, chem_phosphate: 1}), Counter({chem_nitrogen: 2, chem_oxygen: 3, chem_nitrogen_secondary: 2, chem_carboxy: 2, chem_phosphate: 1}), ]), ("3dkq", [ Counter({chem_nitrogen: 4, chem_oxygen: 1, chem_nitrogen_secondary: 4, chem_carboxy: 1}), Counter({chem_nitrogen: 2, chem_oxygen: 1, chem_nitrogen_secondary: 2, chem_carboxy: 1}), Counter({chem_nitrogen: 4, chem_oxygen: 1, chem_nitrogen_secondary: 4, chem_carboxy: 1}), ]), ("2o8q", [ Counter({chem_nitrogen: 3, chem_oxygen: 3, chem_nitrogen_secondary: 3, chem_water: 3}), Counter({chem_nitrogen: 3, chem_oxygen: 3, chem_nitrogen_secondary: 3, chem_water: 3}), ]), ("1tgg", [ Counter({chem_oxygen: 5, chem_chloride: 1, chem_carboxy: 4, chem_water: 1}), Counter({chem_oxygen: 3, chem_chloride: 2, chem_carboxy: 3}), Counter({chem_oxygen: 4, chem_chloride: 2, chem_carboxy: 4}), ]), ("3zu8", [ Counter({chem_oxygen: 7, chem_carboxy: 3, chem_water: 1, chem_backbone: 2}), Counter({chem_nitrogen: 4, chem_oxygen: 1, chem_nitrogen_primary: 1, chem_nitrogen_secondary: 3, chem_carboxy: 1, chem_backbone: 3}), ]), ("1ofs", [ Counter({chem_nitrogen: 1, chem_oxygen: 4, chem_nitrogen_secondary: 1, chem_carboxy: 3, chem_water: 1}), Counter({chem_oxygen: 7, chem_amide: 1, chem_carboxy: 3, chem_water: 2, chem_backbone: 1}), Counter({chem_nitrogen: 1, chem_oxygen: 5, chem_nitrogen_secondary: 1, chem_carboxy: 3, chem_water: 2}), Counter({chem_oxygen: 7, chem_amide: 1, chem_carboxy: 3, chem_water: 2, chem_backbone: 1}), ]), ("3ul2", [ Counter({chem_oxygen: 7, chem_amide: 1, chem_carboxy: 3, chem_water: 2, chem_backbone: 1}), Counter({chem_nitrogen: 1, chem_oxygen: 5, chem_nitrogen_secondary: 1, chem_carboxy: 3, chem_water: 2}), Counter({chem_oxygen: 7, chem_amide: 1, chem_carboxy: 3, chem_backbone: 1, chem_water: 2}), Counter({chem_nitrogen: 1, chem_oxygen: 5, chem_nitrogen_secondary: 1, chem_carboxy: 3, chem_water: 2}), Counter({chem_oxygen: 7, chem_amide: 1, chem_carboxy: 3, chem_water: 2, chem_backbone: 1}), Counter({chem_nitrogen: 1, chem_oxygen: 5, chem_nitrogen_secondary: 1, chem_carboxy: 3, chem_water: 2}), Counter({chem_oxygen: 7, chem_amide: 1, chem_carboxy: 3, chem_water: 2, chem_backbone: 1}), Counter({chem_nitrogen: 1, chem_oxygen: 5, chem_nitrogen_secondary: 1, chem_carboxy: 3, chem_water: 2}), ]), ("3snm", [ Counter({chem_oxygen: 5, chem_amide: 1, chem_carboxy: 3, chem_backbone: 1}), Counter({chem_nitrogen: 1, chem_oxygen: 3, chem_nitrogen_secondary: 1, chem_carboxy: 3}), ]), ("3qlq", [ Counter({chem_oxygen: 7, chem_amide: 1, chem_carboxy: 3, chem_water: 2, chem_backbone: 1}), Counter({chem_nitrogen: 1, chem_oxygen: 5, chem_nitrogen_secondary: 1, chem_carboxy: 3, chem_water: 2}), Counter({chem_nitrogen: 1, chem_oxygen: 5, chem_nitrogen_secondary: 1, chem_carboxy: 3, chem_water: 2}), Counter({chem_oxygen: 7, chem_amide: 1, chem_carboxy: 3, chem_water: 2, chem_backbone: 1}), Counter({chem_nitrogen: 1, chem_oxygen: 5, chem_nitrogen_secondary: 1, chem_carboxy: 3, chem_water: 2}), Counter({chem_oxygen: 7, chem_amide: 1, chem_carboxy: 3, chem_water: 2, chem_backbone: 1}), Counter({chem_oxygen: 7, chem_amide: 1, chem_carboxy: 3, chem_water: 2, chem_backbone: 1}), Counter({chem_nitrogen: 1, chem_oxygen: 5, chem_nitrogen_secondary: 1, chem_carboxy: 3, chem_water: 2}), ]), ("2gdf", [ Counter({chem_nitrogen: 1, chem_oxygen: 4, chem_nitrogen_secondary: 1, chem_carboxy: 3, chem_water: 1}), Counter({chem_oxygen: 6, chem_amide: 1, chem_carboxy: 3, chem_water: 1, chem_backbone: 1}), Counter({chem_nitrogen: 1, chem_oxygen: 4, chem_nitrogen_secondary: 1, chem_carboxy: 3, chem_water: 1}), Counter({chem_oxygen: 6, chem_amide: 1, chem_carboxy: 3, chem_water: 1, chem_backbone: 1}), ]), ("1q8h", [ Counter({chem_oxygen: 7, chem_carboxy: 6, chem_water: 1}), Counter({chem_oxygen: 7, chem_carboxy: 4, chem_water: 3}), Counter({chem_oxygen: 8, chem_carboxy: 6, chem_water: 2}), ]), ]) for model, expected_environments in models.items(): pdb_path = libtbx.env.find_in_repositories( relative_path = os.path.join( "phenix_regression", "mmtbx", "ions", model + ".pdb"), test = os.path.isfile ) mon_lib_srv = monomer_library.server.server() ener_lib = monomer_library.server.ener_lib() processed_pdb_file = monomer_library.pdb_interpretation.process( mon_lib_srv = mon_lib_srv, ener_lib = ener_lib, file_name = pdb_path, raw_records = None, force_symmetry = True, log = libtbx.utils.null_out() ) geometry = \ processed_pdb_file.geometry_restraints_manager(show_energies = False) xray_structure = processed_pdb_file.xray_structure() pdb_hierarchy = processed_pdb_file.all_chain_proxies.pdb_hierarchy connectivity = geometry.shell_sym_tables[0].full_simple_connectivity() manager = mmtbx.ions.identify.manager( fmodel = None, pdb_hierarchy = pdb_hierarchy, xray_structure = xray_structure, connectivity = connectivity) elements = set(ions.DEFAULT_IONS + ions.TRANSITION_METALS) elements.difference_update(["CL"]) metals = [i_seq for i_seq, atom in enumerate(manager.pdb_atoms) if atom.fetch_labels().resname.strip().upper() in elements] assert len(metals) == len(expected_environments) for index, metal, expected_environment in \ zip(range(len(metals)), metals, expected_environments): env = ChemicalEnvironment( metal, manager.find_nearby_atoms(metal, filter_by_two_fofc = False), manager ) if env.chemistry != expected_environment: print("Problem detecting chemistry environment in", model, index) print("Found: ", env.chemistry) print("Should be:", expected_environment) sys.exit() print("OK") if __name__ == "__main__": exercise()