from __future__ import absolute_import, division, print_function try: from phenix.program_template import ProgramTemplate except ImportError: from libtbx.program_template import ProgramTemplate import mmtbx.validation.ligands from mmtbx.validation import validate_ligands from libtbx.utils import null_out, Sorry from iotbx import crystal_symmetry_from_any from libtbx.str_utils import make_sub_header from iotbx import extract_xtal_data master_phil_str = """ include scope mmtbx.validation.validate_ligands.master_params ligand_code = None .type = str .multiple = True reference_structure = None .type = path only_segid = None .type = str verbose = False .type = bool update_scales = True .type = bool """ # TODO update_scales if for development only, delete for production! # ============================================================================= class Program(ProgramTemplate): description = ''' mmtbx.validate_ligands model.pdb data.mtz LIGAND_CODE [...] Print out basic statistics for residue(s) with the given code(s), including electron density values/CC. ''' datatypes = ['model', 'phil', 'miller_array'] master_phil_str = master_phil_str # --------------------------------------------------------------------------- def validate(self): print('Validating inputs...\n', file=self.logger) self.data_manager.has_models( raise_sorry = True, expected_n = 1, exact_count = True) # if (self.params.ligand_code is None or self.params.ligand_code[0] is None): # raise Sorry("Ligand code required!") # --------------------------------------------------------------------------- def get_crystal_symmetry(self): crystal_symmetries = [] files = [self.data_manager.get_default_model_name()] if self.data_manager.get_default_miller_array_name() is not None: files.append(self.data_manager.get_default_miller_array_name()) for f in files: cs = crystal_symmetry_from_any.extract_from(f) if (cs is not None): crystal_symmetries.append(cs) if (len(crystal_symmetries) == 1): crystal_symmetry = crystal_symmetries[0] elif (len(crystal_symmetries) == 0): raise Sorry("No crystal symmetry found.") else: if (not crystal_symmetries[0].is_similar_symmetry(crystal_symmetries[1])): raise Sorry("Crystal symmetry mismatch between different files.") crystal_symmetry = crystal_symmetries[0] return crystal_symmetry # --------------------------------------------------------------------------- def get_fobs_rfree(self, crystal_symmetry): rfs = self.data_manager.get_reflection_file_server( filenames = [self.data_manager.get_default_miller_array_name()], crystal_symmetry = crystal_symmetry, logger=null_out()) parameters = extract_xtal_data.data_and_flags_master_params().extract() determined_data_and_flags = extract_xtal_data.run( reflection_file_server = rfs, parameters = parameters, keep_going = True, working_point_group = crystal_symmetry.space_group().build_derived_point_group()) f_obs = determined_data_and_flags.f_obs r_free_flags = determined_data_and_flags.r_free_flags return f_obs, r_free_flags # --------------------------------------------------------------------------- def run(self): model_fn = self.data_manager.get_default_model_name() print('Using model file:', model_fn, file=self.logger) print('Using reflection file:', self.data_manager.get_default_miller_array_name(), file=self.logger) cs = self.get_crystal_symmetry() model = self.data_manager.get_model() #grm = model.get_restraints_manager() ph = model.get_hierarchy() xrs = model.get_xray_structure() fmodel = None if self.data_manager.get_default_miller_array_name(): f_obs, r_free_flags = self.get_fobs_rfree(crystal_symmetry = cs) print('\nInput data...', file=self.logger) print(' Reflection data:', f_obs.info().labels, file=self.logger) if (r_free_flags is not None): print(' Free-R flags:', r_free_flags.info().labels, file=self.logger) else: print(' Free-R flags: not present or not found', file=self.logger) fmodel = mmtbx.f_model.manager( f_obs = f_obs, r_free_flags = r_free_flags, xray_structure = xrs) print('\n', file = self.logger) fmodel.show(log=self.logger, show_header=False) # TODO: delete this keyword for production #if self.params.update_scales: fmodel.update_all_scales() fmodel.show(log=self.logger, show_header=False) print('\nWorking crystal symmetry after inspecting all inputs:', file=self.logger) cs.show_summary(f=self.logger) # This is the new class, currently a stub but will be developed # spring 2019 by DL and NWM #t0 = time.time() # TODO: Decide if H should be placed here or in the class # if readyset is used, filename is needed # if readyset can be run as class, filename could be avoided ligand_manager = validate_ligands.manager( model = model, # model_fn = model_fn, fmodel = fmodel, params = self.params.validate_ligands, log = self.logger) ligand_manager.run() ligand_manager.show_ligand_counts() ligand_manager.show_ligand_occupancies() ligand_manager.show_adps() ligand_manager.show_ccs() ligand_manager.show_nonbonded_overlaps() #print('time running manager: ', time.time()-t0) # TODO # DL: Eventually, delete "old" call below, but leave it for now to keep the # funcitonality alive, just in case if self.params.ligand_code and self.data_manager.get_default_miller_array_name() is not None: if (not(self.params.ligand_code is None or self.params.ligand_code[0] is None)): make_sub_header("Validating ligands", out=self.logger) for ligand_code in self.params.ligand_code : validations = mmtbx.validation.ligands.validate_ligands( pdb_hierarchy = ph, fmodel = fmodel, ligand_code = ligand_code, reference_structure = self.params.reference_structure, only_segid = self.params.only_segid) if (validations is None): raise Sorry("No ligands named '%s' found." % ligand_code) mmtbx.validation.ligands.show_validation_results(validations=validations, out = self.logger, verbose = self.params.verbose)