from __future__ import absolute_import, division, print_function try: from phenix.program_template import ProgramTemplate except ImportError: from libtbx.program_template import ProgramTemplate import os import libtbx.phil from libtbx.utils import Sorry from libtbx import easy_pickle import mmtbx.ringer.emringer # ============================================================================= program_citations = libtbx.phil.parse(''' citation { article_id = emringer1 authors = Barad BA, Echols N, Wang RY, Cheng Y, DiMaio F, Adams PD, Fraser JS title = Side-chain-directed model and map validation for 3D Electron Cryomicroscopy. journal = Nature Methods volume = 10 pages = 943-46 year = 2015 doi_id = "10.1038/nmeth.3541" pmid = 26280328 external = True } citation { article_id = emringer2 authors = Lang PT, Ng HL, Fraser JS, Corn JE, Echols N, Sales M, Holton JM, Alber T title = Automated electron-density sampling reveals widespread conformational polymorphism in proteins. journal = Protein Sci. volume = 7 pages = 1420-31 year = 2010 doi_id = "" pmid = 20499387 external = True } ''') # ============================================================================= master_phil_str = ''' include scope libtbx.phil.interface.tracking_params include scope mmtbx.ringer.emringer.master_params map_label = 2FOFCWT,PH2FOFCWT .type = str .input_size = 200 .short_caption = 2Fo-FC map labels .help = Labels for 2Fo-Fc map coefficients show_gui = False .type = bool output_base = None .type = str output_dir = None .type = path .short_caption = Output directory quiet = False .type = bool .short_caption = no graphs .help = Don't output files or graphs ''' # ============================================================================= class Program(ProgramTemplate): description = ''' Program for calculating the EMRinger score.\n Minimum required inputs: Model file Map file (or file with map coefficients) How to run: phenix.emringer model.pdb map.ccp4 ''' datatypes = ['model', 'real_map', 'phil', 'map_coefficients'] citations = program_citations master_phil_str = master_phil_str # --------------------------------------------------------------------------- def validate(self): print('Validating inputs', file=self.logger) self.data_manager.has_models(raise_sorry=True) if not (self.data_manager.has_real_maps() or self.data_manager.has_map_coefficients()): raise Sorry("Supply a map file or a file with map coefficients.") elif (self.data_manager.has_real_maps() and self.data_manager.has_map_coefficients()): raise Sorry("Supply either a map file or a file with map coefficients.") # --------------------------------------------------------------------------- def run(self): map_inp = None miller_array = None print('Using model: %s' % self.data_manager.get_default_model_name(), file=self.logger) model = self.data_manager.get_model() if self.data_manager.has_map_coefficients(): miller_arrays = self.data_manager.get_miller_arrays() miller_array = self.find_label(miller_arrays = miller_arrays) print('Using miller array: %s' % miller_array.info().label_string(), file=self.logger) elif self.data_manager.has_real_maps(): print('Using map: %s' % self.data_manager.get_default_real_map_name(), file=self.logger) map_inp = self.data_manager.get_real_map() print("CCP4 map statistics:", file=self.logger) map_inp.show_summary(out=self.logger, prefix=" ") if (self.params.output_base is None): pdb_base = os.path.basename(self.data_manager.get_default_model_name()) self.params.output_base = os.path.splitext(pdb_base)[0] + "_emringer" if not self.params.quiet: plots_dir = self.params.output_base + "_plots" if (not os.path.isdir(plots_dir)): os.makedirs(plots_dir) task_obj = mmtbx.ringer.emringer.emringer( model = model, miller_array = miller_array, map_inp = map_inp, params = self.params, out = self.logger) task_obj.validate() task_obj.run() self.results = task_obj.get_results() ringer_result = self.results.ringer_result if not self.params.quiet: # save as pickle easy_pickle.dump("%s.pkl" % self.params.output_base, ringer_result) print ('Wrote %s.pkl' % self.params.output_base, file=self.logger) # save as CSV csv = "\n".join([ r.format_csv() for r in ringer_result]) open("%s.csv" % self.params.output_base, "w").write(csv) print ('Wrote %s.csv' % self.params.output_base, file=self.logger) scoring_result = self.results.scoring_result scoring_result.show_summary(out = self.logger) #rolling_result = self.results.rolling_result # It would be good to have central code for this # --------------------------------------------------------------------------- def find_label(self, miller_arrays): best_guess = None best_labels = [] all_labels = [] miller_array = None for array in miller_arrays: label = array.info().label_string().replace(" ", "") if (self.params.map_label is not None): if (label == self.params.map_label.replace(" ", "")): miller_array = array return miller_array elif (self.params.map_label is None): if (array.is_complex_array()): all_labels.append(label) if (label.startswith("2FOFCWT") or label.startswith("2mFoDFc") or label.startswith("FWT")): best_guess = array best_labels.append(label) if (miller_array is None): if (len(all_labels) == 0): raise Sorry("No valid (pre-weighted) map coefficients found in file.") elif (len(best_labels) == 0): raise Sorry("Couldn't automatically determine appropriate map labels. "+ "Choices:\n %s" % " \n".join(all_labels)) elif (len(best_labels) > 1): raise Sorry("Multiple appropriate map coefficients found in file. "+ "Choices:\n %s" % "\n ".join(best_labels)) elif (len(best_labels) == 1): miller_array = best_guess print(" Guessing %s for input map coefficients"% best_labels[0], file=self.logger) return miller_array # --------------------------------------------------------------------------- def get_results(self): return self.results