h_mov_new_fname = os.path.join( os.path.dirname(p_mov), params.output.prefix + params.output.suffix.join( os.path.splitext(os.path.basename(p_mov)))) assert os.path.abspath(h_mov_new_fname) != os.path.abspath( p_mov), 'output filename is same as input filename' print 'Saving output structure to {}'.format(h_mov_new_fname) h_mov_new.write_pdb_file(file_name=h_mov_new_fname) t_end = time.time() print pretty_string('\n===========================>').bold() print pretty_string('Finished!').bold() print pretty_string('Total Runtime: {!s}'.format( time.strftime("%H hours:%M minutes:%S seconds", time.gmtime(t_end - t_start)))).bold() print pretty_string('Avg/Structure: {!s}'.format( time.strftime("%H hours:%M minutes:%S seconds", time.gmtime( (t_end - t_start) / len(params.input.pdb))))).bold() print pretty_string('===========================>').bold() ####################################### if __name__ == '__main__': from giant.jiffies import run_default run_default(run=run, master_phil=master_phil, args=sys.argv[1:], blank_arg_prepend=blank_arg_prepend)
pruning_rmsd=params.options.pruning_rmsd, in_place=True, verbose=params.settings.verbose) # Update the atoms numbering final.sort_atoms_in_place() # Write output file filename = os.path.splitext(pdb)[0] + params.output.suffix + '.pdb' log('Writing output structure to {}'.format(filename)) final.write_pdb_file(file_name=filename, crystal_symmetry=obj.crystal_symmetry()) log.heading('FINISHED') log.heading('Final Parameters') log(master_phil.format(params).as_str().strip()) return ############################################################################ if __name__ == '__main__': from giant.jiffies import run_default run_default(run=run, master_phil=master_phil, args=sys.argv[1:], blank_arg_prepend=blank_arg_prepend, program=PROGRAM, description=DESCRIPTION)
dataset_prefix=params.input.xtal_name, out_dir=params.output.out_dir, params=params, ) logging.info("Plotting occupancy, bfactor and mean |Fobs-Fcalc| " "for each simulated occupancy") for simul_occ in np.arange( params.validate.options.start_simul_occ, params.validate.options.end_simul_occ, params.validate.options.step_simulation, ): # TODO remove duplication of this code: utils.get_minimum_fofc: 59 csv_name = params.exhaustive.output.csv_prefix + "_occ_{}_b_{}.csv".format( str(simul_occ).replace(".", "_"), str(params.validate.options.set_b).replace(".", "_"), ) scatter_plot(csv_name, title_text="Phenix.fmodel at occ {}".format(simul_occ)) logging.info("Validation script finished") if __name__ == "__main__": from giant.jiffies import run_default run_default(run=run, master_phil=master_phil, args=sys.argv[1:])