def generateMap(nativePdb, nativeMtz): logging.debug("Parsing MTZ file %s to determine column labels", nativeMtz) F, SIGF, FREE = mtz_util.get_labels(nativeMtz) logging.debug("Generating map from: %s %s", nativeMtz, nativePdb) return phenixer.generateMap(nativeMtz, nativePdb, FP=F, SIGFP=SIGF, FREE=FREE)
def test_process_mtz_labels2(self): # Get MTZ flags os.chdir(self.thisd) # Need as otherwise tests that happen in other directories change os.cwd() mtz = os.path.join( self.testfiles_dir, "1dtx.mtz" ) FP,SIGFP,FREE=mtz_util.get_labels(mtz) self.assertEqual(FP,'FP') self.assertEqual(SIGFP,'SIGFP') self.assertEqual(FREE,'FreeR_flag')
def test_process_mtz_labels(self): # Get MTZ flags os.chdir( self.thisd ) # Need as otherwise tests that happen in other directories change os.cwd() mtz = os.path.join(self.testfiles_dir, "2uui_sigmaa.mtz") FP, SIGFP, FREE = mtz_util.get_labels(mtz) self.assertEqual(FP, 'F') self.assertEqual(SIGFP, 'SIGF') self.assertEqual(FREE, None)
required=True) parser.add_argument('-native_pdb', help="Input native PDB file", required=False) parser.add_argument('-f_label', help="F label from native MTZ file", required=False) parser.add_argument('-sigf_label', help="SIGF label from native MTZ file", required=False) args = parser.parse_args() # Extract F & SIGF from file if not give on command-line if args.f_label and args.sigf_label: f_label, sigf_label = args.f_label, args.sigf_label else: f_label, sigf_label, _ = mtz_util.get_labels(args.native_mtz) _logger.info("Using F, SIGF labels from mtz file: {0}, {1} ".format( f_label, sigf_label)) if args.native_pdb: before_origin, after_origin, change_of_hand, origin_shift = calc_phase_error_pdb( args.native_pdb, args.native_mtz, args.mr_mtz, f_label, sigf_label) else: before_origin, after_origin, change_of_hand, origin_shift = calc_phase_error_mtz( args.native_mtz, args.mr_mtz, f_label, sigf_label) print "Calculated phase error: {0}".format(after_origin) print "Calculated origin shift: {0}".format(origin_shift)
import argparse parser = argparse.ArgumentParser(description='Run cphasematch on two mtz files', prefix_chars="-") parser.add_argument('-native_mtz', help="Input native MTZ file", required=True) parser.add_argument('-mr_mtz', help="Input MTZ file from Molecular Replacement", required=True) parser.add_argument('-native_pdb', help="Input native PDB file", required=False) parser.add_argument('-f_label', help="F label from native MTZ file", required=False) parser.add_argument('-sigf_label', help="SIGF label from native MTZ file", required=False) args = parser.parse_args() # Extract F & SIGF from file if not give on command-line if args.f_label and args.sigf_label: f_label, sigf_label = args.f_label, args.sigf_label else: f_label, sigf_label, _ = mtz_util.get_labels(args.native_mtz) logger.info("Using F, SIGF labels from mtz file: {0}, {1} ".format(f_label, sigf_label)) if args.native_pdb: before_origin, after_origin, change_of_hand, origin_shift = calc_phase_error_pdb( args.native_pdb, args.native_mtz, args.mr_mtz, f_label, sigf_label ) else: before_origin, after_origin, change_of_hand, origin_shift = calc_phase_error_mtz( args.native_mtz, args.mr_mtz, f_label, sigf_label ) print("Calculated phase error:", after_origin) print("Calculated origin shift:", origin_shift)