inlist.close() else: FileList = False # archive_listfile contains a list of archived files (typically one for each aminoacid). archive_list = [] if archive_listfile !="": archhandle = open(archive_listfile, 'r') flines = archhandle.readlines() archhandle.close() for line in flines: archive_list.append( line.rstrip('\n')) # initialize ResTypesStatisticsCollector statistics_collector_from_pdb = ResTypesStatisticsCollector() statistics_collector_from_archive = ResTypesStatisticsCollector() #initialize PoseEnergies for each file in list if FileList: for filename in FileList: pe_instance = PoseEnergies() try: pe_instance.loadFile(filename) except: print "Caught exception when trying to read %s" % filename continue try: statistics_collector_from_pdb.add_pose_energies(pe_instance)
from ResidueEnergies import ResidueEnergies, PoseEnergies,critical_distance_squared from ResTypeAverageScores import ResTypeAverageScores from constants import * import cPickle import numpy as np FileList = ['12as_nohet_1_relax.pdb', '12e8_nohet_1_relax.pdb', '12ca_nohet_1_relax.pdb', '12gs_nohet_1_relax.pdb'] FileList_modified = ['12as_nohet_1_relax.pdb', '12e8_nohet_1_relax.pdb', 'test_modified_12ca_nohet_1_relax.pdb', '12gs_nohet_1_relax.pdb'] statistics_collector = ResTypesStatisticsCollector() statistics_collector_mod = ResTypesStatisticsCollector() for name in FileList: filename = name pe_instance = PoseEnergies() pe_instance.loadFile(filename) statistics_collector.add_pose_energies(pe_instance) for name in FileList_modified: filename = name pe_instance = PoseEnergies() pe_instance.loadFile(filename) statistics_collector_mod.add_pose_energies(pe_instance)
#!/usr/bin/python import sys sys.path.append('../../src') from ResidueEnergies import ResidueEnergies, PoseEnergies,critical_distance_squared from ResTypeAverageScores import ResTypeAverageScores from ResTypesStatisticsCollector import ResTypesStatisticsCollector from constants import * import numpy as np statistics_collector = ResTypesStatisticsCollector() pdbfile1 = "../stddev_and_mean/avetest_mock.pdb" pdbfile2 = "../stddev_and_mean/avetest_mock2.pdb" pe_instance_1 = PoseEnergies() pe_instance_1.loadFile( pdbfile1 ) pe_instance_2 = PoseEnergies() pe_instance_2.loadFile( pdbfile2) statistics_collector.add_pose_energies( pe_instance_1) statistics_collector.add_pose_energies( pe_instance_2) ######################################### error_combined_scored = False #combination of score terms score_terms_to_be_combined = ['faketerm1', 'faketerm2']
archive_listfile = '../../src/archive_files.txt' archive_list = [] if archive_listfile !="": archhandle = open(archive_listfile, 'r') flines = archhandle.readlines() archhandle.close() for line in flines: archive_list.append( line.rstrip('\n')) statistics_collector_from_archive = ResTypesStatisticsCollector() #deserialize archives for archive in archive_list: f = file(archive, 'rb') statistics_collector_from_archive.add_archived_data( cPickle.load(f) ) f.close() #combination of score terms score_terms_to_be_combined = ['hbond_bb_sc', 'hbond_sc'] for aminoacid in aminoacids: statistics_collector_from_archive.restype_av_scores[aminoacid].calculate_sum_of_several_score_terms(score_terms_to_be_combined) #subtraction of score_terms ---- important for subtraction of fa_dun from total
print 'No error when counting neighbors' else: print 'ERROR: Error in counting neighbors' ########################################################################### #extracting subgroup depending on number of neighbors filename1 = '10gs_nohet_1_relax.pdb' filename2 = 'serin-only-test-pdb.txt' statistics_collector_from_pdb1 = ResTypesStatisticsCollector() statistics_collector_from_pdb2 = ResTypesStatisticsCollector() pe_instance1 = PoseEnergies() pe_instance1.loadFile(filename1) statistics_collector_from_pdb1.add_pose_energies(pe_instance1) pe_instance2 = PoseEnergies() pe_instance2.loadFile(filename2) statistics_collector_from_pdb2.add_pose_energies(pe_instance2) mean1 = statistics_collector_from_pdb1.calculate_averages_and_stddevs_from_subset('SER', 'rama', range(10,21))[0] stddev1 = statistics_collector_from_pdb1.calculate_averages_and_stddevs_from_subset('SER', 'rama', range(10,21))[1] mean2 = statistics_collector_from_pdb2.calculate_averages_and_stddevs('SER', 'rama')[0] stddev2 = statistics_collector_from_pdb2.calculate_averages_and_stddevs('SER', 'rama')[1]
from constants import * import cPickle import numpy as np import sys pdb_listfile = 'shortlist1.txt' inlist = open(pdb_listfile, 'r') liste = inlist.readlines() FileList = [] for item in liste: FileList.append(item.rstrip('\n')) inlist.close() statistics_collector_from_pdb = ResTypesStatisticsCollector() for filename in FileList: pe_instance = PoseEnergies() pe_instance.loadFile(filename) statistics_collector_from_pdb.add_pose_energies(pe_instance) #Serialization for aminoacid in aminoacids: statistics_collector_from_pdb.restype_av_scores[aminoacid].pickle_res_type_average_scores('archived/'+aminoacid+'.txt') #print 'shortlist1:', statistics_collector_from_pdb.calculate_averages_and_stddevs('SER', 'rama') ####################################################################################
import cPickle import sys sys.path.append('../src') from ResidueEnergies import ResidueEnergies, PoseEnergies from ResTypeAverageScores import ResTypeAverageScores import numpy as np from ResTypesStatisticsCollector import ResTypesStatisticsCollector aminoacids = ['ALA', 'CYS', 'ASP', 'GLU', 'PHE', 'GLY', 'HIS', 'ILE', 'LYS', 'LEU', 'MET', 'ASN', 'PRO', 'GLN', 'ARG', 'SER', 'THR', 'VAL', 'TRP', 'TYR'] pose_energies = PoseEnergies() # creates instance of PoseEnergies pose_energies.loadFile('stddev_and_mean/avetest_mock.pdb') statistics_collector = ResTypesStatisticsCollector() pdbfile1 = "stddev_and_mean/avetest_mock.pdb" pdbfile2 = "stddev_and_mean/avetest_mock2.pdb" pe_instance_1 = PoseEnergies() pe_instance_1.loadFile( pdbfile1 ) pe_instance_2 = PoseEnergies() pe_instance_2.loadFile( pdbfile2) statistics_collector.add_pose_energies( pe_instance_1) statistics_collector.add_pose_energies( pe_instance_2) ########################################################################