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)
########################################################################
