def _showRingerResults(self, e=None):
i = int(self.residue)
index = int(self.dataDict['_residues_dict'][self.residueList[i]])
# emringer main file
mainDataFile = glob.glob(
self.protocol._getExtraPath("*_emringer.pkl"))[0]
command = """from mmtbx.ringer.em_rolling import easy_pickle
import matplotlib.pyplot as plt
# process file '%s'
file_name='%s'
ringer_results = easy_pickle.load(file_name)
figure = plt.figure() # (figsize=(20,1000))
def show_residue (residue, show_background_boxes=True) :
subplots = []
for i in range(1, residue.n_chi + 1) :
chi = residue.get_angle(i)
if (chi is None) : continue
if (len(subplots) > 0) :
p = figure.add_subplot(4, 1, i, sharex=subplots[0])
else:
p = figure.add_subplot(4, 1, i)
p.set_title(residue.format())
p.set_position([0.15, 0.725 - 0.225*(i-1), 0.8, 0.225])
x = [ k*chi.sampling for k in range(len(chi.densities)) ]
p.plot(x, chi.densities, 'r-', linewidth=1)
if (chi.fofc_densities is not None) :
p.plot(x, chi.fofc_densities, linestyle='--', color=[0.5,0.0,1.0])
p.axvline(chi.angle_current, color='b', linewidth=2, linestyle='--')
p.axhline(0, color=(0.4,0.4,0.4), linestyle='--', linewidth=1)
if show_background_boxes:
p.axhspan(0.3,1,facecolor="green",alpha=0.5)
p.axhspan(-1,0.3,facecolor="grey",alpha=0.5)
p.set_xlim(0,360)
p.set_ylabel("Rho")
p.set_xlabel("Chi" + str(i))
subplots.append(p)
plt.subplots_adjust(left = 0.18, bottom = 0.00, right = 0.94,
top = 0.93,
wspace = 0.80, hspace = 0.43)
plt.tight_layout()
plt.show()
index = %d
show_residue(ringer_results[index])
""" % (mainDataFile, mainDataFile, index)
with open(self.EMRINGERSUBPLOTSFILENAME, "w") as f:
f.write(command)
# execute file with phenix.python
Plugin.runPhenixProgram("", self.EMRINGERSUBPLOTSFILENAME)
def runSuperposePDBsStep(self):
args = os.path.abspath(self.inputStructureFixed.get().getFileName())
args += " "
args += os.path.abspath(self.inputStructureMoving.get().getFileName())
cwd = os.getcwd() + "/" + self._getExtraPath()
try:
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE), args,
extraEnvDict=None, cwd=cwd)
except:
# This exception will run when using phenix v. 1.16 after running
# real space refine the .cif file generated can not be recognized by
# superpose pdbs program and an error is produced
list_args = args.split()
self._runChangingCifFormatSuperpose(list_args)
def _readValidationPklFile(self, fileName):
self.SUMMARYFILENAME = self._getTmpPath(self.SUMMARYFILENAME)
command = """import pickle
import collections
import json
def pickleData(file):
with open(file,"r") as f:
return pickle.load(f)
# process file {VALIDATIONCRYOEMPKLFILENAME}"
data = pickleData('{VALIDATIONCRYOEMPKLFILENAME}')
dictSummary = collections.OrderedDict()
dictSummary['Rhama_Outliers'] = data.model.geometry.ramachandran.outliers
dictSummary['Rhama_Favored'] = data.model.geometry.ramachandran.favored
dictSummary['Rota_Outliers'] = data.model.geometry.rotamer.outliers
dictSummary['Cbeta_Outliers_n'] = data.model.geometry.c_beta.cbetadev.n_outliers
dictSummary['Clash_score'] = data.model.geometry.clash.score
dictSummary['MolProbity_score'] = data.model.geometry.molprobity_score
""".format(VALIDATIONCRYOEMPKLFILENAME=fileName)
command += """with open('%s',"w") as f:
f.write(json.dumps(dictSummary))
""" % (self.SUMMARYFILENAME)
pythonFileName = self.SUMMARYFILENAME.replace('.txt', '.py')
# write script file
with open(pythonFileName, "w") as f:
f.write(command)
# execute file with phenix.python
Plugin.runPhenixProgram("", pythonFileName)
# read file in scipion python
with open(self.SUMMARYFILENAME, "r") as f:
dictSummary = f.read()
dictSummary = json.loads(dictSummary,
object_pairs_hook=collections.OrderedDict)
self.ramachandranOutliers = Float(dictSummary['Rhama_Outliers'])
self.ramachandranFavored = Float(dictSummary['Rhama_Favored'])
self.rotamerOutliers = Float(dictSummary['Rota_Outliers'])
self.cbetaOutliers = Integer(dictSummary['Cbeta_Outliers_n'])
self.clashscore = Float(dictSummary['Clash_score'])
self.overallScore = Float(dictSummary['MolProbity_score'])
def createOutputStep(self):
# get emringer information
# values are stored in python pickle files
# string to be run by phenix python
# temporary file with emringer values
test = self.doTest
if test == True:
EMRINGERTRANSFERFILENAME = self._getExtraPath(
self.EMRINGERTRANSFERFILENAME)
else:
EMRINGERTRANSFERFILENAME = self._getTmpPath(
self.EMRINGERTRANSFERFILENAME)
# directory with files
plots = glob.glob(self._getExtraPath("*_plots"))[0]
# emringer main file
mainDataFile = glob.glob(self._getExtraPath("*_emringer.pkl"))[0]
# file with emringer score
EMRINGERSCORESFILENAME = os.path.join(plots,
self.EMRINGERSCORESFILENAME)
EMRINGERFILES = []
keyList = []
# files with other scores
EMRINGEROPTIMALTHRESHOLDFILENAME = \
os.path.join(plots, self.EMRINGEROPTIMALTHRESHOLDFILENAME)
EMRINGERFILES.append(EMRINGEROPTIMALTHRESHOLDFILENAME)
keyList.append('Optimal Threshold')
EMRINGERROTAMERRATIOSFILENAME = \
os.path.join(plots, self.EMRINGERROTAMERRATIOSFILENAME)
EMRINGERFILES.append(EMRINGERROTAMERRATIOSFILENAME)
keyList.append('Rotamer-Ratio')
EMRINGERMAXZSCOREFILENAME = \
os.path.join(plots, self.EMRINGERMAXZSCOREFILENAME)
EMRINGERFILES.append(EMRINGERMAXZSCOREFILENAME)
keyList.append('Max Zscore')
# I do not want to use the local pickle version
# but the version used to create the files
# that is the phenix.python version
command = """import pickle
import json
import sys
import collections
from mmtbx.ringer.em_scoring import parse_pickle
from mmtbx.ringer.em_rolling import easy_pickle, RingerDict
def pickleData(file):
with open(file,"r") as f:
return pickle.load(f)
# process file %s"
data = pickleData('%s')
dataDict = collections.OrderedDict()
# index to maxscore
maxScore = max(data)
maxScoreIndex = data.index(maxScore)
""" % (EMRINGERSCORESFILENAME, EMRINGERSCORESFILENAME)
for key, fileName in zip(keyList, EMRINGERFILES):
command += "# process file %s\n" % fileName
command += "data = pickleData('%s')\n" % fileName
command += "dataDict['%s'] = data[maxScoreIndex]\n" % key
command += """file_name='%s'
waves, thresholds = parse_pickle(file_name, out=sys.stdout)
# waves: list of ringer_residue objects (Non-gamma-branched, non-proline
# aminoacids with a non-H gamma atom) used in global EMRinger score
# computation
dataDict['Model Length'] = len(waves)
dataDict['EMRinger Score'] = maxScore # find max score
# dataDict is shown in a table
# except for those attributes starting with "_"
dataDict['_thresholds'] = thresholds
dataDict['_maxScoreIndex'] = maxScoreIndex
ringer_results = easy_pickle.load(file_name)
# ringer_results: list of ringer_residue objects (aminoacids with gamma
# carbon; at least one Chi angle)
hierarchy = RingerDict(ringer_results, 0)
chains = sorted(hierarchy.get_chains())
dataDict['_chains'] = chains
# Aminoacids that contain non-H gamma atom (at least one Chi angle; included in
# ringer_results)
dictResidue = {}
formatResidue = []
for residue in ringer_results:
resFormatTmp = residue.format()
formatResidue.append(resFormatTmp)
dictResidue[resFormatTmp] = ringer_results.index(residue)
dataDict['_residues_format'] = formatResidue
dataDict['_residues_dict'] = dictResidue
""" % mainDataFile
command += """with open('%s',"w") as f:
f.write(json.dumps(dataDict))
""" % (EMRINGERTRANSFERFILENAME)
pythonFileName = EMRINGERTRANSFERFILENAME.replace('.txt', '.py')
# write script file
with open(pythonFileName, "w") as f:
f.write(command)
# execute file with phenix.python
Plugin.runPhenixProgram("", pythonFileName)
# read file in scipion python
with open(EMRINGERTRANSFERFILENAME, "r") as f:
self.stringDataDict = String(f.read())
# self.dataDict = json.loads(f.read())
self._store()
def _runChangingCifFormatSuperpose(self, list_args):
cwd = os.getcwd() + "/" + self._getExtraPath()
try:
if list_args[0].endswith(".cif") and list_args[1].endswith(".cif"):
try:
# upgrade cifs
list_args1 = []
for i in range(0, 2):
list_args1.append(fromCIFTommCIF(list_args[i], list_args[i]))
args1 = list_args1[0] + " " + list_args1[1]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE), args1,
extraEnvDict=None, cwd=cwd)
except:
# convert cifs to pdbs
list_args2 = []
for i in range(0, 2):
list_args2.append(fromCIFToPDB(
list_args[i], list_args[i].replace('.cif', '.pdb')))
args2 = list_args2[0] + " " + list_args2[1]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE), args2,
extraEnvDict=None, cwd=cwd)
elif list_args[0].endswith(".cif") and list_args[1].endswith(".pdb"):
try:
# pdbs: convert cif to pdb
list_args1 = []
list_args1.append(fromCIFToPDB(
list_args[0], list_args[0].replace('.cif', '.pdb')))
args1 = list_args1[0] + " " + list_args[1]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE), args1,
extraEnvDict=None, cwd=cwd)
except:
try:
# cifs: convert pdb to cif
list_args2 = []
list_args2.append(fromPDBToCIF(
list_args[1], list_args[1].replace('.pdb', '.cif')))
args2 = list_args[0] + " " + list_args2[0]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE), args2,
extraEnvDict=None, cwd=cwd)
except:
# upgrade cif
list_args3 = []
list_args0 = args2.split()
for i in range(0, 2):
list_args3[i].append(fromCIFTommCIF(
list_args0[i], list_args0[i]))
args3 = list_args3[0] + " " + list_args3[1]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE),
args3, extraEnvDict=None, cwd=cwd)
elif list_args[0].endswith(".pdb") and list_args[1].endswith(".cif"):
try:
# pdbs: convert cif to pdb
list_args1 = []
list_args1.append(fromCIFToPDB(
list_args[1], list_args[1].replace('.cif', '.pdb')))
args1 = list_args[0] + " " + list_args1[0]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE), args1,
extraEnvDict=None, cwd=cwd)
except:
try:
# cifs: convert pdb to cif
list_args2 = []
list_args2.append(fromPDBToCIF(
list_args[0], list_args[0].replace('.pdb', '.cif')))
args2 = list_args2[0] + " " + list_args[1]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE), args2,
extraEnvDict=None, cwd=cwd)
except:
# upgrade cifs
list_args3 = []
list_args0 = args2.split()
for i in range(0, 2):
list_args3.append(fromCIFTommCIF(
list_args0[i], list_args0[i]))
args3 = list_args3[0] + " " + list_args3[1]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE),
args3, extraEnvDict=None, cwd=cwd)
except:
# biopython conversion
aSH = AtomicStructHandler()
try:
for i in range(0, 2):
aSH.read(list_args[i])
aSH.write(list_args[i])
args = list_args[0] + " " + list_args[1]
Plugin.runPhenixProgram(Plugin.getProgram(SUPERPOSE),
args, extraEnvDict=None, cwd=cwd)
except:
print("CIF file standarization failed.")
