def runValidationCryoEMStep(self):
version = Plugin.getPhenixVersion()
if version == '1.13':
print("PHENIX version: 1.13")
else:
print("PHENIX version: ", version)
fileName = self.inputStructure.get().getFileName()
atomStruct = os.path.abspath(fileName)
# starting volume (.mrc)
if self.vol is not None:
tmpMapFile = self.VALIDATIONCRYOEMFILE
volume = os.path.abspath(self._getExtraPath(tmpMapFile))
else:
volume = None
# MolProbity is run to get the file molprobity.out
# (necessary to get geometry outliers)
numberOfThreads = self.numberOfThreads.get()
args = self._writeArgsMolProbity(atomStruct, vol=volume)
cwd = os.getcwd() + "/" + self._getExtraPath()
# script with auxiliary files
retry(Plugin.runPhenixProgram, Plugin.getProgram(MOLPROBITY),
args, cwd=cwd, listAtomStruct=[atomStruct], log=self._log)
args = self._writeArgsValCryoEM(atomStruct, volume, self.vol)
if Plugin.getPhenixVersion() != PHENIXVERSION and self.vol is not None:
retry(Plugin.runPhenixProgram, Plugin.getProgram(VALIDATION_CRYOEM),
args, cwd=cwd, listAtomStruct=[atomStruct], log=self._log)
def _validate(self):
errors = []
# Check that the program exists
program = Plugin.getProgram(EMRINGER)
if program is None:
errors.append("Missing variables EMRINGER and/or PHENIX_HOME")
elif not os.path.exists(program):
errors.append("Binary '%s' does not exists.\n" % program)
elif not self.is_tool(DISPLAY):
errors.append("display program missing.\n "
"Please install imagemagick package")
# If there is any error at this point it is related to config variables
if errors:
errors.append("Check configuration file: " +
Config.SCIPION_LOCAL_CONFIG)
errors.append("and set EMRINGER and PHENIX_HOME variables "
"properly.")
if program is not None:
errors.append("Current values:")
errors.append("PHENIX_HOME = %s" % Plugin.getVar(PHENIX_HOME))
errors.append("EMRINGER = %s" % EMRINGER)
# Check that the input volume exist
if self._getInputVolume() is None:
errors.append("Error: You should provide a volume.\n")
return errors
def runMolprobityStep(self):
version = Plugin.getPhenixVersion()
if version == '1.13':
print("PHENIX version: 1.13")
else:
print(("PHENIX version: ", version))
# PDBx/mmCIF
fileName = self.inputStructure.get().getFileName()
# self.atomStruct = os.path.abspath(fileName)
self.atomStruct = os.getcwd() + "/" + fileName
# starting volume (.mrc)
if (self.inputVolume.get() or self.inputStructure.get().getVolume()) \
is not None:
tmpMapFile = self.MOLPROBITYFILE
# self.vol = os.path.abspath(self._getExtraPath(tmpMapFile))
self.vol = os.getcwd() + "/" + self._getExtraPath(tmpMapFile)
args = self._writeArgsMolProbityExpand(self.atomStruct, self.vol)
else:
args = self._writeArgsMolProbityExpand(self.atomStruct, vol=None)
# script with auxiliary files
retry(
Plugin.runPhenixProgram,
Plugin.getProgram(MOLPROBITY),
# args, cwd=os.path.abspath(self._getExtraPath()),
args,
cwd=self._getExtraPath(),
listAtomStruct=[self.atomStruct],
log=self._log)
def runRSrefineStep(self, tmpMapFile):
atomStruct = os.path.abspath(self.inputStructure.get().getFileName())
vol = os.path.abspath(self._getExtraPath(tmpMapFile))
args = self._writeArgsRSR(atomStruct, vol)
cwd = os.getcwd() + "/" + self._getExtraPath()
retry(
Plugin.runPhenixProgram,
Plugin.getProgram(REALSPACEREFINE),
args,
# cwd=os.path.abspath(self._getExtraPath()),
cwd=cwd,
listAtomStruct=[atomStruct],
log=self._log)
self.refinedFile = False
for item in os.listdir(self._getExtraPath()):
p = re.compile('\d+')
if p.search(item) is not None and item.endswith(".cif"):
self.refinedFile = True
break
if self.refinedFile == False:
print("WARNING!!!\nPHENIX error:\n pdb_interpretation.clash_guard" \
" failure: High number of nonbonded interaction distances " \
"< 0.5. This error has been disable by running the same " \
"command with the same following additional " \
"argument:\npdb_interpretation.clash_guard." \
"nonbonded_distance_threshold=None ")
args += " pdb_interpretation.clash_guard." \
"nonbonded_distance_threshold=None"
retry(
Plugin.runPhenixProgram,
Plugin.getProgram(REALSPACEREFINE),
args,
# cwd=os.path.abspath(self._getExtraPath()),
cwd=cwd,
listAtomStruct=[atomStruct],
log=self._log)
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 runMolprobityStep(self, tmpMapFile):
# PDBx/mmCIF
self._getRSRefineOutput()
atomStruct = os.path.abspath(self.outAtomStructName)
# starting volume (.mrc)
vol = os.path.abspath(self._getExtraPath(tmpMapFile))
args = self._writeArgsMolProbity(atomStruct, vol)
cwd = os.getcwd() + "/" + self._getExtraPath()
retry(
Plugin.runPhenixProgram,
Plugin.getProgram(MOLPROBITY2),
# args, cwd=os.path.abspath(self._getExtraPath()),
args,
cwd=cwd,
listAtomStruct=[atomStruct],
log=self._log)
def _validate(self):
errors = []
# Check that the program exists
program = Plugin.getProgram(SUPERPOSE)
if not os.path.exists(program):
errors.append("Cannot find " + program)
# If there is any error at this point it is related to config variables
errors.append("Check configuration file: " +
Config.SCIPION_LOCAL_CONFIG)
errors.append("and set PHENIX_HOME variables properly.")
if program is not None:
errors.append("Current values:")
errors.append("PHENIX_HOME = %s" % Plugin.getVar(PHENIX_HOME))
errors.append("SUPERPOSE = %s" % SUPERPOSE)
return errors
def runDockInMapStep(self):
# starting structure
atomStructFileName = self.inputStructure.get().getFileName()
atomStruct = os.getcwd() + "/" + atomStructFileName
# starting map (.mrc)
mapFile = self.DOCKINMAPFILE
vol = os.getcwd() + "/" + self._getExtraPath(mapFile)
args = self._writeArgsDocKInMap(vol, atomStruct)
cwd = os.getcwd() + "/" + self._getExtraPath()
retry(
Plugin.runPhenixProgram,
Plugin.getProgram(DOCKINMAP),
# args, cwd=os.path.abspath(self._getExtraPath()),
args,
cwd=cwd,
listAtomStruct=[atomStruct],
log=self._log)
def runValidationCryoEMStep(self, tmpMapFile):
# PDBx/mmCIF
atomStruct = os.path.abspath(self.outAtomStructName)
# starting volume (.mrc)
volume = os.path.abspath(self._getExtraPath(tmpMapFile))
if self.inputVolume.get() is not None:
vol = self.inputVolume.get()
else:
vol = self.inputStructure.get().getVolume()
args = self._writeArgsValCryoEM(atomStruct, volume, vol)
cwd = os.getcwd() + "/" + self._getExtraPath()
retry(
Plugin.runPhenixProgram,
Plugin.getProgram(VALIDATION_CRYOEM),
# args, cwd=os.path.abspath(self._getExtraPath()),
args,
cwd=cwd,
listAtomStruct=[atomStruct],
log=self._log)
def runEMRingerStep(self):
inPDBAtomStructFile = self.inputStructure.get().getFileName()
# atomStruct = os.path.abspath(inPDBAtomStructFile)
if not inPDBAtomStructFile == os.path.abspath(inPDBAtomStructFile):
atomStruct = os.getcwd() + "/" + inPDBAtomStructFile
else:
atomStruct = inPDBAtomStructFile
# vol = os.path.abspath(self._getExtraPath(self.EMRINGERFILE))
vol = os.getcwd() + "/" + self._getExtraPath(self.EMRINGERFILE)
args = self._writeArgsEMRinger(atomStruct, vol)
# script with auxiliary files
import sys
sys.stdout.flush()
# import time
# time.sleep(30)
retry(
Plugin.runPhenixProgram,
Plugin.getProgram(EMRINGER),
# args, cwd=os.path.abspath(self._getExtraPath()),
args,
cwd=self._getExtraPath(),
listAtomStruct=[atomStruct],
log=self._log)
def createOutputStep(self):
MOLPROBITYOUTFILENAME = self._getExtraPath(self.MOLPROBITYOUTFILENAME)
try:
self._parseFile(MOLPROBITYOUTFILENAME)
except:
if self.MOLPROBITYFILE is not None:
# self.vol = os.path.abspath(self._getExtraPath(self.MOLPROBITYFILE))
self.vol = self._getExtraPath(self.MOLPROBITYFILE)
args = self._writeArgsMolProbityExpand(self.atomStruct,
self.vol)
else:
args = self._writeArgsMolProbityExpand(self.atomStruct,
vol=None)
args += " allow_polymer_cross_special_position=True "
retry(
Plugin.runPhenixProgram,
Plugin.getProgram(MOLPROBITY),
# args, cwd=os.path.abspath(self._getExtraPath()),
args,
cwd=self._getExtraPath(),
listAtomStruct=[self.atomStruct],
log=self._log)
self._parseFile(MOLPROBITYOUTFILENAME)
self._store()
def validateBase(self, program, label):
errors = []
# Check that the program exists
program = Plugin.getProgram(program)
if program is None:
errors.append("Missing variables %s and/or PHENIX_HOME" % label)
elif not os.path.exists(program):
errors.append("Binary '%s' does not exists.\n" % program)
errors.append("Check if you need to upgrade your PHENIX version"
" to run %s.\nYour current PHENIX version is %s.\n" %
(label, PHENIXVERSION))
# If there is any error at this point it is related to config variables
if errors:
errors.append("Check configuration file: " +
Config.SCIPION_LOCAL_CONFIG)
errors.append("and set %s and PHENIX_HOME variables "
"properly." % label)
if program is not None:
errors.append("Current values:")
errors.append("PHENIX_HOME = %s" % Plugin.getHome())
#errors.append("%s = %s" % label, program)
return errors
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.")
def refineStep2(self):
# atomStruct = os.path.abspath(self.inputStructure.get().getFileName())
## vol = os.path.abspath(self._getInputVolume().getFileName())
vol = os.path.abspath(self._getExtraPath(self.FITTEDFILE))
cwd = os.getcwd() + "/" + self._getExtraPath()
conn = sqlite3.connect(os.path.abspath(self._getExtraPath(DATAFILE)))
c = conn.cursor()
while 1:
command = """SELECT filename from %s
WHERE done=0
LIMIT 1""" % TABLE
c.execute(command)
myrow = c.fetchone()
if not myrow:
print("refineStep: no more available works")
break # break while if no job is available
atomStructFn, = myrow
c.execute("""UPDATE %s
SET done=1
WHERE filename='%s' AND done=0""" %
(TABLE, atomStructFn))
# ^^^^^^ This will return the number of rows updated (c.rowcount).
# Note that we only update if done is still '0', so if we get 1 updated
# row, we're sure no one else took our job. This works because UPDATE is atomic.
if not c.rowcount:
# Whoops this job was taken! Try again and get another one
continue
conn.commit()
args = self._writeArgsRSR(atomStructFn, vol)
retry(
Plugin.runPhenixProgram,
Plugin.getProgram(REALSPACEREFINE),
args,
# cwd=os.path.abspath(self._getExtraPath()),
cwd=cwd,
listAtomStruct=[atomStructFn],
log=self._log)
if Plugin.getPhenixVersion() >= PHENIXVERSION19:
# update data base with phenix version
logFileFn = atomStructFn[:-4] + "_real_space_refined_???.log"
# last file
lastLogFile = sorted(glob.glob(logFileFn))[-1]
phenix_id = lastLogFile[-8:-4] # _000
c.execute("""UPDATE %s
SET phenix_id='%s'
WHERE filename='%s'""" %
(TABLE, phenix_id, atomStructFn))
else:
phenix_id = ''
conn.commit()
# refinedFile = False
# for item in os.listdir(self._getExtraPath()):
# p = re.compile('\d+')
# if p.search(item) is not None and item.endswith(".cif"):
# self.refinedFile = True
# break
#
# if self.refinedFile == False:
# print("WARNING!!!\nPHENIX error:\n pdb_interpretation.clash_guard" \
# " failure: High number of nonbonded interaction distances " \
# "< 0.5. This error has been disable by running the same " \
# "command with the same following additional " \
# "argument:\npdb_interpretation.clash_guard." \
# "nonbonded_distance_threshold=None ")
# args += " "
# args += "pdb_interpretation.clash_guard." \
# "nonbonded_distance_threshold=None"
# retry(Plugin.runPhenixProgram,
# Plugin.getProgram(REALSPACEREFINE), args,
# # cwd=os.path.abspath(self._getExtraPath()),
# cwd=cwd,
# listAtomStruct=[atomStructFn], log=self._log)
# coot_000000_Imol_0000_version_0004_real_space_refined_001.eff
# coot_000000_Imol_0000_version_0030.pdb
# glob
logFileFn = atomStructFn[:-4] + "_real_space_refined%s.log" % phenix_id
model_to_map_fit = self.extractNumber(logFileFn)
accepted = c.execute(
"""UPDATE %s
SET model_to_map_fit=%f
WHERE filename='%s'""" %
(TABLE, float(model_to_map_fit), atomStructFn))
conn.commit()
c.close()
conn.close()