def createRefmacOutputStep(self):
pdb = AtomStruct()
pdb.setFileName(self._getOutPdbFileName(self.OutPdbFileName))
self._defineOutputs(outputPdb=pdb)
self._defineSourceRelation(self.inputStructure, self.outputPdb)
fnVol = self._getInputVolume()
self._defineSourceRelation(fnVol, self.outputPdb)
def createOutput(self):
""" Copy the PDB structure and register the output object.
"""
# Check vol and pdb files
directory = self._getExtraPath()
for filename in sorted(os.listdir(directory)):
if not filename.startswith("tmp"):
# files starting with "tmp" will not be converted in scipion objects
if filename.endswith(".mrc"):
volFileName = os.path.join(directory, filename)
vol = Volume()
vol.setFileName(volFileName)
# fix mrc header
ccp4header = Ccp4Header(volFileName, readHeader=True)
sampling = ccp4header.computeSampling()
origin = Transform()
shifts = ccp4header.getOrigin()
origin.setShiftsTuple(shifts)
vol.setOrigin(origin)
vol.setSamplingRate(sampling)
keyword = filename.split(".mrc")[0]
kwargs = {keyword: vol}
self._defineOutputs(**kwargs)
if filename.endswith(".pdb") or filename.endswith(".cif"):
path = os.path.join(directory, filename)
pdb = AtomStruct()
pdb.setFileName(path)
if filename.endswith(".cif"):
keyword = filename.split(".cif")[0].replace(".", "_")
else:
keyword = filename.split(".pdb")[0].replace(".", "_")
kwargs = {keyword: pdb}
self._defineOutputs(**kwargs)
def createOutput(self):
# Check vol and pdb files
directory = self._getExtraPath()
for filename in sorted(os.listdir(directory)):
if filename.endswith(".mrc"):
volFileName = os.path.join(directory, filename)
vol = Volume()
vol.setFileName(volFileName)
# fix mrc header
ccp4header = Ccp4Header(volFileName, readHeader=True)
sampling = ccp4header.computeSampling()
origin = Transform()
shifts = ccp4header.getOrigin()
origin.setShiftsTuple(shifts)
vol.setOrigin(origin)
vol.setSamplingRate(sampling)
keyword = filename.split(".mrc")[0]
kwargs = {keyword: vol}
self._defineOutputs(**kwargs)
elif filename.endswith(".pdb") or filename.endswith(".cif"):
path = os.path.join(directory, filename)
pdb = AtomStruct()
pdb.setFileName(path)
keyword = filename.split(".pdb")[0].replace(".","_")
kwargs = {keyword: pdb}
self._defineOutputs(**kwargs)
def createOutputStep(self):
""" Copy the PDB structure and register the output object.
"""
# Check vol and pdb files
directory = self._getExtraPath()
for filename in sorted(os.listdir(directory)):
if filename.endswith(".mrc"):
volFileName = os.path.join(directory, filename)
vol = Volume()
vol.setFileName(volFileName)
# fix mrc header
ccp4header = Ccp4Header(volFileName, readHeader=True)
sampling = ccp4header.computeSampling()
origin = Transform()
shifts = ccp4header.getOrigin()
origin.setShiftsTuple(shifts)
vol.setOrigin(origin)
vol.setSamplingRate(sampling)
keyword = filename.split(".mrc")[0]
kwargs = {keyword: vol}
self._defineOutputs(**kwargs)
if filename.endswith(".pdb") or filename.endswith(".cif"):
path = os.path.join(directory, filename)
pdb = AtomStruct()
pdb.setFileName(path)
if filename.endswith(".cif"):
keyword = filename.split(".cif")[0].replace(".", "_")
else:
keyword = filename.split(".pdb")[0].replace(".", "_")
kwargs = {keyword: pdb}
self._defineOutputs(**kwargs)
# upodate config file flag enablebundle
# so scipionwrite is disabled
config = configparser.ConfigParser()
config.read(self._getExtraPath(CHIMERA_CONFIG_FILE))
config.set('chimerax', 'enablebundle', 'False')
with open(self._getExtraPath(CHIMERA_CONFIG_FILE), 'w') as configfile:
config.write(configfile)
def createOutputStep(self):
self._getDockInMapOutput()
pdb = AtomStruct()
pdb.setFileName(relpath(self.outAtomStructName))
if self.inputVolume1.get() is not None:
pdb.setVolume(self.inputVolume1.get())
else:
pdb.setVolume(self.inputStructure.get().getVolume())
self._defineOutputs(outputPdb=pdb)
self._defineSourceRelation(self.inputStructure.get(), pdb)
if self.inputVolume1.get() is not None:
self._defineSourceRelation(self.inputVolume1.get(), pdb)
def createOutputStep(self):
# viewer: extract cc from database and plot it
# make 5 pdbs with higher score available to scipion
conn = sqlite3.connect(os.path.abspath(self._getExtraPath(DATAFILE)))
c = conn.cursor()
sqlCommand = """SELECT filename, model_to_map_fit, phenix_id
FROM %s
ORDER BY model_to_map_fit DESC
LIMIT 5""" % TABLE
c.execute(sqlCommand)
rows = c.fetchall()
argsOutput = {}
for counter, row in enumerate(rows):
atomStructFn = row[0][:-4] + "_real_space_refined%s.log" % row[2]
atomStruct = AtomStruct()
atomStruct.setFileName(atomStructFn)
argsOutput["outputAtomStruct_%d" % counter] = atomStruct
c.close()
conn.close()
self._defineOutputs(**argsOutput)
def createOutputStep(self, outFileName, twoRelations=False, suffix=''):
outFileName = os.path.abspath(outFileName)
fnCmd = self._getExtraPath("chimera_output.cxc")
f = open(fnCmd, 'a+')
f.write("open %s\n" % outFileName)
f.close()
pdb = AtomStruct()
pdb.setFileName(outFileName)
# MM: to get appropriate cif files to be visualize with Chimera
# Transform the output cif file in mmcif
log = self._log
fromCIFTommCIF(outFileName, outFileName, log)
if suffix == "":
self._defineOutputs(outputPdb=pdb)
else:
outputDict = {'outputPdb_chain%s' % suffix: pdb}
self._defineOutputs(**outputDict)
self._defineSourceRelation(self.pdbFileToBeRefined, pdb)
if twoRelations:
self._defineSourceRelation(self.InputAtomStruct2, pdb)
def createOutputStep(self, targetSym, targetAtomStructFn):
""" save new atomic structure"""
pdb = AtomStruct()
pdb.setFileName(targetAtomStructFn)
# MM: to get appropriate cif files to be visualize with Chimera
# Transform the output cif file in mmcif
log = self._log
fromCIFTommCIF(pdb.getFileName(), pdb.getFileName(), log)
self._defineOutputs(rotatedAtomStruct=pdb)
self._defineSourceRelation(self.pdbFileToBeRefined, pdb)
def createOutputStep(self):
# self._getRSRefineOutput()
pdb = AtomStruct()
pdb.setFileName(self.outAtomStructName)
if self.inputVolume.get() is not None:
pdb.setVolume(self.inputVolume.get())
else:
pdb.setVolume(self.inputStructure.get().getVolume())
self._defineOutputs(outputPdb=pdb)
self._defineSourceRelation(self.inputStructure.get(), pdb)
if self.inputVolume.get() is not None:
self._defineSourceRelation(self.inputVolume.get(), pdb)
if Plugin.getPhenixVersion() == PHENIXVERSION:
MOLPROBITYOUTFILENAME = self._getExtraPath(
self.MOLPROBITYOUTFILENAME)
self._parseFile(MOLPROBITYOUTFILENAME)
else:
VALIDATIONCRYOEMPKLFILENAME = self._getExtraPath(
self.VALIDATIONCRYOEMPKLFILE)
self._readValidationPklFile(VALIDATIONCRYOEMPKLFILENAME)
self._store()
def createOutputStep(self):
fnPdb = os.path.basename(self.inputStructureMoving.get().getFileName())
fnPdb = fnPdb.split('.')[0]
for file in os.listdir(self._getExtraPath()):
if file.endswith('_fitted.pdb'):
os.rename(self._getExtraPath() + "/" + file,
self._getExtraPath() + "/" + fnPdb + "_fitted.pdb")
pdb = AtomStruct()
pdb.setFileName(self._getExtraPath(fnPdb + "_fitted.pdb"))
if self.inputStructureFixed.get().getVolume() is not None:
pdb.setVolume(self.inputStructureFixed.get().getVolume())
self._defineOutputs(outputPdb=pdb)
self._defineSourceRelation(self.inputStructureFixed.get(), pdb)
self._defineSourceRelation(self.inputStructureMoving.get(), pdb)
logFile = os.path.abspath(self._getLogsPath()) + "/run.stdout"
self._parseLogFile(logFile)
self._store()
def createOutputStep(self):
inputVol = self.inputStructure.get()
samplingRate = inputVol.getSamplingRate()
volume = Volume()
volume.setFileName(self._getExtraPath("pseudoatoms_approximation.vol"))
volume.setSamplingRate(samplingRate)
x, y, z = volume.getDim()
xv, yv, zv = inputVol.getOrigin(force=True).getShifts()
t = Transform()
t.setShifts((x / 2. * samplingRate) - xv, (y / 2. * samplingRate) - yv,
(z / 2. * samplingRate) - zv)
volume.setOrigin(inputVol.getOrigin())
self._defineOutputs(outputVolume=volume)
self._defineSourceRelation(self.inputStructure.get(), volume)
pdb = AtomStruct(self._getPath('pseudoatoms.pdb'), pseudoatoms=True)
pdb.setVolume(volume)
pdb.setOrigin(t)
self.createChimeraScript(inputVol, pdb)
self._defineOutputs(outputPdb=pdb)
self._defineSourceRelation(self.inputStructure, pdb)
def createOutputStep(self):
outFile = pwutils.removeBaseExt(
self.inputPDB.get().getFileName()) + '_deformed.pdb'
pdb = AtomStruct(self._getExtraPath(outFile))
self._defineOutputs(outputPDB=pdb)
self._defineSourceRelation(self.inputPDB, pdb)
def createOutput(self):
""" Copy the PDB structure and register the output object.
"""
databasePath = self._getExtraPath(OUTPUTDATABASENAMESWITHLABELS)
getModels(databasePath, DATABASETABLENAME)
# open database
conn = sqlite3.connect(databasePath)
if not _checkTableExists(conn, DATABASETABLENAME):
conn.close()
return
c = conn.cursor()
# read atom struct filename and label in a loop
c.execute('SELECT fileName, labelName '
'FROM %s '
'WHERE saved = 0 AND type=%d' %
(DATABASETABLENAME, TYPE_ATOMSTRUCT))
for row in c:
pdbFileName = row[0]
pdbLabelName = row[1]
pdb = AtomStruct()
pdb.setFileName(pdbFileName)
outputs = {str(pdbLabelName): pdb}
self._defineOutputs(**outputs)
self._defineSourceRelation(self.inputPdbFiles, pdb)
# files has been saved
sql = 'UPDATE %s SET saved = 1 WHERE saved=0 ' \
'AND type=%d' % (DATABASETABLENAME, TYPE_ATOMSTRUCT)
c.execute(sql)
# check if normalized files are saved
sql = "SELECT count(*) " \
"FROM %s " \
"WHERE saved = 0 " \
" AND type = %d LIMIT 1" % (DATABASETABLENAME, TYPE_3DMAP)
c.execute(sql)
result = c.fetchone()[0]
# update saved parameter
if result > 0:
sql = 'UPDATE %s SET saved = 1 WHERE saved=0 ' \
'AND type=%d' % (DATABASETABLENAME, TYPE_3DMAP)
c.execute(sql)
conn.commit()
conn.close()
# save normalized vols...
if result > 0:
inVolumes, norVolumesNames = self._getVolumesList()
counter = 1
for inVol, norVolName in zip(inVolumes, norVolumesNames):
outVol = Volume()
sampling = inVol.getSamplingRate()
origin = inVol.getOrigin(force=True)
outVol.setSamplingRate(sampling)
outVol.setOrigin(origin)
if norVolName.endswith('.mrc'):
norVolName = norVolName + ":mrc"
outFileName = self._getVolumeFileName(norVolName)
outVol.setFileName(outFileName)
outputs = {"output3DMap_%04d" % counter: outVol}
counter += 1
self._defineOutputs(**outputs)
self._defineSourceRelation(inVol, outVol)
else:
print("skip save normalized vol")
if os.path.isfile(self._getExtraPath('STOPPROTCOL')):
self.setStatus(STATUS_FINISHED)
# NOTE: (ROB) can a dirty way to make an interactive process finish but I do not
# think there is a clean one
self._steps[self.step - 1].setInteractive(False)