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 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 importTomogramsStep(self, pattern, samplingRate):
""" Copy images matching the filename pattern
Register other parameters.
"""
self.info("Using pattern: '%s'" % pattern)
# Create a Volume template object
tomo = Tomogram()
tomo.setSamplingRate(samplingRate)
imgh = ImageHandler()
tomoSet = self._createSetOfTomograms()
tomoSet.setSamplingRate(samplingRate)
self._parseAcquisitionData()
for fileName, fileId in self.iterFiles():
x, y, z, n = imgh.getDimensions(fileName)
if fileName.endswith('.mrc') or fileName.endswith('.map'):
fileName += ':mrc'
if z == 1 and n != 1:
zDim = n
n = 1
else:
zDim = z
else:
zDim = z
origin = Transform()
if self.setOrigCoord.get():
origin.setShiftsTuple(self._getOrigCoord())
else:
origin.setShifts(x / -2. * samplingRate,
y / -2. * samplingRate,
zDim / -2. * samplingRate)
tomo.setOrigin(origin) # read origin from form
newFileName = _getUniqueFileName(self.getPattern(),
fileName.split(':')[0])
tsId = removeExt(newFileName)
tomo.setTsId(tsId)
if fileName.endswith(':mrc'):
fileName = fileName[:-4]
createAbsLink(fileName, abspath(self._getExtraPath(newFileName)))
tomo.setAcquisition(self._extractAcquisitionParameters(fileName))
if n == 1: # One volume per file
tomo.cleanObjId()
tomo.setFileName(self._getExtraPath(newFileName))
tomoSet.append(tomo)
else: # A stack of volumes per file (not common)
for index in range(1, n + 1):
tomo.cleanObjId()
tomo.setLocation(index, self._getExtraPath(newFileName))
tomoSet.append(tomo)
self._defineOutputs(outputTomograms=tomoSet)
def _visualize(self, obj, **args):
""" Visualize any saved pdb and map if none were saved
show the input files.
"""
_inputVolFlag = False
_inputPDBFlag = False
directory = self.protocol._getExtraPath()
fnCmd = os.path.abspath(self.protocol._getTmpPath("chimera_output.cxc"))
f = open(fnCmd, 'w')
f.write('cd %s\n' % os.getcwd())
counter = 0
# Find all saved maps and pdbs from protocl. If none
# are found show the input files to the protocol
for filename in sorted(os.listdir(directory)):
if filename.endswith(".mrc"):
_inputVolFlag = True
counter += 1
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)
f.write("open %s\n" % volFileName)
f.write("volume #%d style surface voxelSize %f\n"
"volume #%d origin %0.2f,%0.2f,%0.2f\n"
% (counter, sampling, counter, shifts[0], shifts[1], shifts[2]))
# Set volume to translucent
f.write("volume #%d transparency 0.5\n" % counter)
for filename in os.listdir(directory):
if filename.endswith(".pdb") or filename.endswith(".cif"):
_inputPDBFlag = True
path = os.path.join(directory, filename)
f.write("open %s\n" % path)
# If no pdbs or maps found use inputs to protocol
if not _inputVolFlag:
counter += 1
f.write("open %s \n" % os.path.abspath(self.protocol.inputVolume.get().getFileName()))
# Set volume to translucent
f.write("volume #%d transparency 0.5\n" % counter)
if not _inputPDBFlag:
f.write("open %s \n" % os.path.abspath(self.protocol.pdbFileToBeRefined.get().getFileName()))
f.close()
# run in the background
Chimera.runProgram(chimera.getProgram(), fnCmd + "&")
return []
def createOutput(self):
volume = Volume()
volume.setSamplingRate(self.sampling.get())
volume.setFileName(self._getVolName())
if self.vol:
origin = Transform()
origin.setShiftsTuple(self.shifts)
volume.setOrigin(origin)
self._defineOutputs(outputVolume=volume)
if self.inputPdbData == self.IMPORT_OBJ:
self._defineSourceRelation(self.pdbObj, volume)
def createOutputStep(self):
vol1 = self.vol1.get()
volume = Volume()
volume.setSamplingRate(vol1.getSamplingRate())
if vol1.getFileName().endswith('mrc'):
origin = Transform()
ccp4header = headers.Ccp4Header(vol1.getFileName(), readHeader=True)
shifts = ccp4header.getOrigin()
origin.setShiftsTuple(shifts)
volume.setOrigin(origin)
volume.setFileName(self._getExtraPath("output_volume.mrc"))
filename = volume.getFileName()
if filename.endswith('.mrc') or filename.endswith('.map'):
volume.setFileName(filename + ':mrc')
self._defineOutputs(outputVolume=volume)
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 _visualize(self, obj, **args):
# THe input map or pdb may be a parameter from the protocol
# or from the parent protocol.
dim = 150.
sampling = 1.
_inputVol = None
directory = self.protocol._getExtraPath()
try:
try:
if self.protocol.inputVolume.get() is not None:
_inputVol = self.protocol.inputVolume.get()
elif self.protocol.pdbFileToBeRefined.get().getVolume(
) is not None:
_inputVol = self.protocol.pdbFileToBeRefined.get(
).getVolume()
elif self.protocol.inputVolumes[0] is not None:
_inputVol = self.protocol.inputVolumes[0].get()
except:
output3DMapList = []
for filename in sorted(os.listdir(directory)):
if filename.endswith(".mrc"):
output3DMapList.append(filename.split('.')[0])
output3DMap = str(output3DMapList[0])
if len(output3DMap) > 0:
_inputVol = self.protocol.output3DMap
except:
# TODO: I do not know if we still need this part
# Remark that inputProtocol does not longer exist, it has been replaced by inputProtocolDict
# Compare with the previous code, specially the alternative directory
for item in list(self.protocol.inputProtocolDict().values()):
if item.hasAttribute(
'inputVolume') and item.inputVolume.get() is not None:
_inputVol = item.inputVolume.get()
break
elif item.hasAttribute('pdbFileToBeRefined') and \
item.pdbFileToBeRefined.get().getVolume() is not None:
_inputVol = item.pdbFileToBeRefined.get().getVolume()
break
# directory = item._getExtraPath()
if _inputVol is not None:
dim = _inputVol.getDim()[0]
sampling = _inputVol.getSamplingRate()
bildFileName = self.protocol._getTmpPath("axis_output.bild")
Chimera.createCoordinateAxisFile(dim,
bildFileName=bildFileName,
sampling=sampling)
fnCmd = self.protocol._getTmpPath("chimera_output.cxc")
f = open(fnCmd, 'w')
# change to workingDir
# If we do not use cd and the project name has an space
# the protocol fails even if we pass absolute paths
f.write('cd %s\n' % os.getcwd())
f.write("open %s\n" % bildFileName)
f.write("cofr 0,0,0\n") # set center of coordinates
inputVolFileName = ''
counter = 2
if _inputVol is not None:
# In case we have PDBs only, _inputVol is None:
self.visInputVolume(f, _inputVol, counter)
else:
counter = 1
if (self.protocol.hasAttribute("inputVolume2") and\
self.protocol.inputVolume2.get() is not None):
counter += 1
_inputVol2 = self.protocol.inputVolume2.get()
self.visInputVolume(f, _inputVol2, counter)
for filename in sorted(os.listdir(directory)):
if filename.endswith(".mrc") and filename != inputVolFileName:
counter += 1
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)
f.write("open %s\n" % volFileName)
f.write("volume #%d style surface voxelSize %f\n"
"volume #%d origin %0.2f,%0.2f,%0.2f\n" %
(counter, sampling, counter, shifts[0], shifts[1],
shifts[2]))
f.write("volume #%d level %0.3f\n" % (counter, 0.001))
for filename in os.listdir(directory):
if filename.endswith(".pdb") or filename.endswith(".cif"):
path = os.path.join(directory, filename)
# f.write("open %s\n" % os.path.abspath(path))
f.write("open %s\n" % path)
f.close()
# run in the background
Chimera.runProgram(Chimera.getProgram(), fnCmd + "&")
return []