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 createOutputStep(self):
volume = Volume()
volume.setFileName(self._getExtraPath(POSTPROCESS_VOL_BASENAME))
if self.useHalfMapsInsteadVol.get():
if self.halfMapsAttached.get():
inVol = self.inputVolume.get()
else:
inVol = self.inputHalf1.get()
volume.setSamplingRate(inVol.getSamplingRate())
volume.setOrigin(inVol.getOrigin(force=True))
self._defineOutputs(Volume=volume)
self._defineTransformRelation(inVol, volume)
if not self.halfMapsAttached.get():
self._defineTransformRelation(self.inputHalf2, volume)
else:
inVol = self.inputVolume.get()
volume.setSamplingRate(inVol.getSamplingRate())
volume.setOrigin(inVol.getOrigin(force=True))
self._defineOutputs(Volume=volume)
self._defineTransformRelation(self.inputVolume, volume)
def createOutputStep(self):
metrics = self._getMetrics()
volume = Volume()
volume.setFileName(self._getFileName(RESTA_FILE_MRC))
volume.setSamplingRate(self.inputVolume.get().getSamplingRate())
volume.setOrigin(self.inputVolume.get().getOrigin(True).clone())
self._defineOutputs(fscq_Volume=volume, **metrics)
self._defineTransformRelation(self.inputVolume, volume)
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):
vol = Volume()
vol.setLocation(self._getOutputVol())
sampling = self.inputVolumes.get().getSamplingRate()
vol.setSamplingRate(sampling)
#
ccp4header = Ccp4Header(self._getOutputVol(), readHeader=True)
t = Transform()
x, y, z = ccp4header.getOrigin() # origin output vol
# coordinates
t.setShifts(x, y, z)
vol.setOrigin(t)
#
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self.inputVolumes, self.outputVolume)
def createOutputStep(self):
volumesSet = self._createSetOfVolumes()
volumesSet.setSamplingRate(self.inputVolume.get().getSamplingRate())
for i in range(self.iteration):
vol = Volume()
vol.setOrigin(self.inputVolume.get().getOrigin(True))
if (self.iteration > (i + 1)):
vol.setLocation(
i, self._getExtraPath('sharpenedMap_%d.mrc' % (i + 1)))
vol.setObjComment("Sharpened Map, \n Epoch %d" % (i + 1))
else:
vol.setLocation(i, self._getExtraPath('sharpenedMap_last.mrc'))
vol.setObjComment("Sharpened Map, \n Epoch last")
volumesSet.append(vol)
self._defineOutputs(outputVolumes=volumesSet)
self._defineSourceRelation(self.inputVolume, volumesSet)
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):
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 _visualize(self, obj, **args):
# Input map(s) are a parameter from the protocol
dim = 150.
sampling = 1.
_inputVol = None
_inputHalf1 = None
_inputHalf2 = None
listVol = []
directory = self.protocol._getExtraPath()
if self.protocol.useHalfMapsInsteadVol.get():
if self.protocol.halfMapsAttached.get():
if self.protocol.inputVolume.get() is not None:
_inputVol = self.protocol.inputVolume.get()
dim = _inputVol.getDim()[0]
sampling = _inputVol.getSamplingRate()
listVol.append(_inputVol)
else:
if self.protocol.inputHalf1.get() is not None:
_inputHalf1 = self.protocol.inputHalf1.get()
_inputHalf2 = self.protocol.inputHalf2.get()
dim = _inputHalf1.getDim()[0]
sampling = _inputHalf1.getSamplingRate()
listVol.append(_inputHalf1)
listVol.append(_inputHalf2)
else:
if self.protocol.inputVolume.get() is not None:
_inputVol = self.protocol.inputVolume.get()
dim = _inputVol.getDim()[0]
sampling = _inputVol.getSamplingRate()
listVol.append(_inputVol)
bildFileName = self.protocol._getExtraPath("axis_output.bild")
Chimera.createCoordinateAxisFile(dim,
bildFileName=bildFileName,
sampling=sampling)
fnCxc = self.protocol._getExtraPath("chimera_output.cxc")
f = open(fnCxc, '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
counter = 1
for vol in listVol:
counter += 1
self._visInputVolume(f, vol, counter)
for filename in sorted(os.listdir(directory)):
if filename.endswith(".mrc"):
counter += 1
volFileName = os.path.join(directory, filename)
vol = Volume()
vol.setFileName(volFileName)
if self.protocol.useHalfMapsInsteadVol.get():
if self.protocol.halfMapsAttached.get():
inVol = self.protocol.inputVolume.get()
else:
inVol = self.protocol.inputHalf1.get()
else:
inVol = self.protocol.inputVolume.get()
vol.setSamplingRate(inVol.getSamplingRate())
vol.setOrigin(inVol.getOrigin(True))
self._visInputVolume(f, vol, counter)
f.write("volume #%d level %0.3f\n" % (counter, 0.001))
f.close()
return [ChimeraView(fnCxc)]
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)
