def runChimeraStep(self):
# create CMD file
parentSessionFileName = self.parentProt._getExtraPath(sessionFile)
# if len(self.extraCommands.get()) > 2:
# f.write(self.extraCommands.get())
# args = " --nogui --cmd " + self._getTmpPath(
# chimeraScriptFileName)
# run in the background
cwd = os.path.abspath(self._getExtraPath())
Plugin.runChimeraProgram(Plugin.getProgram(),
os.path.abspath(parentSessionFileName),
cwd=cwd,
extraEnv=getEnvDictionary(self))
def getHome(cls):
""" Returns chimera home, trying first to take it from chimera plugin. If it fails it will return, the default value in the config"""
with pwutils.weakImport("chimera"):
from chimera import Plugin as chimeraPlugin
return chimeraPlugin.getHome()
return os.path.join(emConfig.EM_ROOT, 'chimerax-1.2.5')
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 _viewChimera(self, e=None):
from chimera import Plugin as chimera_plugin
args = ""
fnBaseDir = self.getResultsDir()
if fnBaseDir:
for fn in Path(fnBaseDir).rglob('model*.pdb'):
args += str(fn) + " "
os.system("%s %s &" % (chimera_plugin.getProgram(), args))
def defineBinaries(cls, env):
""" Install ISOLDE with Chimerax toolshed command """
from scipion.install.funcs import \
VOID_TGZ # Local import to avoid having scipion-app installed when building the package.
pathToChimera = chimera_plugin.getProgram()
installPluginsCommand = [
("%s --nogui --exit "
"--cmd 'toolshed install isolde; exit'" % pathToChimera, [])
]
env.addPackage('isolde',
version='1.0',
tar=VOID_TGZ,
default=True,
commands=installPluginsCommand)
def runChimeraStep(self):
""" Run Chimera script to start simulation and enable scipionwrite
"""
self.writeChimeraScript()
fnCmd = os.path.abspath(self._getExtraPath('chimera_script.cxc'))
# Go to extra dir and save there the output of
# scipionwrite
# f.write('cd %s' % os.path.abspath(
# self._getExtraPath()))
# save config file with information
# this is information is pased from scipion to chimerax
config = configparser.ConfigParser()
_chimeraPdbTemplateFileName = \
os.path.abspath(self._getExtraPath(
chimeraPdbTemplateFileName))
_chimeraMapTemplateFileName = \
os.path.abspath(self._getExtraPath(
chimeraMapTemplateFileName))
_sessionFile = os.path.abspath(self._getExtraPath(sessionFile))
protId = self.getObjId()
config['chimerax'] = {
'chimerapdbtemplatefilename': _chimeraPdbTemplateFileName % protId,
'chimeramaptemplatefilename': _chimeraMapTemplateFileName % protId,
'sessionfile': _sessionFile,
'enablebundle': True,
'protid': self.getObjId()
}
# set to True when
# protocol finished
# viewers will check this configuration file
with open(self._getExtraPath(CHIMERA_CONFIG_FILE), 'w') as configfile:
config.write(configfile)
cwd = os.path.abspath(self._getExtraPath())
Chimera.runProgram(chimera.getProgram(), fnCmd + "&", cwd=cwd)
def runChimeraStep(self):
# building script file including the coordinate axes and the input
# volume with samplingRate and Origin information
f = open(self._getTmpPath(chimeraScriptFileName), "w")
# building coordinate axes
dim = 150 # eventually we will create a PDB library that
# computes PDB dim
sampling = 1.
tmpFileName = os.path.abspath(self._getTmpPath("axis_input.bild"))
Chimera.createCoordinateAxisFile(dim,
bildFileName=tmpFileName,
sampling=sampling)
f.write("open %s\n" % tmpFileName)
f.write("cofr 0,0,0\n") # set center of coordinates
# input vol with its origin coordinates
pdbModelCounter = 1
if (not self.addTemplate and self.inputSequence1.get() is not None
and self._getOutFastaSequencesFile is not None):
alignmentFile1 = self._getOutFastaSequencesFile(self.OUTFILE1)
f.write("open %s\n" % alignmentFile1)
f.write("blastprotein %s:%s database %s matrix %s "
"cutoff %.3f maxSeqs %d log true\n" %
(alignmentFile1.split("/")[-1], self.targetSeqID1,
self.OptionForDataBase[int(self.dataBase)],
self.OptionForMatrix[int(self.similarityMatrix)],
self.cutoffValue, self.maxSeqs))
if (hasattr(self, 'pdbFileToBeRefined')
and self.pdbFileToBeRefined.get() is not None):
pdbModelCounter += 1
pdbFileToBeRefined = self.pdbFileToBeRefined.get()
f.write("open %s\n" %
os.path.abspath(pdbFileToBeRefined.getFileName()))
if pdbFileToBeRefined.hasOrigin():
x, y, z = (pdbFileToBeRefined.getOrigin().getShifts())
f.write("move %0.2f,%0.2f,%0.2f model #%d "
"coord #0\n" % (x, y, z, pdbModelCounter))
# Alignment of sequence and structure
if (hasattr(self, 'inputSequence1')
and hasattr(self, 'inputStructureChain')):
if (self.inputSequence1.get() is not None
and self.inputStructureChain.get() is not None):
pdbModelCounter = 2
if str(self.selectedModel) != '0':
f.write("select #%s.%s/%s\n" %
(pdbModelCounter, str(self.selectedModel + 1),
str(self.selectedChain1)))
else:
f.write("select #%s/%s\n" %
(pdbModelCounter, str(self.selectedChain1)))
if self._getOutFastaSequencesFile is not None:
alignmentFile1 = self._getOutFastaSequencesFile(
self.OUTFILE1)
f.write("open %s\n" % alignmentFile1)
f.write("sequence disassociate #%s %s\n" %
(pdbModelCounter, alignmentFile1.split("/")[-1]))
if str(self.selectedModel) != '0':
f.write("sequence associate #%s.%s/%s %s:1\n" %
(pdbModelCounter, str(self.selectedModel + 1),
str(self.selectedChain1),
alignmentFile1.split("/")[-1]))
else:
f.write("sequence associate #%s/%s %s:1\n" %
(pdbModelCounter, str(self.selectedChain1),
alignmentFile1.split("/")[-1]))
if (self.additionalTargetSequence.get() is True
and self.inputSequence2.get() is not None
and self.inputStructureChain.get() is not None):
f.write("select clear\n")
f.write("select #%s/%s,%s\n" %
(pdbModelCounter, str(
self.selectedChain1), str(self.selectedChain2)))
if self._getOutFastaSequencesFile is not None:
alignmentFile2 = self._getOutFastaSequencesFile(
self.OUTFILE2)
f.write("open %s\n" % alignmentFile2)
f.write("sequence disassociate #%s %s\n" %
(pdbModelCounter, alignmentFile2.split("/")[-1]))
if str(self.selectedModel) != '0':
f.write("sequence associate #%s.%s/%s %s:1\n" %
(pdbModelCounter, str(self.selectedModel + 1),
str(self.selectedChain2),
alignmentFile2.split("/")[-1]))
else:
f.write("sequence associate #%s/%s %s:1\n" %
(pdbModelCounter, str(self.selectedChain2),
alignmentFile2.split("/")[-1]))
# run the text:
_chimeraScriptFileName = os.path.abspath(
self._getTmpPath(chimeraScriptFileName))
if len(self.extraCommands.get()) > 2:
f.write(self.extraCommands.get())
args = " --nogui " + _chimeraScriptFileName
else:
args = " " + _chimeraScriptFileName
f.close()
self._log.info('Launching: ' + Plugin.getProgram() + ' ' + args)
# run in the background
cwd = os.path.abspath(self._getExtraPath())
Plugin.runChimeraProgram(Plugin.getProgram(),
args,
cwd=cwd,
extraEnv=getEnvDictionary(self))
def runChimeraStep(self):
# building script file including the coordinate axes and the input
# volume with samplingRate and Origin information
f = open(self._getTmpPath(chimeraScriptFileName), "w")
f.write("from chimerax.core.commands import run\n")
# building coordinate axes
dim = self.vol.getDim()[0]
sampling = self.vol.getSamplingRate()
bildFileName = os.path.abspath(self._getTmpPath("axis_input.bild"))
Chimera.createCoordinateAxisFile(dim, bildFileName=bildFileName,
sampling=sampling)
# origin coordinates
modelId = 1 # axis
f.write("run(session, 'open %s')\n" % (bildFileName))
f.write("run(session, 'cofr 0,0,0')\n") # set center of coordinates
# input volume
modelMapM = modelId + 1 # 2, Minuend, result = minuend − subtrahend
f.write("run(session,'open %s')\n" % self.fnVolName)
# step = 1 -> no binning
f.write("run(session,'volume #%d style surface voxelSize %f')\n"
% (modelMapM, sampling))
x, y, z = self.vol.getShiftsFromOrigin()
f.write("run(session,'volume #%d origin %0.2f,%0.2f,%0.2f')\n"
% (modelMapM, x, y, z))
modelMapS =7
modelAtomStruct = 3
modelAtomStructChain = 4
modelAtomStructChainSym = 5
modelIdZone = 6
modelMapDiff = 8
modelMapDiffFil = 9
if self.mapOrModel == 0: # subtrahend is a 3D Map
# input map
# with its origin coordinates
# modelMapS = modelMapM + 1 # 3 Subtrahend
f.write("run(session,'open %s')\n" %
(self.subVolName))
f.write("run(session, 'rename #3 id #%d')\n" % modelMapS)
f.write("run(session,'volume #%d style surface voxelSize %f step 1')\n"
% (modelMapS, sampling))
x, y, z = self.subVol.getShiftsFromOrigin()
f.write("run(session,'volume #%d origin %0.2f,%0.2f,%0.2f')\n"
% (modelMapS, x, y, z))
if self.subtractOrMask == 1 and self.level.get() is not None:
f.write("run(session,'volume #%d level %f')\n" %
(modelMapS, self.level))
else: # subtrahend is an atomic structure
f.write("run(session,'open %s')\n" % self.atomStructName)
# input atomic structure
if self.selectChain == True:
# model and chain selected
if self.selectStructureChain.get() is not None:
chain = self.selectStructureChain.get()
self.selectedModel = chain.split(',')[0].split(':')[1].strip()
#TODO: Study problems with multimodels
if int(self.selectedModel) != 0:
modelId = int(modelAtomStruct +
int(self.selectedModel))
f.write("run(session, 'rename #%d id #%d')\n" %
(modelId, modelAtomStruct))
self.selectedChain = \
chain.split(',')[1].split(':')[1].strip().split('"')[1]
print("Selected chain: %s from model: %s from structure: %s" \
% (self.selectedChain, self.selectedModel,
os.path.basename(self.atomStructName)))
f.write("run(session,'sel #%d/%s')\n"
% (modelAtomStruct, self.selectedChain))
tmpPath = os.path.abspath(self._getTmpPath('chain.cif'))
f.write("run(session,"
"'save %s format mmcif models #%d relModel #%d selectedOnly true')\n"
% (tmpPath, modelAtomStruct, modelId))
f.write("run(session,'open %s')\n" % tmpPath)
f.write("run(session,'scipionwrite #%d prefix chain_%s_ ')\n"
% (modelAtomStructChain, self.selectedChain))
if self.selectAreaMap == True: # mask the minuend using the atomic structure
if self.applySymmetry == True and self.symmetryGroup.get() is not None:
sym = CHIMERA_SYM_NAME[self.symmetryGroup.get()]
modelId = modelAtomStructChain #4
self.symMethod(f, modelId, sym, self.symmetryOrder)
f.write("run(session,'volume zone #%d nearAtoms #%d "
"range %d newMap true modelId #%d')\n"
% (modelMapM, modelAtomStructChainSym,
self.radius, modelIdZone))
if not self.removeResidues:
f.write("run(session,'scipionwrite #%d prefix sym_ ')\n"
% modelAtomStructChainSym)
f.write("run(session,'close #%d')\n" % (modelAtomStructChainSym))
else:
f.write("run(session,'volume zone #%d nearAtoms #%d "
"range %d newMap true modelId #%d')\n"
% (modelMapM, modelAtomStructChain,
self.radius, modelIdZone))
f.write("run(session,'scipionwrite #%d prefix zone_ ')\n" % modelIdZone)
if self.removeResidues == True:
if (self.firstResidueToRemove.get() is not None and
self.lastResidueToRemove.get() is not None):
self.firstResidue = self.firstResidueToRemove.get().\
split(":")[1].split(",")[0].strip()
self.lastResidue = self.lastResidueToRemove.get(). \
split(":")[1].split(",")[0].strip()
f.write("run(session,'sel #%d/%s:%d-%d')\n"
% (modelAtomStructChain, self.selectedChain,
int(self.firstResidue), int(self.lastResidue)))
f.write("run(session,'del sel')\n")
f.write("run(session,'sel #%d/%s:%d-%d')\n" %
(modelAtomStructChain, self.selectedChain,
int(self.firstResidue) - 10,
int(self.lastResidue) + 10))
if self.applySymmetry == True:
if self.symmetryGroup.get() is not None:
sym = CHIMERA_SYM_NAME[self.symmetryGroup.get()]
modelId = modelAtomStructChain
self.symMethod(f, modelId, sym, self.symmetryOrder, self.rangeDist)
f.write("run(session,'scipionwrite #%d prefix sym_ ')\n"
% modelAtomStructChainSym)
f.write("v=run(session,'molmap #%d %0.3f gridSpacing %f')\n"
% (modelAtomStructChainSym, self.resolution, sampling))
f.write("run(session,'rename #%d id #7' % v.id[0])\n") ## #7 is modelMapS id
if self.subtractOrMask == 1 and self.level.get() is not None:
f.write("run(session,'volume #%d level %f')\n" %
(modelMapS, self.level))
if self.removeResidues == True:
if (self.firstResidueToRemove.get() is not None and
self.lastResidueToRemove.get() is not None):
f.write("run(session,'sel #%d:%d-%d')\n" %
(modelAtomStructChainSym,
int(self.firstResidue) - 10,
int(self.lastResidue) + 10))
else:
f.write("v=run(session,'molmap #%d %0.3f gridSpacing %f')\n"
% (modelAtomStructChain, self.resolution, sampling))
f.write("run(session,'rename #%d id #7' % v.id[0])\n") ## #7 is modelMapS id
if self.subtractOrMask == 1 and self.level.get() is not None:
f.write("run(session,'volume #%d level %f')\n" %
(modelMapS, self.level))
f.write("run(session,'scipionwrite #%d prefix molmap_chain%s_')\n"
% (modelMapS, self.selectedChain))
else: # use whole atomic model
f.write("run(session,'scipionwrite #%d')\n" % modelAtomStruct)
if self.selectAreaMap == True:
if self.applySymmetry == True and self.symmetryGroup.get() is not None:
sym = CHIMERA_SYM_NAME[self.symmetryGroup.get()]
modelId = modelAtomStruct
self.symMethod(f, modelId, sym, self.symmetryOrder, self.rangeDist)
f.write("run(session, 'rename #4 id #%d')\n" % modelAtomStructChainSym)
f.write("run(session,'volume zone #%d nearAtoms #%d "
"range %d newMap true modelId #%d')\n"
% (modelMapM, modelAtomStructChainSym,
self.radius, modelIdZone))
f.write("run(session,'close #%d')\n" % (modelAtomStructChainSym))
else:
f.write("run(session,'volume zone #%d nearAtoms #%d "
"range %d newMap true modelId #%d')\n"
% (modelMapM, modelAtomStruct,
self.radius, modelIdZone))
f.write("run(session,'scipionwrite #%d prefix zone_ ')\n" % modelIdZone)
if self.removeResidues == True:
if (self.inputStructureChain.get() is not None and
self.firstResidueToRemove.get() is not None and
self.lastResidueToRemove.get() is not None):
chain = self.inputStructureChain.get()
self.selectedModel = chain.split(',')[0].split(':')[1].strip()
# TODO: Study problems with multimodels
if int(self.selectedModel) != 0:
modelId = int(modelAtomStruct +
int(self.selectedModel))
f.write("run(session, 'rename #%d id #%d')\n" %
(modelId, modelAtomStruct))
self.selectedChain = \
chain.split(',')[1].split(':')[1].strip().split('"')[1]
print("Selected chain: %s from model: %s from structure: %s"\
% (self.selectedChain, self.selectedModel,
os.path.basename(self.atomStructName)))
f.write("run(session,'sel #%d/%s')\n"
% (modelAtomStruct, self.selectedChain))
self.firstResidue = self.firstResidueToRemove.get(). \
split(":")[1].split(",")[0].strip()
self.lastResidue = self.lastResidueToRemove.get(). \
split(":")[1].split(",")[0].strip()
f.write("run(session,'sel #%d/%s:%d-%d')\n"
% (modelAtomStruct, self.selectedChain,
int(self.firstResidue), int(self.lastResidue)))
f.write("run(session,'del sel')\n")
f.write("run(session,'scipionwrite #%d prefix mutated_ ')\n"
% modelAtomStruct)
f.write("run(session,'sel #%d/%s:%d-%d')\n" %
(modelAtomStruct, self.selectedChain,
int(self.firstResidue) - 10,
int(self.lastResidue) + 10))
if self.applySymmetry == True:
if self.symmetryGroup.get() is not None:
sym = CHIMERA_SYM_NAME[self.symmetryGroup.get()]
modelId = modelAtomStruct
self.symMethod(f, modelId, sym, self.symmetryOrder, self.rangeDist)
f.write("run(session, 'rename #4 id #%d')\n" % modelAtomStructChainSym)
f.write("run(session,'scipionwrite #%d prefix sym_ ')\n"
% modelAtomStructChainSym)
if (self.inputStructureChain.get() is not None and
self.firstResidueToRemove.get() is not None and
self.lastResidueToRemove.get() is not None):
f.write("run(session, 'sel #%d/%s:%d-%d')\n" %
(modelAtomStructChainSym,
self.selectedChain,
int(self.firstResidue) - 10,
int(self.lastResidue) + 10))
f.write("v=run(session,'molmap #%d %0.3f gridSpacing %f')\n"
% (modelAtomStructChainSym, self.resolution, sampling))
f.write("run(session,'rename #%d id #7' % v.id[0])\n") ## #7 is modelMapS id
# modelMapS = modelAtomStructChainSym + 1
if self.subtractOrMask == 1 and self.level.get() is not None:
f.write("run(session,'volume #%d level %f')\n" %
(modelMapS, self.level))
else: # no symmetry
f.write("v=run(session,'molmap #%d %0.3f gridSpacing %f')\n"
% (modelAtomStruct, self.resolution, sampling))
f.write("run(session,'rename #%d id #7' % v.id[0])\n") ## #7 is modelMapS id
if self.subtractOrMask == 1 and self.level.get() is not None:
f.write("run(session,'volume #%d level %f')\n" %
(modelMapS, self.level))
f.write("run(session,'scipionwrite #%d prefix molmap_ ')\n" % modelMapS)
# Generation of the differential map
if self.selectAreaMap == True:
modelId = modelIdZone
else:
modelId = modelMapM
if self.subtractOrMask == 0:
f.write("run(session, 'volume subtract #%d #%d modelId #%d "
"minRms true onGrid #%d')\n" %
(modelId, modelMapS, modelMapDiff, modelId))
else:
f.write("run(session, 'volume mask #%d surfaces #%d invertMask "
"true modelId #%d')\n" %
(modelId, modelMapS, modelMapDiff))
f.write("run(session,'scipionwrite #%d prefix difference_')\n" % modelMapDiff)
# Generation of the filtered map
if self.filterToApplyToDiffMap.get() == 0:
f.write("run(session,'volume gaussian #%d sd %0.3f modelId %#d')\n"
% (modelMapDiff, self.widthFilter.get(), modelMapDiffFil))
else:
f.write("run(session,'volume laplacian #%d')\n" % modelMapDiff)
f.write("run(session,'scipionwrite #%d prefix filtered_')\n" % modelMapDiffFil)
if self.inputPdbFiles is not None: # Other atomic models different
# from the subtrahend
for atomStruct in self.inputPdbFiles:
f.write("run(session,'open %s')\n" %
os.path.abspath(atomStruct.get().getFileName()))
# Finally save session
f.write("run(session,'scipionss')\n")
# run the script:
if len(self.extraCommands.get()) > 2:
f.write(self.extraCommands.get())
args = " --nogui --script " + \
os.path.abspath(self._getTmpPath(chimeraScriptFileName))
else:
args = " --script " + \
os.path.abspath(self._getTmpPath(chimeraScriptFileName))
f.close()
self._log.info('Launching: ' + Plugin.getProgram() + ' ' + args)
# run in the background
cwd = os.path.abspath(self._getExtraPath())
Plugin.runChimeraProgram(Plugin.getProgram(), args, cwd=cwd, extraEnv=getEnvDictionary(self))