def _insertAllSteps(self):
atomsFn = self.getInputPdb().getFileName()
# Define some outputs filenames
self.imgsFn = self._getExtraPath('images.xmd')
self.modesFn = self._getExtraPath('modes.xmd')
self.structureEM = self.inputModes.get().getPdb().getPseudoAtoms()
if self.structureEM:
self.atomsFn = self._getExtraPath(basename(atomsFn))
copyFile(atomsFn, self.atomsFn)
else:
localFn = self._getExtraPath(
replaceBaseExt(basename(atomsFn), 'pdb'))
cifToPdb(atomsFn, localFn)
self.atomsFn = self._getExtraPath(basename(localFn))
self._insertFunctionStep('convertInputStep', atomsFn)
if self.copyDeformations.empty(): #ONLY FOR DEBUGGING
self._insertFunctionStep("performNmaStep", self.atomsFn,
self.modesFn)
else:
# TODO: for debugging and testing it will be useful to copy the deformations
# metadata file, not just the deformation.txt file
self._insertFunctionStep('copyDeformationsStep',
self.copyDeformations.get())
self._insertFunctionStep('createOutputStep')
def getBestVolumesStep(self):
volumes = []
inliers = []
for n in range(self.nRansac.get()):
fnAngles = self._getTmpPath("angles_ransac%05d"%n+".xmd")
md=xmipp.MetaData("inliers@"+fnAngles)
numInliers=md.getValue(xmipp.MDL_WEIGHT,md.firstObject())
volumes.append(fnAngles)
inliers.append(numInliers)
index = sorted(range(inliers.__len__()), key=lambda k: inliers[k])
fnBestAngles = ''
threshold=self.getCCThreshold()
i = self.nRansac.get()-1
indx = 0
while i >= 0 and indx < self.numVolumes:
fnBestAngles = volumes[index[i]]
fnBestAnglesOut = self._getPath("proposedVolume%05d"%indx+".xmd")
copyFile(fnBestAngles, fnBestAnglesOut)
self._log.info("Best volume %d = %s" % (indx, fnBestAngles))
if not self.useAll:
self.runJob("xmipp_metadata_utilities","-i %s -o %s --query select \"maxCC>%f \" --mode append" %(fnBestAnglesOut,fnBestAnglesOut,threshold))
if not isMdEmpty(fnBestAnglesOut):
indx += 1
else:
indx += 1
i -= 1
# Remove unnecessary files
for n in range(self.nRansac.get()):
fnAngles = self._getTmpPath("angles_ransac%05d"%n+".xmd")
cleanPath(fnAngles)
def exportAtomStructStep(self):
exportAtomStruct = self.exportAtomStruct.get()
originStructPath = exportAtomStruct.getFileName()
dirName = self.filesPath.get()
destinyStructPath = os.path.join(dirName, self.COORDINATEFILENAME)
destinySympleStructPath = os.path.join(dirName, self.SYMPLIFIED_STRUCT)
# save input atom struct with no change
baseName = os.path.basename(originStructPath)
localPath = os.path.abspath(os.path.join(dirName, baseName))
copyFile(originStructPath, localPath)
# call biopython to simplify atom struct and save it
aSH = AtomicStructHandler()
aSH.read(originStructPath)
aSH.write(destinySympleStructPath)
# if pdb convert to mmcif calling maxit twice
if originStructPath.endswith(".pdb"):
# convert pdb to cif using maxit program
log = self._log
fromPDBToCIF(originStructPath, destinyStructPath, log)
try:
# convert cif to mmCIF by using maxit program
fromCIFTommCIF(destinyStructPath, destinyStructPath, log)
except Exception as e:
pass
# if cif convert to mmcif using maxit
elif originStructPath.endswith(".cif"):
# convert cif to mmCIF by using maxit program
log = self._log
try:
fromCIFTommCIF(originStructPath, destinyStructPath, log)
except Exception as e:
pass
def importStep(self):
if not self.multiple.get():
copyFile(self.filePath.get(),self._getPath(os.path.split(self.filePath.get())[1]))
fh = open(self.filePath.get())
for line in fh.readlines():
tokens = line.split(',')
if len(tokens)==2:
fhSmile = open(self._getExtraPath(tokens[0].strip()+".smi"),'w')
fhSmile.write(tokens[1].strip()+"\n")
fhSmile.close()
else:
for filename in glob.glob(os.path.join(self.filesPath.get(), self.filesPattern.get())):
fnSmall = self._getExtraPath(os.path.split(filename)[1])
copyFile(filename, fnSmall)
outputSmallMolecules = SetOfSmallMolecules().create(path=self._getPath(),suffix='SmallMols')
for fnSmall in glob.glob(self._getExtraPath("*")):
smallMolecule = SmallMolecule(smallMolFilename=fnSmall)
if not fnSmall.endswith('.mae') and not fnSmall.endswith('.maegz'):
fnRoot = os.path.splitext(os.path.split(fnSmall)[1])[0]
fnOut = self._getExtraPath("%s.png" % fnRoot)
args = Plugin.getPluginHome('utils/rdkitUtils.py') + " draw %s %s" % (fnSmall, fnOut)
try:
Plugin.runRDKit(self, "python3", args)
smallMolecule._PDBLigandImage = pwobj.String(fnOut)
except:
smallMolecule._PDBLigandImage = pwobj.String("Not available")
outputSmallMolecules.append(smallMolecule)
self._defineOutputs(outputSmallMols=outputSmallMolecules)
def getBestVolumesStep(self):
volumes = []
inliers = []
for n in range(self.nRansac.get()):
fnAngles = self._getTmpPath("angles_ransac%05d"%n+".xmd")
md=emlib.MetaData("inliers@"+fnAngles)
numInliers=md.getValue(emlib.MDL_WEIGHT,md.firstObject())
volumes.append(fnAngles)
inliers.append(numInliers)
index = sorted(range(inliers.__len__()), key=lambda k: inliers[k])
fnBestAngles = ''
threshold=self.getCCThreshold()
i = self.nRansac.get()-1
indx = 0
while i >= 0 and indx < self.numVolumes:
fnBestAngles = volumes[index[i]]
fnBestAnglesOut = self._getPath("proposedVolume%05d"%indx+".xmd")
copyFile(fnBestAngles, fnBestAnglesOut)
self._log.info("Best volume %d = %s" % (indx, fnBestAngles))
if not self.useAll:
self.runJob("xmipp_metadata_utilities","-i %s -o %s --query select \"maxCC>%f \" --mode append" %(fnBestAnglesOut,fnBestAnglesOut,threshold))
if not isMdEmpty(fnBestAnglesOut):
indx += 1
else:
indx += 1
i -= 1
# Remove unnecessary files
for n in range(self.nRansac.get()):
fnAngles = self._getTmpPath("angles_ransac%05d"%n+".xmd")
cleanPath(fnAngles)
def elasticAlignmentStep(self, nVoli, voli, nVolj):
makePath(self._getExtraPath("modes%d"%nVoli))
for i in range(self.numberOfModes.get() + 1):
if i == 0 :
i += 1
copyFile (self._getPath("modes/vec.%d"%i),
self._getExtraPath("modes%d/vec.%d"%(nVoli, i)))
mdVol = xmipp.MetaData()
fnOutMeta = self._getExtraPath('RigidAlignVol_%d_To_Vol_%d.xmd' % (nVolj, nVoli))
mdVol.setValue(xmipp.MDL_IMAGE, self._getPath('outputRigidAlignment_vol_%d_to_%d.vol' %
(nVolj, nVoli)), mdVol.addObject())
mdVol.write(fnOutMeta)
fnPseudo = self._getPath("pseudoatoms_%d.pdb"%nVoli)
fnModes = self._getPath("modes_%d.xmd"%nVoli)
Ts = voli.getSamplingRate()
fnDeform = self._getExtraPath('compDeformVol_%d_To_Vol_%d.xmd' % (nVolj, nVoli))
sigma = Ts * self.pseudoAtomRadius.get()
fnPseudoOut = self._getExtraPath('PseudoatomsDeformedPDB_Vol_%d_To_Vol_%d.pdb' %
(nVolj, nVoli))
self.runJob('xmipp_nma_alignment_vol',
"-i %s --pdb %s --modes %s --sampling_rate %s -o %s --fixed_Gaussian %s --opdb %s"%\
(fnOutMeta, fnPseudo, fnModes, Ts, fnDeform, sigma, fnPseudoOut))
fnVolOut = self._getExtraPath('DeformedVolume_Vol_%d_To_Vol_%d' % (nVolj, nVoli))
self.runJob('xmipp_volume_from_pdb', "-i %s -o %s --sampling %s --fixed_Gaussian %s" %
(fnPseudoOut, fnVolOut, Ts, sigma))
def elasticAlignmentStep(self, nVoli, Ts, nVolj, fnAlignedVolj):
fnVolOut = self._getExtraPath('DeformedVolume_Vol_%d_To_Vol_%d' %
(nVolj, nVoli))
if os.path.exists(fnVolOut + ".pdb"):
return
makePath(self._getExtraPath("modes%d" % nVoli))
for i in range(self.numberOfModes.get() + 1):
if i == 0:
i += 1
copyFile(self._getPath("modes/vec.%d" % i),
self._getExtraPath("modes%d/vec.%d" % (nVoli, i)))
mdVol = xmippLib.MetaData()
fnOutMeta = self._getExtraPath('RigidAlignVol_%d_To_Vol_%d.xmd' %
(nVolj, nVoli))
mdVol.setValue(xmippLib.MDL_IMAGE, fnAlignedVolj, mdVol.addObject())
mdVol.write(fnOutMeta)
fnPseudo = self._getPath("pseudoatoms_%d.pdb" % nVoli)
fnModes = self._getPath("modes_%d.xmd" % nVoli)
fnDeform = self._getExtraPath('compDeformVol_%d_To_Vol_%d.xmd' %
(nVolj, nVoli))
sigma = Ts * self.pseudoAtomRadius.get()
fnPseudoOut = self._getExtraPath(
'PseudoatomsDeformedPDB_Vol_%d_To_Vol_%d.pdb' % (nVolj, nVoli))
self.runJob('xmipp_nma_alignment_vol',
"-i %s --pdb %s --modes %s --sampling_rate %s -o %s --fixed_Gaussian %s --opdb %s"%\
(fnOutMeta, fnPseudo, fnModes, Ts, fnDeform, sigma, fnPseudoOut))
self.runJob(
'xmipp_volume_from_pdb',
"-i %s -o %s --sampling %s --fixed_Gaussian %s" %
(fnPseudoOut, fnVolOut, Ts, sigma))
def maskVolume(self, volFn, maskFn, index, halfString):
ih = ImageHandler()
# Check if there is a mask if not then use a spherical mask
if maskFn is None:
# Compute sphere radius and make a spherical mask
maskFn = self._getFileName('mask', index + 1)
volSize = ih.getDimensions(volFn)[0]
radius = volSize / 2 - 1
emlib.createEmptyFile(maskFn, volSize, volSize, volSize)
program = "xmipp_transform_mask"
args = "-i %s --mask circular %d --create_mask %s " % (
maskFn, -1 * radius, maskFn)
self.runJob(program, args)
else:
putils.copyFile(maskFn, self._getFileName('mask', index + 1))
maskFn = self._getFileName('mask', index + 1)
# Read the volume if it is provided
if volFn.endswith(".mrc"):
volFn = volFn + ":mrc"
# Apply mask to the volume
volMasked = self._getFileName('volume', 'masked', index + 1,
halfString)
program = 'xmipp_image_operate'
args = '-i %s --mult %s -o %s' % (volFn, maskFn, volMasked)
self.runJob(program, args)
def calculateAverage(self, iteration):
fnAvg = self._getExtraPath("volumeAvg.vol")
N = 0
for i in range(self.inputVolumes.get().getSize()):
if iteration <= 2:
fnVol = self._getExtraPath("volume%03d.vol" % i)
if i == 0:
copyFile(fnVol, fnAvg)
else:
self.runJob("xmipp_image_operate",
"-i %s --plus %s" % (fnAvg, fnVol),
numberOfMpi=1)
else:
fnVol = self._getExtraPath("volume%03d_best.vol" % i)
self.runJob("xmipp_image_operate",
"-i %s --plus %s" % (fnAvg, fnVol),
numberOfMpi=1)
N += 1
if iteration > 0:
self.runJob("xmipp_image_operate",
"-i %s --plus %s" %
(fnAvg, self._getExtraPath("volumeBest.vol")),
numberOfMpi=1)
N += 1
self.runJob("xmipp_image_operate",
"-i %s --divide %f" % (fnAvg, N),
numberOfMpi=1)
def convertInputStep(self, atomsFn):
# Write the modes metadata taking into account the selection
self.writeModesMetaData()
# Write a metadata with the normal modes information
# to launch the nma alignment programs
writeSetOfParticles(self.inputParticles.get(), self.imgsFn)
# Copy the atoms file to current working dir
copyFile(atomsFn, self.atomsFn)
def convertInputStep(self, atomsFn):
# Write the modes metadata taking into account the selection
self.writeModesMetaData()
# Write a metadata with the normal modes information
# to launch the nma alignment programs
writeSetOfParticles(self.inputParticles.get(), self.imgsFn)
# Copy the atoms file to current working dir
copyFile(atomsFn, self.atomsFn)
def copyPdbStep(self, inputFn, localFn, isEM):
""" Copy the input pdb file and also create a link 'atoms.pdb' """
copyFile(inputFn, localFn)
if isEM:
fnOut = self._getPath('pseudoatoms.pdb')
else:
fnOut = self._getPath('atoms.pdb')
if not os.path.exists(fnOut):
createLink(localFn, fnOut)
def copyPdbStep(self, inputFn, localFn, isEM):
""" Copy the input pdb file and also create a link 'atoms.pdb' """
copyFile(inputFn, localFn)
if isEM:
fnOut=self._getPath('pseudoatoms.pdb')
else:
fnOut=self._getPath('atoms.pdb')
if not os.path.exists(fnOut):
createLink(localFn, fnOut)
def importMicrographs(self, pattern, suffix, voltage, sphericalAberration,
amplitudeContrast):
""" Copy images matching the filename pattern
Register other parameters.
"""
filePaths = glob(expandPattern(pattern))
#imgSet = SetOfMicrographs(filename=self.micsPairsSqlite, prefix=suffix)
imgSet = self._createSetOfMicrographs(suffix=suffix)
acquisition = imgSet.getAcquisition()
# Setting Acquisition properties
acquisition.setVoltage(voltage)
acquisition.setSphericalAberration(sphericalAberration)
acquisition.setAmplitudeContrast(amplitudeContrast)
# Call a function that should be implemented by each subclass
self._setOtherPars(imgSet)
outFiles = [imgSet.getFileName()]
imgh = ImageHandler()
img = imgSet.ITEM_TYPE()
n = 1
size = len(filePaths)
filePaths.sort()
for i, fn in enumerate(filePaths):
# ext = os.path.splitext(basename(f))[1]
dst = self._getExtraPath(basename(fn))
if self.copyToProj:
copyFile(fn, dst)
else:
createLink(fn, dst)
if n > 1:
for index in range(1, n + 1):
img.cleanObjId()
img.setFileName(dst)
img.setIndex(index)
imgSet.append(img)
else:
img.cleanObjId()
img.setFileName(dst)
# Fill the micName if img is a Micrograph.
self._fillMicName(img, fn, pattern)
imgSet.append(img)
outFiles.append(dst)
sys.stdout.write("\rImported %d/%d" % (i + 1, size))
sys.stdout.flush()
print "\n"
imgSet.write()
return imgSet
def createReport(self):
fnTex = "report.tex"
fhTex = open(self._getExtraPath(fnTex), "w")
template = """
\\documentclass[12pt]{article}
\\usepackage{amsmath,amsthm,amssymb,amsfonts}
\\usepackage{graphicx}
\\usepackage{pdfpages}
\\DeclareGraphicsExtensions{.pdf,.png,.jpg}
\\begin{document}
\\title{User Report}
\\author{Created by Scipion}
\\maketitle
"""
fhTex.write(template)
fnDir = self.filesPath.get()
if not os.path.isdir(fnDir):
fnDir = os.path.basename(fnDir)
for fileName in sorted(glob.glob(os.path.join(fnDir, "*"))):
fnDest = os.path.basename(fileName).lower()
fnDest = fnDest.replace(" ", "_")
fnDest = fnDest.replace(":", "_")
fnDest = fnDest.replace(";", "_")
copyFile(fileName, self._getExtraPath(fnDest))
if fnDest.endswith(".tex") or fnDest.endswith(".txt"):
fhTex.write("\\input{%s}\n" % fnDest)
fhTex.write("\n")
elif fnDest.endswith(".png") or fnDest.endswith(".jpg"):
fhTex.write("\\begin{center}\n")
fhTex.write("\\includegraphics[width=14cm]{%s}\n" % fnDest)
fhTex.write("\\end{center}\n")
fhTex.write("\n")
elif fnDest.endswith(".pdf"):
fhTex.write("\\includepdf[pages=-]{%s}\n" % fnDest)
fhTex.write("\\clearpage\n")
fhTex.write("\n")
template = """
\\end{document}
"""
fhTex.write(template)
fhTex.close()
args = "-interaction=nonstopmode " + fnTex
self.runJob("pdflatex", args, cwd=self._getExtraPath())
fnPDF = self._getExtraPath("report.pdf")
if os.path.exists(fnPDF):
moveFile(fnPDF, self._getPath("report.pdf"))
else:
raise Exception("PDF file was not produced.")
def importMicrographs(self, pattern, suffix, voltage, sphericalAberration, amplitudeContrast):
""" Copy images matching the filename pattern
Register other parameters.
"""
filePaths = glob(expandPattern(pattern))
#imgSet = SetOfMicrographs(filename=self.micsPairsSqlite, prefix=suffix)
imgSet = self._createSetOfMicrographs(suffix=suffix)
acquisition = imgSet.getAcquisition()
# Setting Acquisition properties
acquisition.setVoltage(voltage)
acquisition.setSphericalAberration(sphericalAberration)
acquisition.setAmplitudeContrast(amplitudeContrast)
# Call a function that should be implemented by each subclass
self._setOtherPars(imgSet)
outFiles = [imgSet.getFileName()]
imgh = ImageHandler()
img = imgSet.ITEM_TYPE()
n = 1
size = len(filePaths)
filePaths.sort()
for i, fn in enumerate(filePaths):
# ext = os.path.splitext(basename(f))[1]
dst = self._getExtraPath(basename(fn))
if self.copyToProj:
copyFile(fn, dst)
else:
createLink(fn, dst)
if n > 1:
for index in range(1, n+1):
img.cleanObjId()
img.setFileName(dst)
img.setIndex(index)
imgSet.append(img)
else:
img.cleanObjId()
img.setFileName(dst)
# Fill the micName if img is a Micrograph.
self._fillMicName(img, fn, pattern)
imgSet.append(img)
outFiles.append(dst)
sys.stdout.write("\rImported %d/%d" % (i+1, size))
sys.stdout.flush()
print "\n"
imgSet.write()
return imgSet
def createReport(self):
fnTex = "report.tex"
fhTex = open(self._getExtraPath(fnTex), "w")
template ="""
\\documentclass[12pt]{article}
\\usepackage{amsmath,amsthm,amssymb,amsfonts}
\\usepackage{graphicx}
\\usepackage{pdfpages}
\\DeclareGraphicsExtensions{.pdf,.png,.jpg}
\\begin{document}
\\title{User Report}
\\author{Created by Scipion}
\\maketitle
"""
fhTex.write(template)
fnDir = self.filesPath.get()
if not os.path.isdir(fnDir):
fnDir = os.path.basename(fnDir)
for fileName in sorted(glob.glob(os.path.join(fnDir,"*"))):
fnDest = os.path.basename(fileName).lower()
fnDest = fnDest.replace(" ","_")
fnDest = fnDest.replace(":","_")
fnDest = fnDest.replace(";","_")
copyFile(fileName, self._getExtraPath(fnDest))
if fnDest.endswith(".tex") or fnDest.endswith(".txt"):
fhTex.write("\\input{%s}\n" % fnDest)
fhTex.write("\n")
elif fnDest.endswith(".png") or fnDest.endswith(".jpg"):
fhTex.write("\\begin{center}\n")
fhTex.write("\\includegraphics[width=14cm]{%s}\n" % fnDest)
fhTex.write("\\end{center}\n")
fhTex.write("\n")
elif fnDest.endswith(".pdf"):
fhTex.write("\\includepdf[pages=-]{%s}\n" % fnDest)
fhTex.write("\\clearpage\n")
fhTex.write("\n")
template = """
\\end{document}
"""
fhTex.write(template)
fhTex.close()
args = "-interaction=nonstopmode " + fnTex
self.runJob("pdflatex", args, cwd=self._getExtraPath())
fnPDF = self._getExtraPath("report.pdf")
if os.path.exists(fnPDF):
moveFile(fnPDF,self._getPath("report.pdf"))
else:
raise Exception("PDF file was not produced.")
def _moveCoordsToInfo(self, tomo):
fnCoor = '*%s_info.json' % pwutils.removeBaseExt(tomo.getFileName().split("__")[0])
pattern = os.path.join(self.path, fnCoor)
files = glob.glob(pattern)
if files:
infoDir = pwutils.join(os.path.abspath(self.path), 'info')
pathCoor = os.path.join(infoDir, os.path.basename(files[0]))
pwutils.makePath(infoDir)
copyFile(files[0], pathCoor)
def copyOrLinkFileName(imgRow, prefixDir, outputDir, copyFiles=False):
index, imgPath = relionToLocation(imgRow.getValue(md.RLN_IMAGE_NAME))
baseName = os.path.basename(imgPath)
newName = os.path.join(outputDir, baseName)
if not os.path.exists(newName):
if copyFiles:
copyFile(os.path.join(prefixDir, imgPath), newName)
else:
createLink(os.path.join(prefixDir, imgPath), newName)
imgRow.setValue(md.RLN_IMAGE_NAME, locationToRelion(index, newName))
def copyOrLinkFileName(imgRow, prefixDir, outputDir, copyFiles=False):
index, imgPath = relionToLocation(imgRow.getValue(md.RLN_IMAGE_NAME))
baseName = os.path.basename(imgPath)
newName = os.path.join(outputDir, baseName)
if not os.path.exists(newName):
if copyFiles:
copyFile(os.path.join(prefixDir, imgPath), newName)
else:
createLink(os.path.join(prefixDir, imgPath), newName)
imgRow.setValue(md.RLN_IMAGE_NAME, locationToRelion(index, newName))
def createOutputStep(self, pdbPath):
""" Copy the PDB structure and register the output object.
"""
if not exists(pdbPath):
raise Exception("PDB not found at *%s*" % pdbPath)
baseName = basename(pdbPath)
localPath = self._getExtraPath(baseName)
copyFile(pdbPath, localPath)
pdb = PdbFile()
pdb.setFileName(localPath)
self._defineOutputs(outputPdb=pdb)
def createOutputStep(self, pdbPath):
""" Copy the PDB structure and register the output object.
"""
if not exists(pdbPath):
raise Exception("PDB not found at *%s*" % pdbPath)
baseName = basename(pdbPath)
localPath = self._getExtraPath(baseName)
copyFile(pdbPath, localPath)
pdb = PdbFile()
pdb.setFileName(localPath)
self._defineOutputs(outputPdb=pdb)
def copyDeformationsStep(self, deformationMd):
copyFile(deformationMd, self.imgsFn)
# We need to update the image name with the good ones
# and the same with the ids.
inputSet = self.inputParticles.get()
mdImgs = md.MetaData(self.imgsFn)
for objId in mdImgs:
imgPath = mdImgs.getValue(md.MDL_IMAGE, objId)
index, fn = xmippToLocation(imgPath)
# Conside the index is the id in the input set
particle = inputSet[index]
mdImgs.setValue(md.MDL_IMAGE, getImageLocation(particle), objId)
mdImgs.setValue(md.MDL_ITEM_ID, long(particle.getObjId()), objId)
mdImgs.write(self.imgsFn)
def copyDeformationsStep(self, deformationMd):
copyFile(deformationMd, self.imgsFn)
# We need to update the image name with the good ones
# and the same with the ids.
inputSet = self.inputParticles.get()
md = xmipp.MetaData(self.imgsFn)
for objId in md:
imgPath = md.getValue(xmipp.MDL_IMAGE, objId)
index, fn = xmippToLocation(imgPath)
# Conside the index is the id in the input set
particle = inputSet[index]
md.setValue(xmipp.MDL_IMAGE, getImageLocation(particle), objId)
md.setValue(xmipp.MDL_ITEM_ID, long(particle.getObjId()), objId)
md.write(self.imgsFn)
def weightParticles(self):
iteration = 1
fnDirCurrent = self._getExtraPath("Iter%03d" % iteration)
from math import exp
# Grab file
fnDirGlobal = join(fnDirCurrent, "globalAssignment")
fnAnglesDisc = join(fnDirGlobal, "anglesDisc.xmd")
fnAngles = join(fnDirCurrent, "angles.xmd")
copyFile(fnAnglesDisc, fnAngles)
TsCurrent = self.readInfoField(fnDirGlobal, "sampling",
xmipp.MDL_SAMPLINGRATE)
Xdim = self.readInfoField(fnDirGlobal, "size", xmipp.MDL_XSIZE)
self.writeInfoField(fnDirCurrent, "sampling", xmipp.MDL_SAMPLINGRATE,
TsCurrent)
self.writeInfoField(fnDirCurrent, "size", xmipp.MDL_XSIZE, Xdim)
if self.weightSSNR:
self.runJob("xmipp_metadata_utilities","-i %s --set join %s particleId"%\
(fnAngles,self._getExtraPath("ssnrWeights.xmd")),numberOfMpi=1)
md = xmipp.MetaData(fnAngles)
doWeightSignificance = self.weightSignificance and md.containsLabel(
xmipp.MDL_WEIGHT_SIGNIFICANT)
for objId in md:
weight = 1
if self.weightSSNR:
aux = md.getValue(xmipp.MDL_WEIGHT_SSNR, objId)
weight *= aux
if doWeightSignificance:
aux = md.getValue(xmipp.MDL_WEIGHT_SIGNIFICANT, objId)
weight *= aux
md.setValue(xmipp.MDL_WEIGHT, weight, objId)
md.write(fnAngles)
# Weight by Astigmatism
if self.weightAstigmatism:
self.runJob("xmipp_transform_filter","-i %s --fourier astigmatism %f --sampling %f"%\
(fnAngles,self.weightAstigmatismSigma.get(),TsCurrent))
def _importFromFolderStep(self):
""" This function will copy Xmipp .pos files for
simulating a particle picking run...this is only
for testing purposes.
"""
for f in getFiles(self.importFolder.get()):
copyFile(f, self._getExtraPath())
extradir = self._getExtraPath()
inputset = self.inputMicrographsTiltedPair.get()
uSet = inputset.getUntilted()
tSet = inputset.getTilted()
# Create Untilted and Tilted SetOfCoordinates
uCoordSet = self._createSetOfCoordinates(uSet, suffix='Untilted')
readSetOfCoordinates(extradir, uSet, uCoordSet)
uCoordSet.write()
tCoordSet = self._createSetOfCoordinates(tSet, suffix='Tilted')
readSetOfCoordinates(extradir, tSet, tCoordSet)
tCoordSet.write()
# Read Angles from faked input micrographs
micsFn = self._getExtraPath('input_micrographs.xmd')
setAngles = self._createSetOfAngles()
readAnglesFromMicrographs(micsFn, setAngles)
setAngles.write()
# Create CoordinatesTiltPair object
outputset = CoordinatesTiltPair(filename=self._getPath('coordinates_pairs.sqlite'))
outputset.setTilted(tCoordSet)
outputset.setUntilted(uCoordSet)
outputset.setAngles(setAngles)
outputset.setMicsPair(inputset)
outputset.setObjComment(self.getSummary(outputset))
for coordU, coordT in izip(uCoordSet, tCoordSet):
outputset.append(TiltPair(coordU, coordT))
self._defineOutputs(outputCoordinatesTiltPair=outputset)
self._defineSourceRelation(inputset, outputset)
def weightParticles(self):
iteration=1
fnDirCurrent=self._getExtraPath("Iter%03d"%iteration)
from math import exp
# Grab file
fnDirGlobal=join(fnDirCurrent,"globalAssignment")
fnAnglesDisc=join(fnDirGlobal,"anglesDisc.xmd")
fnAngles=join(fnDirCurrent,"angles.xmd")
copyFile(fnAnglesDisc, fnAngles)
TsCurrent=self.readInfoField(fnDirGlobal,"sampling",xmipp.MDL_SAMPLINGRATE)
Xdim=self.readInfoField(fnDirGlobal,"size",xmipp.MDL_XSIZE)
self.writeInfoField(fnDirCurrent,"sampling",xmipp.MDL_SAMPLINGRATE,TsCurrent)
self.writeInfoField(fnDirCurrent,"size",xmipp.MDL_XSIZE,Xdim)
if self.weightSSNR:
self.runJob("xmipp_metadata_utilities","-i %s --set join %s particleId"%\
(fnAngles,self._getExtraPath("ssnrWeights.xmd")),numberOfMpi=1)
md=xmipp.MetaData(fnAngles)
doWeightSignificance=self.weightSignificance and md.containsLabel(xmipp.MDL_WEIGHT_SIGNIFICANT)
for objId in md:
weight=1
if self.weightSSNR:
aux=md.getValue(xmipp.MDL_WEIGHT_SSNR,objId)
weight*=aux
if doWeightSignificance:
aux=md.getValue(xmipp.MDL_WEIGHT_SIGNIFICANT,objId)
weight*=aux
md.setValue(xmipp.MDL_WEIGHT,weight,objId)
md.write(fnAngles)
# Weight by Astigmatism
if self.weightAstigmatism:
self.runJob("xmipp_transform_filter","-i %s --fourier astigmatism %f --sampling %f"%\
(fnAngles,self.weightAstigmatismSigma.get(),TsCurrent))
def initializeStep(self, protId):
protRef = self.protRefine.get()
protClassName = protRef.getClassName()
if protClassName.startswith('ProtRelionRefine3D'):
protRef._createFilenameTemplates()
half1Map = protRef._getFileName("final_half1_volume", ref3d=1)
half2Map = protRef._getFileName("final_half2_volume", ref3d=1)
putils.copyFile(self._getRelionMapFn(half1Map), self._getTmpPath())
putils.copyFile(self._getRelionMapFn(half2Map), self._getTmpPath())
elif protClassName.startswith('ProtFrealign'):
protRef._createFilenameTemplates()
lastIter = protRef._getLastIter()
half1Map = protRef._getFileName('iter_vol1', iter=lastIter)
half2Map = protRef._getFileName('iter_vol2', iter=lastIter)
putils.copyFile(half1Map, self._getFileName("half1"))
putils.copyFile(half2Map, self._getFileName("half2"))
elif protClassName.startswith('XmippProtProjMatch'):
iterN = protRef.getLastIter()
protRef._initialize()
half1 = protRef._getFileName('reconstructedFileNamesItersSplit1',
iter=iterN,
ref=1)
half2 = protRef._getFileName('reconstructedFileNamesItersSplit2',
iter=iterN,
ref=1)
ih = ImageHandler()
ih.convert(half1, self._getFileName("half1"))
ih.convert(half2, self._getFileName("half2"))
elif protClassName.startswith('EmanProtRefine'):
protRef._createFilenameTemplates()
numRun = protRef._getRun()
protRef._createIterTemplates(numRun)
iterN = protRef._lastIter()
print "RUN ITER: ", numRun, iterN, protRef._iterTemplate
half1 = protRef._getFileName("mapEvenUnmasked", run=numRun)
half2 = protRef._getFileName("mapOddUnmasked", run=numRun)
ih = ImageHandler()
ih.convert(half1, self._getFileName("half1"))
ih.convert(half2, self._getFileName("half2"))
def initializeStep(self, protId):
protRef = self.protRefine.get()
protClassName = protRef.getClassName()
if protClassName.startswith('ProtRelionRefine3D'):
protRef._createFilenameTemplates()
half1Map = protRef._getFileName("final_half1_volume", ref3d=1)
half2Map = protRef._getFileName("final_half2_volume", ref3d=1)
putils.copyFile(self._getRelionMapFn(half1Map), self._getTmpPath())
putils.copyFile(self._getRelionMapFn(half2Map), self._getTmpPath())
elif protClassName.startswith('ProtFrealign'):
protRef._createFilenameTemplates()
lastIter = protRef._getLastIter()
half1Map = protRef._getFileName('iter_vol1', iter=lastIter)
half2Map = protRef._getFileName('iter_vol2', iter=lastIter)
putils.copyFile(half1Map, self._getFileName("half1"))
putils.copyFile(half2Map, self._getFileName("half2"))
elif protClassName.startswith('XmippProtProjMatch'):
iterN = protRef.getLastIter()
protRef._initialize()
half1 = protRef._getFileName('reconstructedFileNamesItersSplit1',
iter=iterN, ref=1)
half2 = protRef._getFileName('reconstructedFileNamesItersSplit2',
iter=iterN, ref=1)
ih = ImageHandler()
ih.convert(half1, self._getFileName("half1"))
ih.convert(half2, self._getFileName("half2"))
elif protClassName.startswith('EmanProtRefine'):
protRef._createFilenameTemplates()
numRun = protRef._getRun()
protRef._createIterTemplates(numRun)
iterN = protRef._lastIter()
print "RUN ITER: ", numRun, iterN, protRef._iterTemplate
half1 = protRef._getFileName("mapEvenUnmasked", run=numRun)
half2 = protRef._getFileName("mapOddUnmasked", run=numRun)
ih = ImageHandler()
ih.convert(half1, self._getFileName("half1"))
ih.convert(half2, self._getFileName("half2"))
def managingOutputFilesStep(self):
volList = [vol.clone() for vol in self._iterInputVolumes()]
copyFile (self._getExtraPath ("CoordinateMatrixColumnF1.txt"),
self._defineResultsName1())
copyFile (self._getExtraPath ("CoordinateMatrixColumnF2.txt"),
self._defineResultsName2())
copyFile (self._getExtraPath ("CoordinateMatrixColumnF3.txt"),
self._defineResultsName3())
cleanPattern(self._getExtraPath('pseudoatoms*'))
cleanPattern(self._getExtraPath('vec_ani.pkl'))
cleanPattern(self._getExtraPath('CoordinateMatrixColumnF*'))
cleanPattern(self._getPath('modes/vec*'))
cleanPath(self._getPath('modes'))
if not self.keepingOutputFiles.get():
cleanPattern(self._getPath('warnings*'))
cleanPattern(self._getPath('outputRigid*'))
cleanPattern(self._getExtraPath('RigidAlign*'))
cleanPattern(self._getExtraPath('Pseudoatoms*'))
cleanPattern(self._getExtraPath('comp*'))
cleanPattern(self._getExtraPath('Deform*'))
def managingOutputFilesStep(self):
volList = [vol.clone() for vol in self._iterInputVolumes()]
copyFile(self._getExtraPath("CoordinateMatrixColumnF1.txt"),
self._defineResultsName1())
copyFile(self._getExtraPath("CoordinateMatrixColumnF2.txt"),
self._defineResultsName2())
copyFile(self._getExtraPath("CoordinateMatrixColumnF3.txt"),
self._defineResultsName3())
cleanPattern(self._getExtraPath('pseudoatoms*'))
cleanPattern(self._getExtraPath('vec_ani.pkl'))
cleanPattern(self._getExtraPath('CoordinateMatrixColumnF*'))
cleanPattern(self._getPath('modes/vec*'))
cleanPath(self._getPath('modes'))
if not self.keepingOutputFiles.get():
cleanPattern(self._getPath('warnings*'))
cleanPattern(self._getPath('outputRigid*'))
cleanPattern(self._getExtraPath('RigidAlign*'))
cleanPattern(self._getExtraPath('Pseudoatoms*'))
cleanPattern(self._getExtraPath('comp*'))
cleanPattern(self._getExtraPath('Deform*'))
def globalAssignment(self):
iteration=1
fnDirCurrent=self._getExtraPath("Iter%03d"%iteration)
makePath(fnDirCurrent)
fnGlobal=join(fnDirCurrent,"globalAssignment")
makePath(fnGlobal)
targetResolution=self.significantMaxResolution.get()
TsCurrent=max(self.TsOrig,targetResolution/3)
self.prepareImages(fnGlobal,TsCurrent)
self.prepareReferences(fnGlobal,TsCurrent,targetResolution)
# Calculate angular step at this resolution
ResolutionAlignment=targetResolution
newXdim=self.readInfoField(fnGlobal,"size",xmipp.MDL_XSIZE)
angleStep=self.calculateAngStep(newXdim, TsCurrent, ResolutionAlignment)
self.writeInfoField(fnGlobal,"angleStep",xmipp.MDL_ANGLE_DIFF,float(angleStep))
# Significant alignment
alpha=1-0.01*self.significantSignificance.get()
fnDirSignificant=join(fnGlobal,"significant")
fnImgs=join(fnGlobal,"images.xmd")
makePath(fnDirSignificant)
# Create defocus groups
row=getFirstRow(fnImgs)
if row.containsLabel(xmipp.MDL_CTF_MODEL) or row.containsLabel(xmipp.MDL_CTF_DEFOCUSU):
self.runJob("xmipp_ctf_group","--ctfdat %s -o %s/ctf:stk --pad 2.0 --sampling_rate %f --phase_flipped --error 0.1 --resol %f"%\
(fnImgs,fnDirSignificant,TsCurrent,targetResolution),numberOfMpi=1)
moveFile("%s/ctf_images.sel"%fnDirSignificant,"%s/ctf_groups.xmd"%fnDirSignificant)
cleanPath("%s/ctf_split.doc"%fnDirSignificant)
md = xmipp.MetaData("numberGroups@%s"%join(fnDirSignificant,"ctfInfo.xmd"))
fnCTFs="%s/ctf_ctf.stk"%fnDirSignificant
numberGroups=md.getValue(xmipp.MDL_COUNT,md.firstObject())
ctfPresent=True
else:
numberGroups=1
ctfPresent=False
# Generate projections
fnReferenceVol=join(fnGlobal,"volumeRef.vol")
fnGallery=join(fnDirSignificant,"gallery.stk")
fnGalleryMd=join(fnDirSignificant,"gallery.xmd")
args="-i %s -o %s --sampling_rate %f --sym %s --min_tilt_angle %f --max_tilt_angle %f"%\
(fnReferenceVol,fnGallery,angleStep,self.symmetryGroup,self.angularMinTilt.get(),self.angularMaxTilt.get())
self.runJob("xmipp_angular_project_library",args)
cleanPath(join(fnDirSignificant,"gallery_angles.doc"))
moveFile(join(fnDirSignificant,"gallery.doc"), fnGalleryMd)
fnAngles=join(fnGlobal,"anglesDisc.xmd")
for j in range(1,numberGroups+1):
fnAnglesGroup=join(fnDirSignificant,"angles_group%02d.xmd"%j)
if not exists(fnAnglesGroup):
if ctfPresent:
fnGroup="ctfGroup%06d@%s/ctf_groups.xmd"%(j,fnDirSignificant)
fnGalleryGroup=join(fnDirSignificant,"gallery_group%06d.stk"%j)
fnGalleryGroupMd=join(fnDirSignificant,"gallery_group%06d.xmd"%j)
self.runJob("xmipp_transform_filter",
"-i %s -o %s --fourier binary_file %d@%s --save_metadata_stack %s --keep_input_columns"%\
(fnGalleryMd,fnGalleryGroup,j,fnCTFs,fnGalleryGroupMd))
else:
fnGroup=fnImgs
fnGalleryGroupMd=fnGalleryMd
args='-i %s --initgallery %s --odir %s --sym %s --iter 1 --alpha0 %f --alphaF %f --angularSampling %f --maxShift %d '\
'--minTilt %f --maxTilt %f --useImed --angDistance %f --dontReconstruct'%\
(fnGroup,fnGalleryGroupMd,fnDirSignificant,self.symmetryGroup,alpha,alpha,angleStep,\
round(self.angularMaxShift.get()*newXdim/100),self.angularMinTilt.get(),self.angularMaxTilt.get(),2*angleStep)
self.runJob('xmipp_reconstruct_significant',args,numberOfMpi=self.numberOfThreads.get())
moveFile(join(fnDirSignificant,"angles_iter001_00.xmd"),join(fnDirSignificant,"angles_group%02d.xmd"%j))
self.runJob("rm -f",fnDirSignificant+"/images_*iter00?_*.xmd",numberOfMpi=1)
if j==1:
copyFile(fnAnglesGroup, fnAngles)
else:
self.runJob("xmipp_metadata_utilities","-i %s --set union %s"%(fnAngles,fnAnglesGroup),numberOfMpi=1)
if ctfPresent:
self.runJob("rm -f",fnDirSignificant+"/gallery*",numberOfMpi=1)
def importStep(self):
if not self.multiple.get():
fnSmall = self._getExtraPath(os.path.split(self.filePath.get())[1])
copyFile(self.filePath.get(), fnSmall)
if fnSmall.endswith(".mol2"): # Multiple mol2
with open(fnSmall) as f:
lines = f.readlines()
i = 0
for line in lines:
if line.startswith("#"):
continue
if line.startswith("@<TRIPOS>MOLECULE"):
zincID = lines[i + 1].split()[0]
fname_small = self._getExtraPath("%s.mol2" %
zincID)
f_small = open(fname_small, 'w+')
f_small.write(line)
f_small.write(line)
try:
if lines[i + 1].startswith("@<TRIPOS>MOLECULE"):
f_small.close()
except:
f_small.close()
i += 1
os.remove(fnSmall)
elif fnSmall.endswith(".sdf"): # Multiple sdf
with open(fnSmall) as f:
lines = f.readlines()
lines2write = []
i = 0
for line in lines:
lines2write.append(i)
if line.startswith("$$$$"):
zincID = lines[i - 5].split()[0]
fname_small = self._getExtraPath("%s.sdf" % zincID)
f_small = open(fname_small, 'w+')
for l in lines2write:
f_small.write(lines[l])
lines2write = []
f_small.close()
i += 1
os.remove(fnSmall)
else:
fh = open(self.filePath.get())
for line in fh.readlines():
tokens = line.split(',')
if len(tokens) == 2:
fhSmile = open(
self._getExtraPath(tokens[0].strip() + ".smi"),
'w')
fhSmile.write(tokens[1].strip() + "\n")
fhSmile.close()
fh.close()
else:
for filename in glob.glob(
os.path.join(self.filesPath.get(),
self.filesPattern.get())):
fnSmall = self._getExtraPath(os.path.split(filename)[1])
copyFile(filename, fnSmall)
outputSmallMolecules = SetOfSmallMolecules().create(
path=self._getPath(), suffix='SmallMols')
for fnSmall in glob.glob(self._getExtraPath("*")):
smallMolecule = SmallMolecule(smallMolFilename=fnSmall)
if len(os.listdir(self._getExtraPath())) <= 100: # costly
if not fnSmall.endswith('.mae') or not fnSmall.endswith(
'.maegz'):
fnRoot = os.path.splitext(os.path.split(fnSmall)[1])[0]
fnOut = self._getExtraPath("%s.png" % fnRoot)
args = Plugin.getPluginHome(
'utils/rdkitUtils.py') + " draw %s %s" % (fnSmall,
fnOut)
try:
Plugin.runRDKit(self, "python3", args)
smallMolecule._PDBLigandImage = pwobj.String(fnOut)
except:
smallMolecule._PDBLigandImage = pwobj.String(
"Not available")
outputSmallMolecules.append(smallMolecule)
self._defineOutputs(outputSmallMols=outputSmallMolecules)
def exportImageStep(self):
imageBaseFileName = os.path.basename(self.exportPicture.get())
outputFile = os.path.join(self.dirName, imageBaseFileName)
copyFile(self.exportPicture.get(), outputFile)
def globalAssignment(self):
iteration = 1
fnDirCurrent = self._getExtraPath("Iter%03d" % iteration)
makePath(fnDirCurrent)
fnGlobal = join(fnDirCurrent, "globalAssignment")
makePath(fnGlobal)
targetResolution = self.significantMaxResolution.get()
TsCurrent = max(self.TsOrig, targetResolution / 3)
self.prepareImages(fnGlobal, TsCurrent)
self.prepareReferences(fnGlobal, TsCurrent, targetResolution)
# Calculate angular step at this resolution
ResolutionAlignment = targetResolution
newXdim = self.readInfoField(fnGlobal, "size", xmipp.MDL_XSIZE)
angleStep = self.calculateAngStep(newXdim, TsCurrent,
ResolutionAlignment)
self.writeInfoField(fnGlobal, "angleStep", xmipp.MDL_ANGLE_DIFF,
float(angleStep))
# Significant alignment
alpha = 1 - 0.01 * self.significantSignificance.get()
fnDirSignificant = join(fnGlobal, "significant")
fnImgs = join(fnGlobal, "images.xmd")
makePath(fnDirSignificant)
# Create defocus groups
row = getFirstRow(fnImgs)
if row.containsLabel(xmipp.MDL_CTF_MODEL) or row.containsLabel(
xmipp.MDL_CTF_DEFOCUSU):
self.runJob("xmipp_ctf_group","--ctfdat %s -o %s/ctf:stk --pad 2.0 --sampling_rate %f --phase_flipped --error 0.1 --resol %f"%\
(fnImgs,fnDirSignificant,TsCurrent,targetResolution),numberOfMpi=1)
moveFile("%s/ctf_images.sel" % fnDirSignificant,
"%s/ctf_groups.xmd" % fnDirSignificant)
cleanPath("%s/ctf_split.doc" % fnDirSignificant)
md = xmipp.MetaData("numberGroups@%s" %
join(fnDirSignificant, "ctfInfo.xmd"))
fnCTFs = "%s/ctf_ctf.stk" % fnDirSignificant
numberGroups = md.getValue(xmipp.MDL_COUNT, md.firstObject())
ctfPresent = True
else:
numberGroups = 1
ctfPresent = False
# Generate projections
fnReferenceVol = join(fnGlobal, "volumeRef.vol")
fnGallery = join(fnDirSignificant, "gallery.stk")
fnGalleryMd = join(fnDirSignificant, "gallery.xmd")
args="-i %s -o %s --sampling_rate %f --sym %s --min_tilt_angle %f --max_tilt_angle %f"%\
(fnReferenceVol,fnGallery,angleStep,self.symmetryGroup,self.angularMinTilt.get(),self.angularMaxTilt.get())
self.runJob("xmipp_angular_project_library", args)
cleanPath(join(fnDirSignificant, "gallery_angles.doc"))
moveFile(join(fnDirSignificant, "gallery.doc"), fnGalleryMd)
fnAngles = join(fnGlobal, "anglesDisc.xmd")
for j in range(1, numberGroups + 1):
fnAnglesGroup = join(fnDirSignificant, "angles_group%02d.xmd" % j)
if not exists(fnAnglesGroup):
if ctfPresent:
fnGroup = "ctfGroup%06d@%s/ctf_groups.xmd" % (
j, fnDirSignificant)
fnGalleryGroup = join(fnDirSignificant,
"gallery_group%06d.stk" % j)
fnGalleryGroupMd = join(fnDirSignificant,
"gallery_group%06d.xmd" % j)
self.runJob("xmipp_transform_filter",
"-i %s -o %s --fourier binary_file %d@%s --save_metadata_stack %s --keep_input_columns"%\
(fnGalleryMd,fnGalleryGroup,j,fnCTFs,fnGalleryGroupMd))
else:
fnGroup = fnImgs
fnGalleryGroupMd = fnGalleryMd
args='-i %s --initgallery %s --odir %s --sym %s --iter 1 --alpha0 %f --alphaF %f --angularSampling %f --maxShift %d '\
'--minTilt %f --maxTilt %f --useImed --angDistance %f --dontReconstruct'%\
(fnGroup,fnGalleryGroupMd,fnDirSignificant,self.symmetryGroup,alpha,alpha,angleStep,\
round(self.angularMaxShift.get()*newXdim/100),self.angularMinTilt.get(),self.angularMaxTilt.get(),2*angleStep)
self.runJob('xmipp_reconstruct_significant',
args,
numberOfMpi=self.numberOfThreads.get())
moveFile(join(fnDirSignificant, "angles_iter001_00.xmd"),
join(fnDirSignificant, "angles_group%02d.xmd" % j))
self.runJob("rm -f",
fnDirSignificant + "/images_*iter00?_*.xmd",
numberOfMpi=1)
if j == 1:
copyFile(fnAnglesGroup, fnAngles)
else:
self.runJob("xmipp_metadata_utilities",
"-i %s --set union %s" %
(fnAngles, fnAnglesGroup),
numberOfMpi=1)
if ctfPresent:
self.runJob("rm -f", fnDirSignificant + "/gallery*", numberOfMpi=1)
def ligPrepStep(self):
progLigPrep = Plugin.getHome('ligprep')
progStructConvert = Plugin.getHome('utilities/structconvert')
outputSmallMolecules = SetOfSmallMolecules().create(
path=self._getPath(), suffix='SmallMols')
outputSmallMoleculesDropped = SetOfSmallMolecules().create(
path=self._getPath(), suffix='SmallMolsDropped')
for mol in self.inputSmallMols.get():
fnSmall = mol.smallMoleculeFile.get()
fnMol = os.path.split(fnSmall)[1]
fnRoot = os.path.splitext(fnMol)[0]
existingFiles = glob.glob(self._getExtraPath(fnRoot + "*"))
if len(existingFiles) == 0:
fnSmallExtra = self._getTmpPath(fnMol)
copyFile(fnSmall, fnSmallExtra)
args = '-WAIT -LOCAL'
if self.ionization.get() != 0:
if self.ionization.get() == 1:
args += " -epik"
if self.emb.get():
args += " -epik_metal_binding"
else:
args += " -i %d" % self.ionization.get() - 2
args += " -ph %f -pht %f" % (self.pH.get(),
self.pHrange.get())
if self.stereoisomers.get():
args += " -g"
else:
args += " -ac -s %d" % self.Niso.get()
if self.optimization.get() == 1:
args += " -bff 14"
elif self.optimization.get() == 2:
args += " -bff 16"
if fnMol.endswith('.smi'):
args += " -ismi tmp/%s" % (fnMol)
elif fnMol.endswith('.mae') or fnMol.endswith('.maegz'):
args += " -imae tmp/%s" % (fnMol)
elif fnMol.endswith('.sdf'):
args += " -isd tmp/%s" % (fnMol)
else:
print("Skipping %s" % fnSmall)
continue
fnMae = "extra/%s.maegz" % fnRoot
if not os.path.exists(fnMae):
args += " -omae %s" % fnMae
self.runJob(progLigPrep, args, cwd=self._getPath())
if os.path.exists(self._getPath(fnMae)):
fnOmae = "extra/o%s.maegz" % fnRoot
args = "-imae %s -omae %s -split-nstructures 1" % (fnMae,
fnOmae)
self.runJob(progStructConvert, args, cwd=self._getPath())
for fn in glob.glob(
self._getExtraPath("o%s*.maegz" % fnRoot)):
fnDir, fnOut = os.path.split(fn)
fnOut = self._getExtraPath(fnOut[1:])
moveFile(fn, fnOut)
smallMolecule = SmallMolecule(smallMolFilename=fnOut)
outputSmallMolecules.append(smallMolecule)
if len(glob.glob(self._getExtraPath(
"%s-*.maegz" % fnRoot))) > 0:
cleanPath(self._getPath(fnMae))
else:
smallMolecule = SmallMolecule(smallMolFilename=fnSmall)
outputSmallMoleculesDropped.append(smallMolecule)
else:
for fn in glob.glob(self._getExtraPath("%s*.maegz" % fnRoot)):
print("Reading %s" % fn)
smallMolecule = SmallMolecule(smallMolFilename=fn)
outputSmallMolecules.append(smallMolecule)
if len(outputSmallMolecules) > 0:
self._defineOutputs(outputSmallMols=outputSmallMolecules)
self._defineSourceRelation(self.inputSmallMols,
outputSmallMolecules)
if len(outputSmallMoleculesDropped) > 0:
self._defineOutputs(
outputSmallMolsDropped=outputSmallMoleculesDropped)
self._defineSourceRelation(self.inputSmallMols,
outputSmallMoleculesDropped)
def evaluateIndividuals(self,iteration):
fnDir = self._getExtraPath()
newXdim = self.readInfoField(fnDir,"size",xmippLib.MDL_XSIZE)
angleStep = max(math.atan2(1,newXdim/2),self.minAngle.get())
TsOrig=self.inputParticles.get().getSamplingRate()
TsCurrent = self.readInfoField(fnDir,"sampling",xmippLib.MDL_SAMPLINGRATE)
fnMask = self._getExtraPath("mask.vol")
fnImages = join(fnDir,"images.xmd")
maxShift=round(0.1*newXdim)
R=self.particleRadius.get()
if R<=0:
R=self.inputParticles.get().getDimensions()[0]/2
R=R*TsOrig/TsCurrent
bestWeightVol={}
bestIterVol={}
if iteration>0:
mdPrevious = xmippLib.MetaData("bestByVolume@"+self._getExtraPath("swarm.xmd"))
for objId in mdPrevious:
idx = int(mdPrevious.getValue(xmippLib.MDL_IDX,objId))
bestWeightVol[idx]=mdPrevious.getValue(xmippLib.MDL_WEIGHT,objId)
bestIterVol[idx]=mdPrevious.getValue(xmippLib.MDL_ITER,objId)
# Global alignment
md=xmippLib.MetaData()
if iteration>1:
mdBest = xmippLib.MetaData("best@"+self._getExtraPath("swarm.xmd"))
objId = mdBest.firstObject()
bestWeight = mdBest.getValue(xmippLib.MDL_WEIGHT,objId)
else:
bestWeight = -1e38
for i in range(self.inputVolumes.get().getSize()):
# Filter and mask volumes
fnVol = self._getExtraPath("volume%03d.vol"%i)
self.runJob("xmipp_transform_filter","-i %s --fourier low_pass %f --sampling %f"%(fnVol,self.targetResolution,TsCurrent),numberOfMpi=1)
if exists(fnMask):
self.runJob("xmipp_image_operate","-i %s --mult %s"%(fnVol,fnMask),numberOfMpi=1)
# Prepare subset of experimental images
fnTest = join(fnDir,"imgs_%03d.xmd"%i)
self.runJob("xmipp_metadata_utilities","-i %s --operate random_subset %d -o %s"%(fnImages,self.NimgTest,fnTest),numberOfMpi=1)
# Generate projections
fnGallery=join(fnDir,"gallery%02d.stk"%i)
fnGalleryMd=join(fnDir,"gallery%02d.doc"%i)
# args="-i %s -o %s --sampling_rate %f --perturb %f --sym %s"%\
# (fnVol,fnGallery,angleStep,math.sin(angleStep*math.pi/180.0)/4,self.symmetryGroup)
args="-i %s -o %s --sampling_rate %f --sym %s"%\
(fnVol,fnGallery,angleStep,self.symmetryGroup)
args+=" --compute_neighbors --angular_distance -1 --experimental_images %s"%fnTest
self.runJob("xmipp_angular_project_library",args,numberOfMpi=self.numberOfMpi.get()*self.numberOfThreads.get())
# Assign angles
args='-i %s --initgallery %s --maxShift %d --odir %s --dontReconstruct --useForValidation 1'%\
(fnTest,fnGalleryMd,maxShift,fnDir)
self.runJob('xmipp_reconstruct_significant',args,numberOfMpi=self.numberOfMpi.get()*self.numberOfThreads.get())
# Evaluate
fnAngles = join(fnDir,"angles_iter001_00.xmd")
if exists(fnAngles):
# Significant may decide not to write it if it is not significant
mdAngles = xmippLib.MetaData(fnAngles)
weight = mdAngles.getColumnValues(xmippLib.MDL_MAXCC)
avgWeight = reduce(lambda x, y: x + y, weight) / len(weight)
print("Average weight for "+fnVol+" = "+str(avgWeight))
objId = md.addObject()
md.setValue(xmippLib.MDL_IDX,long(i),objId)
md.setValue(xmippLib.MDL_IMAGE,fnVol,objId)
md.setValue(xmippLib.MDL_WEIGHT,avgWeight,objId)
md.setValue(xmippLib.MDL_ITER,iteration,objId)
# Is global best
if avgWeight>bestWeight:
bestWeight = avgWeight
if iteration==0:
# None of the input volumes can be the best volume in the first iteration since their gray values may significantly
# differ from those in the projections
self.runJob("xmipp_image_operate","-i %s --mult 0 -o %s"%(fnVol,self._getExtraPath("volumeBest.vol")),numberOfMpi=1)
else:
copyFile(fnVol, self._getExtraPath("volumeBest.vol"))
mdBest=xmippLib.MetaData()
objId=mdBest.addObject()
mdBest.setValue(xmippLib.MDL_IMAGE,fnVol,objId)
mdBest.setValue(xmippLib.MDL_WEIGHT,bestWeight,objId)
mdBest.setValue(xmippLib.MDL_ITER,iteration,objId)
mdBest.write("best@"+self._getExtraPath("swarm.xmd"),xmippLib.MD_APPEND)
# Is local best
if iteration==0:
self.runJob("xmipp_image_operate","-i %s --mult 0 -o %s"%(fnVol, self._getExtraPath("volume%03d_best.vol"%i)),numberOfMpi=1)
elif avgWeight>bestWeightVol[i] or iteration==1:
bestWeightVol[i]=avgWeight
bestIterVol[i]=iteration
copyFile(fnVol,self._getExtraPath("volume%03d_best.vol"%i))
# Clean
cleanPath(fnTest)
self.runJob("rm -f",fnDir+"/*iter00?_00.xmd",numberOfMpi=1)
self.runJob("rm -f",fnDir+"/gallery*",numberOfMpi=1)
md.write("evaluations_%03d@"%iteration+self._getExtraPath("swarm.xmd"),xmippLib.MD_APPEND)
# Update best by volume
if iteration==0:
md.write("bestByVolume@"+self._getExtraPath("swarm.xmd"),xmippLib.MD_APPEND)
else:
md.clear()
for i in range(self.inputVolumes.get().getSize()):
objId = md.addObject()
md.setValue(xmippLib.MDL_IDX,long(i),objId)
md.setValue(xmippLib.MDL_IMAGE,self._getExtraPath("volume%03d_best.vol"%i),objId)
md.setValue(xmippLib.MDL_WEIGHT,bestWeightVol[i],objId)
md.setValue(xmippLib.MDL_ITER,bestIterVol[i],objId)
md.write("bestByVolume@"+self._getExtraPath("swarm.xmd"),xmippLib.MD_APPEND)
