def reformatOutputPDB(log,WorkingDir,NumberOfModes):
currentDir=os.getcwd()
changeDir(log,WorkingDir)
createDir(log,"modes")
Natoms=countAtoms("atoms.pdb")
fhIn=open('diagrtb.eigenfacs')
fhAni=open('vec_ani.txt','w')
for n in range(NumberOfModes):
# Skip two lines
fhIn.readline()
fhIn.readline()
fhOut=open('modes/vec.%d'%(n+1),'w')
for i in range(Natoms):
line=fhIn.readline()
fhOut.write(line)
fhAni.write(line.rstrip().lstrip()+" ")
fhOut.close()
if n!=(NumberOfModes-1):
fhAni.write("\n")
fhIn.close()
fhAni.close()
runJob(log,"nma_prepare_for_animate.py","")
runJob(log,"rm","vec_ani.txt")
moveFile(log,'vec_ani.pkl','extra/vec_ani.pkl')
changeDir(log,currentDir)
def reformatOutput(log,WorkingDir):
currentDir=os.getcwd()
changeDir(log,WorkingDir)
Natoms=countAtoms("pseudoatoms.pdb")
runJob(log,"nma_reformat_vector_foranimate.pl","%d fort.11"%Natoms)
runJob(log,"cat","vec.1* > vec_ani.txt")
runJob(log,"rm","-f vec.1*")
runJob(log,"nma_reformat_vector.pl","%d fort.11"%Natoms)
createDir(log,"modes")
runJob(log,"mv","-f vec.* modes")
runJob(log,"nma_prepare_for_animate.py","")
runJob(log,"rm","vec_ani.txt fort.11 matrice.sdijf")
moveFile(log,'vec_ani.pkl','extra/vec_ani.pkl')
changeDir(log,currentDir)
def ransacIteration(log,WorkingDir,n,SymmetryGroup,Xdim,Xdim2,NumGrids,NumSamples,DimRed,InitialVolume,AngularSampling,UseSA,
NIterRandom,Rejection):
fnBase="ransac%05d"%n
TmpDir=os.path.join(WorkingDir,"tmp")
fnRoot=os.path.join(TmpDir,fnBase)
fnOutputReducedClass = os.path.join(WorkingDir,"extra/reducedClasses.xmd")
if (DimRed=='Yes'):
# Get a random sample of images
runJob(log,"xmipp_transform_dimred","-i %s --randomSample %s.xmd %d -m LTSA "%(fnOutputReducedClass,fnRoot,NumGrids))
else:
runJob(log,"xmipp_metadata_utilities","-i %s -o %s.xmd --operate random_subset %d --mode overwrite "%(fnOutputReducedClass,fnRoot,NumSamples))
runJob(log,"xmipp_metadata_utilities","-i %s.xmd --fill angleRot rand_uniform -180 180 "%(fnRoot))
runJob(log,"xmipp_metadata_utilities","-i %s.xmd --fill angleTilt rand_uniform 0 180 "%(fnRoot))
runJob(log,"xmipp_metadata_utilities","-i %s.xmd --fill anglePsi rand_uniform 0 360 "%(fnRoot))
# If there is an initial volume, assign angles
if (InitialVolume != ''):
fnGallery=os.path.join(TmpDir,'gallery_InitialVolume.stk')
runJob(log,"xmipp_angular_projection_matching", "-i %s.xmd -o %s.xmd --ref %s --Ri 0 --Ro %s --max_shift %s --append"\
%(fnRoot,fnRoot,fnGallery,str(Xdim/2),str(Xdim/20)))
# Reconstruct with the small sample
reconstruct(log,fnRoot,SymmetryGroup,Xdim2/2)
fnVol = fnRoot+'.vol'
# Simulated annealing
if UseSA:
smallIter=int(min(floor(NIterRandom/5.0),0));
runJob(log,"xmipp_volume_initial_simulated_annealing","-i %s --initial %s --oroot %s_sa --sym %s --randomIter %d --rejection %f --dontApplyPositive"
%(fnRoot+".xmd",fnVol,fnRoot,SymmetryGroup,smallIter,Rejection))
moveFile(log, fnRoot+"_sa.vol", fnVol)
deleteFile(log, fnRoot+"_sa.xmd")
# Generate projections from this reconstruction
fnGallery=os.path.join(TmpDir,'gallery_'+fnBase+'.stk')
runJob(log,"xmipp_angular_project_library", "-i %s -o %s --sampling_rate %f --sym %s --method fourier 1 0.25 bspline --compute_neighbors --angular_distance -1 --experimental_images %s"\
%(fnVol,fnGallery,float(AngularSampling),SymmetryGroup,fnOutputReducedClass))
# Assign angles to the rest of images
fnAngles=os.path.join(TmpDir,'angles_'+fnBase+'.xmd')
runJob(log,"xmipp_angular_projection_matching", "-i %s -o %s --ref %s --Ri 0 --Ro %s --max_shift %s --append"\
%(fnOutputReducedClass,fnAngles,fnGallery,str(Xdim/2),str(Xdim/20)))
# Delete intermediate files
deleteFile(log,fnGallery)
deleteFile(log,os.path.join(TmpDir,'gallery_'+fnBase+'_sampling.xmd'))
deleteFile(log,os.path.join(TmpDir,'gallery_'+fnBase+'.doc'))
deleteFile(log,fnVol)
deleteFile(log,os.path.join(TmpDir,fnBase+'.xmd'))
def runCrop(log, stack, cropSize, tmpStack):
runJob(log,"xmipp_transform_window","-i %(stack)s --size %(cropSize)d -o %(tmpStack)s" % locals())
moveFile(log, tmpStack, stack)
