def animateModes(log,WorkingDir,LastMode,Amplitude,NFrames,Downsample,PseudoAtomThreshold,PseudoAtomRadius,Sampling,StructureType):
createDir(log,os.path.join(WorkingDir,"extra/animations"))
currentDir=os.getcwd()
changeDir(log,WorkingDir)
if StructureType=="EM":
fn="pseudoatoms.pdb"
runJob(log,"nma_animate_pseudoatoms.py","%s extra/vec_ani.pkl 7 %d %f extra/animations/animated_mode %d %d %f"%\
(fn,LastMode,Amplitude,NFrames,Downsample,PseudoAtomThreshold))
else:
fn="atoms.pdb"
runJob(log,"nma_animate_atoms.py","%s extra/vec_ani.pkl 7 %d %f extra/animations/animated_mode %d"%\
(fn,LastMode,Amplitude,NFrames))
for mode in range(7,LastMode+1):
fnAnimation="extra/animations/animated_mode_%03d"%mode
fhCmd=open(fnAnimation+".vmd",'w')
fhCmd.write("mol new "+os.path.join(WorkingDir,fnAnimation)+".pdb\n")
fhCmd.write("animate style Loop\n")
fhCmd.write("display projection Orthographic\n")
if StructureType=="EM":
fhCmd.write("mol modcolor 0 0 Beta\n")
fhCmd.write("mol modstyle 0 0 Beads %f 8.000000\n"%(PseudoAtomRadius*Sampling))
else:
fhCmd.write("mol modcolor 0 0 Index\n")
fhCmd.write("mol modstyle 0 0 Beads 1.000000 8.000000\n")
fhCmd.write("animate speed 0.5\n")
fhCmd.write("animate forward\n")
fhCmd.close();
changeDir(log,currentDir)
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 computeSAXS(log, WorkingDir,NumberOfHarmonics,MaxFreq, NumberOfSamples, OtherCrysol, ExperimentalSAXS):
if ExperimentalSAXS!="":
ExperimentalSAXS=os.path.abspath(ExperimentalSAXS)
currentDir=os.getcwd()
changeDir(log,WorkingDir)
if ExperimentalSAXS!="":
ExperimentalSAXS=os.path.relpath(ExperimentalSAXS)
runJob(log,"crysol","pseudoatoms.pdb %s /lm %d /sm %f /ns %d %s"%(ExperimentalSAXS,NumberOfHarmonics,MaxFreq,NumberOfSamples,OtherCrysol))
runJob(log,"mv","*log *txt extra")
if ExperimentalSAXS=="":
runJob(log,"mv","*alm extra")
changeDir(log,currentDir)
def qualifyModes(log,WorkingDir,NumberOfModes,StructureType,CollectivityThreshold):
currentDir=os.getcwd()
changeDir(log,WorkingDir)
fnVec=glob.glob("modes/vec.*")
if len(fnVec)<NumberOfModes:
fhWarning=open("warnings.xmd",'w')
fhWarning.write(redStr("There are only "+str(len(fnVec))+" modes instead of "+str(NumberOfModes)+". Check the number of modes you asked to compute and/or consider increasing cut-off distance. The maximum number of modes allowed by the method for atomic normal mode analysis is 6 times the number of RTB blocks and for pseudoatomic normal mode analysis 3 times the number of pseudoatoms. However, the protocol allows only up to 200 modes as 20-100 modes are usually enough. If the number of modes is below the minimum between these two numbers, consider increasing cut-off distance.")+"\n")
fhWarning.close()
fnDiag="diagrtb.eigenfacs"
if StructureType=="EM":
runJob(log,"nma_reformatForElNemo.sh","%d"%NumberOfModes)
fnDiag="diag_arpack.eigenfacs"
runJob(log,"echo","%s | nma_check_modes"%fnDiag)
deleteFile(log,fnDiag)
fh=open("Chkmod.res")
MDout=MetaData()
collectivityList=[]
for n in range(NumberOfModes):
line=fh.readline()
collectivity=float(line.split()[1])
collectivityList.append(collectivity)
id=MDout.addObject()
MDout.setValue(MDL_NMA_MODEFILE,os.path.join(WorkingDir,"modes/vec.%d"%(n+1)),id)
MDout.setValue(MDL_ORDER,long(n+1),id)
if n>=6:
MDout.setValue(MDL_ENABLED,1,id)
else:
MDout.setValue(MDL_ENABLED,-1,id)
MDout.setValue(MDL_NMA_COLLECTIVITY,collectivity,id)
if collectivity<CollectivityThreshold:
MDout.setValue(MDL_ENABLED,-1,id)
fh.close()
idxSorted=[i[0] for i in sorted(enumerate(collectivityList), key=lambda x:x[1])]
score=[0]*NumberOfModes
for i in range(NumberOfModes):
score[i]+=i+1
score[idxSorted[i]]+=NumberOfModes-i
i=0
for id in MDout:
score_i=float(score[i])/(2.0*NumberOfModes)
MDout.setValue(MDL_NMA_SCORE,score_i,id)
i+=1
MDout.write("modes.xmd")
deleteFile(log,"Chkmod.res")
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 computeModesPDB(log, WorkingDir, NumberOfModes, CutoffMode, Rc, RcPercentage, RTBblockSize, RTBForceConstant):
if CutoffMode=="Relative":
Rc=computeCutoff(WorkingDir,os.path.join(WorkingDir,"extra/atoms_distance.hist"),RcPercentage)
currentDir=os.getcwd()
changeDir(log,WorkingDir)
runJob(log,"nma_record_info_PDB.py","%d %d atoms.pdb %f %f"%(NumberOfModes,RTBblockSize,Rc,RTBForceConstant))
runJob(log,"nma_elnemo_pdbmat","")
runJob(log,"nma_diagrtb","")
if not os.path.exists("diagrtb.eigenfacs"):
fhWarning=open("warnings.xmd",'w')
fhWarning.write(redStr("Modes cannot be computed. Check the number of modes you asked to compute and/or consider increasing cut-off distance. The maximum number of modes allowed by the method for atomic normal mode analysis is 6 times the number of RTB blocks but the protocol allows only up to 200 modes as 20-100 modes are usually enough. If the number of modes is below the minimum between 200 and 6 times the number of RTB blocks, consider increasing cut-off distance.")+"\n")
fhWarning.close()
runJob(log,"rm","*.dat_run diagrtb.dat pdbmat.xyzm pdbmat.sdijf pdbmat.dat")
changeDir(log,currentDir)
def computeModes(log, WorkingDir, NumberOfModes, CutoffMode, Rc, RcPercentage):
if CutoffMode=="Relative":
Rc=computeCutoff(WorkingDir,os.path.join(WorkingDir,"extra/pseudoatoms_distance.hist"),RcPercentage)
currentDir=os.getcwd()
changeDir(log,WorkingDir)
runJob(log,"nma_record_info.py","%d pseudoatoms.pdb %d"%(NumberOfModes,int(Rc)))
runJob(log,"nma_pdbmat.pl","pdbmat.dat")
runJob(log,"nma_diag_arpack","")
if not os.path.exists("fort.11"):
fhWarning=open("warnings.xmd",'w')
fhWarning.write(redStr("Modes cannot be computed. Check the number of modes you asked to compute and/or consider increasing cut-off distance. The maximum number of modes allowed by the method for pseudoatomic normal mode analysis is 3 times the number of pseudoatoms but the protocol allows only up to 200 modes as 20-100 modes are usually enough. If the number of modes is below the minimum between 200 and 3 times the number of pseudoatoms, consider increasing cut-off distance.")+"\n")
fhWarning.close()
runJob(log,"rm","diag_arpack.in pdbmat.dat")
changeDir(log,currentDir)