def computeModesStep(self, fnPseudoatoms, numberOfModes, cutoffStr):
(baseDir,fnBase)=os.path.split(fnPseudoatoms)
fnBase=fnBase.replace(".pdb","")
fnDistanceHist=os.path.join(baseDir,'extra',fnBase+'_distance.hist')
rc = self._getRc(fnDistanceHist)
self._enterWorkingDir()
self.runJob('nma_record_info.py', "%d %s.pdb %d" % (numberOfModes, fnBase, rc),env=getNMAEnviron())
self.runJob("nma_pdbmat.pl","pdbmat.dat",env=getNMAEnviron())
self.runJob("nma_diag_arpack","",env=getNMAEnviron())
if not exists("fort.11"):
self._printWarnings(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."))
cleanPath("diag_arpack.in", "pdbmat.dat")
self._leaveWorkingDir()
def reformatOutputStep(self, fnPseudoatoms):
self._enterWorkingDir()
n = self._countAtoms(fnPseudoatoms)
self.runJob("nma_reformat_vector_foranimate.pl", "%d fort.11" % n, env=getNMAEnviron())
self.runJob("cat", "vec.1* > vec_ani.txt")
self.runJob("rm", "-f vec.1*")
self.runJob("nma_reformat_vector.pl", "%d fort.11" % n, env=getNMAEnviron())
makePath("modes")
self.runJob("mv", "-f vec.* modes")
self.runJob("nma_prepare_for_animate.py", "", env=getNMAEnviron())
self.runJob("rm", "-f vec_ani.txt fort.11 matrice.sdijf")
moveFile("vec_ani.pkl", "extra/vec_ani.pkl")
self._leaveWorkingDir()
def reformatPdbOutputStep(self, numberOfModes):
self._enterWorkingDir()
makePath('modes')
Natoms = self._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()
self.runJob("nma_prepare_for_animate.py", "", env=getNMAEnviron())
cleanPath("vec_ani.txt")
moveFile('vec_ani.pkl', 'extra/vec_ani.pkl')
self._leaveWorkingDir()
def animateModesStep(self, numberOfModes,amplitude,nFrames,downsample,pseudoAtomThreshold,pseudoAtomRadius):
makePath(self._getExtraPath('animations'))
self._enterWorkingDir()
if self.structureEM:
fn = "pseudoatoms.pdb"
self.runJob("nma_animate_pseudoatoms.py","%s extra/vec_ani.pkl 7 %d %f extra/animations/animated_mode %d %d %f"%\
(fn,numberOfModes,amplitude,nFrames,downsample,pseudoAtomThreshold),env=getNMAEnviron())
else:
fn="atoms.pdb"
self.runJob("nma_animate_atoms.py","%s extra/vec_ani.pkl 7 %d %f extra/animations/animated_mode %d"%\
(fn,numberOfModes,amplitude,nFrames),env=getNMAEnviron())
for mode in range(7,numberOfModes+1):
fnAnimation = join("extra", "animations", "animated_mode_%03d" % mode)
fhCmd=open(fnAnimation+".vmd",'w')
fhCmd.write("mol new %s.pdb\n" % self._getPath(fnAnimation))
fhCmd.write("animate style Loop\n")
fhCmd.write("display projection Orthographic\n")
if self.structureEM:
fhCmd.write("mol modcolor 0 0 Beta\n")
fhCmd.write("mol modstyle 0 0 Beads %f 8.000000\n"%(pseudoAtomRadius))
else:
fhCmd.write("mol modcolor 0 0 Index\n")
#fhCmd.write("mol modstyle 0 0 Beads 1.000000 8.000000\n")
fhCmd.write("mol modstyle 0 0 NewRibbons 1.800000 6.000000 2.600000 0\n")
fhCmd.write("animate speed 0.5\n")
fhCmd.write("animate forward\n")
fhCmd.close();
self._leaveWorkingDir()
def reformatPdbOutputStep(self, numberOfModes):
self._enterWorkingDir()
makePath('modes')
Natoms = self._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()
self.runJob("nma_prepare_for_animate.py","",env=getNMAEnviron())
cleanPath("vec_ani.txt")
moveFile('vec_ani.pkl', 'extra/vec_ani.pkl')
self._leaveWorkingDir()
def animateModesStep(self, numberOfModes,amplitude,nFrames,downsample,pseudoAtomThreshold,pseudoAtomRadius):
makePath(self._getExtraPath('animations'))
self._enterWorkingDir()
if self.structureEM:
fn = "pseudoatoms.pdb"
self.runJob("nma_animate_pseudoatoms.py","%s extra/vec_ani.pkl 7 %d %f extra/animations/animated_mode %d %d %f"%\
(fn,numberOfModes,amplitude,nFrames,downsample,pseudoAtomThreshold),env=getNMAEnviron())
else:
fn="atoms.pdb"
self.runJob("nma_animate_atoms.py","%s extra/vec_ani.pkl 7 %d %f extra/animations/animated_mode %d"%\
(fn,numberOfModes,amplitude,nFrames),env=getNMAEnviron())
for mode in range(7,numberOfModes+1):
fnAnimation = join("extra", "animations", "animated_mode_%03d" % mode)
fhCmd=open(fnAnimation+".vmd",'w')
fhCmd.write("mol new %s.pdb\n" % self._getPath(fnAnimation))
fhCmd.write("animate style Loop\n")
fhCmd.write("display projection Orthographic\n")
if self.structureEM:
fhCmd.write("mol modcolor 0 0 Beta\n")
fhCmd.write("mol modstyle 0 0 Beads %f 8.000000\n"%(pseudoAtomRadius))
else:
fhCmd.write("mol modcolor 0 0 Index\n")
#fhCmd.write("mol modstyle 0 0 Beads 1.000000 8.000000\n")
fhCmd.write("mol modstyle 0 0 NewRibbons 1.800000 6.000000 2.600000 0\n")
fhCmd.write("animate speed 0.5\n")
fhCmd.write("animate forward\n")
fhCmd.close();
self._leaveWorkingDir()
def reformatOutputStep(self, fnPseudoatoms):
self._enterWorkingDir()
n = self._countAtoms(fnPseudoatoms)
self.runJob("nma_reformat_vector_foranimate.pl",
"%d fort.11" % n,
env=getNMAEnviron())
self.runJob("cat", "vec.1* > vec_ani.txt")
self.runJob("rm", "-f vec.1*")
self.runJob("nma_reformat_vector.pl",
"%d fort.11" % n,
env=getNMAEnviron())
makePath("modes")
self.runJob("mv", "-f vec.* modes")
self.runJob("nma_prepare_for_animate.py", "", env=getNMAEnviron())
self.runJob("rm", "-f vec_ani.txt fort.11 matrice.sdijf")
moveFile('vec_ani.pkl', 'extra/vec_ani.pkl')
self._leaveWorkingDir()
def computeModesStep(self, fnPseudoatoms, numberOfModes, cutoffStr):
(baseDir, fnBase) = os.path.split(fnPseudoatoms)
fnBase = fnBase.replace(".pdb", "")
fnDistanceHist = os.path.join(baseDir, 'extra',
fnBase + '_distance.hist')
rc = self._getRc(fnDistanceHist)
self._enterWorkingDir()
self.runJob('nma_record_info.py',
"%d %s.pdb %d" % (numberOfModes, fnBase, rc),
env=getNMAEnviron())
self.runJob("nma_pdbmat.pl", "pdbmat.dat", env=getNMAEnviron())
self.runJob("nma_diag_arpack", "", env=getNMAEnviron())
if not exists("fort.11"):
self._printWarnings(
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."
))
cleanPath("diag_arpack.in", "pdbmat.dat")
self._leaveWorkingDir()
def computePdbModesStep(self, numberOfModes, RTBblockSize, RTBForceConstant, cutoffStr):
rc = self._getRc(self._getExtraPath('atoms_distance.hist'))
self._enterWorkingDir()
self.runJob('nma_record_info_PDB.py', "%d %d atoms.pdb %f %f" % (numberOfModes, RTBblockSize, rc, RTBForceConstant),
env=getNMAEnviron())
self.runJob("nma_elnemo_pdbmat","",env=getNMAEnviron())
self.runJob("nma_diagrtb","",env=getNMAEnviron())
if not exists("diagrtb.eigenfacs"):
msg = "Modes cannot be computed. Check the number of modes you asked to compute and/or consider "
msg += "increasing cut-off distance. The maximum number of modes allowed by the method for atomic "
msg += "normal mode analysis is 6 times the number of RTB blocks but the protocol allows only up "
msg += "to 200 modes as 20-100 modes are usually enough. If the number of modes is below the minimum "
msg += "between 200 and 6 times the number of RTB blocks, consider increasing cut-off distance."
self._printWarnings(redStr(msg) + '\n')
self.runJob("rm","-f *.dat_run diagrtb.dat pdbmat.xyzm pdbmat.sdijf pdbmat.dat")
self._leaveWorkingDir()
def computePdbModesStep(self, numberOfModes, RTBblockSize, RTBForceConstant, cutoffStr):
rc = self._getRc(self._getExtraPath('atoms_distance.hist'))
self._enterWorkingDir()
self.runJob('nma_record_info_PDB.py', "%d %d atoms.pdb %f %f" % (numberOfModes, RTBblockSize, rc, RTBForceConstant),
env=getNMAEnviron())
self.runJob("nma_elnemo_pdbmat","",env=getNMAEnviron())
self.runJob("nma_diagrtb","",env=getNMAEnviron())
if not exists("diagrtb.eigenfacs"):
msg = "Modes cannot be computed. Check the number of modes you asked to compute and/or consider "
msg += "increasing cut-off distance. The maximum number of modes allowed by the method for atomic "
msg += "normal mode analysis is 6 times the number of RTB blocks but the protocol allows only up "
msg += "to 200 modes as 20-100 modes are usually enough. If the number of modes is below the minimum "
msg += "between 200 and 6 times the number of RTB blocks, consider increasing cut-off distance."
self._printWarnings(redStr(msg) + '\n')
self.runJob("rm","-f *.dat_run diagrtb.dat pdbmat.xyzm pdbmat.sdijf pdbmat.dat")
self._leaveWorkingDir()
def qualifyModesStep(self, numberOfModes, collectivityThreshold,
structureEM):
self._enterWorkingDir()
fnVec = glob("modes/vec.*")
if len(fnVec) < numberOfModes:
msg = "There are only %d modes instead of %d. "
msg += "Check the number of modes you asked to compute and/or consider increasing cut-off distance."
msg += "The maximum number of modes allowed by the method for atomic normal mode analysis is 6 times"
msg += "the number of RTB blocks and for pseudoatomic normal mode analysis 3 times the number of pseudoatoms. "
msg += "However, the protocol allows only up to 200 modes as 20-100 modes are usually enough. If the number of"
msg += "modes is below the minimum between these two numbers, consider increasing cut-off distance."
self._printWarnings(redStr(msg % (len(fnVec), numberOfModes)))
fnDiag = "diagrtb.eigenfacs"
if structureEM:
self.runJob("nma_reformatForElNemo.sh",
"%d" % numberOfModes,
env=getNMAEnviron())
fnDiag = "diag_arpack.eigenfacs"
self.runJob("echo",
"%s | nma_check_modes" % fnDiag,
env=getNMAEnviron())
cleanPath(fnDiag)
fh = open("Chkmod.res")
mdOut = xmipp.MetaData()
collectivityList = []
for n in range(numberOfModes):
line = fh.readline()
collectivity = float(line.split()[1])
collectivityList.append(collectivity)
objId = mdOut.addObject()
modefile = self._getPath("modes", "vec.%d" % (n + 1))
mdOut.setValue(xmipp.MDL_NMA_MODEFILE, modefile, objId)
mdOut.setValue(xmipp.MDL_ORDER, long(n + 1), objId)
if n >= 6:
mdOut.setValue(xmipp.MDL_ENABLED, 1, objId)
else:
mdOut.setValue(xmipp.MDL_ENABLED, -1, objId)
mdOut.setValue(xmipp.MDL_NMA_COLLECTIVITY, collectivity, objId)
if collectivity < collectivityThreshold:
mdOut.setValue(xmipp.MDL_ENABLED, -1, objId)
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 objId in mdOut:
score_i = float(score[i]) / (2.0 * numberOfModes)
mdOut.setValue(xmipp.MDL_NMA_SCORE, score_i, objId)
i += 1
mdOut.write("modes.xmd")
cleanPath("Chkmod.res")
self._leaveWorkingDir()
def qualifyModesStep(self, numberOfModes, collectivityThreshold, structureEM, suffix=''):
self._enterWorkingDir()
fnVec = glob("modes/vec.*")
if len(fnVec) < numberOfModes:
msg = "There are only %d modes instead of %d. "
msg += "Check the number of modes you asked to compute and/or consider increasing cut-off distance."
msg += "The maximum number of modes allowed by the method for atomic normal mode analysis is 6 times"
msg += "the number of RTB blocks and for pseudoatomic normal mode analysis 3 times the number of pseudoatoms. "
msg += "However, the protocol allows only up to 200 modes as 20-100 modes are usually enough. If the number of"
msg += "modes is below the minimum between these two numbers, consider increasing cut-off distance."
self._printWarnings(redStr(msg % (len(fnVec), numberOfModes)))
print redStr('Warning: There are only %d modes instead of %d.'% (len(fnVec), numberOfModes))
print redStr("Check the number of modes you asked to compute and/or consider increasing cut-off distance.")
print redStr("The maximum number of modes allowed by the method for atomic normal mode analysis is 6 times")
print redStr("the number of RTB blocks and for pseudoatomic normal mode analysis 3 times the number of pseudoatoms.")
print redStr("However, the protocol allows only up to 200 modes as 20-100 modes are usually enough. If the number of")
print redStr("modes is below the minimum between these two numbers, consider increasing cut-off distance.")
fnDiag = "diagrtb.eigenfacs"
if structureEM:
self.runJob("nma_reformatForElNemo.sh", "%d" % len(fnVec),env=getNMAEnviron())
fnDiag = "diag_arpack.eigenfacs"
self.runJob("echo", "%s | nma_check_modes" % fnDiag,env=getNMAEnviron())
cleanPath(fnDiag)
fh = open("Chkmod.res")
mdOut = xmipp.MetaData()
collectivityList = []
for n in range(len(fnVec)):
line = fh.readline()
collectivity = float(line.split()[1])
collectivityList.append(collectivity)
objId = mdOut.addObject()
modefile = self._getPath("modes", "vec.%d" % (n+1))
mdOut.setValue(xmipp.MDL_NMA_MODEFILE, modefile, objId)
mdOut.setValue(xmipp.MDL_ORDER, long(n+1), objId)
if n >= 6:
mdOut.setValue(xmipp.MDL_ENABLED, 1, objId)
else:
mdOut.setValue(xmipp.MDL_ENABLED, -1, objId)
mdOut.setValue(xmipp.MDL_NMA_COLLECTIVITY, collectivity, objId)
if collectivity < collectivityThreshold:
mdOut.setValue(xmipp.MDL_ENABLED,-1,objId)
fh.close()
idxSorted = [i[0] for i in sorted(enumerate(collectivityList), key=lambda x:x[1])]
score = []
for j in range(len(fnVec)):
score.append(0)
modeNum = []
l = 0
for k in range(len(fnVec)):
modeNum.append(k)
l += 1
#score = [0]*numberOfModes
for i in range(len(fnVec)):
score[i] += i+1
score[idxSorted[i]] += modeNum[i] - i
i = 0
for objId in mdOut:
score_i = float(score[i])/(2.0*l)
mdOut.setValue(xmipp.MDL_NMA_SCORE, score_i, objId)
i+=1
mdOut.write("modes%s.xmd"%suffix)
cleanPath("Chkmod.res")
self._leaveWorkingDir()
