def convertPdbStep(self):
""" Although is not mandatory, usually is used by the protocol to
register the resulting outputs in the database.
"""
pdbFn = self._getPdbFileName()
outFile = removeExt(self._getVolName())
if getExt(pdbFn) == ".cif":
pdbFn2 = replaceBaseExt(pdbFn, 'pdb')
cifToPdb(pdbFn, pdbFn2)
pdbFn = pdbFn2
args = '-i %s --sampling %f -o %s' % (pdbFn, self.sampling.get(),
outFile)
if self.centerPdb:
args += ' --centerPDB'
if self.setSize:
args += ' --size'
if self.size.hasValue():
args += ' %d' % self.size.get()
self.info("Input file: " + pdbFn)
self.info("Output file: " + outFile)
program = "xmipp_volume_from_pdb"
self.runJob(program, args)
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 copyPdbStep(self, inputFn, localFn, isEM):
""" Copy the input pdb file and also create a link 'atoms.pdb'
"""
cifToPdb(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 _generateAnimation(self):
prot = self.protocol
projectorFile = prot.getProjectorFile()
animation = self.trajectoriesWindow.getAnimationName()
animationPath = prot._getExtraPath('animation_%s' % animation)
cleanPath(animationPath)
makePath(animationPath)
animationRoot = join(animationPath, 'animation_%s' % animation)
trajectoryPoints = np.array(
[p.getData() for p in self.trajectoriesWindow.pathData])
np.savetxt(join(animationPath, 'trajectory.txt'), trajectoryPoints)
if projectorFile:
M = np.loadtxt(projectorFile)
deformations = np.dot(trajectoryPoints, np.linalg.pinv(M))
else:
Y = np.loadtxt(prot.getOutputMatrixFile())
X = np.loadtxt(prot.getDeformationFile())
# Find closest points in deformations
deformations = [
X[np.argmin(np.sum((Y - p)**2, axis=1))]
for p in trajectoryPoints
]
pdb = prot.getInputPdb()
pdbFile = pdb.getFileName()
structureEM = prot.getInputPdb().getPseudoAtoms()
if not structureEM:
localFn = replaceBaseExt(basename(pdbFile), 'pdb')
cifToPdb(pdbFile, localFn)
pdbFile = basename(localFn)
modesFn = prot.inputNMA.get()._getExtraPath('modes.xmd')
for i, d in enumerate(deformations):
atomsFn = animationRoot + 'atomsDeformed_%02d.pdb' % (i + 1)
cmd = '-o %s --pdb %s --nma %s --deformations %s' % (
atomsFn, pdbFile, modesFn, str(d)[1:-1])
runJob(None, 'xmipp_pdb_nma_deform', cmd, env=prot._getEnviron())
# Join all deformations in a single pdb
# iterating going up and down through all points
# 1 2 3 ... n-2 n-1 n n-1 n-2 ... 3, 2
n = len(deformations)
r1 = list(range(1, n + 1))
r2 = list(range(2, n)) # Skip 1 at the end
r2.reverse()
loop = r1 + r2
trajFn = animationRoot + '.pdb'
trajFile = open(trajFn, 'w')
for i in loop:
atomsFn = animationRoot + 'atomsDeformed_%02d.pdb' % i
atomsFile = open(atomsFn)
for line in atomsFile:
trajFile.write(line)
trajFile.write('TER\nENDMDL\n')
atomsFile.close()
trajFile.close()
# Delete temporary atom files
cleanPattern(animationRoot + 'atomsDeformed_??.pdb')
# Generate the vmd script
vmdFn = animationRoot + '.vmd'
vmdFile = open(vmdFn, 'w')
vmdFile.write("""
mol new %s
animate style Loop
display projection Orthographic
mol modcolor 0 0 Index
mol modstyle 0 0 Beads 1.000000 8.000000
animate speed 0.5
animate forward
""" % trajFn)
vmdFile.close()
VmdView(' -e ' + vmdFn).show()