def __runEman2Program(self, program, args):
""" Internal workaround to launch an EMAN2 program. """
from pwem import Domain
eman2 = Domain.importFromPlugin('eman2')
from pyworkflow.utils.process import runJob
runJob(self._log, eman2.Plugin.getProgram(program), args,
env=eman2.Plugin.getEnviron())
def __runEman2Program(self, program, args):
""" Internal workaround to launch an EMAN2 program. """
import pyworkflow.em.packages.eman2 as eman2
from pyworkflow.utils.process import runJob
runJob(self._log,
eman2.getEmanProgram(program),
args,
env=eman2.getEnviron())
def __runEman2Program(cls, program, args):
""" Internal workaround to launch an EMAN2 program. """
eman2 = pwutils.importFromPlugin('eman2')
from pyworkflow.utils.process import runJob
runJob(None,
eman2.Plugin.getProgram(program),
args,
env=eman2.Plugin.getEnviron())
def runJob(self, log, programName, params,
numberOfMpi=1, numberOfThreads=1,
env=None, cwd=None):
""" This function is a wrapper around runJob,
providing the host configuration.
"""
process.runJob(log, programName, params,
numberOfMpi, numberOfThreads,
self.hostConfig,
env=env, cwd=cwd)
def _computePSD(self, inputFn, outputFn, scaleFactor=6):
""" Generate a thumbnail of the PSD with EMAN2"""
args = "%s %s " % (inputFn, outputFn)
args += "--process=math.realtofft --meanshrink %s " % scaleFactor
args += "--fixintscaling=sane"
from pwem import Domain
eman2 = Domain.importFromPlugin('eman2')
from pyworkflow.utils.process import runJob
runJob(self._log,
eman2.Plugin.getProgram('e2proc2d.py'),
args,
env=eman2.Plugin.getEnviron())
return outputFn
def runJob(self,
log,
programName,
params,
numberOfMpi=1,
numberOfThreads=1,
env=None,
cwd=None):
""" This function is a wrapper around runJob,
providing the host configuration.
"""
process.runJob(log,
programName,
params,
numberOfMpi,
numberOfThreads,
self.hostConfig,
env=env,
cwd=cwd)
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])
if projectorFile:
M = np.loadtxt(projectorFile)
deformations = np.dot(trajectoryPoints, np.linalg.pinv(M))
np.savetxt(animationRoot + 'trajectory.txt', trajectoryPoints)
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()
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 = range(1, n + 1)
r2 = 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()
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])
if projectorFile:
M = np.loadtxt(projectorFile)
deformations = np.dot(trajectoryPoints, np.linalg.pinv(M))
np.savetxt(animationRoot + 'trajectory.txt', trajectoryPoints)
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()
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 = range(1, n+1)
r2 = 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()
def lanchEmanForTomogram(self, tomo):
# self._moveCoordsToInfo(tomo)
program = emantomo.Plugin.getProgram("e2spt_boxer.py")
arguments = "%s" % os.path.abspath(tomo.getFileName())
runJob(None, program, arguments, env=emantomo.Plugin.getEnviron(), cwd=self.path)
def __runEman2Program(self, program, args):
""" Internal workaround to launch an EMAN2 program. """
import pyworkflow.em.packages.eman2 as eman2
from pyworkflow.utils.process import runJob
runJob(None, eman2.getEmanProgram(program), args,
env=eman2.getEnviron())
