def generate_hopgraph(topology, trajectory, densityfile, filename, localcopy=False, **hopargs):
density = hop.sitemap.Density(filename=densityfile)
def _generate_hopgraph(trajectory):
hoptraj = hop.trajectory.HoppingTrajectory(hoppsf=topology, hopdcd=trajectory)
tgraph = hop.interactive.build_hoppinggraph(hoptraj,density)
return tgraph
if localcopy:
# should probably also write locally and then copy back
from tempfile import mkstemp
from shutil import copy
root,ext = os.path.splitext(trajectory)
fd, tmptrajectory = mkstemp(suffix=ext)
logger.info("Making local copy to improve read performance: %(trajectory)r --> %(tmptrajectory)r" % vars())
try:
copy(trajectory, tmptrajectory)
tgraph = _generate_hopgraph(tmptrajectory)
finally:
unlink_f(tmptrajectory)
else:
tgraph = _generate_hopgraph(trajectory)
h = tgraph.hopgraph # main result is the 'hopgraph'
h.save(filename) # save result
logger.info("Saved hopgraph as %(filename)s.pickle", vars())
hop.interactive.hopgraph_basic_analysis(h, density, filename)
return h
def generate_densities_locally(topology,
trajectory,
atomselection,
localcopy=False):
def _generate_densities(traj):
return hop.interactive.generate_densities(topology,
traj,
atomselection=atomselection)
if localcopy:
from tempfile import mkstemp
from shutil import copy
root, ext = os.path.splitext(trajectory)
fd, tmptrajectory = mkstemp(suffix=ext)
logger.info(
"Making local copy to improve read performance: %(trajectory)r --> %(tmptrajectory)r"
% vars())
try:
copy(trajectory, tmptrajectory)
densities = _generate_densities(tmptrajectory)
finally:
unlink_f(tmptrajectory)
else:
densities = _generate_densities(trajectory)
return densities
def generate_densities_locally(topology, trajectory, atomselection, localcopy=False):
def _generate_densities(traj):
return hop.interactive.generate_densities(topology, traj, atomselection=atomselection)
if localcopy:
from tempfile import mkstemp
from shutil import copy
root,ext = os.path.splitext(trajectory)
fd, tmptrajectory = mkstemp(suffix=ext)
logger.info("Making local copy to improve read performance: %(trajectory)r --> %(tmptrajectory)r" % vars())
try:
copy(trajectory, tmptrajectory)
densities = _generate_densities(tmptrajectory)
finally:
unlink_f(tmptrajectory)
else:
densities = _generate_densities(trajectory)
return densities
def generate_hopgraph(topology,
trajectory,
densityfile,
filename,
localcopy=False,
**hopargs):
density = hop.sitemap.Density(filename=densityfile)
def _generate_hopgraph(trajectory):
hoptraj = hop.trajectory.HoppingTrajectory(hoppsf=topology,
hopdcd=trajectory)
tgraph = hop.interactive.build_hoppinggraph(hoptraj, density)
return tgraph
if localcopy:
# should probably also write locally and then copy back
from tempfile import mkstemp
from shutil import copy
root, ext = os.path.splitext(trajectory)
fd, tmptrajectory = mkstemp(suffix=ext)
logger.info(
"Making local copy to improve read performance: %(trajectory)r --> %(tmptrajectory)r"
% vars())
try:
copy(trajectory, tmptrajectory)
tgraph = _generate_hopgraph(tmptrajectory)
finally:
unlink_f(tmptrajectory)
else:
tgraph = _generate_hopgraph(trajectory)
h = tgraph.hopgraph # main result is the 'hopgraph'
h.save(filename) # save result
logger.info("Saved hopgraph as %(filename)s.pickle", vars())
hop.interactive.hopgraph_basic_analysis(h, density, filename)
return h
hops = hop.trajectory.HoppingTrajectory(u.trajectory,group,density,**hopargs)
hops.write(filename)
return hops
if localcopy:
# should probably also write locally and then copy back
from tempfile import mkstemp
from shutil import copy
root,ext = os.path.splitext(trajectory)
fd, tmptrajectory = mkstemp(suffix=ext)
logger.info("Making local copy to improve read performance: %(trajectory)r --> %(tmptrajectory)r" % vars())
try:
copy(trajectory, tmptrajectory)
hops = _generate_hoptraj(tmptrajectory)
finally:
unlink_f(tmptrajectory)
else:
hops = _generate_hoptraj(trajectory)
return hops
if __name__ == "__main__":
import sys
from optparse import OptionParser
parser = OptionParser(usage=__doc__)
parser.add_option("-s", "--topology", dest="topology",
metavar="FILE",
help="topology to go with the trajectories; can be a PSF "
"PDB, GRO, or whatever else MDAnalysis accepts; default is to "
"try the path recorded in DENSITY")
parser.add_option("-f", "--trajectory", dest="trajectory",
