def count_solvent_molecules(tpr, solvent="water"):
"""Count number of solvent molecules from index file.
.. Note:: Only solvent="water" or "octanol" supported. New
selections can be added to :data:`solvent_selections`.
"""
# This would be MUCH easier in MDAnalysis but I don't want to add
# this as a dependency to mdpow. g_select would also work but that's
# more recent and also requires reading of an xvg file.
solventgroup = "solvent_%(solvent)s" % vars() # should not start with a number for make_ndx!!
try:
cmd = ['keep 0', 'del 0', solvent_selections[solvent],
'name 0 %(solventgroup)s' % vars(), 'q']
except KeyError:
raise NotImplementedError("solvent %(solvent)r not supported" % vars())
fd, tmpndx = tempfile.mkstemp(suffix=".ndx")
try:
# silent, no screen output!!
rc,output,junk = gromacs.cbook.make_ndx_captured(f=tpr, o=tmpndx,
input=cmd, stderr=False)
if rc != 0:
out = "\n".join(["GMX_FATAL: %s" % s for s in (junk + "\n\n" + output).split("\n")])
errmsg = "Failed to build index. Look at the output below for hints:\n" + out
logger.error(errmsg)
raise GromacsError(errmsg)
finally:
unlink_gmx(tmpndx)
try:
ndx = gromacs.cbook.parse_ndxlist(output)
except AttributeError:
logger.error("Failed to find solvent %(solvent)r. Maybe specify solvent='octanol'?",
vars())
raise ValueError("Failed to properly construct/parse make_ndx output.")
N_solvent = None
for rec in ndx:
if rec['name'] == solventgroup:
N_solvent = rec['natoms'] # == number of molecules as one atom per molecule
break
if N_solvent is None:
errmsg = "Failed to find solvent %(solvent)r in %(tpr)r" % vars()
logger.error(errmsg)
raise ValueError(errmsg)
logger.info("Found %(N_solvent)d %(solvent)s solvent molecules in %(tpr)r", vars())
return N_solvent
def get_observables(edr, observables=None, **kwargs):
"""Run :program:`g_energy` to get thermodynamic averages.
:Arguments:
*edr*
Gromacs energy file
*observables*
list of energy (thermodynamic) averages to be computed;
the default (for ``None``) is ::
["Pressure", "Volume", "Density", "Temperature"]
*kwargs*
other keywords are passed to
:class:`gromacs.tools.G_energy`; for instance, *b* sets
the start time (in ps) and *o* sets the output file name
:Returns: :class:`~numpy.core.records.recarray` with the
observable name in the first column ("*Energy*") and
subsequent columns containing the exact averages
produced by :program:`g_energy`.
"""
if observables is None:
observables = ["Pressure", "Volume", "Density", "Temperature"]
logger.info("Analyzing observables %(observables)r in energy file %(edr)r...", vars())
kwargs['input'] = observables
kwargs['f'] = edr
kwargs['stdout'] = False # required for processing
kwargs['stderr'] = False # suppress stderr
fd, kwargs['o'] = tempfile.mkstemp(suffix=".xvg")
try:
rc, data, stderr = gromacs.g_energy(**kwargs)
if rc != 0:
logger.error("g_energy failed")
raise GromacsError("g_energy failed --- see output below:\n\n" + stderr + data)
finally:
unlink_gmx(kwargs['o'])
return parse_energy(data)
