def __init__(self,
universe,
force_field,
subset1=None,
subset2=None,
threads=None,
mpi_communicator=None):
if not Universe.isUniverse(universe):
raise TypeError("energy evaluator defined only for universes")
self.universe = universe
self.universe_version = self.universe._version
self.ff = force_field
self.configuration = self.universe.configuration()
self.global_data = ForceFieldData()
if subset1 is not None and subset2 is None:
subset2 = subset1
terms = self.ff.evaluatorTerms(self.universe, subset1, subset2,
self.global_data)
if not isinstance(terms, type([])):
raise ValueError("evaluator term list not a list")
from MMTK_forcefield import Evaluator
if threads is None:
import MMTK.ForceFields
threads = MMTK.ForceFields.default_energy_threads
self.evaluator = Evaluator(Numeric.array(terms), threads,
mpi_communicator)
def viewConfigurationVMD(object, configuration=None, format='pdb', label=None):
from MMTK import Universe
format = format.lower()
if format != 'pdb':
return genericViewConfiguration(object, configuration, format)
tempfile.tempdir = tempdir
filename = tempfile.mktemp()
filename_tcl = filename.replace('\\', '\\\\')
script = tempfile.mktemp()
script_tcl = script.replace('\\', '\\\\')
tempfile.tempdir = None
object.writeToFile(filename, configuration, format)
file = open(script, 'w')
file.write('mol load pdb ' + filename_tcl + '\n')
if isCalpha(object):
file.write('mol modstyle 0 all trace\n')
file.write('color Name 1 white\n')
file.write('color Name 2 white\n')
file.write('color Name 3 white\n')
if Universe.isUniverse(object):
# add a box around periodic universes
basis = object.basisVectors()
if basis is not None:
v1, v2, v3 = basis
p = -0.5 * (v1 + v2 + v3)
for p1, p2 in [(p, p + v1), (p, p + v2), (p + v1, p + v1 + v2),
(p + v2, p + v1 + v2), (p, p + v3),
(p + v1, p + v1 + v3), (p + v2, p + v2 + v3),
(p + v1 + v2, p + v1 + v2 + v3),
(p + v3, p + v1 + v3), (p + v3, p + v2 + v3),
(p + v1 + v3, p + v1 + v2 + v3),
(p + v2 + v3, p + v1 + v2 + v3)]:
file.write('graphics 0 line {%f %f %f} {%f %f %f}\n' %
(tuple(p1 / Units.Ang) + tuple(p2 / Units.Ang)))
file.write('file delete ' + filename_tcl + '\n')
if sys.platform != 'win32':
# Under Windows, it seems to be impossible to delete
# the script file while it is still in use. For the moment
# we just don't delete it at all.
file.write('file delete ' + script_tcl + '\n')
file.close()
subprocess.Popen([viewer['pdb'][1], '-nt', '-e', script])
def __init__(self, universe, force_field, subset1=None, subset2=None,
threads=None, mpi_communicator=None):
if not Universe.isUniverse(universe):
raise TypeError, "energy evaluator defined only for universes"
self.universe = universe
self.universe_version = self.universe._version
self.ff = force_field
self.configuration = self.universe.configuration()
self.global_data = ForceFieldData()
if subset1 is not None and subset2 is None:
subset2 = subset1
terms = self.ff.evaluatorTerms(self.universe,
subset1, subset2,
self.global_data)
from MMTK_forcefield import Evaluator
if threads is None:
import MMTK.ForceFields
threads = MMTK.ForceFields.default_energy_threads;
self.evaluator = Evaluator(Numeric.array(terms), threads,
mpi_communicator)
def viewConfigurationVMD(object, configuration = None, format = 'pdb',
label = None):
from MMTK import Universe
format = format.lower()
if format != 'pdb':
return genericViewConfiguration(object, configuration, format)
tempfile.tempdir = tempdir
filename = tempfile.mktemp()
filename_tcl = filename.replace('\\', '\\\\')
script = tempfile.mktemp()
script_tcl = script.replace('\\', '\\\\')
tempfile.tempdir = None
object.writeToFile(filename, configuration, format)
file = open(script, 'w')
file.write('mol load pdb ' + filename_tcl + '\n')
if isCalpha(object):
file.write('mol modstyle 0 all trace\n')
file.write('color Name 1 white\n')
file.write('color Name 2 white\n')
file.write('color Name 3 white\n')
if Universe.isUniverse(object):
# add a box around periodic universes
basis = object.basisVectors()
if basis is not None:
v1, v2, v3 = basis
p = -0.5*(v1+v2+v3)
for p1, p2 in [(p, p+v1), (p, p+v2), (p+v1, p+v1+v2),
(p+v2, p+v1+v2), (p, p+v3), (p+v1, p+v1+v3),
(p+v2, p+v2+v3), (p+v1+v2, p+v1+v2+v3),
(p+v3, p+v1+v3), (p+v3, p+v2+v3),
(p+v1+v3, p+v1+v2+v3), (p+v2+v3, p+v1+v2+v3)]:
file.write('graphics 0 line {%f %f %f} {%f %f %f}\n' %
(tuple(p1/Units.Ang) + tuple(p2/Units.Ang)))
file.write('file delete ' + filename_tcl + '\n')
if sys.platform != 'win32':
# Under Windows, it seems to be impossible to delete
# the script file while it is still in use. For the moment
# we just don't delete it at all.
file.write('file delete ' + script_tcl + '\n')
file.close()
subprocess.Popen([viewer['pdb'][1], '-nt', '-e', script])