def _GetEnergyModel(self):
if hasattr(self, "parent"):
site = self.parent
ceModel = site.parent
energyModel = ceModel.energyModel
else:
raise ContinuumElectrostaticsError("Energy model is undefined.")
return energyModel
def interactions(self):
# . Return a list of interactions of the current instance with other instances
if not hasattr(self, "parent"):
raise ContinuumElectrostaticsError("Energy model is undefined.")
site = self.parent
ceModel = site.parent
energyModel = ceModel.energyModel
energies = []
for indexOther in range(ceModel.ninstances):
energies.append(
energyModel.GetInteractionSymmetric(self._instIndexGlobal,
indexOther))
return energies
def WriteJobFiles(self, log=logFile):
"""Write files: PQR, FPT, OGM and MGM."""
if self.isInitialized:
# . Get atomic charges and radii for the system
system = self.owner
systemCharges = system.AtomicCharges()
systemRadii = []
systemTypes = system.energyModel.mmAtoms.AtomTypes()
radii = YAMLUnpickle("%s/%s" % (YAMLPATHIN, "radii.yaml"))
for atomType in systemTypes:
if radii.has_key(atomType):
radius = radii[atomType]
else:
generalAtomType = "%s*" % atomType[0]
if radii.has_key(generalAtomType):
radius = radii[generalAtomType]
else:
raise ContinuumElectrostaticsError(
"Cannot find atomic radius for atom type %s" %
atomType)
systemRadii.append(radius)
# . Prepare scratch space
if not os.path.exists(self.pathScratch):
try:
os.makedirs(self.pathScratch)
except:
raise ContinuumElectrostaticsError(
"Cannot create scratch directory %s" %
self.pathScratch)
# . Create subdirectories, if necessary
if self.splitToDirectories:
for site in self.sites:
sitePqr = site.instances[0].sitePqr
directory = os.path.dirname(sitePqr)
if not os.path.exists(directory):
try:
os.makedirs(directory)
except:
raise ContinuumElectrostaticsError(
"Cannot create directory %s" % directory)
# . Write PQR, OGM and MGM files of all instances of all sites
for site in self.sites:
site._WriteMEADFiles(system, systemCharges, systemRadii)
# . Write background PQR file
PQRFile_FromSystem(self.pathPqrBack,
system,
selection=Selection(self.backAtomIndices),
charges=systemCharges,
radii=systemRadii)
# . Write full-protein PQR file (to be used as eps2set_region)
PQRFile_FromSystem(self.pathPqrProtein,
system,
selection=Selection(self.proteinAtomIndices),
charges=systemCharges,
radii=systemRadii)
# . Write FPT-file
lines = []
for siteIndex, site in enumerate(self.sites):
for instanceIndex, instance in enumerate(site.instances):
for atomIndex, charge in zip(site.siteAtomIndices,
instance.charges):
x, y, z = system.coordinates3[atomIndex]
line = "%d %d %f %f %f %f\n" % (
siteIndex, instanceIndex, x, y, z, charge)
lines.append(line)
WriteInputFile(self.pathFptSites, lines)
self.isFilesWritten = True
