def _WriteMEADFiles(self, system, systemCharges, systemRadii):
"""For each instance of each site, write:
- PQR file for the site - PQR file for the model compound
- OGM file for the site - MGM file for the model compound"""
grids = []
model = self.parent
for stepIndex, (nodes, resolution) in enumerate(model.focusingSteps):
if stepIndex < 1:
grids.append("ON_GEOM_CENT %d %f\n" % (nodes, resolution))
else:
x, y, z = self.center
grids.append("(%f %f %f) %d %f\n" %
(x, y, z, nodes, resolution))
selectSite = Selection(self.siteAtomIndices)
selectModel = Selection(self.modelAtomIndices)
# . In the PQR file of the model compound, charges of the site atoms must be set to zero (requirement of the my_2diel_solver program)
chargesZeroSite = Clone(systemCharges)
for atomIndex in self.siteAtomIndices:
chargesZeroSite[atomIndex] = 0.0
for instance in self.instances:
PQRFile_FromSystem(
instance.modelPqr,
system,
selection=selectModel,
charges=chargesZeroSite,
radii=systemRadii,
)
# . Update system charges with instance charges
chargesInstance = Clone(systemCharges)
for chargeIndex, atomIndex in enumerate(self.siteAtomIndices):
chargesInstance[atomIndex] = instance.charges[chargeIndex]
PQRFile_FromSystem(
instance.sitePqr,
system,
selection=selectSite,
charges=chargesInstance,
radii=systemRadii,
)
del chargesInstance
# . Write OGM and MGM files (they have the same content)
for fileGrid in (instance.modelGrid, instance.siteGrid):
WriteInputFile(fileGrid, grids)
del chargesZeroSite
def SetUpSystem(path, forceNoQC=False, useSystemWithTimings=True):
"""Set up the system."""
# . Get system data.
systemData = YAMLUnpickle(os.path.join(path, _TestDataFileName))
# . Get the parameters.
parameters = CHARMMParameterFiles_ToParameters(
glob.glob(os.path.join(path, "*.prm")))
# . Get the test name.
name = os.path.split(path)[-1]
# . Generate the system.
system = CHARMMPSFFile_ToSystem(os.path.join(path, name + ".psfx"),
isXPLOR=True,
parameters=parameters)
if useSystemWithTimings: system = SystemWithTimings.FromSystem(system)
system.coordinates3 = XYZFile_ToCoordinates3(
os.path.join(path, name + ".xyz"))
system.label = systemData["Label"]
# . Symmetry.
if systemData.get("Crystal Class", None) is not None:
symmetryOptions = systemData["Symmetry Parameters"]
symmetryOptions["crystalClass"] = _CrystalClasses[
systemData["Crystal Class"]]
system.DefineSymmetry(**symmetryOptions)
# . QC data.
if not forceNoQC:
qcData = systemData.get(_QCRegionKey, None)
if qcData is not None:
# . Electronic state.
system.electronicState = ElectronicState(
charge=qcData.get("Charge", 0),
multiplicity=qcData.get("Multiplicity", 1))
# . QC atoms.
qcAtoms = set()
for path in qcData["Atoms"]:
index = system.sequence.AtomIndex(path)
qcAtoms.add(index)
system.DefineQCModel(_QCModel, qcSelection=Selection(qcAtoms))
# . Finish set up.
system.DefineNBModel(_NBModel)
return system
def ExtractDisorderData ( self, dataBlock, system, disorderGroup = _DefaultDisorderGroup ):
"""Extract atom data from a data block."""
result = system
table = dataBlock.get ( "atom_site", None )
if table is not None:
# . Disorder and multiplicity information.
assemblies = table.ColumnValues ( "atom_site_disorder_assembly" )
groups = table.ColumnValues ( "atom_site_disorder_group" )
multiplicities = table.ColumnValues ( "atom_site_symmetry_multiplicity" )
# . Check for the disorder groups to include.
if groups is not None:
uniqueGroups = set ( groups )
uniqueGroups.discard ( disorderGroup )
uniqueGroups.discard ( "-" + disorderGroup )
uniqueGroups.discard ( _UndefinedCharacter )
if len ( uniqueGroups ) > 0:
toInclude = set ( [ _UndefinedCharacter, disorderGroup, "-" + disorderGroup ] )
indices = []
for ( i, group ) in enumerate ( groups ):
if group in toInclude: indices.append ( i )
if len ( indices ) < len ( groups ):
result = system.Prune ( Selection ( indices ) )
result.label = system.label
return result
def runTest ( self ):
"""The test."""
# . Initialization.
failures = 0
otherFailures = 0
successes = 0
# . Paths.
dataPath = os.path.join ( os.getenv ( "PDYNAMO_PMOLECULE" ), "data", "pdb" )
if self.resultPath is None: outPath = os.path.join ( os.getenv ( "PDYNAMO_SCRATCH" ), _Destination )
else: outPath = os.path.join ( self.resultPath, _Destination )
if not os.path.exists ( outPath ): os.mkdir ( outPath )
log = self.GetLog ( )
# . Models.
mmModel = MMModelCHARMM ( "c36a2" )
nbModel = NBModelABFS ( )
qcModel = QCModelMNDO ( )
# . Get the file.
pdbFile = os.path.join ( dataPath, "2E4E_folded_solvated.pdb" )
( head, tail ) = os.path.split ( pdbFile )
tag = tail[0:-4]
if log is not None: log.Text ( "\nProcessing " + pdbFile + ":\n" )
system = PDBFile_ToSystem ( pdbFile, log = log, useComponentLibrary = True )
try:
# . Fixed atoms.
fixedAtoms = Selection ( ~ AtomSelection.FromAtomPattern ( system, "A:*:*" ) )
# . QC selection.
indices = set ( )
for atomTag in _Tags:
indices.add ( system.sequence.AtomIndex ( "A:TYR.2:" + atomTag ) )
tyrosine = Selection ( indices )
# . Setup.
system.electronicState = ElectronicState ( charge = 0, multiplicity = 1 )
system.DefineFixedAtoms ( fixedAtoms )
system.DefineSymmetry ( crystalClass = CrystalClassCubic ( ), a = _BoxSize )
system.DefineMMModel ( mmModel, log = log )
system.DefineQCModel ( qcModel, qcSelection = tyrosine )
system.DefineNBModel ( nbModel )
system.Summary ( log = log )
referenceEnergy = system.Energy ( log = log, doGradients = True )
# . Pickling.
pklFile = os.path.join ( outPath, tag + ".pkl" )
yamlFile = os.path.join ( outPath, tag + ".yaml" )
Pickle ( pklFile , system )
YAMLPickle ( yamlFile, system )
# . Unpickling.
pklSystem = Unpickle ( pklFile )
pklSystem.label += " (Pickled)"
pklSystem.Summary ( log = log )
pklEnergy = pklSystem.Energy ( log = log, doGradients = True )
if math.fabs ( referenceEnergy - pklEnergy <= _Tolerance ): successes += 1
else: failures += 1
yamlSystem = YAMLUnpickle ( yamlFile )
yamlSystem.label += " (YAMLPickled)"
yamlSystem.Summary ( log = log )
yamlEnergy = yamlSystem.Energy ( log = log, doGradients = True )
if math.fabs ( referenceEnergy - yamlEnergy <= _Tolerance ): successes += 1
else: failures += 1
except Exception as e:
otherFailures += 1
if log is not None: log.Text ( "\nError occurred> " + e.args[0] + "\n" )
# . Summary of results.
if log is not None:
summary = log.GetSummary ( )
summary.Start ( "Pickle Tests" )
summary.Entry ( "Pickle Successes", "{:d}".format ( successes ) )
summary.Entry ( "Pickle Failures" , "{:d}".format ( failures ) )
summary.Entry ( "Total Tests" , "2" )
summary.Entry ( "Loop Failures" , "{:d}".format ( otherFailures ) )
summary.Stop ( )
# . Success/failure.
self.assertTrue ( ( failures == 0 ) and ( otherFailures == 0 ) )
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