def GetSystem ( self, log = logFile ):
"""Get the system."""
if self.setUpType == "CHARMM":
parameters = CHARMMParameterFiles_ToParameters ( self.parameterFiles, log = log )
system = CHARMMPSFFile_ToSystem ( self.setUpFile, isXPLOR = True, log = log, parameters = parameters )
elif self.setUpType == "MOL" : system = MOLFile_ToSystem ( self.setUpFile )
elif self.setUpType == "MOL2" : system = MOL2File_ToSystem ( self.setUpFile )
if self.xyzFile is not None: system.coordinates3 = XYZFile_ToCoordinates3 ( self.xyzFile )
if self.mmModel is not None: system.DefineMMModel ( self.mmModel )
if self.hasSymmetry: system.DefineSymmetry ( crystalClass = CrystalClassCubic ( ), a = self.a )
system.label = self.label
system.Summary ( log = log )
return system
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
# Example script
from pCore import logFile
from pBabel import CHARMMParameterFiles_ToParameters, CHARMMPSFFile_ToSystem, CHARMMCRDFile_ToCoordinates3
from ContinuumElectrostatics import MEADModel, MEADSubstate, StateVector, TitrationCurves, MCModelDefault, MCModelGMCT
parameters = ["toppar/par_all27_prot_na.inp", ]
mol = CHARMMPSFFile_ToSystem ("defensin_xplor.psf", isXPLOR=True, parameters=CHARMMParameterFiles_ToParameters (parameters))
mol.coordinates3 = CHARMMCRDFile_ToCoordinates3 ("defensin.crd")
electrostaticModel = MEADModel (system=mol, pathMEAD="/home/mikolaj/local/bin/", pathScratch="mead", nthreads=1)
electrostaticModel.Initialize ()
electrostaticModel.Summary ()
electrostaticModel.SummarySites ()
electrostaticModel.WriteJobFiles ()
electrostaticModel.CalculateElectrostaticEnergies ()
sites = (
("PRTA", "ASP" , 2),
("PRTA", "GLU", 14),
("PRTA", "ARG", 15), )
mcModelGMCT = MCModelGMCT (pathGMCT="/home/mikolaj/local/bin/")
mcModelDefault = MCModelDefault ()
for mcModel, folded, direc, message, sedFile, substateFile in (
(None , True , "curves_analytic" , "analytically" , "prob_ph7_analytic.sed" , "substate_ph7_analytic.tex" ),
(mcModelGMCT , True , "curves_gmct" , "using GMCT" , "prob_ph7_gmct.sed" , "substate_ph7_gmct.tex" ),
pcetk_root = os.path.join(os.environ["HOME"], "devel", "pcetk_testing")
sys.path.append(pcetk_root)
os.environ["PDYNAMO_PCETK"] = pcetk_root
#-------------------------------------------------------------------------------
from pBabel import CHARMMParameterFiles_ToParameters, CHARMMPSFFile_ToSystem, CHARMMCRDFile_ToCoordinates3
from ContinuumElectrostatics import MEADModel, MCModelDefault, TitrationCurves, StateVector
parameters = [
"toppar/par_all27_prot_na.inp",
]
mol = CHARMMPSFFile_ToSystem(
"setup/lysozyme1977_xplor.psf",
isXPLOR=True,
parameters=CHARMMParameterFiles_ToParameters(parameters))
mol.coordinates3 = CHARMMCRDFile_ToCoordinates3("setup/lysozyme1977.crd")
cem = MEADModel(system=mol,
pathMEAD="/home/mikolaj/local/bin/",
pathScratch="mead",
nthreads=1)
exclusions = (
("PRTA", "CYS", 6),
("PRTA", "CYS", 127),
("PRTA", "CYS", 30),
("PRTA", "CYS", 115),
("PRTA", "CYS", 64),
("PRTA", "CYS", 80),
"""Example: Protonation states in IFP2.0."""
from pBabel import CHARMMParameterFiles_ToParameters, CHARMMPSFFile_ToSystem, CHARMMCRDFile_ToCoordinates3
from ContinuumElectrostatics import MEADModel, MEADSubstate, MCModelDefault, TitrationCurves
parameters = ("toppar/par_all27_prot_na.inp", "toppar/blf.inp")
mol = CHARMMPSFFile_ToSystem(
"setup/ifp20_xplor_separated.psf",
isXPLOR=True,
parameters=CHARMMParameterFiles_ToParameters(parameters))
mol.coordinates3 = CHARMMCRDFile_ToCoordinates3("setup/ifp20.crd")
mol.Summary()
mead = MEADModel(system=mol,
pathMEAD="/home/mikolaj/local/bin/",
pathScratch="mead",
nthreads=1)
mead.Initialize(excludeResidues=(("PRTA", "CYS", 24), ))
mead.Summary()
mead.WriteJobFiles()
mead.CalculateElectrostaticEnergies(calculateETA=False)
sampling = MCModelDefault()
mead.DefineMCModel(sampling)
tc = TitrationCurves(mead)
tc.CalculateCurves()
tc.WriteCurves(directory="curves")
),
(
"new",
"setup/2LZT/lysozyme1990_xplor.psf",
"setup/2LZT/lysozyme1990.crd",
"mead/2LZT",
"curves/2LZT",
"New lysozyme",
),
):
logFile.Text("\n*** Now calculating: %s ***\n" % message)
protein = CHARMMPSFFile_ToSystem(
proteinPsf,
isXPLOR=True,
parameters=CHARMMParameterFiles_ToParameters(parameters),
)
protein.coordinates3 = CHARMMCRDFile_ToCoordinates3(proteinCrd)
model = MEADModel(
system=protein,
pathMEAD="/home/mikolaj/local/bin/",
pathScratch=meadDir,
nthreads=1,
)
model.Initialize(excludeResidues=exclusions, includeTermini=True)
model.Summary()
model.SummarySites()
model.WriteJobFiles()
model.CalculateElectrostaticEnergies()
MEADModel,
StateVector,
MCModelDefault,
TitrationCurves,
)
logFile.Header(
"Calculate protonation states of two titratable sites in a hypothetical peptide."
)
parameters = [
"charmm/toppar/par_all27_prot_na.inp",
]
mol = CHARMMPSFFile_ToSystem(
"charmm/testpeptide_xplor.psf",
isXPLOR=True,
parameters=CHARMMParameterFiles_ToParameters(parameters),
)
mol.coordinates3 = CHARMMCRDFile_ToCoordinates3("charmm/testpeptide.crd")
cem = MEADModel(system=mol,
pathMEAD="/home/mikolaj/local/bin/",
pathScratch="mead",
nthreads=1)
cem.Initialize()
cem.Summary()
cem.SummarySites()
cem.WriteJobFiles()
cem.CalculateElectrostaticEnergies()
logFile.Text(
def runTest(self):
"""The test."""
# . Initialization.
if self.generateReferenceData:
referenceData = TestDataSet("Charmm Test")
else:
observed = {}
# . Output setup.
dataPath = os.path.join(os.getenv("PDYNAMO_PBABEL"), "data", "charmm")
outPath = None
if self.resultPath is not None:
outPath = os.path.join(self.resultPath, "pdb")
if not os.path.exists(outPath): os.mkdir(outPath)
log = self.GetLog()
# . Get the parameters.
parameterPaths = []
for parameterPath in _ParameterPaths:
parameterPaths.append(
os.path.join(dataPath, parameterPath + ".prm"))
parameters = CHARMMParameterFiles_ToParameters(parameterPaths, log=log)
# . Generate systems.
for label in _SystemLabels:
if log is not None:
log.Text("\n" + (80 * "=") + "\n")
log.Text(label + "\n")
log.Text(80 * "=" + "\n")
system = CHARMMPSFFile_ToSystem(os.path.join(
dataPath, label + ".psfx"),
isXPLOR=True,
parameters=parameters,
log=log)
system.coordinates3 = CHARMMCRDFile_ToCoordinates3(os.path.join(
dataPath, label + ".chm"),
log=log)
system.label = label
system.DefineNBModel(NBModelFull())
system.Summary(log=log)
energy = system.Energy(log=log)
log.Text("\nEnergy (kcal/mole) = {:.4f}\n".format(
energy /
UNITS_ENERGY_KILOCALORIES_PER_MOLE_TO_KILOJOULES_PER_MOLE))
# . Get the dictionary of energies.
localObserved = system.configuration.energyTerms.Terms(
asDictionary=True)
localObserved["Potential Energy"] = energy
# . Test gradients.
if len(system.atoms) <= _MaximumAtoms:
of = SystemGeometryObjectiveFunction.FromSystem(system)
of.TestGradients(log=log)
localObserved["Gradient Error"] = of.TestGradients(log=log)
# . Write PDB file and do various sequence tests.
if not self.generateReferenceData:
if outPath is not None:
PDBFile_FromSystem(os.path.join(outPath, label + ".pdb"),
system,
useSegmentEntityLabels=True)
system.sequence.PrintComponentSequence(log=log)
log.Text("\nSelections:\n\n")
for pattern in _Patterns[label]:
log.Text("{:<30s} {:5d}\n".format(
pattern,
len(AtomSelection.FromAtomPattern(system, pattern))))
# . Generate reference data.
if self.generateReferenceData:
localData = TestDataSet(label, parent=referenceData)
for (key, value) in localObserved.iteritems():
if key == "Gradient Error":
localData.AddDatum(
TestReal(key,
value,
localData,
absoluteErrorTolerance=
_GradientAbsoluteErrorTolerance))
else:
localData.AddDatum(
TestReal(
key,
value,
localData,
absoluteErrorTolerance=_AbsoluteErrorTolerance,
toleranceFormat="{:.3f}",
valueFormat="{:.3f}"))
referenceData.AddDatum(localData)
# . Accumulate observed data.
else:
observed[label] = localObserved
# . Generate the reference data.
if self.generateReferenceData:
referenceData.Summary(log=log)
Pickle(self.referenceDataPath, referenceData)
isOK = True
# . Verify the observed data against the reference data.
else:
referenceData = Unpickle(self.referenceDataPath)
results = referenceData.VerifyAgainst(observed)
results.Summary(log=log, fullSummary=self.fullVerificationSummary)
isOK = results.WasSuccessful()
# . Success/failure.
self.assertTrue(isOK)
from pCore import logFile
from pBabel import CHARMMParameterFiles_ToParameters, CHARMMPSFFile_ToSystem, XYZFile_ToCoordinates3, XYZFile_FromSystem
from XTCTrajectory import XTCTrajectoryFileReader, XTCTrajectory_ToSystemGeometryTrajectory
import os
#===========================================================
logFile.Header("Infrared fluorescent protein (parent)")
parameters = (
"par_all27_prot_na.inp",
"par.inp",
)
mol = CHARMMPSFFile_ToSystem(
"parent_waterbox.psf",
isXPLOR=True,
parameters=CHARMMParameterFiles_ToParameters(parameters))
mol.coordinates3 = XYZFile_ToCoordinates3("geometry.xyz")
mol.Summary()
trajectory = XTCTrajectoryFileReader("heat.xtc", mol)
trajectory.Summary()
while trajectory.RestoreOwnerData():
logFile.Text("Frame count: %d\n" % trajectory.currentFrame)
XYZFile_FromSystem("sav%03d.xyz" % trajectory.currentFrame, mol)
trajectory.Summary()
#===========================================================
# This part takes a bit more time to execute, uncomment if you like