def runTest ( self ):
"""The test."""
# . Initialization.
log = self.GetLog ( )
# . Set up the generators.
_NVALUES = 11
generators = [ ( "Direct" , PairListGenerator ( minimumPoints = 100000 ) ) ]
for i in range ( _NVALUES ):
s = float ( i + 1 ) * 0.25
generators.append ( ( "CC {:6.3f}".format ( s ), PairListGenerator ( cutoffCellSizeFactor = s, minimumCellExtent = 0, minimumPoints = 100, sortIndices = False, useGridByCell = True ) ) )
for i in range ( _NVALUES ):
s = float ( i + 1 ) * 0.25
generators.append ( ( "PC {:6.3f}".format ( s ), PairListGenerator ( cutoffCellSizeFactor = s, minimumCellExtent = 0, minimumPoints = 100, sortIndices = False, useGridByCell = False ) ) )
# . Loop over test systems.
numberEnergyFailures = 0
for testSystem in testSystems:
# . Get the system.
system = testSystem.GetSystem ( log = log )
# . Energies.
energies = []
for ( label, generator ) in generators:
nbModel = NBModelABFS ( generator = generator )
nbModel.Summary ( log = log )
system.DefineNBModel ( nbModel )
cpuTime = CPUTime ( )
e = system.Energy ( doGradients = True, log = log )
c = cpuTime.CurrentAsString ( )
energies.append ( ( e, c, label ) )
system.configuration.nbState.StatisticsSummary ( log = log )
# . Print summary of results.
if log is not None:
e0 = energies[0][0]
n = 0
table = log.GetTable ( columns = [ 6, 10, 16, 16, 16, 20 ] )
table.Start ( )
table.Title ( "Energies and CPU Times for {:s}:".format ( system.label ) )
for ( i, ( e, c, l ) ) in enumerate ( energies ):
deltaE = math.fabs ( e - e0 )
if deltaE > 1.0e-2: n += 1
table.Entry ( "{:d}".format ( i ) )
table.Entry ( l )
table.Entry ( "{:15.3f}".format ( e ) )
table.Entry ( "{:15.3f}".format ( e0 ) )
table.Entry ( "{:15.3f}".format ( deltaE ) )
table.Entry ( " {:s}".format ( c ) )
table.Stop ( )
if log is not None:
if n == 0: log.Paragraph ( "All tests were successful." )
else: log.Paragraph ( "{:d} tests failed.".format ( n ) )
numberEnergyFailures += n
# . Check for success/failure.
self.assertTrue ( ( numberEnergyFailures == 0 ) )
def __init__ ( self, **kwargs ):
"""Constructor."""
for ( attribute, value ) in kwargs.iteritems ( ):
setattr ( self, attribute, value )
self.mmModel = MMModelOPLS ( )
self.nbModel = NBModelABFS ( )
self.p1Factor = 1.0
def runTest(self):
"""The test."""
# . Initialization.
isOK = True
numberErrors = 0
# . Energy models.
mmModel = MMModelOPLS("protein")
nbModel = NBModelABFS()
# . Paths.
dataPath = os.path.join(os.getenv("PDYNAMO_PBABEL"), "data")
modelPath = os.path.join(dataPath, "pdbModel")
pdbPath = os.path.join(dataPath, "pdb")
outPath = None
if self.resultPath is not None:
outPath = os.path.join(self.resultPath, "xyz")
log = self.GetLog()
# . Set up the output directory.
if outPath is not None:
if not os.path.exists(outPath): os.mkdir(outPath)
outFiles = glob.glob(os.path.join(outPath, "*.xyz"))
for outFile in outFiles:
os.remove(outFile)
# . Get the files to process.
modelFiles = glob.glob(os.path.join(modelPath, "*.model"))
# . Get the model file names.
pdbNames = set()
for modelFile in modelFiles:
(head, tail) = os.path.split(modelFile)
pdbNames.add(tail[0:-6])
pdbNames = list(pdbNames)
pdbNames.sort()
# . Loop over the files.
for pdbName in pdbNames:
# . Check file names.
modelFile = os.path.join(modelPath, pdbName + ".model")
pdbFile = os.path.join(pdbPath, pdbName + ".pdb")
if os.path.exists(modelFile) and os.path.exists(pdbFile):
# . Get the model and its raw counterpart.
model1 = PDBModel_FromModelFile(modelFile, log=log)
rawModel = PDBFile_ToPDBModel(pdbFile, log=log)
# . Route 1 - make an atomic model.
model1.Summary(log=log)
try:
# . Make the atomic model.
model1.MakeAtomicModelFromComponentLibrary(log=log)
model1.ExtractAtomData(rawModel, log=log)
model1.Summary(log=log)
# . Make a system.
system1 = model1.MakeSystem()
system1.Summary(log=log)
# . Add energy models.
system1.DefineMMModel(mmModel, log=log)
system1.DefineNBModel(nbModel)
# . Build as many undefined coordinates as possible.
if system1.coordinates3.numberUndefined > 0:
rng = RandomNumberGenerator.WithSeed(117513)
BuildHydrogenCoordinates3FromConnectivity(
system1, log=log, randomNumberGenerator=rng)
# . Calculate an energy if all coordinates have been defined.
if system1.coordinates3.numberUndefined <= 0:
system1.Energy(log=log, doGradients=True)
# . Error.
except Exception as e:
numberErrors += 1
if log is not None:
log.Text("\nError occurred> " + e.args[0] + "\n")
# . Route 2 - extract atoms.
model2 = PDBModel_FromModelFile(modelFile, log=log)
model2.ExtractAtoms(rawModel, log=log)
model2.Summary(log=log)
system2 = model2.MakeSystem()
system2.Summary(log=log)
# . Output the xyz file if there are no undefined coordinates.
n = system2.coordinates3.numberUndefined
if n > 0:
if log is not None:
log.Paragraph(
"System has {:d} undefined coordinates.".format(n))
elif outPath is not None:
XYZFile_FromSystem(os.path.join(outPath, pdbName + ".xyz"),
system2)
# . Separator.
if log is not None: log.Separator()
# . Success/failure.
self.assertTrue(isOK and (numberErrors == 0))
def runTest(self):
"""The test."""
# . Paths.
dataPath = os.path.join(os.getenv("PDYNAMO_PMOLECULE"), "data", "pdb")
log = self.GetLog()
# . Models.
mmModel = MMModelOPLS("protein")
nbModel = NBModelABFS()
# . Get all files.
pdbFiles = glob.glob(os.path.join(dataPath, "*.pdb"))
pdbFiles.sort()
# . Read all PDB files.
numberFailed = 0
for pdbFile in pdbFiles:
if log is not None: log.Text("\nProcessing " + pdbFile + ":\n")
system = PDBFile_ToSystem(pdbFile,
log=log,
useComponentLibrary=True)
BuildHydrogenCoordinates3FromConnectivity(system)
try:
# . Setup.
if system.coordinates3.numberUndefined > 0: raise
system.DefineMMModel(mmModel, log=log)
system.DefineNBModel(nbModel)
system.Summary(log=log)
system.Energy(log=log, doGradients=True)
# . Selection.
selector = SQLAtomSelector(system)
# . Standard selections.
aromatics = selector.aromatics
backbone = selector.backbone
boundaryAtoms = selector.boundaryAtoms
counterions = selector.counterions
heavyAtoms = selector.heavyAtoms
hydrogens = selector.hydrogens
mmAtoms = selector.mmAtoms
polymerAtoms1 = selector.linearPolymerAtoms
protein = selector.protein
qcAtoms = selector.qcAtoms
ringAtoms = selector.ringAtoms
water = selector.water
# . Where selections.
nearOrigin1 = selector.Where("X*X + Y*Y + Z*Z < 25.0")
positive = selector.Where("Charge > 0.0")
threonines1 = selector.Where("Path LIKE '%:THR.%:%'")
threonines2 = selector.Where("ResNam='THR'")
# . Atom selection methods.
nearOrigin2 = nearOrigin1.Within(5.0).ByComponent()
polymerAtoms2 = threonines1.ByLinearPolymer()
neighbors = threonines1.ByBondedNeighbor(iterations=3)
# . Atom selection operators.
complementNearOrigin2 = ~nearOrigin2
null = (nearOrigin2 & complementNearOrigin2)
total1 = (nearOrigin2 | complementNearOrigin2)
total2 = (nearOrigin2 ^ complementNearOrigin2)
# . Basic checks.
n = len(system.atoms)
isOK = ( len ( boundaryAtoms ) == 0 ) and \
( len ( qcAtoms ) == 0 ) and \
( len ( mmAtoms ) == n ) and \
( len ( heavyAtoms ) + len ( hydrogens ) == n ) and \
( len ( polymerAtoms1 ) == len ( polymerAtoms2 ) ) and \
( len ( counterions ) + len ( protein ) + len ( water ) == n ) and \
( len ( threonines1 ) == len ( threonines2 ) ) and \
( len ( null ) == 0 ) and \
( len ( total1 ) == len ( total2 ) ) and \
( len ( total1 ) == n )
if not isOK: raise
except Exception as e:
numberFailed += 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("SQL Atom Selection Tests")
summary.Entry("Successes",
"{:d}".format(len(pdbFiles) - numberFailed))
summary.Entry("Failures", "{:d}".format(numberFailed))
summary.Stop()
# . Success/failure.
self.assertTrue((numberFailed == 0))
from pCore import Selection, Pickle, Unpickle
from pMolecule import NBModelABFS
from pMoleculeScripts import BuildHydrogenCoordinates3FromConnectivity
# . Define the atoms IDs and the parameters.
_ToBuild = ( ( "A:LYS.8:CB" , "A:LYS.8:CA" , "A:LYS.8:N" , "A:LYS.8:CG" , 1.54, 109.5, 0.0 ), \
( "I:SER.17:OG", "I:SER.17:CB", "I:SER.17:CA", "A:ATP.400:PG", 1.40, 109.5, 0.0 ) )
# . Get the system.
system = Unpickle ( os.path.join ( outPath, "step4.pkl" ) )
system.Summary ( )
# . Build the coordinates of the missing heavy atoms.
for ( id1, id2, id3, id4, r, theta, phi ) in _ToBuild:
i = system.sequence.AtomIndex ( id1 )
j = system.sequence.AtomIndex ( id2 )
k = system.sequence.AtomIndex ( id3 )
l = system.sequence.AtomIndex ( id4 )
system.coordinates3.BuildPointFromDistanceAngleDihedral ( i, j, k, l, r, theta, phi )
# . Build the hydrogen atom coordinates.
BuildHydrogenCoordinates3FromConnectivity ( system )
# . Save the system.
Pickle ( os.path.join ( outPath, "step6.pkl" ), system )
# . Calculate an energy if all atoms now have coordinates.
if system.coordinates3.numberUndefined <= 0:
system.DefineNBModel ( NBModelABFS ( ) )
system.Energy ( doGradients = True )
sys.path.append ( os.path.join ( os.path.dirname ( os.path.realpath ( __file__ ) ), "..", "data" ) ) from Definitions import outPath from pBabel import PDBFile_FromSystem from pCore import Clone, NormalDeviateGenerator, Pickle, RandomNumberGenerator, Selection, Unpickle from pMolecule import AtomSelection, MMModelOPLS, NBModelABFS, SoftConstraintContainer, SoftConstraintEnergyModelHarmonic, SoftConstraintMultipleTether from pMoleculeScripts import ConjugateGradientMinimize_SystemGeometry, LangevinDynamics_SystemGeometry, SolvateSystemBySuperposition # . Parameters. # . Refine options. _Optimize = True _Refine = True _Steps = 2000 # . Define the MM and NB models. nbModel = NBModelABFS ( ) # . Get the solute system. solute = Unpickle ( os.path.join ( outPath, "step8_a.pkl" ) ) solute.Summary ( ) # . Get the solvent system. solvent = Unpickle ( os.path.join ( outPath, "waterBox.pkl" ) ) solvent.DefineNBModel ( nbModel ) solvent.Summary ( ) # . Create the solvated system. solution = SolvateSystemBySuperposition ( solute, solvent, reorientSolute = False ) solution.label = "Solvated PKA Simulation System - Chains A and I Only" solution.DefineNBModel ( nbModel ) solution.Summary ( )
def runTest ( self ):
"""The test."""
# . 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" )
# mmModel = MMModelOPLS ( "protein" )
nbModel = NBModelABFS ( )
# . Get all files.
pdbFiles = glob.glob ( os.path.join ( dataPath, "*.pdb" ) )
pdbFiles.sort ( )
# . Read all PDB files.
failures = 0
otherFailures = 0
successes = 0
for pdbFile in pdbFiles:
( 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 )
BuildHydrogenCoordinates3FromConnectivity ( system )
try:
# . Setup.
if system.coordinates3.numberUndefined > 0: raise
system.DefineMMModel ( mmModel, log = log )
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" , "{:d}".format ( 2 * len ( pdbFiles ) ) )
summary.Entry ( "Loop Failures" , "{:d}".format ( otherFailures ) )
summary.Stop ( )
# . Success/failure.
self.assertTrue ( ( failures == 0 ) and ( otherFailures == 0 ) )
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 runTest(self):
"""The test."""
# . Initialization.
observed = {}
gromacsReference = True
# . We have two references: One for energies obtained with Gromacs; another for pDynamo energies
if gromacsReference:
referenceDataPath = os.path.join(
os.getenv("PDYNAMO_PBABEL"), "data",
"reference/GromacsTopCrdRead_gromacsValues.pkl")
else:
referenceDataPath = os.path.join(
os.getenv("PDYNAMO_PBABEL"), "data",
"reference/GromacsTopCrdRead_pDynamoValues.pkl")
# . Output setup.
dataPath = os.path.join(os.getenv("PDYNAMO_PBABEL"), "data", "gromacs")
outPath = None
self.resultPath = dataPath
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()
# . Generate systems.
for label in _SystemLabels:
# . Force field.
for ff in _ForceFields:
# . Header.
if log is not None:
log.Text("\n" + (120 * "=") + "\n")
log.Text(label + "-" + ff + "\n")
log.Text(120 * "=" + "\n")
# . Get the parameters.
filename = os.path.join(dataPath, label + "_" + ff)
parameters = GromacsParameters_ToParameters(filename + ".top",
log=log)
system = GromacsDefinitions_ToSystem(filename + ".top",
parameters=parameters,
log=log)
system.coordinates3 = GromacsCrdFile_ToCoordinates3(filename +
".gro",
log=log)
system.label = label
if hasattr(system.configuration, "symmetryParameters"):
system.DefineNBModel(NBModelABFS(**ABFS_options))
else:
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
# . U-B term in Gromacs includes harmonic angle contribution, but not in pDynamo. Their sum should be equal, though.
if gromacsReference and (ff == "CHARMM"):
localObserved["Harmonic Angle + U-B"] = localObserved[
"Harmonic Angle"] + localObserved["Urey-Bradley"]
del localObserved["Harmonic Angle"]
del localObserved["Urey-Bradley"]
# . 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
if outPath is not None:
PDBFile_FromSystem(os.path.join(outPath, label + ".pdb"),
system)
# . Accumulate current data
dataLabel = label + "-" + ff
observed[dataLabel] = localObserved
# . Verify the observed data against the reference data.
referenceData = Unpickle(referenceDataPath)
results = referenceData.VerifyAgainst(observed)
isOK = results.WasSuccessful()
results.Summary(log=log, fullSummary=True)
# . Success/failure.
self.assertTrue(isOK)
#===========================================================
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()
nb_model = NBModelABFS()
mol.DefineNBModel(nb_model)
#===========================================================
# traj = XTCTrajectoryFileWriter ("saved_geometry.xtc", mol)
# traj.WriteOwnerData ()
# traj.Summary ()
#===========================================================
traj3 = XTCTrajectoryFileWriter("optimize.xtc", mol)
ConjugateGradientMinimize_SystemGeometry(mol,
logFrequency=1,
maximumIterations=50,
rmsGradientTolerance=0.04,
trajectories=[(traj3, 1)])
traj3.Summary()
def runTest ( self ):
"""The test."""
# . Paths.
dataPath = os.path.join ( os.getenv ( "PDYNAMO_PMOLECULE" ), "data", "mol2" )
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 ( )
# . NB models.
nbModelNoC = NBModelABFS ( useCentering = False )
nbModelC = NBModelABFS ( useCentering = True )
# . Set up the system.
system = ImportSystem ( os.path.join ( dataPath, "waterBox.mol2" ), log = log )
system.DefineMMModel ( MMModelOPLS ( "bookSmallExamples" ) )
system.DefineNBModel ( nbModelC )
system.Summary ( log = log )
system.Energy ( log = log )
# . Do a short dynamics.
# . Define a normal deviate generator in a given state.
normalDeviateGenerator = NormalDeviateGenerator.WithRandomNumberGenerator ( RandomNumberGenerator.WithSeed ( 614108 ) )
# . Dynamics.
trajectoryPath = os.path.join ( outPath, "waterBox_C_1ps.dcd" )
trajectory = DCDTrajectoryFileWriter ( trajectoryPath, system )
LangevinDynamics_SystemGeometry ( system ,
collisionFrequency = 25.0 ,
log = log ,
logFrequency = _NLog ,
normalDeviateGenerator = normalDeviateGenerator ,
steps = _NSteps ,
temperature = 300.0 ,
timeStep = 0.001 ,
trajectories = [ ( trajectory, _NSave ) ] )
# . Calculate trajectory energies with different NB models.
energies = []
for ( i, nbModel ) in enumerate ( ( nbModelC, nbModelNoC ) ):
system.DefineNBModel ( nbModel )
trajectory = DCDTrajectoryFileReader ( trajectoryPath, system )
trajectory.ReadHeader ( )
e = []
while trajectory.RestoreOwnerData ( ):
e.append ( system.Energy ( log = None ) )
trajectory.Close ( )
energies.append ( e )
# . Check deviations.
( e0, e1 ) = energies
maximumDeviation = 0.0
for i in range ( len ( e0 ) ):
maximumDeviation = max ( maximumDeviation, math.fabs ( e0[i] - e1[i] ) )
# . Summary of results.
if log is not None:
log.Paragraph ( "Maximum deviation = {:.5f}".format ( maximumDeviation ) )
# . Success/failure.
self.assertTrue ( ( maximumDeviation <= _Tolerance ) )