q /= float ( len ( self.charge ) )
for i in range ( len ( self.charge ) ): self.charge[i] -= q
# . Units.
for i in range ( len ( self.bond_force_constant ) ): self.bond_force_constant[i] *= UNITS_ENERGY_KILOCALORIES_PER_MOLE_TO_KILOJOULES_PER_MOLE
for i in range ( len ( self.angle_force_constant ) ): self.angle_force_constant[i] *= UNITS_ENERGY_KILOCALORIES_PER_MOLE_TO_KILOJOULES_PER_MOLE
for i in range ( len ( self.dihedral_force_constant ) ): self.dihedral_force_constant[i] *= UNITS_ENERGY_KILOCALORIES_PER_MOLE_TO_KILOJOULES_PER_MOLE
for i in range ( len ( self.lennard_jones_acoef ) ): self.lennard_jones_acoef[i] *= UNITS_ENERGY_KILOCALORIES_PER_MOLE_TO_KILOJOULES_PER_MOLE
for i in range ( len ( self.lennard_jones_bcoef ) ): self.lennard_jones_bcoef[i] *= UNITS_ENERGY_KILOCALORIES_PER_MOLE_TO_KILOJOULES_PER_MOLE
self.QVERIFIED = True
#===================================================================================================================================
# . Helper functions.
#===================================================================================================================================
def AmberTopologyFile_ToSystem ( filename, log = logFile, mmModel = None ):
"""Helper function that reads a system from an Amber Topology file."""
infile = AmberTopologyFileReader ( filename )
infile.Parse ( log = log )
infile.Verify ( )
infile.Summary ( log = log )
system = infile.ToSystem ( mmModel = mmModel )
return system
# . Importer definitions.
_Importer.AddHandler ( { System : AmberTopologyFile_ToSystem } , [ "top", "TOP" ], "Amber Topology", defaultFunction = AmberTopologyFile_ToSystem )
#===================================================================================================================================
# . Test.
#===================================================================================================================================
if __name__ == "__main__":
pass
return infile.ToCoordinates3()
def GromacsCrdFile_ToCoordinates3(filename, log=logFile):
"""Helper function that returns a set of coordinates from a Gromacs .gro file."""
infile = GromacsCrdFileReader(filename)
infile.Parse(log=log)
infile.Summary(log=log)
return infile.ToCoordinates3()
def GromacsCrdFile_ToSymmetry(filename, log=logFile):
"""Helper function that reads symmetryparamters from a Gromacs .gro file."""
infile = GromacsCrdFileReader(filename)
infile.Parse(log=log)
infile.Summary(log=log)
return infile.ToSymmetryParameters()
# . Importer definitions.
_Importer.AddHandler({Coordinates3: GromacsCrdFile_ToCoordinates3},
["gro", "GRO"],
"Gromacs Coordinates",
defaultFunction=GromacsCrdFile_ToCoordinates3)
#===================================================================================================================================
# . Testing.
#===================================================================================================================================
if __name__ == "__main__":
pass
def MOL2File_ToCoordinates3(filename, log=logFile):
"""Helper function that reads coordinates from a MOL2 file."""
infile = MOL2FileReader(filename)
infile.Parse(log=log)
coordinates3 = infile.ToCoordinates3()
return coordinates3
def MOL2File_ToSystem(filename, log=logFile):
"""Helper function that reads a system from a MOL2 file."""
infile = MOL2FileReader(filename)
infile.Parse(log=log)
system = infile.ToSystem()
return system
# . Importer definitions.
_Importer.AddHandler(
{
Coordinates3: MOL2File_ToCoordinates3,
System: MOL2File_ToSystem
}, ["mol2", "MOL2"],
"Tripos MOL2",
defaultFunction=MOL2File_ToSystem)
#===================================================================================================================================
# . Testing.
#===================================================================================================================================
if __name__ == "__main__":
pass
def JaguarOutputFile_ToCoordinates3(filename):
"""Helper function that reads the coordinates from a Jaguar output file."""
outfile = JaguarOutputFileReader(filename)
outfile.Parse()
coordinates3 = outfile.ToCoordinates3()
return coordinates3
def JaguarOutputFile_ToSystem(filename):
"""Helper function that reads a system from a Jaguar outputfile."""
outfile = JaguarOutputFileReader(filename)
outfile.Parse()
system = outfile.ToSystem()
return system
# . Importer definitions.
_Importer.AddHandler(
{
Coordinates3: JaguarOutputFile_ToCoordinates3,
System: JaguarOutputFile_ToSystem
}, ["jagout", "jout", "JAGOUT", "JOUT"],
"Jaguar Output",
defaultFunction=JaguarOutputFile_ToSystem)
#===================================================================================================================================
# . Test.
#===================================================================================================================================
if __name__ == "__main__":
pass
log=logFile,
useComponentLibrary=False):
"""Helper function that returns a system defined by the atom data in a whitespace-delimited PQR file."""
return PDBFile_ToSystem(fileName,
embeddedHydrogens=embeddedHydrogens,
libraryPaths=libraryPaths,
log=log,
pqrFormat=True,
useComponentLibrary=useComponentLibrary)
# . Importer definitions.
_Importer.AddHandler(
{
Coordinates3: PDBFile_ToCoordinates3,
PDBModel: PDBFile_ToPDBModel,
System: PDBFile_ToSystem
}, ["ent", "ENT", "pdb", "PDB"],
"Protein Data Bank",
defaultFunction=PDBFile_ToSystem)
_Importer.AddHandler(
{
Coordinates3: PQRFile_ToCoordinates3,
System: PQRFile_ToSystem
}, ["pqr", "PQR"],
"PQR",
defaultFunction=PQRFile_ToSystem)
#==================================================================================================================================
# . Test.
#==================================================================================================================================
if __name__ == "__main__":
infile = MOLFileReader(filename)
infile.Parse(log=log)
system = infile.ToSystem(index=index)
return system
def SDFFile_ToSystems(filename, log=logFile):
"""Helper function that reads all the systems from an SDF file."""
infile = MOLFileReader(filename)
infile.Parse(log=log)
systems = []
for i in range(len(infile.molrecords)):
systems.append(infile.ToSystem(index=i))
return systems
# . Importer definitions.
_Importer.AddHandler(
{
Coordinates3: MOLFile_ToCoordinates3,
System: MOLFile_ToSystem
}, ["mol", "MOL"],
"MDL MOL",
defaultFunction=MOLFile_ToSystem)
#===================================================================================================================================
# . Testing.
#===================================================================================================================================
if __name__ == "__main__":
pass
infile = GaussianCubeFileReader(path)
infile.Parse(log=log)
system = infile.ToCoordinates3()
return system
def GaussianCubeFile_ToSystem(path, log=logFile, volumetricdata=None):
"""Helper function that reads a system from a Gaussian cube file."""
infile = GaussianCubeFileReader(path)
infile.Parse(log=log)
system = infile.ToSystem()
if volumetricdata is not None:
volumetricdata.update(infile.ToVolumetricData())
return system
# . Importer definitions.
_Importer.AddHandler(
{
Coordinates3: GaussianCubeFile_ToCoordinates3,
System: GaussianCubeFile_ToSystem
}, ["cub", "CUB", "cube", "CUBE"],
"Gaussian Cube File",
defaultFunction=GaussianCubeFile_ToSystem)
#===================================================================================================================================
# . Test.
#===================================================================================================================================
if __name__ == "__main__":
pass
def ToPolygonalSurface(self):
"""Return a polygonal surface."""
surface = None
if self.QPARSED: surface = self.surface
return surface
#===================================================================================================================================
# . Helper functions.
#===================================================================================================================================
def OOGLOffFile_ToPolygonalSurface(path, log=logFile):
"""Helper function that reads a surface from an OOGL Off file."""
infile = OOGLOffFileReader(path)
infile.Parse()
surface = infile.ToPolygonalSurface()
return surface
# . Importer definitions.
_Importer.AddHandler({PolygonalSurface: OOGLOffFile_ToPolygonalSurface},
["off", "oogloff"],
"OOGL Off",
defaultFunction=OOGLOffFile_ToPolygonalSurface)
#===================================================================================================================================
# . Testing.
#===================================================================================================================================
if __name__ == "__main__":
pass
def ORCAOutputFile_ToCoordinates3(filename, frameIndex=-1):
"""Helper function that reads the coordinates from an ORCA output file."""
infile = ORCAOutputFileReader(filename)
infile.Parse()
return infile.ToCoordinates3(frameIndex=frameIndex)
def ORCAOutputFile_ToSystem(filename, frameIndex=-1):
"""Helper function that reads a system from an ORCA output file."""
infile = ORCAOutputFileReader(filename)
infile.Parse()
return infile.ToSystem(frameIndex=frameIndex)
# . Importer definitions.
_Importer.AddHandler(
{
Coordinates3: ORCAOutputFile_ToCoordinates3,
System: ORCAOutputFile_ToSystem
}, ["olog", "oout", "OLOG", "OOUT"],
"ORCA Output",
defaultFunction=ORCAOutputFile_ToSystem)
#===================================================================================================================================
# . Testing.
#===================================================================================================================================
if __name__ == "__main__":
pass
#===================================================================================================================================
# . Helper functions.
#===================================================================================================================================
def AmberCrdFile_ToCoordinates3(filename, log=logFile):
"""Helper function that reads coordinates from an Amber crd file."""
infile = AmberCrdFileReader(filename)
infile.Parse(log=log)
infile.Summary(log=log)
return infile.ToCoordinates3()
def AmberCrdFile_ToSymmetryParameters(filename, log=logFile):
"""Helper function that reads symmetryparamters from an Amber crd file."""
infile = AmberCrdFileReader(filename)
infile.Parse(log=log)
infile.Summary(log=log)
return infile.ToSymmetryParameters()
# . Importer definitions.
_Importer.AddHandler({Coordinates3: AmberCrdFile_ToCoordinates3},
["crd", "CRD"],
"Amber Coordinates",
defaultFunction=AmberCrdFile_ToCoordinates3)
#===================================================================================================================================
# . Test.
#===================================================================================================================================
if __name__ == "__main__":
pass
def JaguarInputFile_ToCoordinates3(filename):
"""Helper function that reads the coordinates from a Jaguar input file."""
infile = JaguarInputFileReader(filename)
infile.Parse()
coordinates3 = infile.ToCoordinates3()
return coordinates3
def JaguarInputFile_ToSystem(filename, log=logFile):
"""Helper function that reads a system from a Jaguar inputfile."""
infile = JaguarInputFileReader(filename)
infile.Parse()
system = infile.ToSystem()
return system
# . Importer definitions.
_Importer.AddHandler(
{
Coordinates3: JaguarInputFile_ToCoordinates3,
System: JaguarInputFile_ToSystem
}, ["jagin", "jin", "JAGIN", "JIN"],
"Jaguar Input",
defaultFunction=JaguarInputFile_ToSystem)
#===================================================================================================================================
# . Testing.
#===================================================================================================================================
if __name__ == "__main__":
pass
def XYZFiles_ToSystemGeometryTrajectory(inPaths, outPath, system):
"""Convert XYZ files to a SystemGeometryTrajectory.
Files are added in the order that they are supplied.
"""
# . Define the output trajectory.
outTrajectory = SystemGeometryTrajectory(outPath, system, mode="w")
# . Loop over paths.
for inPath in inPaths:
system.coordinates3 = XYZFile_ToCoordinates3(inPath)
outTrajectory.WriteOwnerData()
outTrajectory.Close()
# . Importer definitions.
_Importer.AddHandler(
{
Coordinates3: XYZFile_ToCoordinates3,
System: XYZFile_ToSystem
}, ["xyz"],
"XYZ",
defaultFunction=XYZFile_ToSystem)
#===================================================================================================================================
# . Testing.
#===================================================================================================================================
if __name__ == "__main__":
pass
modelNumber=modelNumber,
embeddedHydrogens=embeddedHydrogens)
# . Print out whether there are undefined coordinates.
if LogFileActive(log) and (system.coordinates3.numberUndefined > 0):
# . Determine the types of atoms with undefined coordinates.
nheavy = 0
nhydrogen = 0
for i in system.coordinates3.undefined:
if system.atoms[i].atomicNumber == 1: nhydrogen += 1
else: nheavy += 1
# . Output a summary.
summary = log.GetSummary()
summary.Start("Undefined Coordinates")
summary.Entry("Heavy Atoms", "{:d}".format(nheavy))
summary.Entry("Hydrogens", "{:d}".format(nhydrogen))
summary.Stop()
# . Finish up.
return system
# . Importer definitions.
_Importer.AddHandler({System: mmCIFFile_ToSystem}, ["mmcif", "MMCIF"],
"Macromolecular Crystallographic Information File",
defaultFunction=mmCIFFile_ToSystem)
#===================================================================================================================================
# . Test.
#===================================================================================================================================
if __name__ == "__main__":
pass
"""Helper function that returns a set of coordinates from a CHARMM CRD file."""
infile = CHARMMCRDFileReader ( filename )
infile.Parse ( log = log )
infile.Summary ( log = log )
return infile.ToCoordinates3 ( )
def CHARMMCRDFile_ToSequence ( filename, log = logFile ):
"""Helper function that returns a sequence from a CHARMM CRD file."""
infile = CHARMMCRDFileReader ( filename )
infile.Parse ( log = log )
infile.Summary ( log = log )
return infile.ToSequence ( )
def CHARMMCRDFile_ToSystem ( filename, log = logFile ):
"""Helper function that returns a system from a CHARMM CRD file."""
infile = CHARMMCRDFileReader ( filename )
infile.Parse ( log = log )
infile.Summary ( log = log )
return infile.ToSystem ( )
# . Importer definitions.
_Importer.AddHandler ( { Coordinates3 : CHARMMCRDFile_ToCoordinates3 ,
System : CHARMMCRDFile_ToSystem } , [ "chm", "CHM" ], "Charmm Coordinates", defaultFunction = CHARMMCRDFile_ToSystem )
#===================================================================================================================================
# . Testing.
#===================================================================================================================================
if __name__ == "__main__":
pass
if not QOK:
self.Warning ( "Unable to build Cartesian coordinates from Z-matrix card number {:d}.".format ( i+1 ), True )
break
#===================================================================================================================================
# . Helper functions.
#===================================================================================================================================
def MopacInputFile_ToCoordinates3 ( filename ):
"""Helper function that reads the coordinates from a Mopac input file."""
infile = MopacInputFileReader ( filename )
infile.Parse ( )
coordinates3 = infile.ToCoordinates3 ( )
return coordinates3
def MopacInputFile_ToSystem ( filename ):
"""Helper function that reads a system from a Mopac input file."""
infile = MopacInputFileReader ( filename )
infile.Parse ( )
system = infile.ToSystem ( )
return system
# . Importer definitions.
_Importer.AddHandler ( { Coordinates3 : MopacInputFile_ToCoordinates3 ,
System : MopacInputFile_ToSystem } , [ "mopin", "MOPIN" ], "MOPAC Input", defaultFunction = MopacInputFile_ToSystem )
#===================================================================================================================================
# . Testing.
#===================================================================================================================================
if __name__ == "__main__":
pass
infile.Parse(log=log)
infile.Summary(log=log)
return infile.ToSequence()
def fDynamoCRDFile_ToSystem(fileName, log=logFile):
"""Helper function that returns a system from an fDynamo CRD file."""
# atomTranslation = kwargs.get ( "atomTranslation", {} ) # . For future use (maybe).
# residueTranslation = kwargs.get ( "residueTranslation", {} )
# subsystemTranslation = kwargs.get ( "subsystemTranslation ", {} )
infile = fDynamoCRDFileReader(fileName)
infile.Parse(log=log)
infile.Summary(log=log)
return infile.ToSystem()
# . Importer definitions.
_Importer.AddHandler(
{
Coordinates3: fDynamoCRDFile_ToCoordinates3,
System: fDynamoCRDFile_ToSystem
}, ["fcrd", "FCRD"],
"Fortran Dynamo Coordinates",
defaultFunction=fDynamoCRDFile_ToSystem)
#===================================================================================================================================
# . Testing.
#===================================================================================================================================
if __name__ == "__main__":
pass
return system
#===================================================================================================================================
# . Helper functions.
#===================================================================================================================================
def CHARMMPSFFile_ToSystem(filename,
isXPLOR=False,
log=logFile,
mmModel=None,
parameters=None):
"""Helper function that generates a system from a CHARMM PSF file."""
infile = CHARMMPSFFileReader(filename)
infile.Parse(isXPLOR=isXPLOR, log=log)
infile.Summary(log=log)
system = infile.ToSystem(mmModel=mmModel, parameters=parameters)
return system
# . Importer definitions.
_Importer.AddHandler({System: CHARMMPSFFile_ToSystem},
["psf", "psfx", "PSF", "PSFX"],
"Charmm PSF",
defaultFunction=CHARMMPSFFile_ToSystem)
#===================================================================================================================================
# . Testing.
#===================================================================================================================================
if __name__ == "__main__":
pass
#===================================================================================================================================
# . Helper functions.
#===================================================================================================================================
def CIFFile_ToSystem ( path, blockCode = None, disorderGroup = _DefaultDisorderGroup, log = logFile ):
"""Helper function that reads a system from a CIF file."""
inFile = CIFFileReader ( path )
inFile.Parse ( )
inFile.Summary ( log = log )
system = inFile.ToSystem ( blockCode = blockCode, disorderGroup = disorderGroup )
return system
def CIFFile_ToSystems ( path, disorderGroup = _DefaultDisorderGroup, log = logFile ):
"""Helper function that reads all the systems from a CIF file."""
inFile = CIFFileReader ( path )
inFile.Parse ( )
inFile.Summary ( log = log )
systems = []
for key in sorted ( inFile.dataBlocks.keys ( ) ):
systems.append ( inFile.ToSystem ( blockCode = key, disorderGroup = disorderGroup ) )
return systems
# . Importer definitions.
_Importer.AddHandler ( { System : CIFFile_ToSystem } , [ "cif", "CIF" ], "Crystallographic Information File", defaultFunction = CIFFile_ToSystem )
#===================================================================================================================================
# . Test.
#===================================================================================================================================
if __name__ == "__main__":
pass