self.file.write("* " + line + "\n")
#===================================================================================================================================
# . Helper functions.
#===================================================================================================================================
def CHARMMPSFFile_FromSystem(path,
system,
extendedFormat=True,
hasCHEQ=True,
isXPLOR=True):
"""Helper function that writes a system to a CHARMM PSF file."""
outFile = CHARMMPSFFileWriter(path)
outFile.Open()
outFile.OutputSystem(system,
extendedFormat=extendedFormat,
hasCHEQ=hasCHEQ,
isXPLOR=isXPLOR)
outFile.Close()
# . Exporter definitions.
_Exporter.AddHandler({System: CHARMMPSFFile_FromSystem},
["psf", "psfx", "PSF", "PSFX"], "Charmm PSF")
#===================================================================================================================================
# . Testing.
#===================================================================================================================================
if __name__ == "__main__":
pass
# . Number of vertices, faces and edges (latter not used).
self.file.write ( "{:d} {:d} 0\n\n".format ( surface.NumberOfVertices ( ), surface.NumberOfPolygons ( ) ) )
# . Vertices.
format = 2 * ndimensions * " {:.10f}" + "\n"
for items in surface.VertexIterator ( ):
self.file.write ( format.format ( items ) )
# . Polygons.
self.file.write ( "\n" )
format = "{:d}".format ( ndimensions ) + ndimensions * " {:d}" + "\n"
for items in surface.PolygonIndexIterator ( ):
self.file.write ( format.format ( items ) )
# . Finish up.
self.Close ( )
#===================================================================================================================================
# . Helper functions.
#===================================================================================================================================
def OOGLOffFile_FromPolygonalSurface ( path, surface, log = logFile ):
"""Helper function that writes a polygonal surface to an OOGL Off file."""
outfile = OOGLOffFileWriter ( path )
outfile.WritePolygonalSurface ( surface )
# . Exporter definitions.
_Exporter.AddHandler ( { PolygonalSurface : OOGLOffFile_FromPolygonalSurface } , [ "off", "oogloff" ], "OOGL Off" )
#===================================================================================================================================
# . Test.
#===================================================================================================================================
if __name__ == "__main__":
pass
self.file.write(_RTISTRING + "CRYSIN\n")
self.file.write(
"{:.3f} {:.3f} {:.3f} {:.1f} {:.1f} {:.1f} 1 1\n".format(
p.a, p.b, p.c, p.alpha, p.beta, p.gamma))
def WriteSingleSystem(self, system, label=None, xyz=None):
"""Write a complete file."""
self.Open()
self.WriteFrame(system, label=label, xyz=xyz)
self.Close()
#===================================================================================================================================
# . Helper functions.
#===================================================================================================================================
def MOL2File_FromSystem(filename, system, label=None, xyz=None):
"""Helper function that writes a system to a MOL2 file."""
outfile = MOL2FileWriter(filename)
outfile.WriteSingleSystem(system, label=label, xyz=xyz)
# . Exporter definitions.
_Exporter.AddHandler({System: MOL2File_FromSystem}, ["mol2", "MOL2"],
"Tripos MOL2")
#===================================================================================================================================
# . Testing.
#===================================================================================================================================
if __name__ == "__main__":
pass
# . Helper functions.
#===================================================================================================================================
def XYZFile_FromSystem ( filename, system, label = None, xyz = None ):
"""Helper function that writes a system to a XYZ file."""
outfile = XYZFileWriter ( filename )
outfile.WriteSingleSystem ( system, label = label, xyz = xyz )
def XYZFiles_FromSystemGeometryTrajectory ( outPath, inPath, system ):
"""Convert a SystemGeometryTrajectory to XYZ files."""
# . Define the paths.
inTrajectory = SystemGeometryTrajectory ( inPath, system, mode = "r" )
if not os.path.exists ( outPath ): os.mkdir ( outPath )
# . Find format.
n = len ( "{:d}".format ( len ( inTrajectory ) ) )
format = "frame{:0" + repr ( n ) + "d}.xyz"
# . Loop over frames.
i = 0
while inTrajectory.RestoreOwnerData ( ):
XYZFile_FromSystem ( os.path.join ( outPath, format.format ( i+1 ) ), system )
i += 1
inTrajectory.Close ( )
# . Exporter definitions.
_Exporter.AddHandler ( { System : XYZFile_FromSystem } , [ "xyz" ], "XYZ" )
#===================================================================================================================================
# . Testing.
#===================================================================================================================================
if __name__ == "__main__":
pass
# . Functions.
#===================================================================================================================================
def PDBFile_FromSystem(filename,
system,
occupancies=None,
QCONECT=False,
selection=None,
suppressICodeField=False,
temperatureFactors=None,
useSegmentEntityLabels=False):
"""Helper function that writes a system to a PDB file."""
outfile = PDBFileWriter(filename)
outfile.WriteSystem(system,
occupancies=occupancies,
QCONECT=QCONECT,
selection=selection,
suppressICodeField=suppressICodeField,
temperatureFactors=temperatureFactors,
useSegmentEntityLabels=useSegmentEntityLabels)
# . Exporter definitions.
_Exporter.AddHandler({System: PDBFile_FromSystem},
["ent", "ENT", "pdb", "PDB"], "Protein Data Bank")
#===================================================================================================================================
# . Test.
#===================================================================================================================================
if __name__ == "__main__":
pass
symbol = PeriodicTable.Symbol(n, index=i + 1)
self.file.write("{:<5s}{:25.15f}{:25.15f}{:25.15f}\n".format(
symbol, xyz[i, 0], xyz[i, 1], xyz[i, 2]))
self.file.write("&\n")
def WriteSingleSystem(self, system, label=None, xyz=None):
"""Write a complete file."""
self.Open()
self.WriteFrame(system, label=label, xyz=xyz)
self.Close()
#===================================================================================================================================
# . Helper functions.
#===================================================================================================================================
def JaguarInputFile_FromSystem(filename, system, label=None, xyz=None):
"""Helper function that writes a system to a Jaguar input file."""
outfile = JaguarInputFileWriter(filename)
outfile.WriteSingleSystem(system, label=label, xyz=xyz)
# . Exporter definitions.
_Exporter.AddHandler({System: JaguarInputFile_FromSystem},
["jagin", "jin", "JAGIN", "JIN"], "Jaguar Input")
#===================================================================================================================================
# . Test.
#===================================================================================================================================
if __name__ == "__main__":
pass
if len ( label ) <= 0: label = _UNDEFINEDCHARACTER
oldname = None
oldsequence = None
for component in entity.children:
fields = sequence.ParseLabel ( component.label, fields = 2 )
name = fields[0]
newSequence = fields[1]
if ( name != oldname ) and ( newSequence != oldsequence ):
self.file.write ( "{:<10s} {:<4s} {:<6s}\n".format ( label, name, newSequence ) )
oldname = name
oldsequence = newSequence
# . Finish up.
self.Close ( )
#===================================================================================================================================
# . Functions.
#===================================================================================================================================
def mmCIFFile_FromSystem ( filename, system, datalabel = _DEFAULTDATALABEL ):
"""Helper function that writes a system to a mmCIF file."""
outfile = mmCIFFileWriter ( filename )
outfile.WriteSystem ( system, datalabel = datalabel )
# . Exporter definitions.
_Exporter.AddHandler ( { System : mmCIFFile_FromSystem } , [ "mmcif", "MMCIF" ], "Macromolecular Crystallographic Information File" )
#===================================================================================================================================
# . Test.
#===================================================================================================================================
if __name__ == "__main__":
pass
if ( ( i + 1 ) % _NumberAtomsPerLine ) == 0: self.write ( "\n" )
if ( ( len ( system.atoms ) + 1 ) % _NumberAtomsPerLine ) == 0: self.write ( "\n" )
# . Symmetry.
if includeSymmetryParameters:
symmetryParameters = getattr ( system.configuration, "symmetryParameters", None )
if symmetryParameters is not None:
self.write ( _SymmetryLineFormat.format ( symmetryParameters.a, symmetryParameters.b, symmetryParameters.c ) )
def WriteSystem ( self, system, includeSymmetryParameters = True, label = None, xyz = None ):
"""Write a system."""
self.Open ( )
self.WriteFrame ( system, includeSymmetryParameters = includeSymmetryParameters, label = label, xyz = xyz )
self.Close ( )
#===================================================================================================================================
# . Helper functions.
#===================================================================================================================================
def AmberCrdFile_FromSystem ( path, system, includeSymmetryParameters = True, label = None, xyz = None ):
"""Helper function that writes coordinates to an Amber crd file."""
inFile = AmberCrdFileWriter ( path )
inFile.WriteSystem ( system, includeSymmetryParameters = includeSymmetryParameters, label = label, xyz = xyz )
# . Exporter definitions.
_Exporter.AddHandler ( { System : AmberCrdFile_FromSystem } , [ "crd", "CRD" ], "Amber Coordinates" )
#===================================================================================================================================
# . Testing.
#===================================================================================================================================
if __name__ == "__main__":
pass
formalCharge = getattr(atom, "formalCharge", 0)
if formalCharge != 0:
self.file.write("M CHG 1{:4d}{:4d}\n".format(
i + 1, formalCharge))
self.file.write("M END\n")
def WriteSingleSystem(self, system, label=None, xyz=None):
"""Write a complete file."""
self.Open()
self.WriteFrame(system, label=label, xyz=xyz)
self.Close()
#===================================================================================================================================
# . Helper functions.
#===================================================================================================================================
def MOLFile_FromSystem(filename, system, label=None, xyz=None):
"""Helper function that writes a system to a MOL file."""
outfile = MOLFileWriter(filename)
outfile.WriteSingleSystem(system, label=label, xyz=xyz)
# . Exporter definitions.
_Exporter.AddHandler({System: MOLFile_FromSystem}, ["mol", "MOL"], "MDL MOL")
#===================================================================================================================================
# . Testing.
#===================================================================================================================================
if __name__ == "__main__":
pass