def __init__(self, file):
"""Load a prmtop file."""
top = Topology()
## The Topology read from the prmtop file
self.topology = top
# Load the prmtop file
prmtop = amber_file_parser.PrmtopLoader(file)
self._prmtop = prmtop
# Add atoms to the topology
PDBFile._loadNameReplacementTables()
lastResidue = None
c = top.addChain()
for index in range(prmtop.getNumAtoms()):
resNumber = prmtop.getResidueNumber(index)
if resNumber != lastResidue:
lastResidue = resNumber
resName = prmtop.getResidueLabel(iAtom=index).strip()
if resName in PDBFile._residueNameReplacements:
resName = PDBFile._residueNameReplacements[resName]
r = top.addResidue(resName, c)
if resName in PDBFile._atomNameReplacements:
atomReplacements = PDBFile._atomNameReplacements[resName]
else:
atomReplacements = {}
atomName = prmtop.getAtomName(index).strip()
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
# Try to guess the element.
upper = atomName.upper()
if upper.startswith('CL'):
element = elem.chlorine
elif upper.startswith('NA'):
element = elem.sodium
elif upper.startswith('MG'):
element = elem.magnesium
else:
try:
element = elem.get_by_symbol(atomName[0])
except KeyError:
element = None
top.addAtom(atomName, element, r)
# Add bonds to the topology
atoms = list(top.atoms())
for bond in prmtop.getBondsWithH():
top.addBond(atoms[bond[0]], atoms[bond[1]])
for bond in prmtop.getBondsNoH():
top.addBond(atoms[bond[0]], atoms[bond[1]])
# Set the periodic box size.
if prmtop.getIfBox():
top.setUnitCellDimensions(tuple(x.value_in_unit(unit.nanometer) for x in prmtop.getBoxBetaAndDimensions()[1:4])*unit.nanometer)
def __init__(self, file, periodicBoxVectors=None, unitCellDimensions=None, includeDir=None, defines=None):
"""Load a top file.
Parameters
----------
file : str
the name of the file to load
periodicBoxVectors : tuple of Vec3=None
the vectors defining the periodic box
unitCellDimensions : Vec3=None
the dimensions of the crystallographic unit cell. For
non-rectangular unit cells, specify periodicBoxVectors instead.
includeDir : string=None
A directory in which to look for other files included from the
top file. If not specified, we will attempt to locate a gromacs
installation on your system. When gromacs is installed in
/usr/local, this will resolve to /usr/local/gromacs/share/gromacs/top
defines : dict={}
preprocessor definitions that should be predefined when parsing the file
"""
if includeDir is None:
includeDir = _defaultGromacsIncludeDir()
self._includeDirs = (os.path.dirname(file), includeDir)
# Most of the gromacs water itp files for different forcefields,
# unless the preprocessor #define FLEXIBLE is given, don't define
# bonds between the water hydrogen and oxygens, but only give the
# constraint distances and exclusions.
self._defines = OrderedDict()
self._defines['FLEXIBLE'] = True
self._genpairs = True
if defines is not None:
for define, value in defines.iteritems():
self._defines[define] = value
# Parse the file.
self._currentCategory = None
self._ifStack = []
self._elseStack = []
self._moleculeTypes = {}
self._molecules = []
self._currentMoleculeType = None
self._atomTypes = {}
self._bondTypes= {}
self._angleTypes = {}
self._dihedralTypes = {}
self._implicitTypes = {}
self._pairTypes = {}
self._cmapTypes = {}
self._processFile(file)
# Create the Topology from it.
top = Topology()
## The Topology read from the prmtop file
self.topology = top
if periodicBoxVectors is not None:
if unitCellDimensions is not None:
raise ValueError("specify either periodicBoxVectors or unitCellDimensions, but not both")
top.setPeriodicBoxVectors(periodicBoxVectors)
else:
top.setUnitCellDimensions(unitCellDimensions)
PDBFile._loadNameReplacementTables()
for moleculeName, moleculeCount in self._molecules:
if moleculeName not in self._moleculeTypes:
raise ValueError("Unknown molecule type: "+moleculeName)
moleculeType = self._moleculeTypes[moleculeName]
if moleculeCount > 0 and moleculeType.has_virtual_sites:
raise ValueError('Virtual sites not yet supported by Gromacs parsers')
# Create the specified number of molecules of this type.
for i in range(moleculeCount):
atoms = []
lastResidue = None
c = top.addChain()
for index, fields in enumerate(moleculeType.atoms):
resNumber = fields[2]
if resNumber != lastResidue:
lastResidue = resNumber
resName = fields[3]
if resName in PDBFile._residueNameReplacements:
resName = PDBFile._residueNameReplacements[resName]
r = top.addResidue(resName, c)
if resName in PDBFile._atomNameReplacements:
atomReplacements = PDBFile._atomNameReplacements[resName]
else:
atomReplacements = {}
atomName = fields[4]
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
# Try to guess the element.
upper = atomName.upper()
if upper.startswith('CL'):
element = elem.chlorine
elif upper.startswith('NA'):
element = elem.sodium
elif upper.startswith('MG'):
element = elem.magnesium
else:
try:
element = elem.get_by_symbol(atomName[0])
except KeyError:
element = None
atoms.append(top.addAtom(atomName, element, r))
# Add bonds to the topology
for fields in moleculeType.bonds:
top.addBond(atoms[int(fields[0])-1], atoms[int(fields[1])-1])
def __init__(self, file):
"""Load a prmtop file."""
top = Topology()
## The Topology read from the prmtop file
self.topology = top
self.elements = []
# Load the prmtop file
prmtop = amber_file_parser.PrmtopLoader(file)
self._prmtop = prmtop
# Add atoms to the topology
PDBFile._loadNameReplacementTables()
lastResidue = None
c = top.addChain()
for index in range(prmtop.getNumAtoms()):
resNumber = prmtop.getResidueNumber(index)
if resNumber != lastResidue:
lastResidue = resNumber
resName = prmtop.getResidueLabel(iAtom=index).strip()
if resName in PDBFile._residueNameReplacements:
resName = PDBFile._residueNameReplacements[resName]
r = top.addResidue(resName, c)
if resName in PDBFile._atomNameReplacements:
atomReplacements = PDBFile._atomNameReplacements[resName]
else:
atomReplacements = {}
atomName = prmtop.getAtomName(index).strip()
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
# Get the element from the prmtop file if available
if prmtop.has_atomic_number:
try:
element = elem.Element.getByAtomicNumber(
int(prmtop._raw_data['ATOMIC_NUMBER'][index]))
except KeyError:
element = None
else:
# Try to guess the element from the atom name.
upper = atomName.upper()
if upper.startswith('CL'):
element = elem.chlorine
elif upper.startswith('NA'):
element = elem.sodium
elif upper.startswith('MG'):
element = elem.magnesium
elif upper.startswith('ZN'):
element = elem.zinc
else:
try:
element = elem.get_by_symbol(atomName[0])
except KeyError:
element = None
top.addAtom(atomName, element, r)
self.elements.append(element)
# Add bonds to the topology
atoms = list(top.atoms())
for bond in prmtop.getBondsWithH():
top.addBond(atoms[bond[0]], atoms[bond[1]])
for bond in prmtop.getBondsNoH():
top.addBond(atoms[bond[0]], atoms[bond[1]])
# Set the periodic box size.
if prmtop.getIfBox():
top.setUnitCellDimensions(
tuple(
x.value_in_unit(unit.nanometer)
for x in prmtop.getBoxBetaAndDimensions()[1:4]) *
unit.nanometer)
def __init__(self, file):
"""Load a prmtop file."""
## The Topology read from the prmtop file
self.topology = top = Topology()
self.elements = []
# Load the prmtop file
prmtop = amber_file_parser.PrmtopLoader(file)
self._prmtop = prmtop
# Add atoms to the topology
PDBFile._loadNameReplacementTables()
lastResidue = None
c = top.addChain()
for index in range(prmtop.getNumAtoms()):
resNumber = prmtop.getResidueNumber(index)
if resNumber != lastResidue:
lastResidue = resNumber
resName = prmtop.getResidueLabel(iAtom=index).strip()
if resName in PDBFile._residueNameReplacements:
resName = PDBFile._residueNameReplacements[resName]
r = top.addResidue(resName, c)
if resName in PDBFile._atomNameReplacements:
atomReplacements = PDBFile._atomNameReplacements[resName]
else:
atomReplacements = {}
atomName = prmtop.getAtomName(index).strip()
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
# Get the element from the prmtop file if available
if prmtop.has_atomic_number:
try:
element = elem.Element.getByAtomicNumber(int(prmtop._raw_data['ATOMIC_NUMBER'][index]))
except KeyError:
element = None
else:
# Try to guess the element from the atom name.
upper = atomName.upper()
if upper.startswith('CL'):
element = elem.chlorine
elif upper.startswith('NA'):
element = elem.sodium
elif upper.startswith('MG'):
element = elem.magnesium
elif upper.startswith('ZN'):
element = elem.zinc
else:
try:
element = elem.get_by_symbol(atomName[0])
except KeyError:
element = None
top.addAtom(atomName, element, r)
self.elements.append(element)
# Add bonds to the topology
atoms = list(top.atoms())
for bond in prmtop.getBondsWithH():
top.addBond(atoms[bond[0]], atoms[bond[1]])
for bond in prmtop.getBondsNoH():
top.addBond(atoms[bond[0]], atoms[bond[1]])
# Set the periodic box size.
if prmtop.getIfBox():
box = prmtop.getBoxBetaAndDimensions()
top.setPeriodicBoxVectors(computePeriodicBoxVectors(*(box[1:4] + box[0:1]*3)))
def __init__(self,
file,
unitCellDimensions=None,
includeDir='/usr/local/gromacs/share/gromacs/top',
defines={}):
"""Load a top file.
Parameters:
- file (string) the name of the file to load
- unitCellDimensions (Vec3=None) the dimensions of the crystallographic unit cell
- includeDir (string=/usr/local/gromacs/share/gromacs/top) a directory in which to look for other files
included from the top file
- defines (map={}) preprocessor definitions that should be predefined when parsing the file
"""
self._includeDirs = (os.path.dirname(file), includeDir)
self._defines = defines
# Parse the file.
self._currentCategory = None
self._ifStack = []
self._moleculeTypes = {}
self._molecules = []
self._currentMoleculeType = None
self._atomTypes = {}
self._bondTypes = {}
self._angleTypes = {}
self._dihedralTypes = {}
self._implicitTypes = {}
self._pairTypes = {}
self._cmapTypes = {}
self._processFile(file)
# Create the Topology from it.
top = Topology()
## The Topology read from the prmtop file
self.topology = top
top.setUnitCellDimensions(unitCellDimensions)
PDBFile._loadNameReplacementTables()
for moleculeName, moleculeCount in self._molecules:
if moleculeName not in self._moleculeTypes:
raise ValueError("Unknown molecule type: " + moleculeName)
moleculeType = self._moleculeTypes[moleculeName]
# Create the specified number of molecules of this type.
for i in range(moleculeCount):
atoms = []
lastResidue = None
c = top.addChain()
for index, fields in enumerate(moleculeType.atoms):
resNumber = fields[2]
if resNumber != lastResidue:
lastResidue = resNumber
resName = fields[3]
if resName in PDBFile._residueNameReplacements:
resName = PDBFile._residueNameReplacements[resName]
r = top.addResidue(resName, c)
if resName in PDBFile._atomNameReplacements:
atomReplacements = PDBFile._atomNameReplacements[
resName]
else:
atomReplacements = {}
atomName = fields[4]
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
# Try to guess the element.
upper = atomName.upper()
if upper.startswith('CL'):
element = elem.chlorine
elif upper.startswith('NA'):
element = elem.sodium
elif upper.startswith('MG'):
element = elem.magnesium
else:
try:
element = elem.get_by_symbol(atomName[0])
except KeyError:
element = None
atoms.append(top.addAtom(atomName, element, r))
# Add bonds to the topology
for fields in moleculeType.bonds:
top.addBond(atoms[int(fields[0]) - 1],
atoms[int(fields[1]) - 1])
def __init__(self, file, unitCellDimensions=None, includeDir='/usr/local/gromacs/share/gromacs/top', defines={}):
"""Load a top file.
Parameters:
- file (string) the name of the file to load
- unitCellDimensions (Vec3=None) the dimensions of the crystallographic unit cell
- includeDir (string=/usr/local/gromacs/share/gromacs/top) a directory in which to look for other files
included from the top file
- defines (map={}) preprocessor definitions that should be predefined when parsing the file
"""
self._includeDirs = (os.path.dirname(file), includeDir)
self._defines = defines
# Parse the file.
self._currentCategory = None
self._ifStack = []
self._moleculeTypes = {}
self._molecules = []
self._currentMoleculeType = None
self._atomTypes = {}
self._bondTypes= {}
self._angleTypes = {}
self._dihedralTypes = {}
self._implicitTypes = {}
self._pairTypes = {}
self._cmapTypes = {}
self._processFile(file)
# Create the Topology from it.
top = Topology()
## The Topology read from the prmtop file
self.topology = top
top.setUnitCellDimensions(unitCellDimensions)
PDBFile._loadNameReplacementTables()
for moleculeName, moleculeCount in self._molecules:
if moleculeName not in self._moleculeTypes:
raise ValueError("Unknown molecule type: "+moleculeName)
moleculeType = self._moleculeTypes[moleculeName]
# Create the specified number of molecules of this type.
for i in range(moleculeCount):
atoms = []
lastResidue = None
c = top.addChain()
for index, fields in enumerate(moleculeType.atoms):
resNumber = fields[2]
if resNumber != lastResidue:
lastResidue = resNumber
resName = fields[3]
if resName in PDBFile._residueNameReplacements:
resName = PDBFile._residueNameReplacements[resName]
r = top.addResidue(resName, c)
if resName in PDBFile._atomNameReplacements:
atomReplacements = PDBFile._atomNameReplacements[resName]
else:
atomReplacements = {}
atomName = fields[4]
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
# Try to guess the element.
upper = atomName.upper()
if upper.startswith('CL'):
element = elem.chlorine
elif upper.startswith('NA'):
element = elem.sodium
elif upper.startswith('MG'):
element = elem.magnesium
else:
try:
element = elem.get_by_symbol(atomName[0])
except KeyError:
element = None
atoms.append(top.addAtom(atomName, element, r))
# Add bonds to the topology
for fields in moleculeType.bonds:
top.addBond(atoms[int(fields[0])-1], atoms[int(fields[1])-1])
