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,
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, periodicBoxVectors=None, unitCellDimensions=None, includeDir=None, defines=None):
"""Load a top file.
Parameters:
- file (string) 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 = {'FLEXIBLE': True}
if defines is not None:
self._defines.update(defines)
# 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]
# 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():
box = prmtop.getBoxBetaAndDimensions()
top.setPeriodicBoxVectors(computePeriodicBoxVectors(*(box[1:4] + box[0:1]*3)))
def __init__(self,
file,
unitCellDimensions=None,
includeDir=None,
defines=None):
"""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=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 = {'FLEXIBLE': True}
if defines is not None:
self._defines.update(defines)
# 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
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):
"""Load a PDB file.
The atom positions and Topology can be retrieved by calling getPositions() and getTopology().
Parameters:
- file (string) the name of the file to load
"""
top = Topology()
## The Topology read from the PDB file
self.topology = top
# Load the PDB file
if isinstance(file, PdbStructure):
pdb = file
else:
inputfile = file
if isinstance(file, str):
inputfile = open(file)
pdb = PdbStructure(inputfile, load_all_models=True)
PDBFile._loadNameReplacementTables()
# Build the topology
atomByNumber = {}
for chain in pdb.iter_chains():
c = top.addChain()
for residue in chain.iter_residues():
resName = residue.get_name()
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 = {}
for atom in residue.atoms:
atomName = atom.get_name()
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
atomName = atomName.strip()
element = atom.element
if element is None:
# 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
elif upper.startswith('BE'):
element = elem.beryllium
elif upper.startswith('LI'):
element = elem.lithium
elif upper.startswith('K'):
element = elem.potassium
elif (len(residue) == 1 and upper.startswith('CA')):
element = elem.calcium
else:
try:
element = elem.get_by_symbol(atomName[0])
except KeyError:
pass
newAtom = top.addAtom(atomName, element, r)
atomByNumber[atom.serial_number] = newAtom
self._positions = []
for model in pdb.iter_models(True):
coords = []
for chain in model.iter_chains():
for residue in chain.iter_residues():
for atom in residue.atoms:
pos = atom.get_position().value_in_unit(nanometers)
coords.append(Vec3(pos[0], pos[1], pos[2]))
self._positions.append(coords * nanometers)
## The atom positions read from the PDB file. If the file contains multiple frames, these are the positions in the first frame.
self.positions = self._positions[0]
self.topology.setUnitCellDimensions(pdb.get_unit_cell_dimensions())
self.topology.createStandardBonds()
self.topology.createDisulfideBonds(self.positions)
self._numpyPositions = None
# Add bonds based on CONECT records.
connectBonds = []
for connect in pdb.models[0].connects:
i = connect[0]
for j in connect[1:]:
if i in atomByNumber and j in atomByNumber:
connectBonds.append((atomByNumber[i], atomByNumber[j]))
if len(connectBonds) > 0:
# Only add bonds that don't already exist.
existingBonds = set(top.bonds())
for bond in connectBonds:
if bond not in existingBonds and (
bond[1], bond[0]) not in existingBonds:
top.addBond(bond[0], bond[1])
existingBonds.add(bond)
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):
"""Load a PDBx/mmCIF file.
The atom positions and Topology can be retrieved by calling getPositions() and getTopology().
Parameters:
- file (string) the name of the file to load. Alternatively you can pass an open file object.
"""
top = Topology()
## The Topology read from the PDBx/mmCIF file
self.topology = top
self._positions = []
# Load the file.
inputFile = file
if isinstance(file, str):
inputFile = open(file)
reader = PdbxReader(inputFile)
data = []
reader.read(data)
block = data[0]
# Build the topology.
atomData = block.getObj('atom_site')
atomNameCol = atomData.getAttributeIndex('label_atom_id')
atomIdCol = atomData.getAttributeIndex('id')
resNameCol = atomData.getAttributeIndex('label_comp_id')
resIdCol = atomData.getAttributeIndex('label_seq_id')
asymIdCol = atomData.getAttributeIndex('label_asym_id')
chainIdCol = atomData.getAttributeIndex('label_entity_id')
elementCol = atomData.getAttributeIndex('type_symbol')
altIdCol = atomData.getAttributeIndex('label_alt_id')
modelCol = atomData.getAttributeIndex('pdbx_PDB_model_num')
xCol = atomData.getAttributeIndex('Cartn_x')
yCol = atomData.getAttributeIndex('Cartn_y')
zCol = atomData.getAttributeIndex('Cartn_z')
lastChainId = None
lastResId = None
lastAsymId = None
atomTable = {}
models = []
for row in atomData.getRowList():
atomKey = ((row[resIdCol], row[asymIdCol], row[atomNameCol]))
model = ('1' if modelCol == -1 else row[modelCol])
if model not in models:
models.append(model)
self._positions.append([])
modelIndex = models.index(model)
if row[altIdCol] != '.' and atomKey in atomTable and len(self._positions[modelIndex]) > atomTable[atomKey].index:
# This row is an alternate position for an existing atom, so ignore it.
continue
if modelIndex == 0:
# This row defines a new atom.
if lastChainId != row[chainIdCol]:
# The start of a new chain.
chain = top.addChain()
lastChainId = row[chainIdCol]
lastResId = None
lastAsymId = None
if lastResId != row[resIdCol] or lastAsymId != row[asymIdCol]:
# The start of a new residue.
res = top.addResidue(row[resNameCol], chain)
lastResId = row[resIdCol]
if lastResId == '.':
lastResId = None
lastAsymId = row[asymIdCol]
element = None
try:
element = elem.get_by_symbol(row[elementCol])
except KeyError:
pass
atom = top.addAtom(row[atomNameCol], element, res)
atomTable[atomKey] = atom
else:
# This row defines coordinates for an existing atom in one of the later models.
try:
atom = atomTable[atomKey]
except KeyError:
raise ValueError('Unknown atom %s in residue %s %s for model %s' % (row[atomNameCol], row[resNameCol], row[resIdCol], model))
if atom.index != len(self._positions[modelIndex]):
raise ValueError('Atom %s for model %s does not match the order of atoms for model %s' % (row[atomIdCol], model, models[0]))
self._positions[modelIndex].append(Vec3(float(row[xCol]), float(row[yCol]), float(row[zCol]))*0.1)
for i in range(len(self._positions)):
self._positions[i] = self._positions[i]*nanometers
## The atom positions read from the PDBx/mmCIF file. If the file contains multiple frames, these are the positions in the first frame.
self.positions = self._positions[0]
self.topology.createStandardBonds()
self._numpyPositions = None
# Record unit cell information, if present.
cell = block.getObj('cell')
if cell is not None and cell.getRowCount() > 0:
row = cell.getRow(0)
cellSize = [float(row[cell.getAttributeIndex(attribute)]) for attribute in ('length_a', 'length_b', 'length_c')]*angstroms
self.topology.setUnitCellDimensions(cellSize)
# Add bonds based on struct_conn records.
connectData = block.getObj('struct_conn')
if connectData is not None:
res1Col = connectData.getAttributeIndex('ptnr1_label_seq_id')
res2Col = connectData.getAttributeIndex('ptnr2_label_seq_id')
atom1Col = connectData.getAttributeIndex('ptnr1_label_atom_id')
atom2Col = connectData.getAttributeIndex('ptnr2_label_atom_id')
asym1Col = connectData.getAttributeIndex('ptnr1_label_asym_id')
asym2Col = connectData.getAttributeIndex('ptnr2_label_asym_id')
typeCol = connectData.getAttributeIndex('conn_type_id')
connectBonds = []
for row in connectData.getRowList():
type = row[typeCol][:6]
if type in ('covale', 'disulf', 'modres'):
key1 = (row[res1Col], row[asym1Col], row[atom1Col])
key2 = (row[res2Col], row[asym2Col], row[atom2Col])
if key1 in atomTable and key2 in atomTable:
connectBonds.append((atomTable[key1], atomTable[key2]))
if len(connectBonds) > 0:
# Only add bonds that don't already exist.
existingBonds = set(top.bonds())
for bond in connectBonds:
if bond not in existingBonds and (bond[1], bond[0]) not in existingBonds:
top.addBond(bond[0], bond[1])
existingBonds.add(bond)
def __init__(self, file):
"""Load a PDB file.
The atom positions and Topology can be retrieved by calling getPositions() and getTopology().
Parameters:
- file (string) the name of the file to load
"""
top = Topology()
## The Topology read from the PDB file
self.topology = top
# Load the PDB file
if isinstance(file, PdbStructure):
pdb = file
else:
inputfile = file
if isinstance(file, str):
inputfile = open(file)
pdb = PdbStructure(inputfile, load_all_models=True)
PDBFile._loadNameReplacementTables()
# Build the topology
atomByNumber = {}
for chain in pdb.iter_chains():
c = top.addChain()
for residue in chain.iter_residues():
resName = residue.get_name()
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 = {}
for atom in residue.atoms:
atomName = atom.get_name()
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
atomName = atomName.strip()
element = atom.element
if element is None:
# 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
elif upper.startswith('BE'):
element = elem.beryllium
elif upper.startswith('LI'):
element = elem.lithium
elif upper.startswith('K'):
element = elem.potassium
elif upper.startswith('ZN'):
element = elem.zinc
elif( len( residue ) == 1 and upper.startswith('CA') ):
element = elem.calcium
else:
try:
element = elem.get_by_symbol(atomName[0])
except KeyError:
pass
newAtom = top.addAtom(atomName, element, r)
atomByNumber[atom.serial_number] = newAtom
self._positions = []
for model in pdb.iter_models(True):
coords = []
for chain in model.iter_chains():
for residue in chain.iter_residues():
for atom in residue.atoms:
pos = atom.get_position().value_in_unit(nanometers)
coords.append(Vec3(pos[0], pos[1], pos[2]))
self._positions.append(coords*nanometers)
## The atom positions read from the PDB file. If the file contains multiple frames, these are the positions in the first frame.
self.positions = self._positions[0]
self.topology.setUnitCellDimensions(pdb.get_unit_cell_dimensions())
self.topology.createStandardBonds()
self.topology.createDisulfideBonds(self.positions)
self._numpyPositions = None
# Add bonds based on CONECT records.
connectBonds = []
for connect in pdb.models[0].connects:
i = connect[0]
for j in connect[1:]:
if i in atomByNumber and j in atomByNumber:
connectBonds.append((atomByNumber[i], atomByNumber[j]))
if len(connectBonds) > 0:
# Only add bonds that don't already exist.
existingBonds = set(top.bonds())
for bond in connectBonds:
if bond not in existingBonds and (bond[1], bond[0]) not in existingBonds:
top.addBond(bond[0], bond[1])
existingBonds.add(bond)
def __init__(self, file):
"""Load a PDBx/mmCIF file.
The atom positions and Topology can be retrieved by calling getPositions() and getTopology().
Parameters:
- file (string) the name of the file to load. Alternatively you can pass an open file object.
"""
top = Topology()
## The Topology read from the PDBx/mmCIF file
self.topology = top
self._positions = []
# Load the file.
inputFile = file
if isinstance(file, str):
inputFile = open(file)
reader = PdbxReader(inputFile)
data = []
reader.read(data)
block = data[0]
# Build the topology.
atomData = block.getObj('atom_site')
atomNameCol = atomData.getAttributeIndex('label_atom_id')
atomIdCol = atomData.getAttributeIndex('id')
resNameCol = atomData.getAttributeIndex('label_comp_id')
resIdCol = atomData.getAttributeIndex('label_seq_id')
asymIdCol = atomData.getAttributeIndex('label_asym_id')
chainIdCol = atomData.getAttributeIndex('label_entity_id')
elementCol = atomData.getAttributeIndex('type_symbol')
altIdCol = atomData.getAttributeIndex('label_alt_id')
modelCol = atomData.getAttributeIndex('pdbx_PDB_model_num')
xCol = atomData.getAttributeIndex('Cartn_x')
yCol = atomData.getAttributeIndex('Cartn_y')
zCol = atomData.getAttributeIndex('Cartn_z')
lastChainId = None
lastResId = None
lastAsymId = None
atomTable = {}
models = []
for row in atomData.getRowList():
atomKey = ((row[resIdCol], row[asymIdCol], row[atomNameCol]))
model = ('1' if modelCol == -1 else row[modelCol])
if model not in models:
models.append(model)
self._positions.append([])
modelIndex = models.index(model)
if row[altIdCol] != '.' and atomKey in atomTable and len(
self._positions[modelIndex]) > atomTable[atomKey].index:
# This row is an alternate position for an existing atom, so ignore it.
continue
if modelIndex == 0:
# This row defines a new atom.
if lastChainId != row[chainIdCol]:
# The start of a new chain.
chain = top.addChain()
lastChainId = row[chainIdCol]
lastResId = None
lastAsymId = None
if lastResId != row[resIdCol] or lastAsymId != row[asymIdCol]:
# The start of a new residue.
res = top.addResidue(row[resNameCol], chain)
lastResId = row[resIdCol]
if lastResId == '.':
lastResId = None
lastAsymId = row[asymIdCol]
element = None
try:
element = elem.get_by_symbol(row[elementCol])
except KeyError:
pass
atom = top.addAtom(row[atomNameCol], element, res)
atomTable[atomKey] = atom
else:
# This row defines coordinates for an existing atom in one of the later models.
try:
atom = atomTable[atomKey]
except KeyError:
raise ValueError(
'Unknown atom %s in residue %s %s for model %s' %
(row[atomNameCol], row[resNameCol], row[resIdCol],
model))
if atom.index != len(self._positions[modelIndex]):
raise ValueError(
'Atom %s for model %s does not match the order of atoms for model %s'
% (row[atomIdCol], model, models[0]))
self._positions[modelIndex].append(
Vec3(float(row[xCol]), float(row[yCol]), float(row[zCol])) *
0.1)
for i in range(len(self._positions)):
self._positions[i] = self._positions[i] * nanometers
## The atom positions read from the PDBx/mmCIF file. If the file contains multiple frames, these are the positions in the first frame.
self.positions = self._positions[0]
self.topology.createStandardBonds()
self._numpyPositions = None
# Record unit cell information, if present.
cell = block.getObj('cell')
if cell is not None and cell.getRowCount() > 0:
row = cell.getRow(0)
cellSize = [
float(row[cell.getAttributeIndex(attribute)])
for attribute in ('length_a', 'length_b', 'length_c')
] * angstroms
self.topology.setUnitCellDimensions(cellSize)
# Add bonds based on struct_conn records.
connectData = block.getObj('struct_conn')
if connectData is not None:
res1Col = connectData.getAttributeIndex('ptnr1_label_seq_id')
res2Col = connectData.getAttributeIndex('ptnr2_label_seq_id')
atom1Col = connectData.getAttributeIndex('ptnr1_label_atom_id')
atom2Col = connectData.getAttributeIndex('ptnr2_label_atom_id')
asym1Col = connectData.getAttributeIndex('ptnr1_label_asym_id')
asym2Col = connectData.getAttributeIndex('ptnr2_label_asym_id')
typeCol = connectData.getAttributeIndex('conn_type_id')
connectBonds = []
for row in connectData.getRowList():
type = row[typeCol][:6]
if type in ('covale', 'disulf', 'modres'):
key1 = (row[res1Col], row[asym1Col], row[atom1Col])
key2 = (row[res2Col], row[asym2Col], row[atom2Col])
if key1 in atomTable and key2 in atomTable:
connectBonds.append((atomTable[key1], atomTable[key2]))
if len(connectBonds) > 0:
# Only add bonds that don't already exist.
existingBonds = set(top.bonds())
for bond in connectBonds:
if bond not in existingBonds and (
bond[1], bond[0]) not in existingBonds:
top.addBond(bond[0], bond[1])
existingBonds.add(bond)
def __init__(self, pdb_line):
"""Create a new pdb.Atom from an ATOM or HETATM line.
Example line:
ATOM 2209 CB TYR A 299 6.167 22.607 20.046 1.00 8.12 C
00000000011111111112222222222333333333344444444445555555555666666666677777777778
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM line format description from
http://deposit.rcsb.org/adit/docs/pdb_atom_format.html:
COLUMNS DATA TYPE CONTENTS
--------------------------------------------------------------------------------
1 - 6 Record name "ATOM "
7 - 11 Integer Atom serial number.
13 - 16 Atom Atom name.
17 Character Alternate location indicator.
18 - 20 Residue name Residue name.
22 Character Chain identifier.
23 - 26 Integer Residue sequence number.
27 AChar Code for insertion of residues.
31 - 38 Real(8.3) Orthogonal coordinates for X in Angstroms.
39 - 46 Real(8.3) Orthogonal coordinates for Y in Angstroms.
47 - 54 Real(8.3) Orthogonal coordinates for Z in Angstroms.
55 - 60 Real(6.2) Occupancy (Default = 1.0).
61 - 66 Real(6.2) Temperature factor (Default = 0.0).
73 - 76 LString(4) Segment identifier, left-justified.
77 - 78 LString(2) Element symbol, right-justified.
79 - 80 LString(2) Charge on the atom.
"""
# We might modify first/final status during _finalize() methods
self.is_first_atom_in_chain = False
self.is_final_atom_in_chain = False
self.is_first_residue_in_chain = False
self.is_final_residue_in_chain = False
# Start parsing fields from pdb line
self.record_name = pdb_line[0:6].strip()
self.serial_number = int(pdb_line[6:11])
self.name_with_spaces = pdb_line[12:16]
alternate_location_indicator = pdb_line[16]
self.residue_name_with_spaces = pdb_line[17:20]
# In some MD codes, notably ffamber in gromacs, residue name has a fourth character in
# column 21
possible_fourth_character = pdb_line[20:21]
if possible_fourth_character != " ":
# Fourth character should only be there if official 3 are already full
if len(self.residue_name_with_spaces.strip()) != 3:
raise ValueError('Misaligned residue name: %s' % pdb_line)
self.residue_name_with_spaces += possible_fourth_character
self.residue_name = self.residue_name_with_spaces.strip()
self.chain_id = pdb_line[21]
self.residue_number = int(pdb_line[22:26])
self.insertion_code = pdb_line[26]
# coordinates, occupancy, and temperature factor belong in Atom.Location object
x = float(pdb_line[30:38])
y = float(pdb_line[38:46])
z = float(pdb_line[46:54])
try:
occupancy = float(pdb_line[54:60])
except:
occupancy = 1.0
try:
temperature_factor = float(pdb_line[60:66])
except:
temperature_factor = 0.0
self.locations = {}
loc = Atom.Location(alternate_location_indicator, np.array([x,y,z]), occupancy, temperature_factor, self.residue_name_with_spaces)
self.locations[alternate_location_indicator] = loc
self.default_location_id = alternate_location_indicator
# segment id, element_symbol, and formal_charge are not always present
self.segment_id = pdb_line[72:76].strip()
self.element_symbol = pdb_line[76:78].strip()
try: self.formal_charge = int(pdb_line[78:80])
except ValueError: self.formal_charge = None
# figure out atom element
try:
# First try to find a sensible element symbol from columns 76-77
self.element = element.get_by_symbol(self.element_symbol)
except KeyError:
# otherwise, deduce element from first two characters of atom name
# remove digits found in some hydrogen atom names
symbol = self.name_with_spaces[0:2].strip().lstrip("0123456789")
try:
# Some molecular dynamics PDB files, such as gromacs with ffamber force
# field, include 4-character hydrogen atom names beginning with "H".
# Hopefully elements like holmium (Ho) and mercury (Hg) will have fewer than four
# characters in the atom name. This problem is the fault of molecular
# dynamics code authors who feel the need to make up their own atom
# nomenclature because it is too tedious to read that provided by the PDB.
# These are the same folks who invent their own meanings for biochemical terms
# like "dipeptide". Clowntards.
if len(self.name) == 4 and self.name[0:1] == "H":
self.element = element.hydrogen
else:
self.element = element.get_by_symbol(symbol)
except KeyError:
# OK, I give up
self.element = None
def __init__(self, file):
"""Load a PDBx/mmCIF file.
The atom positions and Topology can be retrieved by calling getPositions() and getTopology().
Parameters:
- file (string) the name of the file to load. Alternatively you can pass an open file object.
"""
top = Topology()
## The Topology read from the PDBx/mmCIF file
self.topology = top
self._positions = []
# Load the file.
inputFile = file
if isinstance(file, str):
inputFile = open(file)
reader = PdbxReader(inputFile)
data = []
reader.read(data)
block = data[0]
# Build the topology.
atomData = block.getObj("atom_site")
atomNameCol = atomData.getAttributeIndex("label_atom_id")
atomIdCol = atomData.getAttributeIndex("id")
resNameCol = atomData.getAttributeIndex("label_comp_id")
resIdCol = atomData.getAttributeIndex("label_seq_id")
resNumCol = atomData.getAttributeIndex("auth_seq_id")
asymIdCol = atomData.getAttributeIndex("label_asym_id")
chainIdCol = atomData.getAttributeIndex("label_entity_id")
elementCol = atomData.getAttributeIndex("type_symbol")
altIdCol = atomData.getAttributeIndex("label_alt_id")
modelCol = atomData.getAttributeIndex("pdbx_PDB_model_num")
xCol = atomData.getAttributeIndex("Cartn_x")
yCol = atomData.getAttributeIndex("Cartn_y")
zCol = atomData.getAttributeIndex("Cartn_z")
lastChainId = None
lastResId = None
lastAsymId = None
atomTable = {}
atomsInResidue = set()
models = []
for row in atomData.getRowList():
atomKey = (row[resIdCol], row[asymIdCol], row[atomNameCol])
model = "1" if modelCol == -1 else row[modelCol]
if model not in models:
models.append(model)
self._positions.append([])
modelIndex = models.index(model)
if (
row[altIdCol] != "."
and atomKey in atomTable
and len(self._positions[modelIndex]) > atomTable[atomKey].index
):
# This row is an alternate position for an existing atom, so ignore it.
continue
if modelIndex == 0:
# This row defines a new atom.
if lastChainId != row[chainIdCol]:
# The start of a new chain.
chain = top.addChain(row[asymIdCol])
lastChainId = row[chainIdCol]
lastResId = None
lastAsymId = None
if (
lastResId != row[resIdCol]
or lastAsymId != row[asymIdCol]
or (lastResId == "." and row[atomNameCol] in atomsInResidue)
):
# The start of a new residue.
res = top.addResidue(row[resNameCol], chain, None if resNumCol == -1 else row[resNumCol])
lastResId = row[resIdCol]
lastAsymId = row[asymIdCol]
atomsInResidue.clear()
element = None
try:
element = elem.get_by_symbol(row[elementCol])
except KeyError:
pass
atom = top.addAtom(row[atomNameCol], element, res, row[atomIdCol])
atomTable[atomKey] = atom
atomsInResidue.add(row[atomNameCol])
else:
# This row defines coordinates for an existing atom in one of the later models.
try:
atom = atomTable[atomKey]
except KeyError:
raise ValueError(
"Unknown atom %s in residue %s %s for model %s"
% (row[atomNameCol], row[resNameCol], row[resIdCol], model)
)
if atom.index != len(self._positions[modelIndex]):
raise ValueError(
"Atom %s for model %s does not match the order of atoms for model %s"
% (row[atomIdCol], model, models[0])
)
self._positions[modelIndex].append(Vec3(float(row[xCol]), float(row[yCol]), float(row[zCol])) * 0.1)
for i in range(len(self._positions)):
self._positions[i] = self._positions[i] * nanometers
## The atom positions read from the PDBx/mmCIF file. If the file contains multiple frames, these are the positions in the first frame.
self.positions = self._positions[0]
self.topology.createStandardBonds()
self._numpyPositions = None
# Record unit cell information, if present.
cell = block.getObj("cell")
if cell is not None and cell.getRowCount() > 0:
row = cell.getRow(0)
(a, b, c) = [
float(row[cell.getAttributeIndex(attribute)]) * 0.1
for attribute in ("length_a", "length_b", "length_c")
]
(alpha, beta, gamma) = [
float(row[cell.getAttributeIndex(attribute)]) * math.pi / 180.0
for attribute in ("angle_alpha", "angle_beta", "angle_gamma")
]
self.topology.setPeriodicBoxVectors(computePeriodicBoxVectors(a, b, c, alpha, beta, gamma))
# Add bonds based on struct_conn records.
connectData = block.getObj("struct_conn")
if connectData is not None:
res1Col = connectData.getAttributeIndex("ptnr1_label_seq_id")
res2Col = connectData.getAttributeIndex("ptnr2_label_seq_id")
atom1Col = connectData.getAttributeIndex("ptnr1_label_atom_id")
atom2Col = connectData.getAttributeIndex("ptnr2_label_atom_id")
asym1Col = connectData.getAttributeIndex("ptnr1_label_asym_id")
asym2Col = connectData.getAttributeIndex("ptnr2_label_asym_id")
typeCol = connectData.getAttributeIndex("conn_type_id")
connectBonds = []
for row in connectData.getRowList():
type = row[typeCol][:6]
if type in ("covale", "disulf", "modres"):
key1 = (row[res1Col], row[asym1Col], row[atom1Col])
key2 = (row[res2Col], row[asym2Col], row[atom2Col])
if key1 in atomTable and key2 in atomTable:
connectBonds.append((atomTable[key1], atomTable[key2]))
if len(connectBonds) > 0:
# Only add bonds that don't already exist.
existingBonds = set(top.bonds())
for bond in connectBonds:
if bond not in existingBonds and (bond[1], bond[0]) not in existingBonds:
top.addBond(bond[0], bond[1])
existingBonds.add(bond)
def __init__(self, pdb_line):
"""Create a new pdb.Atom from an ATOM or HETATM line.
Example line:
ATOM 2209 CB TYR A 299 6.167 22.607 20.046 1.00 8.12 C
00000000011111111112222222222333333333344444444445555555555666666666677777777778
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM line format description from
http://deposit.rcsb.org/adit/docs/pdb_atom_format.html:
COLUMNS DATA TYPE CONTENTS
--------------------------------------------------------------------------------
1 - 6 Record name "ATOM "
7 - 11 Integer Atom serial number.
13 - 16 Atom Atom name.
17 Character Alternate location indicator.
18 - 20 Residue name Residue name.
22 Character Chain identifier.
23 - 26 Integer Residue sequence number.
27 AChar Code for insertion of residues.
31 - 38 Real(8.3) Orthogonal coordinates for X in Angstroms.
39 - 46 Real(8.3) Orthogonal coordinates for Y in Angstroms.
47 - 54 Real(8.3) Orthogonal coordinates for Z in Angstroms.
55 - 60 Real(6.2) Occupancy (Default = 1.0).
61 - 66 Real(6.2) Temperature factor (Default = 0.0).
73 - 76 LString(4) Segment identifier, left-justified.
77 - 78 LString(2) Element symbol, right-justified.
79 - 80 LString(2) Charge on the atom.
"""
# We might modify first/final status during _finalize() methods
self.is_first_atom_in_chain = False
self.is_final_atom_in_chain = False
self.is_first_residue_in_chain = False
self.is_final_residue_in_chain = False
# Start parsing fields from pdb line
self.record_name = pdb_line[0:6].strip()
self.serial_number = int(pdb_line[6:11])
self.name_with_spaces = pdb_line[12:16]
alternate_location_indicator = pdb_line[16]
self.residue_name_with_spaces = pdb_line[17:20]
# In some MD codes, notably ffamber in gromacs, residue name has a fourth character in
# column 21
possible_fourth_character = pdb_line[20:21]
if possible_fourth_character != " ":
# Fourth character should only be there if official 3 are already full
if len(self.residue_name_with_spaces.strip()) != 3:
raise ValueError('Misaligned residue name: %s' % pdb_line)
self.residue_name_with_spaces += possible_fourth_character
self.residue_name = self.residue_name_with_spaces.strip()
self.chain_id = pdb_line[21]
self.residue_number = int(pdb_line[22:26])
self.insertion_code = pdb_line[26]
# coordinates, occupancy, and temperature factor belong in Atom.Location object
x = float(pdb_line[30:38])
y = float(pdb_line[38:46])
z = float(pdb_line[46:54])
try:
occupancy = float(pdb_line[54:60])
except:
occupancy = 1.0
try:
temperature_factor = float(pdb_line[60:66])
except:
temperature_factor = 0.0
self.locations = {}
loc = Atom.Location(alternate_location_indicator, np.array([x, y, z]),
occupancy, temperature_factor,
self.residue_name_with_spaces)
self.locations[alternate_location_indicator] = loc
self.default_location_id = alternate_location_indicator
# segment id, element_symbol, and formal_charge are not always present
self.segment_id = pdb_line[72:76].strip()
self.element_symbol = pdb_line[76:78].strip()
try:
self.formal_charge = int(pdb_line[78:80])
except ValueError:
self.formal_charge = None
# figure out atom element
try:
# First try to find a sensible element symbol from columns 76-77
self.element = element.get_by_symbol(self.element_symbol)
except KeyError:
# otherwise, deduce element from first two characters of atom name
# remove digits found in some hydrogen atom names
symbol = self.name_with_spaces[0:2].strip().lstrip("0123456789")
try:
# Some molecular dynamics PDB files, such as gromacs with ffamber force
# field, include 4-character hydrogen atom names beginning with "H".
# Hopefully elements like holmium (Ho) and mercury (Hg) will have fewer than four
# characters in the atom name. This problem is the fault of molecular
# dynamics code authors who feel the need to make up their own atom
# nomenclature because it is too tedious to read that provided by the PDB.
# These are the same folks who invent their own meanings for biochemical terms
# like "dipeptide". Clowntards.
if len(self.name) == 4 and self.name[0:1] == "H":
self.element = element.hydrogen
else:
self.element = element.get_by_symbol(symbol)
except KeyError:
# OK, I give up
self.element = None
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 .gro file.
The atom positions can be retrieved by calling getPositions().
Parameters:
- file (string) the name of the file to load
"""
xyzs = []
elements = [] # The element, most useful for quantum chemistry calculations
atomname = [] # The atom name, for instance 'HW1'
comms = []
resid = []
resname = []
boxes = []
xyz = []
ln = 0
frame = 0
for line in open(file):
if ln == 0:
comms.append(line.strip())
elif ln == 1:
na = int(line.strip())
elif _is_gro_coord(line):
if frame == 0: # Create the list of residues, atom names etc. only if it's the first frame.
(thisresnum, thisresname, thisatomname) = [line[i*5:i*5+5].strip() for i in range(3)]
resname.append(thisresname)
resid.append(int(thisresnum))
atomname.append(thisatomname)
thiselem = thisatomname
if len(thiselem) > 1:
thiselem = thiselem[0] + sub('[A-Z0-9]','',thiselem[1:])
try:
elements.append(elem.get_by_symbol(thiselem))
except KeyError:
elements.append(None)
firstDecimalPos = line.index('.', 20)
secondDecimalPos = line.index('.', firstDecimalPos+1)
digits = secondDecimalPos-firstDecimalPos
pos = [float(line[20+i*digits:20+(i+1)*digits]) for i in range(3)]
xyz.append(Vec3(pos[0], pos[1], pos[2]))
elif _is_gro_box(line) and ln == na + 2:
sline = line.split()
boxes.append(tuple([float(i) for i in sline])*nanometers)
xyzs.append(xyz*nanometers)
xyz = []
ln = -1
frame += 1
else:
raise Exception("Unexpected line in .gro file: "+line)
ln += 1
## The atom positions read from the file. If the file contains multiple frames, these are the positions in the first frame.
self.positions = xyzs[0]
## A list containing the element of each atom stored in the file
self.elements = elements
## A list containing the name of each atom stored in the file
self.atomNames = atomname
## A list containing the ID of the residue that each atom belongs to
self.residueIds = resid
## A list containing the name of the residue that each atom belongs to
self.residueNames = resname
self._positions = xyzs
self._unitCellDimensions = boxes
self._numpyPositions = None
def __init__(self, file):
"""Load a .gro file.
The atom positions can be retrieved by calling getPositions().
Parameters:
- file (string) the name of the file to load
"""
xyzs = []
elements = [
] # The element, most useful for quantum chemistry calculations
atomname = [] # The atom name, for instance 'HW1'
comms = []
resid = []
resname = []
boxes = []
xyz = []
ln = 0
frame = 0
for line in open(file):
if ln == 0:
comms.append(line.strip())
elif ln == 1:
na = int(line.strip())
elif _is_gro_coord(line):
if frame == 0: # Create the list of residues, atom names etc. only if it's the first frame.
(thisresnum, thisresname, thisatomname) = [
line[i * 5:i * 5 + 5].strip() for i in range(3)
]
resname.append(thisresname)
resid.append(int(thisresnum))
atomname.append(thisatomname)
thiselem = thisatomname
if len(thiselem) > 1:
thiselem = thiselem[0] + sub('[A-Z0-9]', '',
thiselem[1:])
try:
elements.append(elem.get_by_symbol(thiselem))
except KeyError:
elements.append(None)
firstDecimalPos = line.index('.', 20)
secondDecimalPos = line.index('.', firstDecimalPos + 1)
digits = secondDecimalPos - firstDecimalPos
pos = [
float(line[20 + i * digits:20 + (i + 1) * digits])
for i in range(3)
]
xyz.append(Vec3(pos[0], pos[1], pos[2]))
elif _is_gro_box(line) and ln == na + 2:
sline = line.split()
boxes.append(_construct_box_vectors(line))
xyzs.append(xyz * nanometers)
xyz = []
ln = -1
frame += 1
else:
raise Exception("Unexpected line in .gro file: " + line)
ln += 1
## The atom positions read from the file. If the file contains multiple frames, these are the positions in the first frame.
self.positions = xyzs[0]
## A list containing the element of each atom stored in the file
self.elements = elements
## A list containing the name of each atom stored in the file
self.atomNames = atomname
## A list containing the ID of the residue that each atom belongs to
self.residueIds = resid
## A list containing the name of the residue that each atom belongs to
self.residueNames = resname
self._positions = xyzs
self._periodicBoxVectors = boxes
self._numpyPositions = None
def __init__(self, file):
"""Load a .gro file.
The atom positions can be retrieved by calling getPositions().
Parameters:
- file (string) the name of the file to load
"""
xyzs = []
elements = [] # The element, most useful for quantum chemistry calculations
atomname = [] # The atom name, for instance 'HW1'
comms = []
resid = []
resname = []
boxes = []
xyz = []
ln = 0
frame = 0
for line in open(file):
sline = line.split()
if ln == 0:
comms.append(line.strip())
elif ln == 1:
na = int(line.strip())
elif _is_gro_coord(line):
if frame == 0: # Create the list of residues, atom names etc. only if it's the first frame.
# Name of the residue, for instance '153SOL1 -> SOL1' ; strips leading numbers
thisresname = sub('^[0-9]*','',sline[0])
resname.append(thisresname)
resid.append(int(sline[0].replace(thisresname,'')))
atomname.append(sline[1])
thiselem = sline[1]
if len(thiselem) > 1:
thiselem = thiselem[0] + sub('[A-Z0-9]','',thiselem[1:])
try:
elements.append(elem.get_by_symbol(thiselem))
except KeyError:
elements.append(None)
pos = [float(i) for i in sline[-3:]]
xyz.append(Vec3(pos[0], pos[1], pos[2]))
elif _is_gro_box(line) and ln == na + 2:
boxes.append([float(i) for i in sline]*nanometers)
xyzs.append(xyz*nanometers)
xyz = []
ln = -1
frame += 1
else:
raise Exception("Unexpected line in .gro file: "+line)
ln += 1
## The atom positions read from the file. If the file contains multiple frames, these are the positions in the first frame.
self.positions = xyzs[0]
## A list containing the element of each atom stored in the file
self.elements = elements
## A list containing the name of each atom stored in the file
self.atomNames = atomname
## A list containing the ID of the residue that each atom belongs to
self.residueIds = resid
## A list containing the name of the residue that each atom belongs to
self.residueNames = resname
self._positions = xyzs
self._unitCellDimensions = boxes
self._numpyPositions = None
