def __init__(self, file, extraParticleIdentifier='EP'):
"""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
extraParticleIdentifier : string='EP'
if this value appears in the element column for an ATOM record, the Atom's element will be set to None to mark it as an extra particle
"""
metalElements = ['Al','As','Ba','Ca','Cd','Ce','Co','Cs','Cu','Dy','Fe','Gd','Hg','Ho','In','Ir','K','Li','Mg',
'Mn','Mo','Na','Ni','Pb','Pd','Pt','Rb','Rh','Sm','Sr','Te','Tl','V','W','Yb','Zn']
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
own_handle = False
if isinstance(file, str):
inputfile = open(file)
own_handle = True
pdb = PdbStructure(inputfile, load_all_models=True, extraParticleIdentifier=extraParticleIdentifier)
if own_handle:
inputfile.close()
PDBFile._loadNameReplacementTables()
# Build the topology
atomByNumber = {}
for chain in pdb.iter_chains():
c = top.addChain(chain.chain_id)
for residue in chain.iter_residues():
resName = residue.get_name()
if resName in PDBFile._residueNameReplacements:
resName = PDBFile._residueNameReplacements[resName]
r = top.addResidue(resName, c, str(residue.number))
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 == 'EP':
element = None
elif element is None:
# Try to guess the element.
upper = atomName.upper()
while len(upper) > 1 and upper[0].isdigit():
upper = upper[1:]
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(upper[0])
except KeyError:
pass
newAtom = top.addAtom(atomName, element, r, str(atom.serial_number))
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.setPeriodicBoxVectors(pdb.get_periodic_box_vectors())
self.topology.createStandardBonds()
self.topology.createDisulfideBonds(self.positions)
self._numpyPositions = None
# Add bonds based on CONECT records. Bonds between metals of elements specified in metalElements and residues in standardResidues are not added.
connectBonds = []
for connect in pdb.models[-1].connects:
i = connect[0]
for j in connect[1:]:
if i in atomByNumber and j in atomByNumber:
if atomByNumber[i].element is not None and atomByNumber[j].element is not None:
if atomByNumber[i].element.symbol not in metalElements and atomByNumber[j].element.symbol not in metalElements:
connectBonds.append((atomByNumber[i], atomByNumber[j]))
elif atomByNumber[i].element.symbol in metalElements and atomByNumber[j].residue.name not in PDBFile._standardResidues:
connectBonds.append((atomByNumber[i], atomByNumber[j]))
elif atomByNumber[j].element.symbol in metalElements and atomByNumber[i].residue.name not in PDBFile._standardResidues:
connectBonds.append((atomByNumber[i], atomByNumber[j]))
else:
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, extraParticleIdentifier='EP'):
"""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
extraParticleIdentifier : string='EP'
if this value appears in the element column for an ATOM record, the Atom's element will be set to None to mark it as an extra particle
"""
metalElements = [
'Al', 'As', 'Ba', 'Ca', 'Cd', 'Ce', 'Co', 'Cs', 'Cu', 'Dy', 'Fe',
'Gd', 'Hg', 'Ho', 'In', 'Ir', 'K', 'Li', 'Mg', 'Mn', 'Mo', 'Na',
'Ni', 'Pb', 'Pd', 'Pt', 'Rb', 'Rh', 'Sm', 'Sr', 'Te', 'Tl', 'V',
'W', 'Yb', 'Zn'
]
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
own_handle = False
if isinstance(file, str):
inputfile = open(file)
own_handle = True
pdb = PdbStructure(inputfile,
load_all_models=True,
extraParticleIdentifier=extraParticleIdentifier)
if own_handle:
inputfile.close()
PDBFile._loadNameReplacementTables()
# Build the topology
atomByNumber = {}
for chain in pdb.iter_chains():
c = top.addChain(chain.chain_id)
for residue in chain.iter_residues():
resName = residue.get_name()
if resName in PDBFile._residueNameReplacements:
resName = PDBFile._residueNameReplacements[resName]
r = top.addResidue(resName, c, str(residue.number),
residue.insertion_code)
if resName in PDBFile._atomNameReplacements:
atomReplacements = PDBFile._atomNameReplacements[resName]
else:
atomReplacements = {}
for atom in residue.iter_atoms():
atomName = atom.get_name()
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
atomName = atomName.strip()
element = atom.element
if element == 'EP':
element = None
elif element is None:
# Try to guess the element.
upper = atomName.upper()
while len(upper) > 1 and upper[0].isdigit():
upper = upper[1:]
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(upper[0])
except KeyError:
pass
newAtom = top.addAtom(atomName, element, r,
str(atom.serial_number))
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.iter_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.setPeriodicBoxVectors(pdb.get_periodic_box_vectors())
self.topology.createStandardBonds()
self.topology.createDisulfideBonds(self.positions)
self._numpyPositions = None
# Add bonds based on CONECT records. Bonds between metals of elements specified in metalElements and residues in standardResidues are not added.
connectBonds = []
for connect in pdb.models[-1].connects:
i = connect[0]
for j in connect[1:]:
if i in atomByNumber and j in atomByNumber:
if atomByNumber[i].element is not None and atomByNumber[
j].element is not None:
if atomByNumber[
i].element.symbol not in metalElements and atomByNumber[
j].element.symbol not in metalElements:
connectBonds.append(
(atomByNumber[i], atomByNumber[j]))
elif atomByNumber[
i].element.symbol in metalElements and atomByNumber[
j].residue.name not in PDBFile._standardResidues:
connectBonds.append(
(atomByNumber[i], atomByNumber[j]))
elif atomByNumber[
j].element.symbol in metalElements and atomByNumber[
i].residue.name not in PDBFile._standardResidues:
connectBonds.append(
(atomByNumber[i], atomByNumber[j]))
else:
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 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
own_handle = False
if isinstance(file, str):
inputfile = open(file)
own_handle = True
pdb = PdbStructure(inputfile, load_all_models=True)
if own_handle:
inputfile.close()
PDBFile._loadNameReplacementTables()
# Build the topology
atomByNumber = {}
for chain in pdb.iter_chains():
c = top.addChain(chain.chain_id)
for residue in chain.iter_residues():
resName = residue.get_name()
if resName in PDBFile._residueNameReplacements:
resName = PDBFile._residueNameReplacements[resName]
r = top.addResidue(resName, c, str(residue.number))
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, str(atom.serial_number))
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.setPeriodicBoxVectors(pdb.get_periodic_box_vectors())
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 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
own_handle = False
if isinstance(file, str):
inputfile = open(file)
own_handle = True
pdb = PdbStructure(inputfile, load_all_models=True)
if own_handle:
inputfile.close()
PDBFile._loadNameReplacementTables()
# Build the topology
atomByNumber = {}
for chain in pdb.iter_chains():
c = top.addChain(chain.chain_id)
for residue in chain.iter_residues():
resName = residue.get_name()
if resName in PDBFile._residueNameReplacements:
resName = PDBFile._residueNameReplacements[resName]
r = top.addResidue(resName, c, str(residue.number))
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,
str(atom.serial_number))
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.setPeriodicBoxVectors(pdb.get_periodic_box_vectors())
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)