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 = []
PDBFile._loadNameReplacementTables()
# Load the file.
inputFile = file
ownHandle = False
if isinstance(file, str):
inputFile = open(file)
ownHandle = True
reader = PdbxReader(inputFile)
data = []
reader.read(data)
if ownHandle:
inputFile.close()
block = data[0]
# Build the topology.
atomData = block.getObj('atom_site')
atomNameCol = atomData.getAttributeIndex('auth_atom_id')
if atomNameCol == -1:
atomNameCol = atomData.getAttributeIndex('label_atom_id')
atomIdCol = atomData.getAttributeIndex('id')
resNameCol = atomData.getAttributeIndex('auth_comp_id')
if resNameCol == -1:
resNameCol = atomData.getAttributeIndex('label_comp_id')
resNumCol = atomData.getAttributeIndex('auth_seq_id')
if resNumCol == -1:
resNumCol = atomData.getAttributeIndex('label_seq_id')
resInsertionCol = atomData.getAttributeIndex('pdbx_PDB_ins_code')
chainIdCol = atomData.getAttributeIndex('auth_asym_id')
if chainIdCol == -1:
chainIdCol = atomData.getAttributeIndex('label_asym_id')
altChainIdCol = -1
else:
altChainIdCol = atomData.getAttributeIndex('label_asym_id')
if altChainIdCol != -1:
# Figure out which column is best to use for chain IDs.
idSet = set(row[chainIdCol] for row in atomData.getRowList())
altIdSet = set(row[altChainIdCol] for row in atomData.getRowList())
if len(altIdSet) > len(idSet):
chainIdCol, altChainIdCol = (altChainIdCol, chainIdCol)
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
lastAltChainId = None
lastResId = None
lastInsertionCode = ''
atomTable = {}
atomsInResidue = set()
models = []
for row in atomData.getRowList():
atomKey = ((row[resNumCol], row[chainIdCol], 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 resInsertionCol == -1:
insertionCode = ''
else:
insertionCode = row[resInsertionCol]
if insertionCode in ('.', '?'):
insertionCode = ''
if lastChainId != row[chainIdCol] or (
altChainIdCol != -1
and lastAltChainId != row[altChainIdCol]):
# The start of a new chain.
chain = top.addChain(row[chainIdCol])
lastChainId = row[chainIdCol]
lastResId = None
if altChainIdCol != -1:
lastAltChainId = row[altChainIdCol]
if lastResId != row[resNumCol] or lastChainId != row[
chainIdCol] or lastInsertionCode != insertionCode or (
lastResId == '.'
and row[atomNameCol] in atomsInResidue):
# The start of a new residue.
resId = (None if resNumCol == -1 else row[resNumCol])
resIC = insertionCode
resName = row[resNameCol]
if resName in PDBFile._residueNameReplacements:
resName = PDBFile._residueNameReplacements[resName]
res = top.addResidue(resName, chain, resId, resIC)
if resName in PDBFile._atomNameReplacements:
atomReplacements = PDBFile._atomNameReplacements[
resName]
else:
atomReplacements = {}
lastResId = row[resNumCol]
lastInsertionCode = insertionCode
atomsInResidue.clear()
element = None
try:
element = elem.get_by_symbol(row[elementCol])
except KeyError:
pass
atomName = row[atomNameCol]
if atomName in atomReplacements:
atomName = atomReplacements[atomName]
atom = top.addAtom(atomName, element, res, row[atomIdCol])
atomTable[atomKey] = atom
atomsInResidue.add(atomName)
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[resNumCol],
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, file, extraParticleIdentifier='EP'):
"""Load a PDB file.
The atom positions and Topology can be retrieved by calling getPositions() and getTopology().
Parameters
----------
file : string or file
the name of the file to load. Alternatively you can pass an open file object.
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
elif upper.startswith('D') and any(
a.name == atomName[1:]
for a in residue.iter_atoms()):
pass # A Drude particle
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)