Source code for MDAnalysis.topology.PDBParser
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# MDAnalysis --- http://www.MDAnalysis.org
# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein
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# Please cite your use of MDAnalysis in published work:
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
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"""
PDB topology parser
===================
Use a PDB file to build a minimum internal structure representation.
.. Note:: Only atoms and their names are read; no bond connectivity of
(partial) charges are deduced. Masses are guessed and set to
0 if unknown.
.. SeeAlso:: :mod:`MDAnalysis.coordinates.PDB` and :mod:`Bio.PDB`
.. SeeAlso:: :mod:`MDAnalysis.topology.PrimitivePDBParser` (which
*can* guess conectivity but does not support all subleties of the full
PDB format)
Classes
-------
.. autoclass:: PDBParser
:members:
:inherited-members:
"""
from __future__ import absolute_import
try:
# BioPython is overkill but potentially extensible (altLoc etc)
import Bio.PDB
except ImportError:
raise ImportError("Bio.PDB from biopython not found."
"Required for PDB topology parser.")
from .base import TopologyReader
from ..core.AtomGroup import Atom
from ..coordinates.pdb.extensions import get_structure
from .core import guess_atom_type, guess_atom_mass, guess_atom_charge
[docs]class PDBParser(TopologyReader):
"""Read minimum topology information from a PDB file."""
format = 'PDB'
[docs] def parse(self):
"""Parse atom information from PDB file *pdbfile*.
Only reads the list of atoms.
This functions uses the :class:`Bio.PDB.PDBParser` as used by
:func:`MDAnalysis.coordinates.pdb.extensions.get_structure`.
:Returns: MDAnalysis internal *structure* dict
.. SeeAlso:: The *structure* dict is defined in `MDAnalysis.topology`.
"""
atoms = self._parseatoms()
structure = {'atoms': atoms}
return structure
def _parseatoms(self):
# use Sloppy PDB parser to cope with big PDBs!
pdb = get_structure(self.filename, "0UNK")
atoms = []
# translate Bio.PDB atom objects to MDAnalysis Atom.
for iatom, atom in enumerate(pdb.get_atoms()):
residue = atom.parent
chain_id = residue.parent.id
atomname = atom.name
atomtype = guess_atom_type(atomname)
resname = residue.resname
resid = int(residue.id[1])
# no empty segids (or Universe throws IndexError)
segid = residue.get_segid().strip() or chain_id or "SYSTEM"
mass = guess_atom_mass(atomname)
charge = guess_atom_charge(atomname)
bfactor = atom.bfactor
# occupancy = atom.occupancy
atoms.append(Atom(iatom, atomname, atomtype, resname, resid, segid,
mass, charge, bfactor=bfactor, universe=self._u))
return atoms