Source code for MDAnalysis.topology.PQRParser
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# MDAnalysis --- http://mdanalysis.googlecode.com
# 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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"""
PQR topology parser
===================
Read atoms with charges from a PQR_ file (as written by PDB2PQR_). No
connectivity is deduced.
.. SeeAlso:: The file format is described in :mod:`MDAnalysis.coordinates.PQR`.
.. _PQR: http://www.poissonboltzmann.org/file-formats/biomolecular-structurw/pqr
.. _APBS: http://www.poissonboltzmann.org/apbs
.. _PDB2PQR: http://www.poissonboltzmann.org/pdb2pqr
.. _PDB: http://www.rcsb.org/pdb/info.html#File_Formats_and_Standards
"""
from MDAnalysis.core.AtomGroup import Atom
import MDAnalysis.coordinates.PQR
from MDAnalysis.topology.core import guess_atom_type, guess_atom_mass
from .base import TopologyReader
[docs]class PQRParser(TopologyReader):
"""Parse atom information from PQR file *filename*.
Only reads the list of atoms. Reads the charges and radii from the
PQR file and populates the
:attr:`MDAnalysis.core.AtomGroup.Atom.charge` and
:attr:`MDAnalysis.core.AtomGroup.Atom.radius` attribute.
:Returns: MDAnalysis internal *structure* dict
.. SeeAlso:: The *structure* dict is defined in
`MDAnalysis.topology` and
:class:`~MDAnalysis.coordinates.PQR.PQRReader` is used to read
the PQR file.
.. versionchanged:: 0.9.0
Read chainID from a PQR file and use it as segid (before we always used
'SYSTEM' as the new segid).
"""
[docs] def parse(self):
"""Parse atom information from PQR file *filename*.
:Returns: MDAnalysis internal *structure* dict
"""
structure = {}
pqr = MDAnalysis.coordinates.PQR.PQRReader(self.filename)
structure['_atoms'] = self._parseatoms(pqr)
return structure
def _parseatoms(self, pqr):
atoms = []
# translate list of atoms to MDAnalysis Atom.
for iatom, atom in enumerate(pqr._atoms):
atomname = atom.name
atomtype = guess_atom_type(atomname)
resname = atom.resName
resid = int(atom.resSeq)
chain = atom.chainID.strip()
# no empty segids (or Universe throws IndexError)
segid = atom.segID.strip() or chain or "SYSTEM"
mass = guess_atom_mass(atomname)
charge = float(atom.charge)
radius = atom.radius
atoms.append(Atom(iatom, atomname, atomtype, resname, resid,
segid, mass, charge, radius=radius))
return atoms