Source code for MDAnalysis.topology.PQRParser
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# MDAnalysis --- http://mdanalysis.googlecode.com
# Copyright (c) 2006-2011 Naveen Michaud-Agrawal,
# Elizabeth J. Denning, Oliver Beckstein,
# and contributors (see website for details)
# Released under the GNU Public Licence, v2 or any higher version
#
# 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
#
"""
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
"""
import MDAnalysis.coordinates.PQR
from MDAnalysis.topology.core import guess_atom_type, guess_atom_mass
class PQRParseError(Exception):
pass
[docs]def parse(filename):
"""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
:func:`MDAnalysis.topology.PSFParser.parse` and
:class:`~MDAnalysis.coordinates.PQR.PQRReader` is used to read
the PQR file.
"""
structure = {}
pqr = MDAnalysis.coordinates.PQR.PQRReader(filename)
__parseatoms_(pqr, structure)
# TODO: reconstruct bonds from CONECT or guess from distance search
# (e.g. like VMD)
return structure
def __parseatoms_(pqr, structure):
from MDAnalysis.core.AtomGroup import Atom
attr = "_atoms" # name of the atoms section
atoms = [] # list of Atom objects
# 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 = atom.resSeq
chain = atom.chainID.strip()
segid = atom.segID.strip() or "SYSTEM" # no empty segids (or Universe throws IndexError)
mass = guess_atom_mass(atomname)
charge = atom.charge
radius = atom.radius
atoms.append(Atom(iatom,atomname,atomtype,resname,int(resid),segid,float(mass),float(charge),
radius=radius))
structure[attr] = atoms