Source code for MDAnalysis.topology.PDBQTParser

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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
#

"""
PDBQT topology parser
=====================

Use a PDBQT_ file to build a minimum internal structure representation (list of
atoms), including AutoDock_ atom types (stored as :attr:`Atom.type`) and
partial charges (:attr:`Atom.charge`).

Reads a PDBQT file line by line and is not fuzzy about numbering.

This does not support multi-model PDBQT files (yet!)

.. Warning:: Only cares for atoms and their names; connectivity is not
             deduced. Masses are guessed and set to 0 if unknown.

.. _PDBQT:
   http://autodock.scripps.edu/faqs-help/faq/what-is-the-format-of-a-pdbqt-file
.. _AutoDock:
   http://autodock.scripps.edu/
"""

import MDAnalysis.coordinates.PDBQT
from MDAnalysis.topology.core import guess_atom_type, guess_atom_mass, guess_atom_charge

[docs]class PDBQTParseError(Exception): """Signifies an error during parsing a PDBQT file.""" pass
[docs]def parse(filename): """Parse atom information from PDBQT file *filename*. :Returns: MDAnalysis internal *structure* dict .. SeeAlso:: The *structure* dict is defined in :func:`MDAnalysis.topology.PSFParser.parse` and the file is read with :class:`MDAnalysis.coordinates.PDBQT.PDBQTReader`. """ structure = {} pdb = MDAnalysis.coordinates.PDBQT.PDBQTReader(filename) __parseatoms_(pdb, structure) # TODO: reconstruct bonds from CONECT or guess from distance search # (e.g. like VMD) return structure
def __parseatoms_(pdb, 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(pdb._atoms): atomname = atom.name atomtype = atom.type # always set in PDBQT resname = atom.resName resid = atom.resSeq chain = atom.chainID.strip() segid = chain or "SYSTEM" # no empty segids (or Universe throws IndexError) mass = guess_atom_mass(atomname) charge = atom.partialCharge # always set in PDBQT bfactor = atom.tempFactor occupancy = atom.occupancy atoms.append(Atom(iatom,atomname,atomtype,resname,int(resid),segid,float(mass),float(charge), bfactor=bfactor)) structure[attr] = atoms