Source code for MDAnalysis.topology.DMSParser

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# MDAnalysis --- http://www.MDAnalysis.org
# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein
# and contributors (see AUTHORS for the full list)
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# 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
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"""
DESRES Molecular Structure file format topology parser
======================================================

Classes to read a topology from a DESRES_ Molecular Structure file
format (DMS_) coordinate files (as used by the Desmond_ MD package).

.. _DESRES: http://www.deshawresearch.com
.. _Desmond: http://www.deshawresearch.com/resources_desmond.html
.. _DMS: http://www.deshawresearch.com/Desmond_Users_Guide-0.7.pdf

Classes
-------

.. autoclass:: DMSParser
   :members:
   :inherited-members:

"""
from __future__ import absolute_import

import sqlite3
import os

from ..core.AtomGroup import Atom
from .core import guess_atom_type
from .base import TopologyReader


[docs]class DMSParser(TopologyReader): """Read a topology from a DESRES_ Molecular Structure file. Format (DMS_) coordinate files (as used by the Desmond_ MD package). .. _DESRES: http://www.deshawresearch.com .. _Desmond: http://www.deshawresearch.com/resources_desmond.html .. _DMS: http://www.deshawresearch.com/Desmond_Users_Guide-0.7.pdf """ format = 'DMS'
[docs] def parse(self): """Parse DMS file *filename* and return the dict `structure`. Only reads the list of atoms. :Returns: MDAnalysis internal *structure* dict, which contains Atom and Bond objects .. SeeAlso:: The *structure* dict is defined in :mod:`MDAnalysis.topology`. """ # Fix by SB: Needed because sqlite3.connect does not raise anything if file is not there if not os.path.isfile(self.filename): raise IOError("No such file: {0}".format(self.filename)) def dict_factory(cursor, row): """ Fetch SQL records as dictionaries, rather than the default tuples. """ d = {} for idx, col in enumerate(cursor.description): d[col[0]] = row[idx] return d with sqlite3.connect(self.filename) as con: try: # This will return dictionaries instead of tuples, # when calling cur.fetch() or fetchall() con.row_factory = dict_factory cur = con.cursor() cur.execute('SELECT * FROM particle') particles = cur.fetchall() except sqlite3.DatabaseError: raise IOError("Failed reading the atoms from DMS Database") else: # p["anum"] contains the atomic number try: atoms = [Atom(p["id"], p["name"].strip(), guess_atom_type(p["name"].strip()), p["resname"].strip(), p["resid"], p["segid"].strip(), p["mass"], p["charge"], universe=self._u) for p in particles] except KeyError: raise ValueError("Failed reading atom information") try: cur.execute('SELECT * FROM bond') bonds = cur.fetchall() except sqlite3.DatabaseError: raise IOError("Failed reading the bonds from DMS Database") else: bondlist = [] bondorder = {} for b in bonds: desc = tuple(sorted([b['p0'], b['p1']])) bondlist.append(desc) bondorder[desc] = b['order'] # All the records below besides donors and acceptors can be contained in a DMS file. # In addition to the coordinates and bonds, DMS may contain the entire force-field # information (terms+parameters), structure = {"atoms": atoms, "bonds": tuple(bondlist), "bondorder": bondorder} return structure