Source code for MDAnalysis.topology.DMSParser
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# 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
#
"""
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
"""
from MDAnalysis.core.AtomGroup import Atom
from MDAnalysis.topology.core import guess_atom_type, Bond
import sqlite3, os
class DMSParseError(Exception):
pass
[docs]def parse(filename):
"""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
:func:`MDAnalysis.topology.PSFParser.parse`.
"""
# Fix by SB: Needed because sqlite3.connect does not raise anything if file is not there
if not os.path.isfile(filename):
raise IOError("No such file: %s" % 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
atoms = None
with sqlite3.connect(filename) as con:
# 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()
# p["anum"] contains the atomic number
atoms = [ (p["id"], Atom(p["id"], p["name"].strip(), guess_atom_type(p["name"].strip()), p["resname"].strip(), p["resid"], p["segid"].strip(), p["mass"], p["charge"])) for p in particles]
atoms_dictionary = dict(atoms)
cur.execute('SELECT * FROM bond')
bonds = cur.fetchall()
bonds = [ Bond(atoms_dictionary[b["p0"]],
atoms_dictionary[b["p1"]],
b["order"] ) for b in bonds]
# 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),
return {"_atoms": [ atom[1] for atom in atoms],
"_bonds": bonds,
"_angles": [],
"_dihe": [],
"_impr": [],
"_donors": [],
"_acceptors": [],
}