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# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the Lesser GNU Public Licence, v2.1 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
#
# 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
Classes
-------
.. autoclass:: DMSParser
:members:
:inherited-members:
"""
import numpy as np
import sqlite3
import os
from .base import TopologyReaderBase, change_squash
from ..core.topology import Topology
from ..core.topologyattrs import (
Atomids,
Atomnames,
Bonds,
Charges,
ChainIDs,
Masses,
Resids,
Resnums,
Resnames,
Segids,
AtomAttr, # for custom Attributes
)
class Atomnums(AtomAttr):
"""The number for each Atom"""
attrname = "atomnums"
singular = "atomnum"
class DMSParser(TopologyReaderBase):
"""Read a topology from a DESRES_ Molecular Structure file.
Format (DMS_) coordinate files (as used by the Desmond_ MD package).
Reads the following attributes:
Atom:
- Atomids
- Atomnums
- Atomnames
- Masses
- Charges
- Chainids
Residue:
- Resnames
- Resids
Segment:
- Segids
.. note::
By default, atomtypes will be guessed on Universe creation.
This may change in release 3.0.
See :ref:`Guessers` for more information.
.. _DESRES: http://www.deshawresearch.com
.. _Desmond: http://www.deshawresearch.com/resources_desmond.html
.. _DMS: http://www.deshawresearch.com/Desmond_Users_Guide-0.7.pdf
.. versionchanged:: 2.8.0
Removed type guessing (attributes guessing takes place now
through universe.guess_TopologyAttrs() API).
"""
format = "DMS"
def parse(self, **kwargs):
"""Parse DMS file *filename* and return the Topology object"""
# 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
attrs = {}
# Row factories for different data types
facs = {
np.int32: lambda c, r: r[0],
np.float32: lambda c, r: r[0],
object: lambda c, r: str(r[0].strip()),
}
with sqlite3.connect(self.filename) as con:
# Selecting single column, so just strip tuple
for attrname, dt in [
("id", np.int32),
("anum", np.int32),
("mass", np.float32),
("charge", np.float32),
("name", object),
("resname", object),
("resid", np.int32),
("chain", object),
("segid", object),
]:
try:
cur = con.cursor()
cur.row_factory = facs[dt]
cur.execute("SELECT {} FROM particle" "".format(attrname))
vals = cur.fetchall()
except sqlite3.DatabaseError:
errmsg = "Failed reading the atoms from DMS Database"
raise IOError(errmsg) from None
else:
attrs[attrname] = np.array(vals, dtype=dt)
try:
cur.row_factory = dict_factory
cur.execute("SELECT * FROM bond")
bonds = cur.fetchall()
except sqlite3.DatabaseError:
errmsg = "Failed reading the bonds from DMS Database"
raise IOError(errmsg) from None
else:
bondlist = []
bondorder = {}
for b in bonds:
desc = tuple(sorted([b["p0"], b["p1"]]))
bondlist.append(desc)
bondorder[desc] = b["order"]
attrs["bond"] = bondlist
attrs["bondorder"] = bondorder
topattrs = []
# Bundle in Atom level objects
for attr, cls in [
("id", Atomids),
("anum", Atomnums),
("mass", Masses),
("charge", Charges),
("name", Atomnames),
("chain", ChainIDs),
]:
topattrs.append(cls(attrs[attr]))
# Residues
atom_residx, (res_resids, res_resnums, res_resnames, res_segids) = (
change_squash(
(attrs["resid"], attrs["resname"], attrs["segid"]),
(
attrs["resid"],
attrs["resid"].copy(),
attrs["resname"],
attrs["segid"],
),
)
)
n_residues = len(res_resids)
topattrs.append(Resids(res_resids))
topattrs.append(Resnums(res_resnums))
topattrs.append(Resnames(res_resnames))
if any(res_segids) and not any(val is None for val in res_segids):
res_segidx, (res_segids,) = change_squash(
(res_segids,), (res_segids,)
)
uniq_seg = np.unique(res_segids)
idx2seg = {idx: res_segids[idx] for idx in res_segidx}
res_segids = uniq_seg
nidx = {segid: nidx for nidx, segid in enumerate(uniq_seg)}
res_segidx = np.array([nidx[idx2seg[idx]] for idx in res_segidx])
n_segments = len(res_segids)
topattrs.append(Segids(res_segids))
else:
n_segments = 1
topattrs.append(Segids(np.array(["SYSTEM"], dtype=object)))
res_segidx = None
topattrs.append(Bonds(attrs["bond"]))
top = Topology(
len(attrs["id"]),
n_residues,
n_segments,
attrs=topattrs,
atom_resindex=atom_residx,
residue_segindex=res_segidx,
)
return top
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