Source code for MDAnalysis.coordinates.DMS

# -*- 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 GNU Public Licence, v2 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 file format --- :mod:`MDAnalysis.coordinates.DMS`
========================================================

Classes to read 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
"""
import numpy as np
import sqlite3

from . import base
from .core import triclinic_box




class DMSReader(base.SingleFrameReaderBase):
    """
    Reads both coordinates and velocities.

    .. versionchanged:: 0.11.0
       Frames now 0-based instead of 1-based
    """
    format = 'DMS'
    units = {'time': None, 'length': 'A', 'velocity': 'A/ps'}

    def get_coordinates(self, cur):
        cur.execute('SELECT * FROM particle')
        particles = cur.fetchall()
        return [(p['x'], p['y'], p['z']) for p in particles]

    def get_particle_by_columns(self, cur, columns=None):
        if columns is None:
            columns = ['x', 'y', 'z']
        cur.execute('SELECT * FROM particle')
        particles = cur.fetchall()
        return [tuple([p[c] for c in columns]) for p in particles]

    def get_global_cell(self, cur):
        cur.execute('SELECT * FROM global_cell')
        rows = cur.fetchall()
        assert len(rows) == 3
        x = [row["x"] for row in rows]
        y = [row["y"] for row in rows]
        z = [row["z"] for row in rows]
        return {'x': x, 'y': y, 'z': z}

    def _read_first_frame(self):
        coords_list = None
        velocities_list = None

        def dict_factory(cursor, row):
            d = {}
            for idx, col in enumerate(cursor.description):
                d[col[0]] = row[idx]
            return d

        with sqlite3.connect(self.filename) as con:
            # This will return dictionaries instead of tuples, when calling cur.fetch() or fetchall()
            con.row_factory = dict_factory
            cur = con.cursor()
            coords_list = self.get_coordinates(cur)
            velocities_list = self.get_particle_by_columns(cur, columns=['vx', 'vy', 'vz'])
            unitcell = self.get_global_cell(cur)

        if not coords_list:
            raise IOError("Found no coordinates")
        self.n_atoms = len(coords_list)

        velocities = np.array(velocities_list, dtype=np.float32)
        if not velocities.any():
            velocities = None

        self.ts = self._Timestep.from_coordinates(
            np.array(coords_list, dtype=np.float32),
            velocities=velocities,
            **self._ts_kwargs)
        self.ts.frame = 0  # 0-based frame number

        self.ts.dimensions = triclinic_box(unitcell['x'], unitcell['y'], unitcell['z'])

        if self.convert_units:
            self.convert_pos_from_native(self.ts._pos)  # in-place !
            if self.ts.dimensions is not None:
                self.convert_pos_from_native(self.ts.dimensions[:3])  # in-place !
            if self.ts.has_velocities:
                # converts nm/ps to A/ps units
                self.convert_velocities_from_native(self.ts._velocities)