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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 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)
|
