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# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; -*-
# 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
#
"""Stub module for distopia --- :mod:`MDAnalysis.analysis.distopia`
===================================================================
This module is a stub to provide distopia distance functions to `distances.py`
as a selectable backend.
"""
import warnings
from packaging.version import Version
MIN_DISTOPIA_VERSION = Version("0.4.0")
# check for distopia
try:
import distopia
except ImportError:
HAS_DISTOPIA = False
distopia_version = Version("0.0.0")
else:
HAS_DISTOPIA = True
# check for compatibility: currently needs to be >=0.4.0,
# some versions of `distopia` don't have a version attribute
try:
distopia_version = Version(distopia.__version__)
except AttributeError:
distopia_version = Version("0.0.0")
if distopia_version < MIN_DISTOPIA_VERSION:
warnings.warn(
f"distopia version {distopia_version} is too old; "
f"need at least {MIN_DISTOPIA_VERSION}, Your installed version of "
"distopia will NOT be used.",
category=RuntimeWarning,
)
HAS_DISTOPIA = False
import numpy as np
def calc_bond_distance_ortho(
coords1: np.ndarray,
coords2: np.ndarray,
box: np.ndarray,
results: np.ndarray,
) -> None:
distopia.distances_ortho(coords1, coords2, box[:3], results=results)
def calc_bond_distance(
coords1: np.ndarray, coords2: np.ndarray, results: np.ndarray
) -> None:
distopia.distances_no_box(coords1, coords2, results=results)
def calc_bond_distance_triclinic(
coords1: np.ndarray,
coords2: np.ndarray,
box: np.ndarray,
results: np.ndarray,
) -> None:
distopia.distances_triclinic(coords1, coords2, box, results=results)
def calc_angle(
coords1: np.ndarray,
coords2: np.ndarray,
coords3: np.ndarray,
results: np.ndarray,
) -> None:
distopia.angles_no_box(coords1, coords2, coords3, results=results)
def calc_angle_ortho(
coords1: np.ndarray,
coords2: np.ndarray,
coords3: np.ndarray,
box: np.ndarray,
results: np.ndarray,
) -> None:
distopia.angles_ortho(coords1, coords2, coords3, box[:3], results=results)
def calc_angle_triclinic(
coords1: np.ndarray,
coords2: np.ndarray,
coords3: np.ndarray,
box: np.ndarray,
results: np.ndarray,
) -> None:
distopia.angles_triclinic(coords1, coords2, coords3, box, results=results)
def calc_dihedral(
coords1: np.ndarray,
coords2: np.ndarray,
coords3: np.ndarray,
coords4: np.ndarray,
results: np.ndarray,
) -> None:
distopia.dihedrals_no_box(
coords1, coords2, coords3, coords4, results=results
)
def calc_dihedral_ortho(
coords1: np.ndarray,
coords2: np.ndarray,
coords3: np.ndarray,
coords4: np.ndarray,
box: np.ndarray,
results: np.ndarray,
) -> None:
distopia.dihedrals_ortho(
coords1, coords2, coords3, coords4, box[:3], results=results
)
def calc_dihedral_triclinic(
coords1: np.ndarray,
coords2: np.ndarray,
coords3: np.ndarray,
coords4: np.ndarray,
box: np.ndarray,
results: np.ndarray,
) -> None:
distopia.dihedrals_triclinic(
coords1, coords2, coords3, coords4, box, results=results
)
def calc_distance_array(
coords1: np.ndarray, coords2: np.ndarray, results: np.ndarray
) -> None:
distopia.distance_array_no_box(coords1, coords2, results=results)
def calc_distance_array_ortho(
coords1: np.ndarray,
coords2: np.ndarray,
box: np.ndarray,
results: np.ndarray,
) -> None:
distopia.distance_array_ortho(coords1, coords2, box[:3], results=results)
def calc_distance_array_triclinic(
coords1: np.ndarray,
coords2: np.ndarray,
box: np.ndarray,
results: np.ndarray,
) -> None:
distopia.distance_array_triclinic(coords1, coords2, box, results=results)
def calc_self_distance_array(coords: np.ndarray, results: np.ndarray) -> None:
distopia.self_distance_array_no_box(coords, results=results)
def calc_self_distance_array_ortho(
coords: np.ndarray, box: np.ndarray, results: np.ndarray
) -> None:
distopia.self_distance_array_ortho(coords, box[:3], results=results)
def calc_self_distance_array_triclinic(
coords: np.ndarray, box: np.ndarray, results: np.ndarray
) -> None:
distopia.self_distance_array_triclinic(coords, box, results=results)
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