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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
#
r"""
Calculating path similarity --- :mod:`MDAnalysis.analysis.psa`
==========================================================================
:Author: Sean Seyler
:Year: 2015
:Copyright: Lesser GNU Public License v2.1+
.. versionadded:: 0.10.0
.. deprecated:: 2.8.0
This module is deprecated in favour of the mdakit
`pathsimanalysis <https://github.com/MDAnalysis/PathSimAnalysis>`_ and
will be removed in MDAnalysis 3.0.0.
See Also
--------
:mod:`pathsimanalysis.psa`
"""
import warnings
try:
from pathsimanalysis import (
get_path_metric_func,
sqnorm,
get_msd_matrix,
reshaper,
get_coord_axes,
hausdorff,
hausdorff_wavg,
hausdorff_avg,
hausdorff_neighbors,
discrete_frechet,
dist_mat_to_vec,
Path,
PSAPair,
PSAnalysis,
)
except ImportError:
wmsg = (
"Please install the PathSimAnalysis mdakit to use it in MDAnalysis.\n"
"More details can be found here: "
"https://www.mdanalysis.org/PathSimAnalysis/getting_started.html"
)
warnings.warn(wmsg, category=UserWarning)
else:
wmsg = (
"Deprecation in version 2.8.0:\n"
"MDAnalysis.analysis.psa is deprecated in favour of the MDAKit "
"PathSimAnalysis (https://github.com/MDAnalysis/PathSimAnalysis) "
"and will be removed in MDAnalysis version 3.0.0"
)
warnings.warn(wmsg, category=DeprecationWarning)
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