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Expansion of dihedrals analysis module #2033
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# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- | ||
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 | ||
# | ||
# 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. | ||
# | ||
# 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 | ||
# | ||
""" | ||
Analysis data files | ||
=================== | ||
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There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Please add brief documentation: Analysis data files
------------------
.. data:: Rama_ref
Reference Ramachandran histogram for :class:`MDAnalysis.analysis.dihedrals.Ramachandran`.
The data were calculated on a data set of 500 PDB structures taken from [Lovell2003]_.
.. data:: Janin_ref
... You are starting this data module so you should set a good example for documentation in the future. There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Insert the docs for |
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:mod:`MDAnalysis.analysis.data` contains data files that are used as part of | ||
analysis. These can be experimental or theoretical data. Files are stored | ||
inside the package and made accessible via variables in | ||
:mod:`MDAnalysis.analysis.data.filenames`. These variables are documented | ||
below, including references to the literature and where they are used | ||
inside :mod:`MDAnalysis.analysis`. | ||
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Data files | ||
---------- | ||
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.. data:: Rama_ref | ||
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Reference Ramachandran histogram for :class:`MDAnalysis.analysis.dihedrals.Ramachandran`. | ||
The data were calculated on a data set of 500 PDB structures taken from [Lovell2003]_. | ||
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.. data:: Janin_ref | ||
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Reference Ramachandran histogram for :class:`MDAnalysis.analysis.dihedrals.Ramachandran`. | ||
The data were calculated on a data set of 500 PDB structures taken from [Lovell2003]_. | ||
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""" | ||
from __future__ import absolute_import | ||
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__all__ = [ | ||
"Rama_ref", "Janin_ref" # reference plots for Ramachandran and Janin classes | ||
] | ||
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from pkg_resources import resource_filename | ||
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Rama_ref = resource_filename(__name__, 'rama_ref_data.npy') | ||
Janin_ref = resource_filename(__name__, 'janin_ref_data.npy') | ||
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# This should be the last line: clean up namespace | ||
del resource_filename |
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The
data
directory also needs an empty file__init__.py
to mark it as an importable module. Just add it withThere was a problem hiding this comment.
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The absence of the file is the reason for the test failures.