Expansion of dihedrals analysis module

package/CHANGELOG

@@ -23,9 +23,9 @@ Enhancements
 
   * Added a wrapper of lib.nsgrid in lib.distances.self_capped_distance
     and lib.distances.capped_distanceto automatically chose the fastest
-    method for distance based calculations. (PR #2008)  
+    method for distance based calculations. (PR #2008)
   * Added Grid search functionality in lib.nsgrid for faster distance based
-    calculations. (PR #2008)   
+    calculations. (PR #2008)
   * Modified around selections to work with KDTree and periodic boundary
     conditions.  Should reduce memory usage (#974 PR #2022)
   * Modified topology.guessers.guess_bonds to automatically select the
@@ -64,7 +64,9 @@ Enhancements
     generated with gromacs -noappend (PR #1728)
   * MDAnalysis.lib.mdamath now supports triclinic boxes and rewrote in Cython (PR #1965)
   * AtomGroup.write can write a trajectory of selected frames (Issue #1037)
-  * Added analysis.dihedrals with Ramachandran class to analysis module (PR #1997)
+  * Added dihedrals.py with Dihedral, Ramachandran, and Janin classes to
+    analysis module (PR #1997, PR #2033)
+  * Added the analysis.data module for reference data used in analysis (PR #2033)
 
 Fixes
   * rewind in the SingleFrameReader now reads the frame from the file (Issue #1929)

package/MDAnalysis/analysis/data/filenames.py

@@ -0,0 +1,59 @@
+# -*- 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
+===================
+
+: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`.
+
+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
+
+   Reference Ramachandran histogram for :class:`MDAnalysis.analysis.dihedrals.Ramachandran`.
+   The data were calculated on a data set of 500 PDB structures taken from [Lovell2003]_.
+
+"""
+from __future__ import absolute_import
+
+__all__ = [
+    "Rama_ref", "Janin_ref" # reference plots for Ramachandran and Janin classes
+]
+
+from pkg_resources import resource_filename
+
+Rama_ref = resource_filename(__name__, 'rama_ref_data.npy')
+Janin_ref = resource_filename(__name__, 'janin_ref_data.npy')
+
+# This should be the last line: clean up namespace
+del resource_filename