Hbond analysis

package/CHANGELOG

@@ -13,9 +13,9 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-mm/dd/yy richardjgowers, kain88-de, lilyminium
+mm/dd/yy richardjgowers, kain88-de, lilyminium, p-j-smith
 
-  * 0.20.2
+  * 0.21.0
 
 Fixes
   * AtomGroup.guess_bonds now uses periodic boundary information when available
@@ -27,7 +27,12 @@ Fixes
 Enhancements
   * Expanded selection wildcards to the start and middle of strings (Issue #2370)
   * Added type checking and conversion to Connection TopologyAttrs (Issue #2373)
+  * New analysis.hydrogenbonds.HydrogenBondAnalysis class for the analysis of
+    hydrogen bonds. Simpler interface, more extensible and better performance
+    than analysis.hbonds.HydrogenBondAnalysis (PR #2237)
 
+Deprecations
+  * analysis.hbonds.HydrogenBondAnalysis will be deprecated in 1.0
 
 09/05/19 IAlibay, richardjgowers
 

package/MDAnalysis/analysis/__init__.py

@@ -118,6 +118,7 @@
     'distances',
     'gnm',
     'hbonds',
+    'hydrogenbonds',
     'helanal',
     'hole',
     'leaflet',

package/MDAnalysis/analysis/hbonds/hbond_analysis.py

@@ -22,13 +22,16 @@
 #
 
 # Hydrogen Bonding Analysis
-r"""Hydrogen Bond analysis --- :mod:`MDAnalysis.analysis.hbonds.hbond_analysis`
-===========================================================================
+r"""Hydrogen Bond analysis (Deprecated) --- :mod:`MDAnalysis.analysis.hbonds.hbond_analysis`
+============================================================================================
 
 :Author: David Caplan, Lukas Grossar, Oliver Beckstein
 :Year: 2010-2017
 :Copyright: GNU Public License v3
 
+..Warning:
+    This module will be deprecated in version 1.0.
+    Please use :mod:`MDAnalysis.analysis.hydrogenbonds.hbond_analysis` instead.
 
 Given a :class:`~MDAnalysis.core.universe.Universe` (simulation
 trajectory with 1 or more frames) measure all hydrogen bonds for each
@@ -336,6 +339,11 @@ class HydrogenBondAnalysis_OtherFF(HydrogenBondAnalysis):
 
 logger = logging.getLogger('MDAnalysis.analysis.hbonds')
 
+warnings.warn(
+            "This module will be deprecated in version 1.0."
+            "Please use MDAnalysis.analysis.hydrogenbonds.hbond_analysis instead.",
+            category=DeprecationWarning
+        )
 
 class HydrogenBondAnalysis(base.AnalysisBase):
     """Perform a hydrogen bond analysis
@@ -557,6 +565,13 @@ def __init__(self, universe, selection1='protein', selection2='all', selection1_
 
         """
         super(HydrogenBondAnalysis, self).__init__(universe.trajectory, **kwargs)
+
+        warnings.warn(
+            "This class will be deprecated in version 1.0."
+            "Please use MDAnalysis.analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis instead.",
+            category=DeprecationWarning
+        )
+
         # per-frame debugging output?
         self.debug = debug
 

package/MDAnalysis/analysis/hydrogenbonds/__init__.py

@@ -0,0 +1,29 @@
+# -*- 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 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.
+# 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
+#
+from __future__ import absolute_import
+
+__all__ = [
+    'HydrogenBondAnalysis'
+]
+
+from .hbond_analysis import HydrogenBondAnalysis