Merge pull request #2523 from lilyminium/hole

Created hole2 module

package/CHANGELOG

@@ -57,6 +57,9 @@ Fixes
   * Added parmed to setup.py
 
 Enhancements
+  * New analysis.hole2 module for HOLE interfacing. Contains a function (hole) 
+    for running HOLE on singular PDB files and class (HoleAnalysis) for 
+    trajectories (PR #2523)
   * Changed selection wildcards to support multiple wildcards (#2436)
   * Added coordinate reader and writer for NAMD binary coordinate format (PR #2485)
   * Improved ClusterCollection and Cluster string representations (Issue #2464)
@@ -134,6 +137,7 @@ Changes
     function calls. (Issue #782)
 
 Deprecations
+  * analysis.hole is deprecated in 1.0 (remove in 2.0)
   * analysis.hbonds.HydrogenBondAnalysis is deprecated in 1.0 (remove in 2.0)
 
 

package/MDAnalysis/analysis/hole2/__init__.py

@@ -0,0 +1,41 @@
+# -*- 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) 2006-2020 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
+from ...due import due, Doi
+from .hole import hole, HoleAnalysis
+from .utils import create_vmd_surface
+
+due.cite(Doi("10.1016/S0006-3495(93)81293-1"),
+         description="HOLE program",
+         path="MDAnalysis.analysis.hole",
+         cite_module=True)
+due.cite(Doi("10.1016/S0263-7855(97)00009-X"),
+         description="HOLE program",
+         path="MDAnalysis.analysis.hole",
+         cite_module=True)
+due.cite(Doi("10.1016/j.jmb.2013.10.024"),
+         description="HOLE trajectory analysis with orderparameters",
+         path="MDAnalysis.analysis.hole",
+         cite_module=True)
+del Doi