Merged changes from main branch

docs/sphinx/autonumber.py

+from docutils.parsers.rst import roles
+from docutils.nodes import Text, reference, section
+from sphinx.roles import XRefRole
+    
+class autonumber(Text):
+    pass
+    
+class autonumber_ref(reference):
+    pass
+
+def autonumber_role(name, rawtext, text, lineno, inliner, options={}, content=[]):
+    return ([autonumber(text)], [])
+
+def doctree_resolved(app, doctree, docname):
+    index = {};
+    refTable = {}
+    if app.config.autonumber_by_chapter:
+        # Record the number of each chapter
+        
+        env = app.builder.env
+        sectionNumbers = {}
+        for doc in env.toc_secnumbers:
+            sections = env.toc_secnumbers[doc]
+            for sectionId in sections:
+                sectionNumbers[sectionId[1:]] = sections[sectionId]
+        lastChapter = -1
+    
+    # Assign numbers to all the autonumbered objects.
+    
+    for node in doctree.traverse(autonumber):
+        category = node.astext().split(',')[0]
+        if category in index:
+            nextNumber = index[category]+1
+        else:
+            nextNumber = 1
+        if app.config.autonumber_by_chapter:
+            parent = node.parent
+            chapter = None
+            while chapter is None:
+                if isinstance(parent, section):
+                    chapter = parent
+                parent = parent.parent
+            chapter = sectionNumbers[chapter.attributes['ids'][0]][0]
+            if chapter != lastChapter:
+                index = {}
+            newNode = Text('%s %d-%d' % (category, chapter, nextNumber))
+            lastChapter = chapter
+        else:
+            newNode = Text('%s %d' % (category, nextNumber))            
+        index[category] = nextNumber
+        refTable[node.astext()] = newNode
+        node.parent.replace(node, newNode)
+    
+    # Replace references with the name of the referenced object
+    
+    for ref_info in doctree.traverse(autonumber_ref):
+        target = ref_info['reftarget']
+        if target not in refTable:
+            raise ValueError('Unknown target for autonumber reference: '+target)
+        ref_info.replace_self(Text(refTable[target].astext()))
+
+def setup(app):
+    app.add_config_value('autonumber_by_chapter', True, False)
+    roles.register_local_role('autonumber', autonumber_role)
+    app.add_node(autonumber)
+    app.add_node(autonumber_ref)
+    app.add_role('numref', XRefRole(nodeclass=autonumber_ref))
+    app.connect('doctree-resolved', doctree_resolved)
+
+

docs/sphinx/caption.py

+from docutils.parsers.rst import Directive
+from docutils.nodes import compound, raw
+
+class CaptionDirective(Directive):
+    
+    has_content = True
+
+    def run(self):
+        latexPrefix = raw('', '{\\centering', format='latex')
+        latexSuffix = raw('', '\\par}\\bigskip', format='latex')
+        text = '\n'.join(self.content)
+        content_node = compound(rawsource=text)
+        self.state.nested_parse(self.content, self.content_offset, content_node)
+        content_node.attributes['classes'].append('caption')
+        return [latexPrefix, content_node, latexSuffix]
+
+def setup(app):
+    app.add_directive('caption', CaptionDirective)

docs/sphinx/samepage.py

+from docutils.parsers.rst import Directive
+from docutils.nodes import compound, raw
+
+class SamepageDirective(Directive):
+    
+    has_content = True
+
+    def run(self):
+        prefix = raw('', '\\par\\begin{samepage}', format='latex')
+        suffix = raw('', '\\end{samepage}\\par', format='latex')
+        text = '\n'.join(self.content)
+        content_node = compound(rawsource=text)
+        self.state.nested_parse(self.content, self.content_offset, content_node)
+        return [prefix, content_node, suffix]
+
+def setup(app):
+    app.add_directive('samepage', SamepageDirective)

docs/usersguide/Makefile

+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	-rm -rf $(BUILDDIR)/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/OpenMMDeveloperGuide.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/OpenMMDeveloperGuide.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/OpenMMDeveloperGuide"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/OpenMMDeveloperGuide"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."

docs/usersguide/conf.py

+# -*- coding: utf-8 -*-
+#
+# OpenMM Developer Guide documentation build configuration file, created by
+# sphinx-quickstart on Fri Feb  7 12:42:06 2014.
+#
+# This file is execfile()d with the current directory set to its containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys, os
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+sys.path.insert(0, os.path.abspath('.'))
+sys.path.append(os.path.abspath('../sphinx'))
+
+# -- General configuration -----------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be extensions
+# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+extensions = ['sphinx.ext.pngmath', 'sphinx.ext.mathjax', 'sphinxcontrib.bibtex', 'autonumber', 'samepage', 'caption', 'numsec']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'OpenMM Users Guide'
+copyright = u'2008-2014, Stanford University'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+version = '6.0'
+# The full version, including alpha/beta/rc tags.
+release = '6.0'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ['_build']
+
+# The reST default role (used for this markup: `text`) to use for all documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+
+# -- Options for HTML output ---------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+html_theme = 'agogo'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'OpenMMUsersGuidedoc'
+
+
+# -- Options for LaTeX output --------------------------------------------------
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+#'papersize': 'letterpaper',
+
+# The font size ('10pt', '11pt' or '12pt').
+#'pointsize': '10pt',
+
+# Additional stuff for the LaTeX preamble.
+'preamble': """
+    \\usepackage[none]{hyphenat}
+    \\usepackage{xstring}
+    \\usepackage{color}
+    \\usepackage{caption}
+    \\setcounter{tocdepth}{3}
+    \\captionsetup[figure]{labelformat=empty}
+    \\renewcommand{\DUspan}[2]{%
+        \\IfEqCase{#1}{%
+            {code}{\\small{}\\texttt{#2}\\normalsize{}}%
+        }[\\PackageError{DUspan}{Unrecognized option passed to DUspan: #1}{}]%
+    }%""",
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass [howto/manual]).
+latex_documents = [
+  ('index', 'OpenMMUsersGuide.tex', u'OpenMM Users Guide',
+   u'Peter Eastman', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output --------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('index', 'openmmusersguide', u'OpenMM Users Guide',
+     [u'Peter Eastman'], 1)
+]
+
+# If true, show URL addresses after external links.
+#man_show_urls = False
+
+
+# -- Options for Texinfo output ------------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+  ('index', 'OpenMMUsersGuide', u'OpenMM Users Guide',
+   u'Peter Eastman', 'OpenMMUsersGuide', 'One line description of project.',
+   'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#texinfo_appendices = []
+
+# If false, no module index is generated.
+#texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#texinfo_show_urls = 'footnote'

docs/usersguide/header.rst

+.. role:: code
+.. raw:: html
+
+    <style> .code {font-family:monospace;} </style>
+    <style> .caption {text-align:center;} </style>
+
+.. |--| replace:: :option:`--`

docs/usersguide/index.rst

+.. include:: header.rst
+
+####################################
+OpenMM Users Manual and Theory Guide
+####################################
+
+
+Portions copyright (c) 2008-2014 Stanford University and the Authors
+
+Contributors:  Kyle Beauchamp, Christopher Bruns, Peter Eastman, Mark
+Friedrichs, Joy P. Ku, Vijay Pande, Randy Radmer, Michael Sherman, Tom Markland
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this document (the "Document"), to deal in the Document without restriction,
+including without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Document, and to permit
+persons to whom the Document is furnished to do so, subject to the following
+conditions:
+
+This copyright and permission notice shall be included in all copies or
+substantial portions of the Document.
+
+THE DOCUMENT IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
+FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL THE AUTHORS,
+CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE DOCUMENT OR THE USE OR OTHER DEALINGS IN THE
+DOCUMENT.
+
+
+.. toctree::
+   :numbered:
+   :maxdepth: 3
+
+   introduction   
+   application
+   library
+   theory
+   zbibliography
+

docs/usersguide/introduction.rst

+.. include:: header.rst
+
+Introduction
+############
+
+OpenMM consists of two parts:
+
+#. A set of libraries that lets programmers easily add molecular simulation
+   features to their programs
+#. An “application layer” that exposes those features to end users who just want
+   to run simulations
+
+
+This guide is devided into three sections:
+
+* Part I (Chapters :ref:`the-openmm-application-layer-introduction`\ -\ :ref:`creating-force-fields`\ )
+  describes the application layer.  It is relevant to all users, but especially relevant to people
+  who want to use OpenMM as a stand-alone application for running simulations.
+* Part II (Chapters :ref:`the-openmm-library-introduction`\ -\ :ref:`drude-plugin`\ )
+  describes how to use the OpenMM libraries within your own applications.  It is primarily
+  relevant to programmers who want to write simulation applications.
+* Part III (Chapters :ref:`the-theory-behind-openmm-introduction`\ -\ :ref:`other-features`\ )
+  describes the mathematical theory behind the features found in OpenMM.  It is relevant to all users.
+
+
+Online Resources
+****************
+
+You can find more documentation and other material at our website
+http://simtk.org/home/openmm.   Among other things there is a discussion forum,
+a wiki, and videos of lectures on using OpenMM.
+
+
+Referencing OpenMM
+******************
+
+Any work that uses OpenMM should cite the following publication:
+
+P. Eastman, M. S. Friedrichs, J. D. Chodera, R. J. Radmer, C. M. Bruns, J. P.
+Ku, K. A. Beauchamp, T. J. Lane, L.-P. Wang, D. Shukla, T. Tye, M. Houston, T.
+Stich, C. Klein, M. R. Shirts, and V. S. Pande. "OpenMM 4: A Reusable,
+Extensible, Hardware Independent Library for High Performance Molecular
+Simulation." J. Chem. Theor. Comput. 9(1): 461-469. (2013).
+
+We depend on academic research grants to fund the OpenMM development efforts;
+citations of our publication will help demonstrate the value of OpenMM.
+
+
+Acknowledgments
+***************
+
+OpenMM software and all related activities, such as this manual, are funded by
+the Simbios National Center for Biomedical Computing through the National
+Institutes of Health Roadmap for Medical Research, Grant U54 GM072970.
+Information on the National Centers can be found at
+http://nihroadmap.nih.gov/bioinformatics.
+

docs/usersguide/numsec.py

+"""
+Changes section references to be the section number
+instead of the title of the section.
+"""
+
+from docutils import nodes
+import sphinx.domains.std
+
+class CustomStandardDomain(sphinx.domains.std.StandardDomain):
+
+    def __init__(self, env):
+        env.settings['footnote_references'] = 'superscript'
+        sphinx.domains.std.StandardDomain.__init__(self, env)
+
+    def resolve_xref(self, env, fromdocname, builder,
+                     typ, target, node, contnode):
+        res = super(CustomStandardDomain, self).resolve_xref(env, fromdocname, builder,
+                                                            typ, target, node, contnode)
+        
+        if res is None:
+            return res
+        
+        if typ == 'ref' and not node['refexplicit']:
+            docname, labelid, sectname = self.data['labels'].get(target, ('','',''))
+            res['refdocname'] = docname
+        
+        return res
+
+def doctree_resolved(app, doctree, docname):
+    secnums = app.builder.env.toc_secnumbers
+    for node in doctree.traverse(nodes.reference):
+        if 'refdocname' in node:
+            refdocname = node['refdocname']
+            if refdocname in secnums:
+                secnum = secnums[refdocname]
+                emphnode = node.children[0]
+                textnode = emphnode.children[0]
+                
+                toclist = app.builder.env.tocs[refdocname]
+                anchorname = None
+                for refnode in toclist.traverse(nodes.reference):
+                    if refnode.astext() == textnode.astext():
+                        anchorname = refnode['anchorname']
+                if anchorname is None:
+                    continue
+                linktext = '.'.join(map(str, secnum[anchorname]))
+                node.replace(emphnode, nodes.Text(linktext))
+
+def setup(app):
+    app.override_domain(CustomStandardDomain)
+    app.connect('doctree-resolved', doctree_resolved)
+

docs/usersguide/references.bib

+@article{Andersen1980
+   author = {Andersen, Hans C.},
+   title = {Molecular dynamics simulations at constant pressure and/or temperature},
+   journal = {Journal of Chemical Physics},
+   volume = {72},
+   number = {4},
+   pages = {2384-2393},
+   year = {1980},
+   type = {Journal Article}
+}
+
+@article{Aqvist2004
+   author = {Åqvist, Johan and Wennerström, Petra and Nervall, Martin and Bjelic, Sinisa and Brandsdal, Bjørn O.},
+   title = {Molecular dynamics simulations of water and biomolecules with a Monte Carlo constant pressure algorithm},
+   journal = {Chemical Physics Letters},
+   volume = {384},
+   pages = {288-294},
+   year = {2004},
+   type = {Journal Article}
+}
+
+@article{Berendsen1987
+   author = {Berendsen, H. J. C. and Grigera, J. R. and Straatsma, T. P.},
+   title = {The missing term in effective pair potentials},
+   journal = {Journal of Physical Chemistry},
+   volume = {91},
+   pages = {6269-6271},
+   year = {1987},
+   type = {Journal Article}
+}
+
+@article{Ceriotti2010
+   author = {Ceriotti, M. and Parrinello, M. and Markland, Thomas E. and Manolopoulos, David E.},
+   title = {Efficient stochastic thermostatting of path integral molecular dynamics},
+   journal = {Journal of Chemical Physics},
+   volume = {133},
+   number = {12},
+   year = {2010},
+   type = {Journal Article}
+}
+
+@article{Chow1995
+   author = {Chow, Kim-Hung and Ferguson, David M.},
+   title = {Isothermal-isobaric molecular dynamics simulations with Monte Carlo volume sampling},
+   journal = {Computer Physics Communications},
+   volume = {91},
+   pages = {283-289},
+   year = {1995},
+   type = {Journal Article}
+}
+
+@article{Craig2004
+   author = {Craig, I. R. and Manolopoulos, David E.},
+   title = {Quantum statistics and classical mechanics: Real time correlation functions from ring polymer molecular dynamics},
+   journal = {Journal of Chemical Physics},
+   volume = {121},
+   pages = {3368-3373},
+   year = {2004},
+   type = {Journal Article}
+}
+
+@article{Duan2003
+   author = {Duan, Y.; Wu, C. and Chowdhury, S. and Lee, M.C. and Xiong, G. and Zhang, W. and Yang, R. and Cieplak, P. and Luo, R. and Lee, T.},
+   title = {A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations},
+   journal = {Journal of Computational Chemistry},
+   volume = {24},
+   pages = {1999-2012},
+   year = {2003},
+   type = {Journal Article}
+}
+
+@article{Essmann1995
+   author = {Essmann, Ulrich and Perera, Lalith and Berkowitz, Max L. and Darden, Tom and Lee, Hsing and Pedersen, Lee G.},
+   title = {A smooth particle mesh Ewald method},
+   journal = {Journal of Chemical Physics},
+   volume = {103},
+   number = {19},
+   pages = {8577-8593},
+   year = {1995},
+   type = {Journal Article}
+}
+
+@article{Hall1984
+   author = {Hall, Randall W. and Berne, B. J.},
+   title = {Nonergodicity in path integral molecular dynamics},
+   journal = {Journal of Chemical Physics},
+   volume = {81},
+   number = {8},
+   year = {1984},
+   type = {Journal Article}
+}
+
+@article{Hawkins1995
+   author = {Hawkins, Gregory D. and Cramer, Christopher J. and Truhlar, Donald G.},
+   title = {Pairwise solute descreening of solute charges from a dielectric medium},
+   journal = {Chemical Physics Letters},
+   volume = {246},
+   number = {1-2},
+   pages = {122-129},
+   year = {1995},
+   type = {Journal Article}
+}
+
+@article{Horn2004
+   author = {Horn, Hans W. and Swope, William C. and Pitera, Jed W. and Madura, Jeffry D. and Dick, Thomas J. and Hura, Greg L. and Head-Gordon, Teresa},
+   title = {Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew},
+   journal = {Journal of Chemical Physics},
+   volume = {120},
+   pages = {9665-9678},
+   year = {2004},
+   type = {Journal Article}
+}
+
+@article{Hornak2006
+   author = {Hornak, V. and Abel, R. and Okur, A. and Strockbine, B. and Roitberg, A. and Simmerling, C.},
+   title = {Comparison of multiple Amber force fields and development of improved protein backbone parameters},
+   journal = {Proteins},
+   volume = {65},
+   pages = {712-725},
+   year = {2006},
+   type = {Journal Article}
+}
+
+@article{Izaguirre2010
+   author = {Izaguirre, Jesús A. and Sweet, Chris R. and Pande, Vijay S.},
+   title = {Multiscale dynamics of macromolecules using Normal Mode Langevin},
+   journal = {Pacific Symposium on Biocomputing},
+   volume = {15},
+   pages = {240-251},
+   year = {2010},
+   type = {Journal Article}
+}
+
+@article{Jorgensen1983
+   author = {Jorgensen, William L. and Chandrasekhar, Jayaraman and Madura, Jeffry D. and Impey, Roger W. and Klein, Michael L.},
+   title = {Comparison of simple potential functions for simulating liquid water},
+   journal = {Journal of Chemical Physics},
+   volume = {79},
+   pages = {926-935},
+   year = {1983},
+   type = {Journal Article}
+}
+
+@inbook{Kollman1997
+   author = {Kollman, P.A. and Dixon, R. and Cornell, W. and Fox, T. and Chipot, C. and Pohorille, A.},
+   title = {Computer Simulation of Biomolecular Systems},
+   editor = {Wilkinson, A. and Weiner, P. and van Gunsteren, Wilfred F.},
+   publisher = {Elsevier},
+   volume = {3},
+   pages = {83-96},
+   year = {1997},
+   type = {Book Section}
+}
+
+@article{Labute2008
+   author = {Labute, Paul},
+   title = {The generalized Born/volume integral implicit solvent model: Estimation of the free energy of hydration using London dispersion instead of atomic surface area},
+   journal = {Journal of Computational Chemistry},
+   volume = {29},
+   number = {10},
+   pages = {1693-1698},
+   year = {2008},
+   type = {Journal Article}
+}
+
+@article{Lamoureux2006
+   author = {Lamoureux, Guillaume and Harder, Edward and Vorobyov, Igor V. and Roux, Benoit and MacKerell Jr., Alexander D.},
+   title = {A polarizable model of water for molecular dynamics simulations of biomolecules},
+   journal = {Chemical Physics Letters},
+   volume = {418},
+   number = {1-3},
+   pages = {245-249},
+   year = {2006},
+   type = {Journal Article}
+}
+
+@article{Lamoureux2003
+   author = {Lamoureux, Guillaume and Roux, Benoit},
+   title = {Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm},
+   journal = {Journal of Chemical Physics},
+   volume = {119},
+   number = {6},
+   pages = {3025-3039},
+   year = {2003},
+   type = {Journal Article}
+}
+
+@article{Li2010
+   author = {Li, D.W. and Br{\"u}schweiler, R.},
+   title = {NMR-based protein potentials},
+   journal = {Angewandte Chemie International Edition},
+   volume = {49},
+   pages = {6778-6780},
+   year = {2010},
+   type = {Journal Article}
+}
+
+@article{Lindorff-Larsen2010
+   author = {Lindorff-Larsen, K. and Piana, S. and Palmo, K. and Maragakis, P. and Klepeis, J. and Dror, R.O. and Shaw, D.E.},
+   title = {Improved side-chain torsion potentials for the Amber ff99SB protein force field},
+   journal = {Proteins},
+   volume = {78},
+   pages = {1950-1958},
+   year = {2010},
+   type = {Journal Article}
+}
+
+@article{Liu1989
+   author = {Liu, Dong C. and Nocedal, Jorge},
+   title = {On the Limited Memory BFGS Method For Large Scale Optimization},
+   journal = {Mathematical Programming},
+   volume = {45},
+   pages = {503-528},
+   year = {1989},
+   type = {Journal Article}
+}
+
+@article{Mahoney2000
+   author = {Mahoney, Michael W. and Jorgensen, William L.},
+   title = {A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions},
+   journal = {Journal of Chemical Physics},
+   volume = {112},
+   pages = {8910-8922},
+   year = {2000},
+   type = {Journal Article}
+}
+
+@article{Markland2008
+   author = {Markland, Thomas E. and Manolopoulos, David E.},
+   title = {An efficient ring polymer contraction scheme for imaginary time path integral simulations},
+   journal = {Journal of Chemical Physics},
+   volume = {129},
+   number = {2},
+   year = {2008},
+   type = {Journal Article}
+}
+
+@article{Mongan2007
+   author = {Mongan, John and Simmerling, Carlos and McCammon, J. Andrew and Case, David A. and Onufriev, Alexey},
+   title = {Generalized Born model with a simple, robust molecular volume correction},
+   journal = {Journal of Chemical Theory and Computation},
+   volume = {3},
+   number = {1},
+   pages = {156-169},
+   year = {2007},
+   type = {Journal Article}
+}
+
+@article{Nguyen2013
+   author = {Nguyen, Hai and Roe, Daniel R. and Simmerling, Carlos},
+   title = {Improved Generalized Born Solvent Model Parameters for Protein Simulations},
+   journal = {Journal of Chemical Theory and Computation},
+   volume = {9},
+   number = {4},
+   pages = {2020-2034},
+   year = {2013},
+   type = {Journal Article}
+}
+
+@article{Onufriev2004
+   author = {Onufriev, Alexey and Bashford, Donald and Case, David A.},
+   title = {Exploring protein native states and large-scale conformational changes with a modified generalized born model},
+   journal = {Proteins},
+   volume = {55},
+   number = {22},
+   pages = {383-394},
+   year = {2004},
+   type = {Journal Article}
+}
+
+@article{Parrinello1984
+   author = {Parrinello, M. and Rahman, A.},
+   title = {Study of an F center in molten KCl},
+   journal = {Journal of Chemical Physics},
+   volume = {80},
+   number = {2},
+   pages = {860-867},
+   year = {1984},
+   type = {Journal Article}
+}
+
+@misc{Ponder
+   author = {Ponder, Jay W.},
+   title = {Personal communication},
+   type = {Personal Communication}
+}
+
+@article{Ren2002
+   author = {Ren, P. and Ponder, Jay W.},
+   title = {A Consistent Treatment of Inter- and Intramolecular Polarization in Molecular Mechanics Calculations},
+   journal = {Journal of Computational Chemistry},
+   volume = {23},
+   pages = {1497-1506},
+   year = {2002},
+   type = {Journal Article}
+}
+
+@article{Ren2003
+   author = {Ren, P. and Ponder, Jay W.},
+   title = {Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation},
+   journal = {Journal of Physical Chemistry B},
+   volume = {107},
+   pages = {5933-5947},
+   year = {2003},
+   type = {Journal Article}
+}
+
+@article{Schaefer1998
+   author = {Schaefer, Michael and Bartels, Christian and Karplus, Martin},
+   title = {Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model},
+   journal = {Journal of Molecular Biology},
+   volume = {284},
+   number = {3},
+   pages = {835-848},
+   year = {1998},
+   type = {Journal Article}
+}
+
+@article{Schnieders2007
+   author = {Schnieders, Michael J. and Ponder, Jay W.},
+   title = {Polarizable Atomic Multipole Solutes in a Generalized Kirkwood Continuum},
+   journal = {Journal of Chemical Theory and Computation},
+   volume = {3},
+   pages = {2083-2097},
+   year = {2007},
+   type = {Journal Article}
+}
+
+@article{Shirts2008
+   author = {Shirts, Michael R. and Chodera, John D.},
+   title = {Statistically optimal analysis of samples from multiple equilibrium states},
+   journal = {Journal of Chemical Physics},
+   volume = {129},
+   pages = {124105},
+   year = {2008},
+   type = {Journal Article}
+}
+
+@article{Shirts2007
+   author = {Shirts, Michael R. and Mobley, David L. and Chodera, John D. and Pande, Vijay S.},
+   title = {Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular
+Simulations},
+   journal = {Journal of Physical Chemistry B},
+   volume = {111},
+   pages = {13052-13063},
+   year = {2007},
+   type = {Journal Article}
+}
+
+@article{Shirts2005
+   author = {Shirts, Michael R. and Pande, Vijay S.},
+   title = {Solvation free energies of amino acid side chain analogs for common molecular mechanics water models},
+   journal = {Journal of Chemical Physics},
+   volume = {132},
+   pages = {134508},
+   year = {2005},
+   type = {Journal Article}
+}
+
+@article{Thole1981
+   author = {Thole, B. T.},
+   title = {Molecular polarizabilities calculated with a modified dipole interaction},
+   journal = {Chemical Physics},
+   volume = {59},
+   number = {3},
+   pages = {341-350},
+   year = {1981},
+   type = {Journal Article}
+}
+
+@article{Tironi1995
+   author = {Tironi, Ilario G. and Sperb, René and Smith, Paul E. and van Gunsteren, Wilfred F.},
+   title = {A generalized reaction field method for molecular dynamics simulations},
+   journal = {Journal of Chemical Physics},
+   volume = {102},
+   number = {13},
+   pages = {5451-5459},
+   year = {1995},
+   type = {Journal Article}
+}
+
+@article{Toukmaji1996
+   author = {Toukmaji, Abdulnour Y.  and Board Jr, John A.},
+   title = {Ewald summation techniques in perspective: a survey},
+   journal = {Computer Physics Communications},
+   volume = {95},
+   pages = {73-92},
+   year = {1996},
+   type = {Journal Article}
+}
+
+@article{Wang2000
+   author = {Wang, J. and Cieplak, P. and Kollman, P.A.},
+   title = {How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?},
+   journal = {Journal of Computational Chemistry},
+   volume = {21},
+   pages = {1049-1074},
+   year = {2000},
+   type = {Journal Article}
+}
+

docs/usersguide/zbibliography.rst

+.. only:: html
+
+   Bibliography
+   ############
+
+.. bibliography:: references.bib
+   :style: unsrt