Sphinx

docs-source/python-api/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) .
+
+all: html
+
+html:	builddir render
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)"
+
+builddir:
+	mkdir -p $(BUILDDIR)
+
+clean:
+	rm -rf $(BUILDDIR)/*
+	rm -rf generated/*.rst
+
+render:
+	python render.py

docs-source/python-api/_templates/class.rst

+{{ objname }}
+{{ underline }}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+
+   {% block methods %}
+   .. automethod:: __init__
+
+   {% if methods %}
+   .. rubric:: Methods
+
+   .. autosummary::
+   {% for item in methods %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Attributes
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

docs-source/python-api/app.rst.jinja2

+Application Layer
+=================
+
+Loaders and Setup
+~~~~~~~~~~~~~~~~~
+.. autosummary::
+    :toctree: generated/
+    :template: class.rst
+
+    ~simtk.openmm.app.pdbfile.PDBFile
+    ~simtk.openmm.app.pdbxfile.PDBxFile
+    ~simtk.openmm.app.gromacsgrofile.GromacsGroFile
+    ~simtk.openmm.app.gromacstopfile.GromacsTopFile
+    ~simtk.openmm.app.amberinpcrdfile.AmberInpcrdFile
+    ~simtk.openmm.app.amberprmtopfile.AmberPrmtopFile
+    ~simtk.openmm.app.charmmpsffile.CharmmPsfFile
+    ~simtk.openmm.app.charmmcrdfiles.CharmmRstFile
+    ~simtk.openmm.app.charmmparameterset.CharmmParameterSet
+    ~simtk.openmm.app.desmonddmsfile.DesmondDMSFile
+
+
+Representation and Manipulation
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.. autosummary::
+    :toctree: generated/
+    :template: class.rst
+
+    ~simtk.openmm.app.topology.Topology
+    ~simtk.openmm.app.modeller.Modeller
+
+Simulation
+~~~~~~~~~~
+.. autosummary::
+    :toctree: generated/
+    :template: class.rst
+
+    ~simtk.openmm.app.forcefield.ForceField
+    ~simtk.openmm.app.simulation.Simulation
+
+
+Reporting Output
+~~~~~~~~~~~~~~~~
+.. autosummary::
+    :toctree: generated/
+    :template: class.rst
+
+{% for reporter in reporters %}
+    ~{{ reporter }}
+{% endfor %}
+    ~simtk.openmm.app.dcdfile.DCDFile

docs-source/python-api/conf.py

+# -*- coding: utf-8 -*-
+#
+# MDTraj documentation build configuration file, created by
+# sphinx-quickstart on Tue Jun 11 21:23:28 2013.
+#
+# 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
+import os
+
+import simtk.openmm.version
+
+# 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('.'))
+
+# -- 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.mathjax', 'sphinx.ext.ifconfig', 'sphinx.ext.autosummary',
+              'sphinx.ext.autodoc', 'numpydoc', 'sphinx.ext.intersphinx',]
+
+autosummary_generate = True
+autodoc_default_flags = ['members', 'inherited-members']
+
+html_theme_options = {
+    'logo': 'OPENMMLogo.png',
+    'description': 'A high performance GPU molecular simulation toolkit',
+    'github_user': 'pandegroup',
+    'github_repo': 'openmm',
+    'travis_button': True,
+}
+
+html_sidebars = {
+    '**': [
+        'about.html',
+        'navigation.html',
+        'searchbox.html',
+    ]
+}
+
+
+_python_doc_base = 'http://docs.python.org/2.7'
+intersphinx_mapping = {
+    _python_doc_base: None,
+}
+
+# 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'
+copyright = u'2015, Stanford University and the Authors'
+
+# 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 = simtk.openmm.version.short_version
+# The full version, including alpha/beta/rc tags.
+release = simtk.openmm.version.full_version
+
+# 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 = False
+
+# 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 = "alabaster"
+
+# 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 = ''
+
+# 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 = ''
+
+autodoc_member_order = 'bysource'
+
+# stackoverflow.com/questions/12206334
+numpydoc_show_class_members = False

docs-source/python-api/index.rst

+.. currentmodule:: simtk.openmm.openmm
+
+OpenMM Python API
+=================
+
+.. toctree::
+   :maxdepth: 2
+
+   app
+   library

docs-source/python-api/library.rst.jinja2

+Library API
+===========
+
+
+Core Objects
+~~~~~~~~~~~~
+.. autosummary::
+    :toctree: generated/
+    :template: class.rst
+
+    simtk.openmm.openmm.System
+    simtk.openmm.openmm.Context
+    simtk.openmm.openmm.Platform
+
+
+Forces
+~~~~~~
+.. autosummary::
+    :toctree: generated/
+    :template: class.rst
+
+    {% for force in forces %}
+    ~{{ force }}
+    {% endfor %}
+
+
+Integrators
+~~~~~~~~~~~
+.. autosummary::
+    :toctree: generated/
+    :template: class.rst
+
+    {% for integrator in integrators %}
+    ~{{ integrator }}
+    {% endfor %}
+
+Extras
+~~~~~~
+.. autosummary::
+    :toctree: generated/
+    :template: class.rst
+
+    {% for extra in library_extras %}
+    ~{{ extra }}
+    {% endfor %}

docs-source/python-api/render.py

+from os.path import dirname, join, splitext
+from glob import glob
+import inspect
+
+import jinja2
+import simtk.openmm as mm
+from simtk.openmm import app
+
+def fullname(klass):
+    return klass.__module__ + '.' + klass.__name__
+
+
+def template_variables():
+    data = {
+        'reporters': [],
+        'forces': [],
+        'integrators': [],
+        'library_extras': []
+    }
+
+
+    app_klasses = inspect.getmembers(app, predicate=inspect.isclass)
+    mm_klasses = inspect.getmembers(mm, predicate=inspect.isclass)
+
+    # gather all Reporters
+    for name, klass in app_klasses:
+        if name.endswith('Reporter'):
+            data['reporters'].append(fullname(klass))
+
+    # gather all Force subclasses
+    for name, klass in mm_klasses:
+        if issubclass(klass, mm.Force):
+            data['forces'].append(fullname(klass))
+
+    # gather all Integrator subclasses
+    for _, klass in mm_klasses:
+        if issubclass(klass, mm.Integrator):
+            data['integrators'].append(fullname(klass))
+
+    # gather all extra subclasses
+    for _, klass in mm_klasses:
+        full = fullname(klass)
+
+        if full in data['forces']:
+            continue
+        if full in data['integrators']:
+            continue
+        if full in ('simtk.openmm.openmm.Platform', 'simtk.openmm.openmm.Context',
+                    'simtk.openmm.openmm.System'):
+            continue
+        if klass.__name__[0].islower():
+            continue
+        if klass.__name__ in ['SwigPyIterator', 'OpenMMException']:
+            continue
+
+        data['library_extras'].append(full)
+
+    return data
+
+
+def main():
+    here = dirname(__file__)
+    templateLoader = jinja2.FileSystemLoader(here)
+    templateEnv = jinja2.Environment(loader=templateLoader)
+    data = template_variables()
+
+    for template_fn in glob(join(here, '*.jinja2')):
+        output_fn = splitext(template_fn)[0]
+        print('Rendering %s to %s...' % (template_fn, output_fn))
+
+        template = templateEnv.get_template(template_fn)
+        output_text = template.render(data)
+        with open(output_fn, 'w') as f:
+            f.write(output_text)
+
+
+if __name__ == '__main__':
+    main()