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Merge pull request #191 from choderalab/docs
Basic documentation for readthedocs
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| MIT License | ||
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| Copyright (c) 2015-2017 Chodera lab // Memorial Sloan Kettering Cancer Center | ||
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| Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| of this software and associated documentation files (the "Software"), to deal | ||
| in the Software without restriction, including without limitation the rights | ||
| to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| copies of the Software, and to permit persons to whom the Software is | ||
| furnished to do so, subject to the following conditions: | ||
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| The above copyright notice and this permission notice shall be included in all | ||
| copies or substantial portions of the Software. | ||
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| THE SOFTWARE 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 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 SOFTWARE OR THE USE OR OTHER DEALINGS IN THE | ||
| SOFTWARE. |
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| # Makefile for Sphinx documentation | ||
| # Minimal makefile for Sphinx documentation | ||
| # | ||
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| # You can set these variables from the command line. | ||
| SPHINXOPTS = | ||
| SPHINXBUILD = sphinx-build | ||
| PAPER = | ||
| SPHINXPROJ = openmmtools | ||
| SOURCEDIR = . | ||
| BUILDDIR = _build | ||
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| # User-friendly check for sphinx-build | ||
| ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1) | ||
| $(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/) | ||
| endif | ||
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| # 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) . | ||
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| .PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext | ||
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| # Put it first so that "make" without argument is like "make help". | ||
| 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 " latexpdfja to make LaTeX files and run them through platex/dvipdfmx" | ||
| @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 " xml to make Docutils-native XML files" | ||
| @echo " pseudoxml to make pseudoxml-XML files for display purposes" | ||
| @echo " linkcheck to check all external links for integrity" | ||
| @echo " doctest to run all doctests embedded in the documentation (if enabled)" | ||
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| clean: | ||
| rm -rf $(BUILDDIR)/* | ||
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| html: | ||
| $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html | ||
| @echo | ||
| @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." | ||
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| dirhtml: | ||
| $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml | ||
| @echo | ||
| @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." | ||
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| singlehtml: | ||
| $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml | ||
| @echo | ||
| @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." | ||
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| pickle: | ||
| $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle | ||
| @echo | ||
| @echo "Build finished; now you can process the pickle files." | ||
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| json: | ||
| $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json | ||
| @echo | ||
| @echo "Build finished; now you can process the JSON files." | ||
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| 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." | ||
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| 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/pymbar.qhcp" | ||
| @echo "To view the help file:" | ||
| @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/pymbar.qhc" | ||
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| devhelp: | ||
| $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp | ||
| @echo | ||
| @echo "Build finished." | ||
| @echo "To view the help file:" | ||
| @echo "# mkdir -p $$HOME/.local/share/devhelp/pymbar" | ||
| @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/pymbar" | ||
| @echo "# devhelp" | ||
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| epub: | ||
| $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub | ||
| @echo | ||
| @echo "Build finished. The epub file is in $(BUILDDIR)/epub." | ||
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| 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)." | ||
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| 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." | ||
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| latexpdfja: | ||
| $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex | ||
| @echo "Running LaTeX files through platex and dvipdfmx..." | ||
| $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja | ||
| @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." | ||
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| text: | ||
| $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text | ||
| @echo | ||
| @echo "Build finished. The text files are in $(BUILDDIR)/text." | ||
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| man: | ||
| $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man | ||
| @echo | ||
| @echo "Build finished. The manual pages are in $(BUILDDIR)/man." | ||
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| 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)." | ||
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| 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." | ||
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| gettext: | ||
| $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale | ||
| @echo | ||
| @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." | ||
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| changes: | ||
| $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes | ||
| @echo | ||
| @echo "The overview file is in $(BUILDDIR)/changes." | ||
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| 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." | ||
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| doctest: | ||
| $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest | ||
| @echo "Testing of doctests in the sources finished, look at the " \ | ||
| "results in $(BUILDDIR)/doctest/output.txt." | ||
| @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) | ||
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| xml: | ||
| $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml | ||
| @echo | ||
| @echo "Build finished. The XML files are in $(BUILDDIR)/xml." | ||
| .PHONY: help Makefile | ||
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| pseudoxml: | ||
| $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml | ||
| @echo | ||
| @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml." | ||
| # Catch-all target: route all unknown targets to Sphinx using the new | ||
| # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). | ||
| %: Makefile | ||
| @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) |
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| .. _alchemy:: | ||
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| Alchemical factories | ||
| ==================== | ||
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| :mod:`openmmtools.alchemy` contains factories for generating `alchemically-modified <http://alchemistry.org>`_ versions of OpenMM `System <http://docs.openmm.org/7.1.0/api-python/generated/simtk.openmm.openmm.System.html>`_ objects for use in alchemical free energy calculations. | ||
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| Absolute alchemical factories | ||
| ----------------------------- | ||
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| Absolute alchical factories modify the ``System`` object to allow part of the system to be alchemically annihilated or decoupled. | ||
| This is useful for computing free energies of transfer, solvation, or binding for small molecules. | ||
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| .. currentmodule:: openmmtools.alchemy | ||
| .. autosummary:: | ||
| :nosignatures: | ||
| :toctree: api/generated/ | ||
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| AlchemicalFunction | ||
| AlchemicalState | ||
| AlchemicalFactory | ||
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| Relative alchemical factories | ||
| ----------------------------- | ||
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| Coming soon! |
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| .. _cache:: | ||
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| Cache | ||
| ===== | ||
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| The module :mod:`openmmtools.cache` implements a shared LRU cache for OpenMM `Context <http://docs.openmm.org/7.1.0/api-python/generated/simtk.openmm.openmm.Context.html>`_ objects that tries to minimize the number of objects in memory at the same time. | ||
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| - :class:`LRUCache`: A simple LRU cache with a dictionary-like interface. It supports a maximum capacity and expiration. | ||
| - :class:`ContextCache`: A LRU cache for OpenMM `Context <http://docs.openmm.org/7.1.0/api-python/generated/simtk.openmm.openmm.Context.html>`_ objects. | ||
| - ``global_context_cache``: A shared :class:`ContextCache` that minimizes the number of `Context <http://docs.openmm.org/7.1.0/api-python/generated/simtk.openmm.openmm.Context.html>`_ creations when employing :class:`MCMCMove`s. | ||
| Cache objects | ||
| ------------- | ||
| .. currentmodule:: openmmtools.cache | ||
| .. autosummary:: | ||
| :nosignatures: | ||
| :toctree: api/generated/ | ||
| LRUCache | ||
| ContextCache |
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