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Commit 088b4910 authored by peastman's avatar peastman
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Renamed docs to docs-source

parent e4ee9efd
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Showing with 1877 additions and 1 deletion
CMakeLists.txt
View file @ 088b4910
......@@ -496,7 +496,7 @@ ELSE (EXECUTABLE_OUTPUT_PATH)
SET (TEST_PATH .)
ENDIF (EXECUTABLE_OUTPUT_PATH)
ADD_SUBDIRECTORY(docs)
ADD_SUBDIRECTORY(docs-source)
ADD_SUBDIRECTORY(tests)
ADD_SUBDIRECTORY(examples)
......
docs-source/C++ API Reference.html 0 → 100644
View file @ 088b4910
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html>
<head>
<meta http-equiv="REFRESH" content="0;url=api-c++/index.html"></HEAD>
<BODY>
</BODY>
</HTML>
\ No newline at end of file
docs-source/CMakeLists.txt 0 → 100644
View file @ 088b4910
#
# Build and install API documentation
#
find_package(Doxygen QUIET)
mark_as_advanced(CLEAR DOXYGEN_EXECUTABLE)
IF(DOXYGEN_EXECUTABLE)
# Generate C++ API documentation
SET(DOXY_CONFIG_C++ "${CMAKE_BINARY_DIR}/DoxyfileC++")
CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/DoxyfileC++.in
${DOXY_CONFIG_C++}
@ONLY )
FILE(GLOB_RECURSE OPENMM_INCLUDES "openmm/include/*.h")
FILE(GLOB_RECURSE OLLA_INCLUDES "olla/include/*.h")
ADD_CUSTOM_COMMAND(
OUTPUT "${CMAKE_BINARY_DIR}/api-c++/index.html"
COMMAND ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG_C++}
DEPENDS ${OPENMM_INCLUDES} ${OLLA_INCLUDES}
WORKING_DIRECTORY "${CMAKE_BINARY_DIR}"
COMMENT "Generating C++ API documentation using Doxygen")
ADD_CUSTOM_TARGET(C++ApiDocs
DEPENDS "${CMAKE_BINARY_DIR}/api-c++/index.html"
COMMENT "Generating C++ API documentation using Doxygen"
SOURCES
"${CMAKE_CURRENT_SOURCE_DIR}/DoxyfileC++.in"
${OPENMM_INCLUDES}
${OLLA_INCLUDES}
)
FILE(MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/api-c++/")
INSTALL(DIRECTORY "${PROJECT_BINARY_DIR}/api-c++/"
DESTINATION "docs/api-c++/")
INSTALL(FILES "C++ API Reference.html"
DESTINATION "docs/")
ADD_CUSTOM_TARGET(DoxygenApiDocs
DEPENDS "${CMAKE_BINARY_DIR}/api-c++/index.html"
COMMENT "Generating C++ API documentation using Doxygen"
SOURCES
"${CMAKE_CURRENT_SOURCE_DIR}/DoxyfileC++.in"
"${CMAKE_CURRENT_SOURCE_DIR}/DoxyfilePython.in"
${OPENMM_INCLUDES}
${OLLA_INCLUDES}
)
set(OPENMM_GENERATE_API_DOCS OFF CACHE BOOL "Whether to create API documentation using Doxygen")
IF (OPENMM_GENERATE_API_DOCS)
SET_TARGET_PROPERTIES(DoxygenApiDocs PROPERTIES EXCLUDE_FROM_ALL FALSE)
ENDIF (OPENMM_GENERATE_API_DOCS)
# Generate Python API documentation
IF (OPENMM_BUILD_PYTHON_WRAPPERS)
SET(DOXY_CONFIG_PYTHON "${CMAKE_BINARY_DIR}/DoxyfilePython")
CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/DoxyfilePython.in
${DOXY_CONFIG_PYTHON}
@ONLY )
ADD_CUSTOM_COMMAND(
OUTPUT "${CMAKE_BINARY_DIR}/api-python/index.html"
COMMAND ${DOXYGEN_EXECUTABLE} ${DOXY_CONFIG_PYTHON}
DEPENDS RunSwig
WORKING_DIRECTORY "${CMAKE_BINARY_DIR}"
COMMENT "Generating Python API documentation using Doxygen")
ADD_CUSTOM_TARGET(PythonApiDocs
DEPENDS "${CMAKE_BINARY_DIR}/api-python/index.html"
COMMENT "Generating Python API documentation using Doxygen"
SOURCES
"${CMAKE_CURRENT_SOURCE_DIR}/DoxyfilePython.in"
${OPENMM_INCLUDES}
${OLLA_INCLUDES}
)
FILE(MAKE_DIRECTORY "${PROJECT_BINARY_DIR}/api-python/")
INSTALL(DIRECTORY "${PROJECT_BINARY_DIR}/api-python/"
DESTINATION "docs/api-python/")
INSTALL(FILES "Python API Reference.html"
DESTINATION "docs/")
ADD_DEPENDENCIES(DoxygenApiDocs PythonApiDocs)
ENDIF (OPENMM_BUILD_PYTHON_WRAPPERS)
ENDIF(DOXYGEN_EXECUTABLE)
#
# Build and install the User Guide and Developer Guide
#
SET(SPHINX_BUILD_DIR "${CMAKE_BINARY_DIR}/sphinx-docs/")
FILE(MAKE_DIRECTORY "${SPHINX_BUILD_DIR}")
ADD_CUSTOM_COMMAND(
OUTPUT "${SPHINX_BUILD_DIR}/userguide/latex/OpenMMUsersGuide.pdf"
COMMAND "${CMAKE_MAKE_PROGRAM}" BUILDDIR="${SPHINX_BUILD_DIR}/userguide" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" latexpdf
WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/usersguide"
COMMENT "Generating PDF user guide"
)
ADD_CUSTOM_COMMAND(
OUTPUT "${SPHINX_BUILD_DIR}/developerguide/latex/OpenMMDeveloperGuide.pdf"
COMMAND "${CMAKE_MAKE_PROGRAM}" BUILDDIR="${SPHINX_BUILD_DIR}/developerguide" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" latexpdf
WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/developerguide"
COMMENT "Generating PDF developer guide"
)
ADD_CUSTOM_TARGET(sphinxpdf
DEPENDS "${SPHINX_BUILD_DIR}/userguide/latex/OpenMMUsersGuide.pdf" "${SPHINX_BUILD_DIR}/developerguide/latex/OpenMMDeveloperGuide.pdf"
)
ADD_CUSTOM_COMMAND(
OUTPUT "${SPHINX_BUILD_DIR}/userguide/html/index.html"
COMMAND "${CMAKE_MAKE_PROGRAM}" BUILDDIR="${SPHINX_BUILD_DIR}/userguide" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" html
WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/usersguide"
COMMENT "Generating PDF user guide"
)
ADD_CUSTOM_COMMAND(
OUTPUT "${SPHINX_BUILD_DIR}/developerguide/html/index.html"
COMMAND "${CMAKE_MAKE_PROGRAM}" BUILDDIR="${SPHINX_BUILD_DIR}/developerguide" OPENMM_VERSION="${OPENMM_MAJOR_VERSION}.${OPENMM_MINOR_VERSION}" html
WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/developerguide"
COMMENT "Generating PDF developer guide"
)
ADD_CUSTOM_TARGET(sphinxhtml
DEPENDS "${SPHINX_BUILD_DIR}/userguide/html/index.html" "${SPHINX_BUILD_DIR}/developerguide/html/index.html"
)
install(FILES "${SPHINX_BUILD_DIR}/userguide/latex/OpenMMUsersGuide.pdf" "${SPHINX_BUILD_DIR}developerguide/latex/OpenMMDeveloperGuide.pdf"
DESTINATION docs/)
FILE(GLOB LICENSE_FILES "licenses/*.txt")
install(FILES ${LICENSE_FILES}
DESTINATION licenses/)
docs-source/DoxyfileC++.in 0 → 100644
View file @ 088b4910
# Doxyfile 1.5.3
#---------------------------------------------------------------------------
# Project related configuration options
#---------------------------------------------------------------------------
DOXYFILE_ENCODING = UTF-8
PROJECT_NAME = @PROJECT_NAME@
PROJECT_NUMBER =
OUTPUT_DIRECTORY =
CREATE_SUBDIRS = NO
OUTPUT_LANGUAGE = English
BRIEF_MEMBER_DESC = YES
REPEAT_BRIEF = YES
ABBREVIATE_BRIEF =
ALWAYS_DETAILED_SEC = NO
INLINE_INHERITED_MEMB = NO
FULL_PATH_NAMES = NO
STRIP_FROM_PATH =
STRIP_FROM_INC_PATH =
SHORT_NAMES = NO
JAVADOC_AUTOBRIEF = YES
QT_AUTOBRIEF = NO
MULTILINE_CPP_IS_BRIEF = NO
DETAILS_AT_TOP = YES
INHERIT_DOCS = YES
SEPARATE_MEMBER_PAGES = NO
TAB_SIZE = 4
ALIASES =
OPTIMIZE_OUTPUT_FOR_C = NO
OPTIMIZE_OUTPUT_JAVA = NO
BUILTIN_STL_SUPPORT = NO
CPP_CLI_SUPPORT = NO
DISTRIBUTE_GROUP_DOC = YES
SUBGROUPING = YES
#---------------------------------------------------------------------------
# Build related configuration options
#---------------------------------------------------------------------------
EXTRACT_ALL = YES
EXTRACT_PRIVATE = NO
EXTRACT_STATIC = NO
EXTRACT_LOCAL_CLASSES = YES
EXTRACT_LOCAL_METHODS = NO
EXTRACT_ANON_NSPACES = NO
HIDE_UNDOC_MEMBERS = NO
HIDE_UNDOC_CLASSES = NO
HIDE_FRIEND_COMPOUNDS = NO
HIDE_IN_BODY_DOCS = YES
INTERNAL_DOCS = NO
CASE_SENSE_NAMES = YES
HIDE_SCOPE_NAMES = YES
SHOW_INCLUDE_FILES = YES
INLINE_INFO = YES
SORT_MEMBER_DOCS = YES
SORT_BRIEF_DOCS = NO
SORT_BY_SCOPE_NAME = NO
GENERATE_TODOLIST = YES
GENERATE_TESTLIST = YES
GENERATE_BUGLIST = YES
GENERATE_DEPRECATEDLIST= YES
ENABLED_SECTIONS =
MAX_INITIALIZER_LINES = 30
SHOW_USED_FILES = YES
SHOW_DIRECTORIES = YES
FILE_VERSION_FILTER =
SHOW_NAMESPACES = NO
SHOW_FILES = NO
SHOW_DIRECTORIES = NO
#---------------------------------------------------------------------------
# configuration options related to warning and progress messages
#---------------------------------------------------------------------------
QUIET = NO
WARNINGS = YES
WARN_IF_UNDOCUMENTED = YES
WARN_IF_DOC_ERROR = YES
WARN_NO_PARAMDOC = NO
WARN_FORMAT = "$file:$line: $text "
WARN_LOGFILE =
#---------------------------------------------------------------------------
# configuration options related to the input files
#---------------------------------------------------------------------------
INPUT = "@CMAKE_SOURCE_DIR@/openmmapi" \
"@CMAKE_SOURCE_DIR@/olla" \
"@CMAKE_SOURCE_DIR@/serialization/include/openmm/serialization/XmlSerializer.h" \
"@CMAKE_SOURCE_DIR@/plugins/drude/openmmapi/include" \
"@CMAKE_SOURCE_DIR@/plugins/rpmd/openmmapi/include" \
"@CMAKE_SOURCE_DIR@/plugins/amoeba/openmmapi/include"
INPUT_ENCODING = UTF-8
FILE_PATTERNS =
RECURSIVE = YES
EXCLUDE =
EXCLUDE_SYMLINKS = NO
EXCLUDE_PATTERNS = */tests/* \
*/openmmapi/src/* \
*/.svn/* \
*/olla/include/openmm/kernels.h \
*/DrudeKernels.h \
*/RpmdKernels.h \
*/amoebaKernels.h \
EXCLUDE_SYMBOLS =
EXAMPLE_PATH =
EXAMPLE_PATTERNS =
EXAMPLE_RECURSIVE = NO
IMAGE_PATH =
INPUT_FILTER =
FILTER_PATTERNS =
FILTER_SOURCE_FILES = NO
#---------------------------------------------------------------------------
# configuration options related to source browsing
#---------------------------------------------------------------------------
SOURCE_BROWSER = NO
INLINE_SOURCES = NO
STRIP_CODE_COMMENTS = YES
REFERENCED_BY_RELATION = YES
REFERENCES_RELATION = YES
REFERENCES_LINK_SOURCE = YES
USE_HTAGS = NO
VERBATIM_HEADERS = YES
#---------------------------------------------------------------------------
# configuration options related to the alphabetical class index
#---------------------------------------------------------------------------
ALPHABETICAL_INDEX = NO
COLS_IN_ALPHA_INDEX = 5
IGNORE_PREFIX =
#---------------------------------------------------------------------------
# configuration options related to the HTML output
#---------------------------------------------------------------------------
GENERATE_HTML = YES
HTML_OUTPUT = api-c++
HTML_FILE_EXTENSION = .html
HTML_HEADER =
HTML_FOOTER =
HTML_STYLESHEET =
HTML_ALIGN_MEMBERS = YES
GENERATE_HTMLHELP = NO
HTML_DYNAMIC_SECTIONS = YES
CHM_FILE =
HHC_LOCATION =
GENERATE_CHI = NO
BINARY_TOC = NO
TOC_EXPAND = NO
DISABLE_INDEX = NO
ENUM_VALUES_PER_LINE = 4
GENERATE_TREEVIEW = YES
TREEVIEW_WIDTH = 250
#---------------------------------------------------------------------------
# configuration options related to the LaTeX output
#---------------------------------------------------------------------------
GENERATE_LATEX = NO
LATEX_OUTPUT = latex
LATEX_CMD_NAME = latex
MAKEINDEX_CMD_NAME = makeindex
COMPACT_LATEX = NO
PAPER_TYPE = a4wide
EXTRA_PACKAGES =
LATEX_HEADER =
PDF_HYPERLINKS = NO
USE_PDFLATEX = NO
LATEX_BATCHMODE = NO
LATEX_HIDE_INDICES = NO
#---------------------------------------------------------------------------
# configuration options related to the RTF output
#---------------------------------------------------------------------------
GENERATE_RTF = NO
RTF_OUTPUT = rtf
COMPACT_RTF = NO
RTF_HYPERLINKS = NO
RTF_STYLESHEET_FILE =
RTF_EXTENSIONS_FILE =
#---------------------------------------------------------------------------
# configuration options related to the man page output
#---------------------------------------------------------------------------
GENERATE_MAN = NO
MAN_OUTPUT = man
MAN_EXTENSION = .3
MAN_LINKS = NO
#---------------------------------------------------------------------------
# configuration options related to the XML output
#---------------------------------------------------------------------------
GENERATE_XML = NO
XML_OUTPUT = xml
XML_SCHEMA =
XML_DTD =
XML_PROGRAMLISTING = YES
#---------------------------------------------------------------------------
# configuration options for the AutoGen Definitions output
#---------------------------------------------------------------------------
GENERATE_AUTOGEN_DEF = NO
#---------------------------------------------------------------------------
# configuration options related to the Perl module output
#---------------------------------------------------------------------------
GENERATE_PERLMOD = NO
PERLMOD_LATEX = NO
PERLMOD_PRETTY = YES
PERLMOD_MAKEVAR_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the preprocessor
#---------------------------------------------------------------------------
ENABLE_PREPROCESSING = YES
MACRO_EXPANSION = YES
EXPAND_ONLY_PREDEF = YES
SEARCH_INCLUDES = YES
INCLUDE_PATH =
INCLUDE_FILE_PATTERNS =
PREDEFINED =
EXPAND_AS_DEFINED =
SKIP_FUNCTION_MACROS = YES
#---------------------------------------------------------------------------
# Configuration::additions related to external references
#---------------------------------------------------------------------------
TAGFILES =
GENERATE_TAGFILE = "api-c++/@PROJECT_NAME@DoxygenTagfile"
ALLEXTERNALS = NO
EXTERNAL_GROUPS = YES
PERL_PATH = /usr/bin/perl
#---------------------------------------------------------------------------
# Configuration options related to the dot tool
#---------------------------------------------------------------------------
CLASS_DIAGRAMS = YES
MSCGEN_PATH = /Applications/Doxygen.app/Contents/Resources/
HIDE_UNDOC_RELATIONS = YES
HAVE_DOT = NO
CLASS_GRAPH = YES
COLLABORATION_GRAPH = YES
GROUP_GRAPHS = YES
UML_LOOK = NO
TEMPLATE_RELATIONS = YES
INCLUDE_GRAPH = YES
INCLUDED_BY_GRAPH = YES
CALL_GRAPH = NO
CALLER_GRAPH = NO
GRAPHICAL_HIERARCHY = YES
DIRECTORY_GRAPH = YES
DOT_IMAGE_FORMAT = png
DOT_PATH =
DOTFILE_DIRS =
DOT_GRAPH_MAX_NODES = 50
MAX_DOT_GRAPH_DEPTH = 0
DOT_TRANSPARENT = NO
DOT_MULTI_TARGETS = NO
GENERATE_LEGEND = YES
DOT_CLEANUP = YES
#---------------------------------------------------------------------------
# Configuration::additions related to the search engine
#---------------------------------------------------------------------------
SEARCHENGINE = YES
docs-source/DoxyfilePython.in 0 → 100644
View file @ 088b4910
# Doxyfile 1.5.3
#---------------------------------------------------------------------------
# Project related configuration options
#---------------------------------------------------------------------------
DOXYFILE_ENCODING = UTF-8
PROJECT_NAME = @PROJECT_NAME@
PROJECT_NUMBER =
OUTPUT_DIRECTORY =
CREATE_SUBDIRS = NO
OUTPUT_LANGUAGE = English
BRIEF_MEMBER_DESC = YES
REPEAT_BRIEF = YES
ABBREVIATE_BRIEF =
ALWAYS_DETAILED_SEC = NO
INLINE_INHERITED_MEMB = NO
FULL_PATH_NAMES = NO
STRIP_FROM_PATH =
STRIP_FROM_INC_PATH =
SHORT_NAMES = NO
JAVADOC_AUTOBRIEF = YES
QT_AUTOBRIEF = NO
MULTILINE_CPP_IS_BRIEF = NO
DETAILS_AT_TOP = YES
INHERIT_DOCS = YES
SEPARATE_MEMBER_PAGES = NO
TAB_SIZE = 4
ALIASES =
OPTIMIZE_OUTPUT_FOR_C = NO
OPTIMIZE_OUTPUT_JAVA = YES
BUILTIN_STL_SUPPORT = NO
CPP_CLI_SUPPORT = NO
DISTRIBUTE_GROUP_DOC = YES
SUBGROUPING = YES
#---------------------------------------------------------------------------
# Build related configuration options
#---------------------------------------------------------------------------
EXTRACT_ALL = YES
EXTRACT_PRIVATE = NO
EXTRACT_STATIC = NO
EXTRACT_LOCAL_CLASSES = YES
EXTRACT_LOCAL_METHODS = NO
EXTRACT_ANON_NSPACES = NO
HIDE_UNDOC_MEMBERS = NO
HIDE_UNDOC_CLASSES = NO
HIDE_FRIEND_COMPOUNDS = NO
HIDE_IN_BODY_DOCS = YES
INTERNAL_DOCS = NO
CASE_SENSE_NAMES = YES
HIDE_SCOPE_NAMES = YES
SHOW_INCLUDE_FILES = YES
INLINE_INFO = YES
SORT_MEMBER_DOCS = YES
SORT_BRIEF_DOCS = NO
SORT_BY_SCOPE_NAME = NO
GENERATE_TODOLIST = YES
GENERATE_TESTLIST = YES
GENERATE_BUGLIST = YES
GENERATE_DEPRECATEDLIST= YES
ENABLED_SECTIONS =
MAX_INITIALIZER_LINES = 30
SHOW_USED_FILES = YES
SHOW_DIRECTORIES = YES
FILE_VERSION_FILTER =
SHOW_NAMESPACES = NO
SHOW_FILES = NO
SHOW_DIRECTORIES = NO
#---------------------------------------------------------------------------
# configuration options related to warning and progress messages
#---------------------------------------------------------------------------
QUIET = NO
WARNINGS = YES
WARN_IF_UNDOCUMENTED = YES
WARN_IF_DOC_ERROR = YES
WARN_NO_PARAMDOC = NO
WARN_FORMAT = "$file:$line: $text "
WARN_LOGFILE =
#---------------------------------------------------------------------------
# configuration options related to the input files
#---------------------------------------------------------------------------
INPUT = "@CMAKE_BINARY_DIR@/python/simtk/openmm" "@CMAKE_BINARY_DIR@/python/simtk/openmm/app"
INPUT_ENCODING = UTF-8
FILE_PATTERNS =
RECURSIVE = NO
EXCLUDE =
EXCLUDE_SYMLINKS = NO
EXCLUDE_PATTERNS =
EXCLUDE_SYMBOLS = SerializationNode SerializationProxy SwigPyIterator
EXAMPLE_PATH =
EXAMPLE_PATTERNS =
EXAMPLE_RECURSIVE = NO
IMAGE_PATH =
INPUT_FILTER = "@PYTHON_EXECUTABLE@ @CMAKE_BINARY_DIR@/python/filterPythonFiles.py"
FILTER_PATTERNS =
FILTER_SOURCE_FILES = YES
#---------------------------------------------------------------------------
# configuration options related to source browsing
#---------------------------------------------------------------------------
SOURCE_BROWSER = NO
INLINE_SOURCES = NO
STRIP_CODE_COMMENTS = YES
REFERENCED_BY_RELATION = YES
REFERENCES_RELATION = YES
REFERENCES_LINK_SOURCE = YES
USE_HTAGS = NO
VERBATIM_HEADERS = YES
#---------------------------------------------------------------------------
# configuration options related to the alphabetical class index
#---------------------------------------------------------------------------
ALPHABETICAL_INDEX = NO
COLS_IN_ALPHA_INDEX = 5
IGNORE_PREFIX =
#---------------------------------------------------------------------------
# configuration options related to the HTML output
#---------------------------------------------------------------------------
GENERATE_HTML = YES
HTML_OUTPUT = api-python
HTML_FILE_EXTENSION = .html
HTML_HEADER =
HTML_FOOTER =
HTML_STYLESHEET =
HTML_ALIGN_MEMBERS = YES
GENERATE_HTMLHELP = NO
HTML_DYNAMIC_SECTIONS = YES
CHM_FILE =
HHC_LOCATION =
GENERATE_CHI = NO
BINARY_TOC = NO
TOC_EXPAND = NO
DISABLE_INDEX = NO
ENUM_VALUES_PER_LINE = 4
GENERATE_TREEVIEW = YES
TREEVIEW_WIDTH = 250
#---------------------------------------------------------------------------
# configuration options related to the LaTeX output
#---------------------------------------------------------------------------
GENERATE_LATEX = NO
LATEX_OUTPUT = latex
LATEX_CMD_NAME = latex
MAKEINDEX_CMD_NAME = makeindex
COMPACT_LATEX = NO
PAPER_TYPE = a4wide
EXTRA_PACKAGES =
LATEX_HEADER =
PDF_HYPERLINKS = NO
USE_PDFLATEX = NO
LATEX_BATCHMODE = NO
LATEX_HIDE_INDICES = NO
#---------------------------------------------------------------------------
# configuration options related to the RTF output
#---------------------------------------------------------------------------
GENERATE_RTF = NO
RTF_OUTPUT = rtf
COMPACT_RTF = NO
RTF_HYPERLINKS = NO
RTF_STYLESHEET_FILE =
RTF_EXTENSIONS_FILE =
#---------------------------------------------------------------------------
# configuration options related to the man page output
#---------------------------------------------------------------------------
GENERATE_MAN = NO
MAN_OUTPUT = man
MAN_EXTENSION = .3
MAN_LINKS = NO
#---------------------------------------------------------------------------
# configuration options related to the XML output
#---------------------------------------------------------------------------
GENERATE_XML = NO
XML_OUTPUT = xml
XML_SCHEMA =
XML_DTD =
XML_PROGRAMLISTING = YES
#---------------------------------------------------------------------------
# configuration options for the AutoGen Definitions output
#---------------------------------------------------------------------------
GENERATE_AUTOGEN_DEF = NO
#---------------------------------------------------------------------------
# configuration options related to the Perl module output
#---------------------------------------------------------------------------
GENERATE_PERLMOD = NO
PERLMOD_LATEX = NO
PERLMOD_PRETTY = YES
PERLMOD_MAKEVAR_PREFIX =
#---------------------------------------------------------------------------
# Configuration options related to the preprocessor
#---------------------------------------------------------------------------
ENABLE_PREPROCESSING = YES
MACRO_EXPANSION = YES
EXPAND_ONLY_PREDEF = YES
SEARCH_INCLUDES = YES
INCLUDE_PATH =
INCLUDE_FILE_PATTERNS =
PREDEFINED =
EXPAND_AS_DEFINED =
SKIP_FUNCTION_MACROS = YES
#---------------------------------------------------------------------------
# Configuration::additions related to external references
#---------------------------------------------------------------------------
TAGFILES =
GENERATE_TAGFILE = "api-python/@PROJECT_NAME@DoxygenTagfile"
ALLEXTERNALS = NO
EXTERNAL_GROUPS = YES
PERL_PATH = /usr/bin/perl
#---------------------------------------------------------------------------
# Configuration options related to the dot tool
#---------------------------------------------------------------------------
CLASS_DIAGRAMS = YES
MSCGEN_PATH = /Applications/Doxygen.app/Contents/Resources/
HIDE_UNDOC_RELATIONS = YES
HAVE_DOT = NO
CLASS_GRAPH = YES
COLLABORATION_GRAPH = YES
GROUP_GRAPHS = YES
UML_LOOK = NO
TEMPLATE_RELATIONS = YES
INCLUDE_GRAPH = YES
INCLUDED_BY_GRAPH = YES
CALL_GRAPH = NO
CALLER_GRAPH = NO
GRAPHICAL_HIERARCHY = YES
DIRECTORY_GRAPH = YES
DOT_IMAGE_FORMAT = png
DOT_PATH =
DOTFILE_DIRS =
DOT_GRAPH_MAX_NODES = 50
MAX_DOT_GRAPH_DEPTH = 0
DOT_TRANSPARENT = NO
DOT_MULTI_TARGETS = NO
GENERATE_LEGEND = YES
DOT_CLEANUP = YES
#---------------------------------------------------------------------------
# Configuration::additions related to the search engine
#---------------------------------------------------------------------------
SEARCHENGINE = YES
docs-source/Python API Reference.html 0 → 100644
View file @ 088b4910
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html>
<head>
<meta http-equiv="REFRESH" content="0;url=api-python/index.html"></HEAD>
<BODY>
</BODY>
</HTML>
\ No newline at end of file
docs-source/developerguide/Makefile 0 → 100644
View file @ 088b4910
# 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-source/developerguide/conf.py 0 → 100644
View file @ 088b4910
# -*- 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 = ['autonumber', '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 Developer Guide'
copyright = u'2011-2014, 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 = os.getenv('OPENMM_VERSION')
# The full version, including alpha/beta/rc tags.
release = os.getenv('OPENMM_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 = 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 = 'OpenMMDeveloperGuidedoc'
# -- 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', 'OpenMMDeveloperGuide.tex', u'OpenMM Developer 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', 'openmmdeveloperguide', u'OpenMM Developer 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', 'OpenMMDeveloperGuide', u'OpenMM Developer Guide',
u'Peter Eastman', 'OpenMMDeveloperGuide', '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-source/developerguide/developer.rst 0 → 100644
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docs-source/developerguide/index.rst 0 → 100644
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######################
OpenMM Developer Guide
######################
Portions copyright (c) 2011-2014 Stanford University and the Authors
Contributors: Peter Eastman
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.
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.
.. toctree::
:maxdepth: 3
:numbered:
developer
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