Accidentally added local copy of /docs as subfolder under /docs. Deleting subfolder and contents.

248e8883 · Joy Ku · 3050314a · 3050314a · 3050314a · 3050314a
Commit 248e8883 authored Mar 18, 2013 by Joy Ku
20 changed files
--- a/docs/docs/About OpenMM.doc
+++ b/docs/docs/About OpenMM.doc
--- a/docs/docs/About OpenMM.pdf
+++ b/docs/docs/About OpenMM.pdf
--- a/docs/docs/C++ API Reference.html
+++ b/docs/docs/C++ API Reference.html
-<!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
--- a/docs/docs/DoxyfileC++.in
+++ b/docs/docs/DoxyfileC++.in
-# 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"
-INPUT_ENCODING         = UTF-8
-FILE_PATTERNS          = 
-RECURSIVE              = YES
-EXCLUDE                = 
-EXCLUDE_SYMLINKS       = NO
-EXCLUDE_PATTERNS       = */tests/* \
-                         */openmmapi/src/* \
-                         */.svn/* \
-                         */olla/include/openmm/kernels.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
--- a/docs/docs/DoxyfilePython.in
+++ b/docs/docs/DoxyfilePython.in
-# 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
--- a/docs/docs/InstallationGuideImages/Thumbs.db
+++ b/docs/docs/InstallationGuideImages/Thumbs.db
--- a/docs/docs/InstallationGuideImages/VisualStudiosSetReleaseMode.jpg
+++ b/docs/docs/InstallationGuideImages/VisualStudiosSetReleaseMode.jpg
--- a/docs/docs/InstructionsForOpenMMInstallationAndExamples.doc
+++ b/docs/docs/InstructionsForOpenMMInstallationAndExamples.doc
--- a/docs/docs/InstructionsForOpenMMInstallationAndExamples.pdf
+++ b/docs/docs/InstructionsForOpenMMInstallationAndExamples.pdf
--- a/docs/docs/Lepton User's Manual.doc
+++ b/docs/docs/Lepton User's Manual.doc
--- a/docs/docs/Lepton User's Manual.pdf
+++ b/docs/docs/Lepton User's Manual.pdf
--- a/docs/docs/OpenMMApplicationGuide.doc
+++ b/docs/docs/OpenMMApplicationGuide.doc
--- a/docs/docs/OpenMMApplicationGuide.jpk.20111107.doc
+++ b/docs/docs/OpenMMApplicationGuide.jpk.20111107.doc
--- a/docs/docs/OpenMMApplicationGuide.jpk.20111117.doc
+++ b/docs/docs/OpenMMApplicationGuide.jpk.20111117.doc
--- a/docs/docs/OpenMMApplicationGuide.pdf
+++ b/docs/docs/OpenMMApplicationGuide.pdf
--- a/docs/docs/OpenMMDeveloperGuide.doc
+++ b/docs/docs/OpenMMDeveloperGuide.doc
--- a/docs/docs/OpenMMDeveloperGuide.pdf
+++ b/docs/docs/OpenMMDeveloperGuide.pdf
--- a/docs/docs/OpenMMUsersGuide.doc
+++ b/docs/docs/OpenMMUsersGuide.doc
--- a/docs/docs/OpenMMUsersGuide.pdf
+++ b/docs/docs/OpenMMUsersGuide.pdf
--- a/docs/docs/Python API Reference.html
+++ b/docs/docs/Python API Reference.html
-<!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