From: Teemu Murtola <teemu.murtola@gmail.com>
Date: Sun, 8 Feb 2015 05:22:20 +0000 (+0200)
Subject: Move flow chart from old-html to Sphinx
X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=1876477ef6075e10c27e90fac7d17508bea3f119;p=alexxy%2Fgromacs.git

Move flow chart from old-html to Sphinx

Get rid of the remaining HTML page generated from old-html/, and all the
machinery that was there just to generate and link to these pages.
The images used by the flowchart still remain in old-html/ and there is
a target to copy them to the output, but this is significantly simpler
than what it was.

For now, replace the flow chart with raw HTML within rst; using
something like sphinx.ext.graphviz could probably work better.
<td align=...> did not work when embedded into a Sphinx-generate page;
replaced with <td style="text-align:...">.

Change-Id: Icbcccd36a9cc157a5a8efe1e9054d6a6741c83ca
---

diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
index 8d75986f1b..c06a10193c 100644
--- a/docs/CMakeLists.txt
+++ b/docs/CMakeLists.txt
@@ -35,7 +35,7 @@
 # This directory provides a unified place for building all kinds of
 # GROMACS documentation. This includes some "static" content (Doxygen
 # code documentation, reference manual, install guide, old online HTML
-# pages), and content generated from the gmx program for the various
+# images), and content generated from the gmx program for the various
 # tools (man and HTML pages). It also provides the "webpage" target,
 # that combines all of the above (except man pages in man format) into
 # a form suitable for automated deployment to the GROMACS website. It
@@ -61,7 +61,6 @@ set(MAN_PAGE_DIR ${CMAKE_CURRENT_SOURCE_DIR})
 find_package(PythonInterp)
 find_package(Sphinx 1.2.3 COMPONENTS pygments)
 
-add_subdirectory(old-html)
 add_subdirectory(doxygen)
 
 option(GMX_BUILD_WEBPAGE "Whether to try to configure to build the GROMACS static webpages" OFF)
@@ -90,11 +89,11 @@ if (SPHINX_FOUND)
     set(SPHINX_SOURCE_FILES
         index.rst
         download.rst
-        online.rst
         install-guide/index.rst
         man/gromacs.7.rst
         user-guide/index.rst
         user-guide/getting-started.rst
+        user-guide/flow.rst
         user-guide/cutoff-schemes.rst
         user-guide/file-formats.rst
         user-guide/tools.rst
@@ -236,11 +235,6 @@ if(GMX_BUILD_WEBPAGE)
     set(HTML_BUILD_IS_POSSIBLE ON)
     # Next, turn it off in any of the preconditions are unsatisified
 
-    if(NOT GMX_BUILD_HELP)
-        set(HTML_BUILD_IS_POSSIBLE OFF)
-        message(STATUS "Cannot build webpage without GMX_BUILD_HELP=on")
-    endif()
-
     if(NOT MANUAL_BUILD_IS_POSSIBLE)
         set(HTML_BUILD_IS_POSSIBLE OFF)
         message(STATUS "Cannot build webpage without being able to build the reference PDF manual")
@@ -267,6 +261,13 @@ if(GMX_BUILD_WEBPAGE)
     endif()
 endif()
 
+# TODO Get rid of the remaining content in old-html
+add_custom_target(webpage-old-images
+    ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/old-html ${HTML_OUTPUT_DIR}
+    COMMENT "Copying flowchart images"
+    VERBATIM
+    )
+
 if(HTML_BUILD_IS_POSSIBLE)
     # If building the webpage from the repo, then tarballs may not
     # exist, and if so, it would not make sense to build that part of
@@ -309,24 +310,6 @@ if(HTML_BUILD_IS_POSSIBLE)
         VERBATIM
         )
 
-    # TODO Move content from the "old" html output into the new user
-    # guide, or delete, as appropriate.
-    if(NOT SOURCE_IS_SOURCE_DISTRIBUTION)
-        # TODO If content remains here once the user guide is in
-        # decent shape, try to make the generated HTML arrive directly
-        # in ${HTML_OUTPUT_DIR}
-        add_custom_target(webpage-html
-            ${CMAKE_COMMAND} -E copy_directory old-html/final ${HTML_OUTPUT_DIR}
-            )
-        add_dependencies(webpage-html html)
-    else()
-        # In the source distribution, the html pages are already
-        # built, so we can avoid making gmx via the html target
-        add_custom_target(webpage-html
-            ${CMAKE_COMMAND} -E copy_directory ${CMAKE_CURRENT_SOURCE_DIR}/old-html/final ${HTML_OUTPUT_DIR}
-            )
-    endif()
-
     # The Doxygen configuration in doxygen/Doxyfile-common.cmakein
     # makes all the Doxygen output directly in
     # ${HTML_OUTPUT_DIR}/doxygen (and makes the directory if it needs
@@ -339,7 +322,7 @@ if(HTML_BUILD_IS_POSSIBLE)
            ${extra_webpage_dependencies}
         VERBATIM
         )
-    add_dependencies(webpage webpage-sphinx webpage-html doxygen-all)
+    add_dependencies(webpage webpage-sphinx webpage-old-images doxygen-all)
 else()
     add_custom_target(webpage
         COMMAND ${CMAKE_COMMAND} -E echo "Cannot build webpage because of missing requirements. Check cmake status output for reasons"
diff --git a/docs/index.rst b/docs/index.rst
index 31d2197bf3..8d0bf87682 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -17,8 +17,6 @@ Contents:
 
    user-guide/index
 
-   online
-
 * `Reference Manual`_ (PDF format)
 
 * Answers to `Frequently Asked Questions <http://www.gromacs.org/Documentation/FAQs>`_
diff --git a/docs/old-html/BuildHtmlHelp.cmake b/docs/old-html/BuildHtmlHelp.cmake
deleted file mode 100644
index 400ea70318..0000000000
--- a/docs/old-html/BuildHtmlHelp.cmake
+++ /dev/null
@@ -1,81 +0,0 @@
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS is free software; you can redistribute it and/or
-# modify it under the terms of the GNU Lesser General Public License
-# as published by the Free Software Foundation; either version 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-# Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-if (NOT DEFINED GMX_EXECUTABLE OR NOT DEFINED OUTPUT_DIR OR NOT DEFINED SOURCE_HTML_DIR)
-    message(FATAL_ERROR "Required input parameter not set")
-endif()
-
-file(MAKE_DIRECTORY ${OUTPUT_DIR})
-file(MAKE_DIRECTORY ${OUTPUT_DIR}/programs)
-file(COPY ${SOURCE_HTML_DIR}/header.html.in DESTINATION .)
-file(COPY ${SOURCE_HTML_DIR}/footer.html DESTINATION .)
-
-# This is generated by gmx help -export html
-set(HEADER_FILE header.html)
-
-execute_process(
-    COMMAND ${GMX_EXECUTABLE} -quiet help -export html
-    RESULT_VARIABLE exitcode)
-if (exitcode)
-    # Ensure that no partial output is left behind.
-    file(REMOVE_RECURSE ${OUTPUT_DIR})
-    file(REMOVE ${HEADER_FILE})
-    message(FATAL_ERROR
-        "Failed to generate HTML help. "
-        "Set GMX_BUILD_HELP=OFF or GMX_BUILD_HELP=AUTO if you want to skip them.\n"
-        "Error/exit code: ${exitcode}")
-endif()
-
-set(FOOTER_FILE ${SOURCE_HTML_DIR}/footer.html)
-file(READ ${HEADER_FILE} HEADER_TEXT)
-file(READ ${FOOTER_FILE} FOOTER_TEXT)
-set(_title_re "[Tt][Ii][Tt][Ll][Ee]")
-
-function(CREATE_HTML_FILE SOURCE_FILE ROOTPATH)
-    file(RELATIVE_PATH _rel_path ${SOURCE_HTML_DIR} ${SOURCE_FILE})
-    file(READ ${SOURCE_FILE} _content)
-    string(REGEX REPLACE "^ *<${_title_re}>(.*)</${_title_re}>\n" "" _content "${_content}")
-    set(TITLE "${CMAKE_MATCH_1}")
-    string(CONFIGURE "${HEADER_TEXT}" _header @ONLY)
-    set(_content "${_header}${_content}${FOOTER_TEXT}")
-    file(WRITE ${OUTPUT_DIR}/${_rel_path} "${_content}")
-endfunction()
-
-file(COPY ${SOURCE_HTML_DIR}/images DESTINATION ${OUTPUT_DIR})
-file(MAKE_DIRECTORY ${OUTPUT_DIR}/online)
-file(COPY ${SOURCE_HTML_DIR}/online/style.css DESTINATION ${OUTPUT_DIR}/online)
-file(GLOB _source_files ${SOURCE_HTML_DIR}/online/*.html)
-foreach(_file ${_source_files})
-    create_html_file(${_file} "../")
-endforeach()
diff --git a/docs/old-html/CMakeLists.txt b/docs/old-html/CMakeLists.txt
deleted file mode 100644
index 798916ed58..0000000000
--- a/docs/old-html/CMakeLists.txt
+++ /dev/null
@@ -1,68 +0,0 @@
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS is free software; you can redistribute it and/or
-# modify it under the terms of the GNU Lesser General Public License
-# as published by the Free Software Foundation; either version 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
-# Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-include(gmxCustomCommandUtilities)
-
-set(OUTPUT_DIR final)
-
-if (GMX_BUILD_HELP)
-    # Unlike the man and completion targets, this target is not built
-    # automatically with GMX_BUILD_HELP=AUTO, since most people will not
-    # notice it missing.
-    file(GLOB_RECURSE deps
-         ${CMAKE_CURRENT_SOURCE_DIR}/images/*
-         ${CMAKE_CURRENT_SOURCE_DIR}/*.html
-         ${CMAKE_CURRENT_SOURCE_DIR}/*.css
-         )
-    list(APPEND deps
-         ${CMAKE_CURRENT_SOURCE_DIR}/BuildHtmlHelp.cmake
-         ${CMAKE_CURRENT_SOURCE_DIR}/header.html.in
-         )
-
-    gmx_add_custom_output_target(html OUTPUT STAMP
-        COMMAND ${CMAKE_COMMAND}
-            -D GMX_EXECUTABLE=$<TARGET_FILE:gmx>
-            -D SOURCE_HTML_DIR=${CMAKE_CURRENT_SOURCE_DIR}
-            -D OUTPUT_DIR=${OUTPUT_DIR}
-            -P ${CMAKE_CURRENT_SOURCE_DIR}/BuildHtmlHelp.cmake
-        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-        DEPENDS gmx ${deps}
-        COMMENT "Generating HTML help")
-
-    if (GMX_BUILD_HELP_FORCE)
-        set_target_properties(html PROPERTIES EXCLUDE_FROM_ALL OFF)
-    endif()
-    set_directory_properties(PROPERTIES
-        ADDITIONAL_MAKE_CLEAN_FILES "${OUTPUT_DIR};header.html")
-endif()
diff --git a/docs/old-html/footer.html b/docs/old-html/footer.html
deleted file mode 100644
index cac6e95fbb..0000000000
--- a/docs/old-html/footer.html
+++ /dev/null
@@ -1,8 +0,0 @@
-
-<P>
-<HR>
-<DIV ALIGN=RIGHT><FONT SIZE="-1">
-<A HREF="http://www.gromacs.org">http://www.gromacs.org</A><BR>
-</FONT></DIV>
-</BODY>
-</HTML>
diff --git a/docs/old-html/header.html.in b/docs/old-html/header.html.in
deleted file mode 100644
index 04b7677e28..0000000000
--- a/docs/old-html/header.html.in
+++ /dev/null
@@ -1,26 +0,0 @@
-<HTML>
-<HEAD>
-  <TITLE>@TITLE@</TITLE>
-  <LINK rel=stylesheet href="@ROOTPATH@online/style.css" type="text/css">
-</HEAD>
-<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
-  <TABLE WIDTH="98%%">
-    <TR>
-      <TD WIDTH="116" ROWSPAN="2">
-        <A HREF="http://www.gromacs.org/"><IMG SRC="@ROOTPATH@images/gmxlogo_small.jpg" BORDER=0></A>
-      </TD>
-      <TD ALIGN="LEFT" VALIGN="CENTER" COLSPAN="2">
-        <H2>@TITLE@</H2>
-      </TD>
-    </TR>
-    <TR>
-      <TD>
-        <FONT SIZE="-1"><A HREF="@ROOTPATH@online.html">Main Table of Contents</A></FONT>
-      </TD>
-      <TD ALIGN="RIGHT" VALIGN="BOTTOM">
-        <B>@VERSION@</B>
-      </TD>
-  </TR>
-</TABLE>
-  <HR>
-
diff --git a/docs/old-html/images/gmxlogo_small.jpg b/docs/old-html/images/gmxlogo_small.jpg
deleted file mode 100644
index 55c9df7847..0000000000
Binary files a/docs/old-html/images/gmxlogo_small.jpg and /dev/null differ
diff --git a/docs/old-html/online/flow.html b/docs/old-html/online/flow.html
deleted file mode 100644
index 900f04c6c5..0000000000
--- a/docs/old-html/online/flow.html
+++ /dev/null
@@ -1,208 +0,0 @@
-<TITLE>Flow Chart</TITLE>
-<p>This is a flow chart of a typical GROMACS MD run of a protein
-in a box of water.
-A more detailed example is available in the
-<A HREF="../user-guide/index.html#getting-started-with-gromacs">Getting Started</A>
-section. Several steps of energy minimization may be necessary,
-these consist of cycles: grompp -&gt; mdrun.
-<p>
-
-<CENTER>
-<TABLE BORDER=0 CELLMARGIN=0 CELLPADDING=0 CELLSPACING=0>
-
-<TR>
-<TD COLSPAN=2 ALIGN=RIGHT> <A HREF=pdb.html onMouseOver="window.status='Protein Databank file'; return true">eiwit.pdb</A></TD>
-<TD ALIGN=RIGHT>&nbsp;<IMG SRC=../images/flow_leftrightdown.gif></TD>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-</TR>
-
-<TR>
-<TD COLSPAN=2 ALIGN=LEFT>Generate a GROMACS topology </TD>
-<TD></TD>
-<TD BGCOLOR=#777777 COLSPAN=3 ALIGN=CENTER>&nbsp;<A HREF=../programs/gmx-pdb2gmx.html onMouseOver="window.status='Convert PDB file to GROMAX coordinate file and topology'; return true"><B>gmx pdb2gmx</B></A>&nbsp;</TD>
-<TD><IMG SRC=../images/flow_vrule.gif></TD>
-</TR>
-
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif BORDER=0></TD>
-<TD WIDTH=20></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><A HREF=gro.html onMouseOver="window.status='GROMACS coordinate file containing molecules from PDB file'; return true">conf.gro</A></TD>
-<TD></TD>
-<TD ALIGN=CENTER> <A HREF=top.html onMouseOver="window.status='GROMACS ascii topology file'; return true">topol.top</A> </TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif BORDER=0></TD>
-<TD></TD>
-<TD ROWSPAN=5 COLSPAN=1 ALIGN=CENTER><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_down.gif></TD>
-</TR>
-
-<TR>
-<TD COLSPAN=2 ALIGN=left>Enlarge the box</TD>
-<TD></TD>
-<TD ALIGN=CENTER BGCOLOR=#777777>&nbsp;&nbsp;<A HREF=../programs/gmx-editconf.html onMouseOver="window.status='Adjust boxsize and placement of molecule'; return true"><B>gmx editconf</B></A>&nbsp;&nbsp;</TD>
-<TD></TD>
-<TD><IMG SRC=../images/flow_vrule.gif></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
-<TD></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER> <A HREF=gro.html onMouseOver="window.status='GROMACS coordinate file with adjusted box etc.'; return true">conf.gro</A> </TD>
-<TD></TD>
-</TR>
-
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
-<TD></TD>
-</TR>
-
-<TR>
-<TD COLSPAN=2 ALIGN=LEFT>Solvate protein</TD>
-<TD></TD>
-<TD COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777>&nbsp;<A HREF=../programs/gmx-solvate.html onMouseOver="window.status='Fill box with water (solvate molecule)'; return true"><B>gmx solvate</B></A>&nbsp;</TD>
-<TD><IMG SRC=../images/flow_vrule.gif></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><A HREF=gro.html onMouseOver="window.status='GROMACS coordinate file with water molecules added'; return true">conf.gro</A></TD>
-<TD></TD>
-<TD ALIGN=CENTER> <A HREF=top.html onMouseOver="window.status='GROMACS ascii topology file with water molecules added'; return true">topol.top</A> </TD>
-</TR>
-
-<TR>
-<TD COLSPAN=2 ALIGN=RIGHT><A HREF=mdp.html onMouseOver="window.status='Parameter file for grompp (controls all MD parameters)'; return true">grompp.mdp</A></TD>
-<TD ALIGN=RIGHT>&nbsp;<IMG SRC=../images/flow_leftrightdown.gif></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
-<TD></TD>
-</TR>
-
-
-<TR>
-<TD COLSPAN=2 ALIGN=LEFT>Generate mdrun input file</TD>
-<TD></TD>
-<TD COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777>&nbsp; <A HREF=../programs/gmx-grompp.html onMouseOver="window.status='Process parameters, coordinates and topology and write binary topology'; return true"><B>gmx grompp</B></A> &nbsp;</TD>
-<TD><IMG SRC=../images/flow_vrule.gif></TD>
-<TD></TD>
-<TD></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
-<TD ROWSPAN=3 ALIGN=RIGHT>
-<IMG SRC=../images/flow_rightleftdown.gif></TD>
-<TD ALIGN=CENTER VALIGN=BOTTOM>Continuation</TD>
-</TR>
-
-<TR>
-<TD COLSPAN=2 ALIGN=LEFT></TD>
-<TD></TD>
-<TD COLSPAN=3 ALIGN=CENTER> <A HREF=tpr.html onMouseOver="window.status='Portable GROMACS binary run input file (contains all information to start MD run)'; return true">topol.tpr</A></TD>
-<TD ALIGN=CENTER >&nbsp;&nbsp;<A HREF=cpt.html onMouseOver="window.status='Checkpoint file'; return true">state.cpt</A>&nbsp;&nbsp;</TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
-<TD ROWSPAN=2 ALIGN=CENTER>
-<IMG SRC=../images/flow_vline.gif><BR>
-<IMG SRC=../images/flow_leftup.gif></TD>
-</TR>
-
-<TR>
-<TD COLSPAN=2>Run the simulation (EM or MD)</TD>
-<TD></TD>
-<TD  COLSPAN=3 ALIGN=CENTER BGCOLOR=#777777>&nbsp;<A HREF=../programs/gmx-mdrun.html onMouseOver="window.status='The moment you have all been waiting for! START YOUR MD RUN'; return true"><B>gmx mdrun</B></A>&nbsp;</TD>
-<TD></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_vline.gif></TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER> <A HREF=xtc.html onMouseOver="window.status='Portable compressed trajectory'; return true">traj.xtc</A> /
-<A HREF=trr.html onMouseOver="window.status='Full precision portable trajectory'; return true">traj.trr</A> </TD>
-<TD></TD>
-<TD ALIGN=CENTER> <A HREF=edr.html onMouseOver="window.status='Portable energy file'; return true">ener.edr</A> </TD>
-</TR>
-
-<TR>
-<TD></TD>
-<TD></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
-<TD></TD>
-<TD ALIGN=CENTER><IMG SRC=../images/flow_down.gif></TD>
-</TR>
-
-<TR>
-<TD COLSPAN=2 ALIGN=LEFT>Analysis</TD>
-<TD></TD>
-<TD ALIGN=CENTER BGCOLOR=#777777>&nbsp;&nbsp;<A HREF=../online.html onMouseOver="window.status='Your favourite GROMACS analysis tool'; return true"><B>g_...</B></A>&nbsp;&nbsp;<BR>&nbsp;&nbsp;<A HREF=../programs/gmx-view.html onMouseOver="window.status='gmx view, the GROMACS trajectory viewer'; return true"><B>gmx view</B></A>&nbsp;&nbsp;</TD>
-<TD></TD>
-<TD ALIGN=CENTER BGCOLOR=#777777>&nbsp;&nbsp;<A HREF=../programs/gmx-energy.html onMouseOver="window.status='Energy plots, averages and  fluctuations'; return true"><B>gmx energy</B></A>&nbsp;&nbsp;</TD>
-<TD><IMG SRC=../images/flow_vrule.gif></TD>
-</TR>
-
-
-</TABLE>
-</CENTER>
diff --git a/docs/old-html/online/style.css b/docs/old-html/online/style.css
deleted file mode 100644
index a296f99f08..0000000000
--- a/docs/old-html/online/style.css
+++ /dev/null
@@ -1,15 +0,0 @@
-H1         { text-indent: 0em; font-size: 24pt; font-family: serif }
-H2         { text-indent: 0em; font-size: 24pt; font-weight: bold; font-family: arial,helvetica,verdana,sans-serif }
-H3         { text-indent: 0em; font-size: 18pt; font-weight: bold; font-family: arial,helvetica,verdana,sans-serif }
-H4         { font-family: arial,helvetica,verdana,sans-serif }
-A:link     { text-decoration: none }
-A:active   { text-decoration: none }
-A:visited  { text-decoration: none } 
-tt         { font-family: courier,"lucida console",serif }
-
-
-
-
-
-
-
diff --git a/docs/online.rst b/docs/online.rst
deleted file mode 100644
index 041e1fbf4d..0000000000
--- a/docs/online.rst
+++ /dev/null
@@ -1,4 +0,0 @@
-Online reference
-================
-
-* `Flow Chart <online/flow.html>`_
diff --git a/docs/user-guide/flow.rst b/docs/user-guide/flow.rst
new file mode 100644
index 0000000000..6579c7c008
--- /dev/null
+++ b/docs/user-guide/flow.rst
@@ -0,0 +1,210 @@
+Flow Chart
+==========
+
+This is a flow chart of a typical GROMACS MD run of a protein
+in a box of water.
+A more detailed example is available in :doc:`getting-started`.
+Several steps of energy minimization may be necessary,
+these consist of cycles: :ref:`gmx grompp` -> :ref:`gmx mdrun`.
+
+.. raw:: html
+
+   <CENTER>
+   <TABLE BORDER=0 CELLMARGIN=0 CELLPADDING=0 CELLSPACING=0>
+
+   <TR>
+   <TD COLSPAN="2" STYLE="text-align:right"> <A HREF="file-formats.html#pdb" onMouseOver="window.status='Protein Databank file'; return true">eiwit.pdb</A></TD>
+   <TD STYLE="text-align:right"><IMG SRC=../images/flow_leftrightdown.gif></TD>
+   <TD></TD>
+   <TD></TD>
+   <TD></TD>
+   </TR>
+
+   <TR>
+   <TD COLSPAN=2>Generate a GROMACS topology </TD>
+   <TD></TD>
+   <TD BGCOLOR=#777777 COLSPAN=3 STYLE="text-align:center"><A HREF=../programs/gmx-pdb2gmx.html onMouseOver="window.status='Convert PDB file to GROMAX coordinate file and topology'; return true"><B>gmx pdb2gmx</B></A></TD>
+   <TD><IMG SRC=../images/flow_vrule.gif></TD>
+   </TR>
+
+
+   <TR>
+   <TD></TD>
+   <TD></TD>
+   <TD></TD>
+   <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif BORDER=0></TD>
+   <TD WIDTH=20></TD>
+   <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif></TD>
+   </TR>
+
+   <TR>
+   <TD></TD>
+   <TD></TD>
+   <TD></TD>
+   <TD STYLE="text-align:center"><A HREF="file-formats.html#gro" onMouseOver="window.status='GROMACS coordinate file containing molecules from PDB file'; return true">conf.gro</A></TD>
+   <TD></TD>
+   <TD STYLE="text-align:center"> <A HREF="file-formats.html#top" onMouseOver="window.status='GROMACS ascii topology file'; return true">topol.top</A> </TD>
+   </TR>
+
+   <TR>
+   <TD></TD>
+   <TD></TD>
+   <TD></TD>
+   <TD STYLE="text-align:center"><IMG SRC=../images/flow_down.gif BORDER=0></TD>
+   <TD></TD>
+   <TD ROWSPAN=5 COLSPAN=1 STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_vline.gif><BR><IMG SRC=../images/flow_down.gif></TD>
+   </TR>
+
+   <TR>
+   <TD COLSPAN=2>Enlarge the box</TD>
+   <TD></TD>
+   <TD STYLE="text-align:center" BGCOLOR=#777777><A HREF=../programs/gmx-editconf.html onMouseOver="window.status='Adjust boxsize and placement of molecule'; return true"><B>gmx editconf</B></A></TD>
+   <TD></TD>
+   <TD><IMG SRC=../images/flow_vrule.gif></TD>
+   </TR>
+
+   <TR>
+   <TD></TD>
+   <TD></TD>
+   <TD></TD>
+   <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif></TD>
+   <TD></TD>
+   </TR>
+
+   <TR>
+   <TD></TD>
+   <TD></TD>
+   <TD></TD>
+   <TD STYLE="text-align:center"> <A HREF="file-formats.html#gro" onMouseOver="window.status='GROMACS coordinate file with adjusted box etc.'; return true">conf.gro</A> </TD>
+   <TD></TD>
+   </TR>
+
+
+   <TR>
+   <TD></TD>
+   <TD></TD>
+   <TD></TD>
+   <TD STYLE="text-align:center"><IMG SRC=../images/flow_down.gif></TD>
+   <TD></TD>
+   </TR>
+
+   <TR>
+   <TD COLSPAN=2>Solvate protein</TD>
+   <TD></TD>
+   <TD COLSPAN=3 STYLE="text-align:center" BGCOLOR=#777777>&nbsp;<A HREF=../programs/gmx-solvate.html onMouseOver="window.status='Fill box with water (solvate molecule)'; return true"><B>gmx solvate</B></A>&nbsp;</TD>
+   <TD><IMG SRC=../images/flow_vrule.gif></TD>
+   </TR>
+
+   <TR>
+   <TD></TD>
+   <TD></TD>
+   <TD></TD>
+   <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif></TD>
+   <TD></TD>
+   <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif></TD>
+   </TR>
+
+   <TR>
+   <TD></TD>
+   <TD></TD>
+   <TD></TD>
+   <TD STYLE="text-align:center"><A HREF="file-formats.html#gro" onMouseOver="window.status='GROMACS coordinate file with water molecules added'; return true">conf.gro</A></TD>
+   <TD></TD>
+   <TD STYLE="text-align:center"> <A HREF="file-formats.html#top" onMouseOver="window.status='GROMACS ascii topology file with water molecules added'; return true">topol.top</A> </TD>
+   </TR>
+
+   <TR>
+   <TD COLSPAN=2 STYLE="text-align:right"><A HREF="file-formats.html#mdp" onMouseOver="window.status='Parameter file for grompp (controls all MD parameters)'; return true">grompp.mdp</A></TD>
+   <TD STYLE="text-align:right">&nbsp;<IMG SRC=../images/flow_leftrightdown.gif></TD>
+   <TD STYLE="text-align:center"><IMG SRC=../images/flow_down.gif></TD>
+   <TD></TD>
+   <TD STYLE="text-align:center"><IMG SRC=../images/flow_down.gif></TD>
+   <TD></TD>
+   </TR>
+
+
+   <TR>
+   <TD COLSPAN=2>Generate mdrun input file</TD>
+   <TD></TD>
+   <TD COLSPAN=3 STYLE="text-align:center" BGCOLOR=#777777><A HREF=../programs/gmx-grompp.html onMouseOver="window.status='Process parameters, coordinates and topology and write binary topology'; return true"><B>gmx grompp</B></A></TD>
+   <TD><IMG SRC=../images/flow_vrule.gif></TD>
+   <TD></TD>
+   <TD></TD>
+   </TR>
+
+   <TR>
+   <TD></TD>
+   <TD></TD>
+   <TD></TD>
+   <TD></TD>
+   <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif></TD>
+   <TD ROWSPAN=3 STYLE="text-align:right"><IMG SRC=../images/flow_rightleftdown.gif></TD>
+   <TD STYLE="text-align:center;vertical-align:bottom">Continuation</TD>
+   </TR>
+
+   <TR>
+   <TD COLSPAN=2></TD>
+   <TD></TD>
+   <TD COLSPAN=3 STYLE="text-align:center"> <A HREF="file-formats.html#tpr" onMouseOver="window.status='Portable GROMACS binary run input file (contains all information to start MD run)'; return true">topol.tpr</A></TD>
+   <TD STYLE="text-align:center"><A HREF="file-formats.html#cpt" onMouseOver="window.status='Checkpoint file'; return true">state.cpt</A></TD>
+   </TR>
+
+   <TR>
+   <TD></TD>
+   <TD></TD>
+   <TD></TD>
+   <TD></TD>
+   <TD STYLE="text-align:center"><IMG SRC=../images/flow_down.gif></TD>
+   <TD ROWSPAN=2 STYLE="text-align:center">
+   <IMG SRC=../images/flow_vline.gif><BR>
+   <IMG SRC=../images/flow_leftup.gif></TD>
+   </TR>
+
+   <TR>
+   <TD COLSPAN=2>Run the simulation (EM or MD)</TD>
+   <TD></TD>
+   <TD  COLSPAN=3 STYLE="text-align:center" BGCOLOR=#777777>&nbsp;<A HREF=../programs/gmx-mdrun.html onMouseOver="window.status='The moment you have all been waiting for! START YOUR MD RUN'; return true"><B>gmx mdrun</B></A>&nbsp;</TD>
+   <TD></TD>
+   </TR>
+
+   <TR>
+   <TD></TD>
+   <TD></TD>
+   <TD></TD>
+   <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif></TD>
+   <TD></TD>
+   <TD STYLE="text-align:center"><IMG SRC=../images/flow_vline.gif></TD>
+   </TR>
+
+   <TR>
+   <TD></TD>
+   <TD></TD>
+   <TD></TD>
+   <TD STYLE="text-align:center"> <A HREF="file-formats.html#xtc" onMouseOver="window.status='Portable compressed trajectory'; return true">traj.xtc</A> /
+   <A HREF="file-formats.html#trr" onMouseOver="window.status='Full precision portable trajectory'; return true">traj.trr</A> </TD>
+   <TD></TD>
+   <TD STYLE="text-align:center"> <A HREF="file-formats.html#edr" onMouseOver="window.status='Portable energy file'; return true">ener.edr</A> </TD>
+   </TR>
+
+   <TR>
+   <TD></TD>
+   <TD></TD>
+   <TD></TD>
+   <TD STYLE="text-align:center"><IMG SRC=../images/flow_down.gif></TD>
+   <TD></TD>
+   <TD STYLE="text-align:center"><IMG SRC=../images/flow_down.gif></TD>
+   </TR>
+
+   <TR>
+   <TD COLSPAN=2>Analysis</TD>
+   <TD></TD>
+   <TD STYLE="text-align:center" BGCOLOR=#777777><A HREF="../programs/bytopic.html" onMouseOver="window.status='Your favourite GROMACS analysis tool'; return true"><B>g_...</B></A><BR><A HREF=../programs/gmx-view.html onMouseOver="window.status='gmx view, the GROMACS trajectory viewer'; return true"><B>gmx view</B></A></TD>
+   <TD></TD>
+   <TD STYLE="text-align:center" BGCOLOR=#777777><A HREF=../programs/gmx-energy.html onMouseOver="window.status='Energy plots, averages and  fluctuations'; return true"><B>gmx energy</B></A></TD>
+   <TD><IMG SRC=../images/flow_vrule.gif></TD>
+   </TR>
+
+
+   </TABLE>
+   </CENTER>
+
diff --git a/docs/user-guide/getting-started.rst b/docs/user-guide/getting-started.rst
index d35bf01b99..5c325d7657 100644
--- a/docs/user-guide/getting-started.rst
+++ b/docs/user-guide/getting-started.rst
@@ -1,6 +1,11 @@
 Getting started
 ===============
 
+.. toctree::
+   :hidden:
+
+   flow
+
 In this chapter we assume the reader is familiar with Molecular Dynamics and
 familiar with Unix, including the use of a text editor such as ``jot``, ``emacs``
 or ``vi``. We furthermore assume the |Gromacs| software is installed properly on
@@ -36,7 +41,7 @@ administrator for more information, and then follow the advice for
 
 Flowchart of typical simulation
 -------------------------------
-A typical simulation workflow with |Gromacs| is `illustrated here <../online/flow.html>`_.
+A typical simulation workflow with |Gromacs| is :doc:`illustrated here <flow>`.
 
 Important files
 ---------------
diff --git a/src/gromacs/commandline/cmdlinehelpmodule.cpp b/src/gromacs/commandline/cmdlinehelpmodule.cpp
index b4fce4cb31..78903210dc 100644
--- a/src/gromacs/commandline/cmdlinehelpmodule.cpp
+++ b/src/gromacs/commandline/cmdlinehelpmodule.cpp
@@ -406,45 +406,6 @@ void initProgramLinks(HelpLinks *links, const CommandLineHelpModuleImpl &helpMod
     }
 }
 
-/********************************************************************
- * HelpExportHtml
- */
-
-/*! \internal
- * \brief
- * Implements export for HTML help.
- *
- * This whole class can go once docs/old-html/ no longer requires header.html
- * that it generates.
- *
- * \ingroup module_commandline
- */
-class HelpExportHtml : public HelpExportInterface
-{
-    public:
-        //! Initializes HTML exporter.
-        HelpExportHtml();
-
-        virtual void startModuleExport() {}
-        virtual void exportModuleHelp(
-            const CommandLineModuleInterface & /*module*/,
-            const std::string                & /*tag*/,
-            const std::string                & /*displayName*/) {}
-        virtual void finishModuleExport() {}
-
-        virtual void startModuleGroupExport() {}
-        virtual void exportModuleGroup(const char                * /*title*/,
-                                       const ModuleGroupContents & /*modules*/) {}
-        virtual void finishModuleGroupExport() {}
-};
-
-HelpExportHtml::HelpExportHtml()
-{
-    std::string header = gmx::File::readToString("header.html.in");
-    header = replaceAll(header, "@VERSION@", gmx_version());
-    gmx::File::writeFileFromString("header.html", header);
-}
-
 /********************************************************************
  * HelpExportReStructuredText
  */
@@ -758,7 +719,7 @@ int CommandLineHelpModule::run(int argc, char *argv[])
     // Add internal topics lazily here.
     addTopic(HelpTopicPointer(new CommandsHelpTopic(*impl_)));
 
-    const char *const exportFormats[] = { "html", "rst", "completion" };
+    const char *const exportFormats[] = { "rst", "completion" };
     std::string       exportFormat;
     Options           options(NULL, NULL);
     options.addOption(StringOption("export").store(&exportFormat)
@@ -767,11 +728,7 @@ int CommandLineHelpModule::run(int argc, char *argv[])
     if (!exportFormat.empty())
     {
         boost::scoped_ptr<HelpExportInterface> exporter;
-        if (exportFormat == "html")
-        {
-            exporter.reset(new HelpExportHtml());
-        }
-        else if (exportFormat == "rst")
+        if (exportFormat == "rst")
         {
             exporter.reset(new HelpExportReStructuredText(*impl_));
         }