From fd397bbc7744e9dcb3728f0c2e6f7372e6d74019 Mon Sep 17 00:00:00 2001 From: Teemu Murtola Date: Tue, 12 May 2015 14:37:54 +0300 Subject: [PATCH] Remove remaining old-html content Replace the HTML table hack + static images that created the flow chart with a graphviz graph. The presentation could potentially be improved, but the essential content from the old chart is there (in case it is useful). Remove all build system references to old-html, simplifying the system and removing the need to document any of this. Change-Id: Ic011c770676d4d6d1b560fcb521bfc523c142ad0 --- docs/CMakeLists.txt | 15 +- docs/conf.py | 1 + docs/old-html/images/flow_down.gif | Bin 300 -> 0 bytes docs/old-html/images/flow_downleft.gif | Bin 696 -> 0 bytes docs/old-html/images/flow_hline.gif | Bin 306 -> 0 bytes docs/old-html/images/flow_left.gif | Bin 305 -> 0 bytes docs/old-html/images/flow_leftright.gif | Bin 697 -> 0 bytes docs/old-html/images/flow_leftrightdown.gif | Bin 696 -> 0 bytes docs/old-html/images/flow_leftrightup.gif | Bin 693 -> 0 bytes docs/old-html/images/flow_leftup.gif | Bin 689 -> 0 bytes docs/old-html/images/flow_right+left.gif | Bin 698 -> 0 bytes docs/old-html/images/flow_right.gif | Bin 306 -> 0 bytes docs/old-html/images/flow_rightleftdown.gif | Bin 701 -> 0 bytes docs/old-html/images/flow_uprightleft.gif | Bin 699 -> 0 bytes docs/old-html/images/flow_vline.gif | Bin 693 -> 0 bytes docs/old-html/images/flow_vrule.gif | Bin 118 -> 0 bytes docs/user-guide/flow.rst | 327 ++++++++------------ 17 files changed, 129 insertions(+), 214 deletions(-) delete mode 100644 docs/old-html/images/flow_down.gif delete mode 100644 docs/old-html/images/flow_downleft.gif delete mode 100644 docs/old-html/images/flow_hline.gif delete mode 100644 docs/old-html/images/flow_left.gif delete mode 100644 docs/old-html/images/flow_leftright.gif delete mode 100644 docs/old-html/images/flow_leftrightdown.gif delete mode 100644 docs/old-html/images/flow_leftrightup.gif delete mode 100644 docs/old-html/images/flow_leftup.gif delete mode 100644 docs/old-html/images/flow_right+left.gif delete mode 100644 docs/old-html/images/flow_right.gif delete mode 100644 docs/old-html/images/flow_rightleftdown.gif delete mode 100644 docs/old-html/images/flow_uprightleft.gif delete mode 100644 docs/old-html/images/flow_vline.gif delete mode 100644 docs/old-html/images/flow_vrule.gif diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt index 8197b4fced..9f48109107 100644 --- a/docs/CMakeLists.txt +++ b/docs/CMakeLists.txt @@ -299,13 +299,6 @@ 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) # Make the PDF reference guide # TODO Try to make the PDF arrive directly in ${HTML_OUTPUT_DIR} @@ -327,12 +320,8 @@ if(HTML_BUILD_IS_POSSIBLE) # Add a top-level target for the others to hook onto add_custom_target(webpage - DEPENDS - ${HTML_OUTPUT_DIR}/manual-${GMX_VERSION_STRING}.pdf - ${extra_webpage_dependencies} - VERBATIM - ) - add_dependencies(webpage webpage-sphinx webpage-old-images doxygen-all) + DEPENDS ${HTML_OUTPUT_DIR}/manual-${GMX_VERSION_STRING}.pdf) + add_dependencies(webpage webpage-sphinx doxygen-all) else() add_custom_target(webpage COMMAND ${CMAKE_COMMAND} -E echo "Cannot build webpage because of missing requirements. Check cmake status output for reasons" diff --git a/docs/conf.py b/docs/conf.py index a7b172b5d6..8a63cd7c43 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -66,6 +66,7 @@ sys.path.append(gmx_sphinx_extension_path) # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ + 'sphinx.ext.graphviz', 'sphinx.ext.pngmath', 'sphinx.ext.ifconfig', 'gmxsphinx' diff --git a/docs/old-html/images/flow_down.gif b/docs/old-html/images/flow_down.gif deleted file mode 100644 index 5944f8a65e4ec63d72f505a7224a843b20e214e4..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 300 zcmb_VI|{-;5PdEw2CI~ov#X_8`)RgHNaqy-CL!Pw2|0iXIf7^N9+o!h&KmFnKA3s) zhBt50EZOezITm<8@DA{Uel3|ZcWK(LIC0rFj?*mR+T~TT=W|hZo2o9MpV16ZSj(}* zSarXxV2l}INsqCDrh!R8`oOsQE(ZjTDN?Y3dO%cf83+^;AZoJsrGFzTSa<^Pze%!w M<)2O2Up@kd53yb@@&Et; diff --git a/docs/old-html/images/flow_downleft.gif b/docs/old-html/images/flow_downleft.gif deleted file mode 100644 index 9881edad97a66d459e05475be8e739353dddebb4..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 696 zcmbVIy9&ZU5S$z-u1uM7BbLG1M-wcRe1nAq@*t2H2?1LbKfxchw29s&If8j0Ivlsd z&g|aqZQad$;h8Y;fW)hUAXaG;x#=;>i@>Ka&r;gD8;Vme3YHWm*=g@*r$Z8i#Vm?L zSWjI87;M=^_H$TypH2jB#+qC50>9GG0l3aC4jE%XL#>I<9~PDRE}tU_kWqu=f%9ef$EG}w2EC1pfUrUMMbsFfHYFIlOJ;i#3+0zkJ2#wWoDu+jhq25SJqyEIV% diff --git a/docs/old-html/images/flow_left.gif b/docs/old-html/images/flow_left.gif deleted file mode 100644 index 6cf841ae03499ec7ca1512179f19573036707d1f..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 305 zcmZ?wbhEHblwjau_{abP|G@yrQ2eK%px~KXkY7}inxc?al%K2M?&+qGnVXoNYNe2t zlV2X6lbTkdm!6r%p!k!8k%57UK?h_4$Sen@Yg1Ghl$4ZO1e`b&K?Ea1lL7}40;xm? 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Several steps of energy minimization may be necessary, these consist of cycles: :ref:`gmx grompp` -> :ref:`gmx mdrun`. -.. raw:: html - -
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
eiwit.pdb
Generate a GROMACS topology gmx pdb2gmx
conf.gro topol.top




Enlarge the boxgmx editconf
conf.gro
Solvate protein gmx solvate 
conf.gro topol.top
grompp.mdp 
Generate mdrun input filegmx grompp
Continuation
topol.tprstate.cpt
-
-
Run the simulation (EM or MD) gmx mdrun 
traj.xtc / - traj.trr ener.edr
Analysisg_...
gmx view		gmx energy
-
- +.. URL="file-formats.html#pdb" +.. ../programs/gmx-pdb2gmx.html + +.. digraph:: flowchart + + node [ shape=box, width=1.5 ] + + input_pdb [ + label="eiwit.pdb" + tooltip="Protein Databank file" + URL="file-formats.html#pdb" + shape=none, width=0, height=0, margin=0 + group=input + ] + pdb2gmx [ + label="Generate a GROMACS topology\ngmx pdb2gmx" + tooltip="Convert PDB file to GROMACS coordinate file and topology" + URL="../programs/gmx-pdb2gmx.html" + width=3 + group=main + ] + + input_pdb -> pdb2gmx [ headport=e ] + + editconf [ + label="Enlarge the box\ngmx editconf" + tooltip="Adjust box size and placement of molecule" + URL="../programs/gmx-editconf.html" + ] + + pdb2gmx -> editconf [ + label="conf.gro" + labeltooltip="GROMACS coordinate file containing molecules from PDB file" + URL="file-formats.html#gro" + ] + + solvate [ + label="Solvate protein\ngmx solvate" + tooltip="Fill box with water (solvate molecule)" + URL="../programs/gmx-solvate.html" + width=3 + group=main + ] + + pdb2gmx -> solvate [ + label="topol.top" + labeltooltip="GROMACS ascii topology file" + URL="file-formats.html#top" + ] + editconf -> solvate [ + label="conf.gro" + labeltooltip="GROMACS coordinate file with adjusted box etc." + URL="file-formats.html#gro" + ] + + input_mdp [ + label="grompp.mdp" + tooltip="Parameter file from grompp (controls all MD parameters)" + URL="file-formats.html#mdp" + shape=none, width=0, height=0, margin=0 + group=input + ] + grompp [ + label="Generate mdrun input file\ngmx grompp" + tooltip="Process parameters, coordinates and topology and write binary topology" + URL="../programs/gmx-grompp.html" + width=3 + group=main + ] + + input_pdb -> input_mdp [ style=invis, minlen=3 ] + + input_mdp -> grompp [ headport=e, weight=0 ] + solvate -> grompp [ + label="conf.gro" + labeltooltip="GROMACS coordinate file with water molecules added" + URL="file-formats.html#gro" + ] + solvate -> grompp [ + label="topol.top" + labeltooltip="GROMACS ascii topology file with water molecules added" + URL="file-formats.html#top" + ] + + mdrun [ + label="Run the simulation (EM or MD)\ngmx mdrun" + tooltip="The moment you have all been waiting for! START YOUR MD RUN" + URL="../programs/gmx-mdrun.html" + width=3 + group=main + ] + + grompp -> mdrun [ + label="topol.tpr" + labeltooltip="Portable GROMACS binary run input file (contains all information to start MD run)" + URL="file-formats.html#tpr" + ] + mdrun -> mdrun [ + label="Continuation\nstate.cpt" + labeltooltip="Checkpoint file" + URL="file-formats.html#cpt" + ] + + analysis [ + label="Analysis\ngmx ...\ngmx view" + tooltip="Your favourite GROMACS analysis tool" + URL="../programs/bytopic.html" + ] + + mdrun -> analysis [ + label="traj.xtc / traj.trr" + labeltooltip="Portable compressed trajectory / full precision portable trajectory" + URL="file-formats.html#xtc" + ] + + energy [ + label="Analysis\ngmx energy" + tooltip="Energy plots, averages and fluctuations" + URL="../programs/gmx-energy.html" + ] + + mdrun -> energy [ + label="ener.edr" + labeltooltip="Portable energy file" + URL="file-formats.html#edr" + ] -- 2.22.0