GROMACS $VER Online Reference

#!/bin/csh -f if ( $#argv < 2 ) then echo "Error: provide the binary directory as first argument," echo "and the location of programs.txt as the second." echo "A html subdirectory will be created in the current dir." exit endif set GMXBINDIR = $1 set PROGFILE = $2 set dir = $cwd set VER = 4.6.5 set MANDIR = online set HTML = $cwd/html set HTMLOL = $HTML/$MANDIR set HTMLIDX = $HTML/$MANDIR.html set GENERAL = "getting_started:Getting_Started flow:Flow_Chart files:File_Formats mdp_opt:mdp_options" cd $GMXBINDIR set PROGRAMS = [a-z]* cd $dir echo "" echo "Generating table of contents in $HTMLIDX" echo "-------------------------------------------" if ( ! -d $HTML ) mkdir $HTML if ( ! -d $HTMLOL ) mkdir $HTMLOL if ( -f $HTMLIDX ) \rm $HTMLIDX touch $HTMLIDX cat > $HTMLIDX << EOD GROMACS $VER Online Reference

GROMACS $VER
Online Reference

VERSION $VER

General

EOD foreach i ( $GENERAL ) set file = `echo $i | cut -d: -f1` set desc = `echo $i | cut -d: -f2 | sed 's/_/ /g'` echo ""$desc"" >> $HTMLIDX echo "

" >> $HTMLIDX end cat >> $HTMLIDX <FAQ

Programs

Options
EOD foreach program ( $PROGRAMS ) if ( ( -x $GMXBINDIR/$program ) && ( $program != "my_dssp" ) && ( $program != "GMXRC" ) && ( $program != "completion.csh" ) && ( $program != "completion.zsh" ) && ( $program != "average" ) && ( $program != "completion.bash" ) && ( $program != "luck" ) && ( $program != "demux.pl" ) && ( $program != "xplor2gmx.pl" ) ) then echo "
$program" >> $HTMLIDX endif end cat >> $HTMLIDX << EOD

Programs by Topic

EOD awk -F '|' -v mandir=$MANDIR '{\ if (NF) {\ if ( $1 == "HEAD" ) {\ hnr++;\ printf("%s
\n",hnr,$2);\ }\ }\ }' $PROGFILE >> $HTMLIDX echo " " >> $HTMLIDX awk -F '|' -v mandir=$MANDIR '{\ if (NF) {\ if ( $1 == "HEAD" ) {\ hnr++;\ printf("\n\n",hnr);\ printf("\n

\n");\ printf("
%s\n",$2);\ } else if ( $1 == "END" ) {\ printf("

\n");\ } else {\ printf("%s%s\n",mandir,$1,$1,$2);\ }\ }\ }' $PROGFILE >> $HTMLIDX cat >> $HTMLIDX <

http://www.gromacs.org
EOD echo "Generating html manual for GROMACS programs" echo "-------------------------------------------" cd $dir setenv GMX_MAXBACKUP -1 foreach program ( $PROGRAMS ) if ( ( -x $GMXBINDIR/$program ) && ( $program != "my_dssp" ) && ( $program != "GMXRC" ) && ( $program != "completion.csh" ) && ( $program != "completion.zsh" ) && ( $program != "average" ) && ( $program != "completion.bash" ) && ( $program != "luck" ) && ( $program != "demux.pl" ) ) then echo -n "$program " cd $HTMLOL $GMXBINDIR/$program -quiet -man html >& /dev/null cd .. endif endif end echo #last line