#!/bin/csh -f

setenv MOLDIR `pwd`

# accept namelist format directory names, 1 line

if ( $1 != '' ) then

	setenv MOLNAME `cut -f1 -d' ' ${1}/names | tr -s ' ' | tr -d ')' | tr -d '(' | tr -d '[' | tr -d ']' | sed s/' -'/' '/ | sed s/' -'/' '/ | sed s/' -'/' '/ | tr -s ' ' | tr -d '*' | tr -d '\"' | tr -d "\'" | tr / ' '`
	# make raster images
	if ( -f ${1}/${MOLNAME}-balls.png ) then
		echo image in place
	else
		balls < ${1}/*.pdb | render -png > ${1}/${MOLNAME}-balls.png
	endif
	
	if ( -f ${1}/${MOLNAME}-rods.png ) then
		echo image in place
	else
		rods  < ${1}/*.pdb | render -png > ${1}/${MOLNAME}-rods.png
	endif

	echo  "<title>Molecules@GNU-Darwin.org:"`echo "$*" | \
	tr -s ' ' | tr -d ')' | tr -d '(' | tr -d '[' | tr -d ']' | sed s/' -'/' '/ | sed s/' -'/' '/ | sed s/' -'/' '/ | tr -s ' ' | tr -d '*' | tr -d '\"' | tr -d "\'" | tr / ' ' | cut -f1-5 -d ' ' | tr ' ' /`"</title>" \
> ${1}/index.html
	echo  "<h1>"`echo "$*" | \
	tr -s ' ' | tr -d ')' | tr -d '(' | tr -d '[' | tr -d ']' | sed s/' -'/' '/ | sed s/' -'/' '/ | sed s/' -'/' '/ | tr -s ' ' | tr -d '*' | tr -d '\"' | tr -d "\'" | tr / ' ' | cut -f2,3 -d ' ' | tr ' ' /`" Index</h1>" \
>> ${1}/index.html

#
#	echo -n "<title>${1} " > ${1}/index.html
#	echo -n `cat ${1}/names` > ${1}/index.html
#	echo    "Index</title>" > ${1}/index.html
#	echo    "<h1>${1} index</h1>" > ${1}/index.html



	echo "$*" | tr -s ' ' | tr -d ')' | tr -d '(' | tr -d '[' | tr -d ']' | sed s/' -'/' '/ | sed s/' -'/' '/ | sed s/' -'/' '/ | tr -s ' ' | tr -d '*' | tr -d '\"' | tr -d "\'" | tr / ' ' | awk '{print("babel -isdf "$1"/"$2"/"$3"/"$3".sdf -osmiles > "$1"/"$2"/"$3"/\${MOLNAME}.smiles ; echo \"<table cellpadding=0 cellspacing=0 border=0><tr bgcolor=#000000><td valign=top ><a href="$3".png><img src="$3".png border=0 width=320 height=240 ></a></td><td valign=top ><a href=\${MOLNAME}-balls.png><img src=\${MOLNAME}-balls.png border=0 width=320 height=240 ></a></td><td valign=top ><a href=\${MOLNAME}-rods.png><img src=\${MOLNAME}-rods.png border=0 width=320 height=240 ></a></td></tr><tr><td valign=top colspan=2><br><a href="$3".png>\" && echo -n "$3"\" \"  && cat "$1"/"$2"/"$3"/names | fold -w 60 | tr \"\\n\" % | sed s/\"%\"/\"<br>\"/g  && echo \"</a><br>Smiles: \" && cat "$1"/"$2"/"$3"/\${MOLNAME}.smiles | fold -w 60 | sed s/%%%%$%%%%/\"<br>\"/ && echo \"<br>pdb file: <a href="$3".pdb>"$3".pdb</a><br>sdf file: <a href="$3".sdf>"$3".sdf</a><p>\"")}' | sed s/%%%%/"\'"/g | csh -f \
>> ${1}/index.html

	cd ${MOLDIR}/$1 && \
	echo "$*" | tr / ' ' | cut -f3-104 -d ' ' | tr -s ' ' | tr ' ' '\n' | grep . | \
	tr -d ')' | tr -d '(' | tr -d '[' | tr -d ']' | \
	sed s/' -'/' '/ | sed s/' -'/' '/ | sed s/' -'/' '/ | tr -s ' ' | tr -d '*' | tr -d '\"' | tr -d "\'" | \
	awk '{print("ln -s index.html "$1".html")}' | csh -f ; \
	cd ${MOLDIR}

	echo "<p>Please note: images may show incorrect connectivity due to improper geometry.  We will be working to improve this situation.  For now, the left image should be correct, and the other two are correct, if they match the first.<br>" >> ${1}/index.html
	echo "<p><hr><p><b>Image Links</b><p><ul>"\
>> ${1}/index.html
	\ls $1/ | grep '\.png$' | awk '{print("<a href="$1">"$1"</a><br>")}'\
>> ${1}/index.html
	echo "</ul><p><hr><p><b>Molecule Name Links</b><ul>"\
>> ${1}/index.html
	\ls $1/ | grep '\.html$' | grep -v index.html | sed s/'\.html$'// | awk '{print("<a href="$1".html>"$1"</a><br>")}'\
>> ${1}/index.html
	echo "</ul><p>More coming soon!</td><td valign=top align=right><p><b><p><a href=/>Back to top</a><p><a href=/mod.rss><img src=/mod-rss.png border=0 width=140 height=60 ><br>RSS News Feed</a><br><a href=http://us.rd.yahoo.com/my/atm/Molecules@GNU-Darwin.org/MOD/*http://add.my.yahoo.com/rss?url=http%3A//molecules.gnu-darwin.org/mod.rss><img src=http://us.i1.yimg.com/us.yimg.com/i/us/my/addtomyyahoo6.gif width=89 height=33 border=0 alt="Add to My Yahoo"!></a><br><a href=http://www.newsgator.com/ngs/subscriber/subext.aspx?url=http://molecules.gnu-darwin.org/mod.rss><img src=http://www.newsgator.com/images/ngsub1.gif alt="Subscribe in NewsGator Online" border=0></a><br><a href=http://fusion.google.com/add?source=atgs&feedurl=http%3A//molecules.gnu-darwin.org/mod.rss><img src=http://gmodules.com/ig/images/plus_google.gif border=0 alt="Add to Google"></a><br>(syndicate freely:)<p>" \
>> ${1}/index.html
	echo "</ul></td></tr><ul></table><p><hr><p><b>PubChem Fields</b></ul><ul>"\
>> ${1}/index.html
	cat ${1}/*.sdf | tr "\n" "%" | sed s/"%%"/"#"/g | tr "#" "\n" | tr "%" " " | sed s/"> <"// | sed s/">"// | awk '{print(tolower($1)": "$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$12,$13,$14,$15,$16,$17,$18,$19,$20,$21,$22,$23,$24,$25,$26,$27,$28,$29,$30,$31,$32,$33,$34,$35,$36,$37,$38,$39,$40,$41,$42,$43,$44,$45,$46,$47,$48,$49,$50,$51,$52,$53,$54,$55,$56,$57,$58,$59,$60,$61,$62,$63,$64,$65,$66,$67,$68,$69,$70,$71,$72,$73,$74,$75,$76,$77,$78,$79,$80,$81,$82,$83,$84,$85,$86,$87,$88,$89,$90,$91,$92,$93,$94,$95,$96,$97,$98,$99,$100)}' | grep pubchem | tr -s ' ' '\n' | fold -w 154 | txt2html | grep -v "DOCTYPE" |  grep -v "http://www.w3.org/TR/html4/strict.dtd" |  grep -v "<HTML>" |  grep -v "<HEAD>" |  grep -v "<TITLE></TITLE>" |  grep -v "<META" |  grep -v "</HEAD>" |  grep -v "<BODY>" |  grep -v "</BODY>" |  grep -v "</HTML>" | sed s/pubchem_/'<br>pubchem_'/ | sed s/'<BR>'// | sed s/'<br>pubchem_total_charge'/pubchem_total_charge/ \
>> ${1}/index.html
#sed s/pubchem/'<a href=http:\/\/pubchem.ncbi.nlm.nih.gov\/>pubchem<\/a>'/ \
	echo "</ul><p><hr><p><b>Other Related Links</b><ul>"\
>> ${1}/index.html
	\ls $1/ | grep -v '\.html$' | grep -v '\.png$' | grep -v index.html | awk '{print("<a href="$1">"$1"</a><br>")}'\
>> ${1}/index.html
	echo "</ul><p>More coming soon!" \
>> ${1}/index.html
	echo '<pre><br>' \
>> ${1}/index.html
	smiley \
>> ${1}/index.html
	echo '</pre>' \
>> ${1}/index.html



	echo inserting header
	~/grabHtmlHeader ${1}/index.html ; ~/insertSidebar2 ${1}/index.html
else 
	echo argument required
endif