#!/bin/csh 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 balls < ${1}/*.pdb | render -png > ${1}/${MOLNAME}-balls.png rods < ${1}/*.pdb | render -png > ${1}/${MOLNAME}-rods.png echo "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 ' ' /`"" \ > ${1}/index.html echo "

"`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

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

${1} index

" > ${1}/index.html echo "$*" | 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("echo \"

\" && echo -n "$3"\" \" && cat "$1"/"$2"/"$3"/names && echo \"
Smiles: \" && babel -isdf "$1"/"$2"/"$3"/"$3".sdf -osmiles && echo \"
pdb file: "$3".pdb
sdf file: "$3".sdf

\"")}' | csh \ >> ${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 && \ cd ${MOLDIR} echo "

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.
" >> ${1}/index.html echo "

Image Links

    "\ >> ${1}/index.html \ls $1/ | grep '\.png$' | awk '{print(""$1"
    ")}'\ >> ${1}/index.html echo "

Molecule Name Links

    "\ >> ${1}/index.html \ls $1/ | grep '\.html$' | grep -v index.html | sed s/'\.html$'// | awk '{print(""$1"
    ")}'\ >> ${1}/index.html echo "

PubChem Fields

    "\ >> ${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)}' | tr -s ' ' | grep pubchem | txt2html | grep -v "DOCTYPE" | grep -v "http://www.w3.org/TR/html4/strict.dtd" | grep -v "" | grep -v "" | grep -v "" | grep -v "" | grep -v "" | grep -v "" | grep -v "" | sed s/pubchem_/'
    pubchem_'/ | sed s/'
    '// | sed s/'
    pubchem_total_charge'/pubchem_total_charge/\ >> ${1}/index.html #sed s/pubchem/'pubchem<\/a>'/ \ echo "

Other Related Links

More coming soon!

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