#!/bin/bash - TEMP=`getopt -o ch -n 'pdb2svg' -- "$@"` if [ $? != 0 ] ; then echo "Terminating..." >&2 ; exit 1 ; fi eval set -- "$TEMP" fill='colour[$12]' while true ; do case "$1" in -c) fill='numcolour[chain[$5]]' shift ;; -h) echo $0 '[-c] [file.pdb]' echo Converts a PDB file to SVG. File can come through stdin or on command line. Atoms will be coloured by element unless -c is given, in which case, they will be coloured by chain. exit 0 ;; --) shift break ;; *) echo "Internal error!" 1>&2; exit 1 ;; esac done if [ $# -gt 1 ] then echo Too many files. 1>&2 exit 1 fi ( [ $# = 0 ] && cat || cat "$1" ) | egrep '^ATOM ' | sed -e 's/ */ /g' | sort -rnk 9 | awk 'BEGIN {colour["C"]="black";colour["H"]="grey";colour["O"]="red";colour["N"]="blue";colour["S"]="yellow";colour["P"]="violet"; radius["C"]=1.7; radius["H"]=1.2; radius["O"]=1.5; radius["N"]=1.4; radius["S"]=1.8; radius["P"]=1.8; numcolour[1]="blue"; numcolour[2]="green"; numcolour[3]="violet"; numcolour[4]="aqua"; numcolour[5]="darkorange"; numcolours[6]="darkred"; numcolours[7]="darkslateblue"; numcolours[8]="firebrick"; numcolours[9]="yellow"; numcolours[10]="teal"; numcolour[11]="darkmagenta"; chainidx=0; print "" }'