#!/bin/bash

rm -f $5/va_*.*

((count=0))

./search_bonds $1 $2 $3 $4 | grep ' # atoms' | while read a b c d e f; do

	ca=`echo $c | awk -F/ '{ print $1}'`
	ma=`echo $d | awk -F/ '{ print $1}'`

	./visual_atoms $1 $ca 12.0 5.429 $ma | \
		grep ^[A-Z] > $5/va_${count}.xyz

	which povray
	ret=$?
	if [ "$ret" = "0" ]; then
		./visualize -w 640 -h 480 -d $5/va_${count}.xyz \
                            -nll -0.76 -0.76 -0.76 -fur 0.76 0.76 0.76 \
                            -b -0.5 -0.5 -0.5 0.5 0.5 0.5 \
                            -c -0.2 -2.0 0.6 -L 0 0 -0.1 \
                            -r 0.6 -B 0.1
	fi

	echo -en "$count "

	((count+=1))
done

echo "done"

qiv $5/va_*.png