#!/bin/bash

# write out an AB layer from Alliance AB construct and add to CIF file
sed 's/\,/\ /' $1.cif | \
sed '1,/^(AB :/ s/^(AB\ :\(.*\)/L\ AB;\1/' > temp
x1=$(grep '^L AB' temp | awk '{printf "%1d\n", $3*100 }')
y1=$(grep '^L AB' temp | awk '{printf "%1d\n", $4*100 }')
x2=$(grep '^L AB' temp | awk '{printf "%1d\n", $5*100 }')
y2=$(grep '^L AB' temp | awk '{printf "%1d\n", $6*100 }')
width=$(echo $[ ($x2-$x1)*2 ] | awk '{printf "%1d\n", $1/100 }')
height=$(echo $[ ($y2-$y1)*2 ] | awk '{printf "%1d\n", $1/100 }')
centerx=$(echo $[ ($x1+($x2-$x1)/2)*2 ] | awk '{printf "%1d\n", $1/100 }')
centery=$(echo $[ ($y1+($y2-$y1)/2)*2 ] | awk '{printf "%1d\n", $1/100 }')
echo "sed 's/L\ AB;.*$/L\ AB;\nB\ "$width"\ "$height"\ "$centerx"\ "$centery";/' temp > \$1" > temp1
chmod 755 temp1
./temp1 $1.cif
rm -f temp temp1
