#!/bin/bash
# iteratively removes all water molecules that are not buried

while read fname; do
	echo "Processing $fname"
	cat ${fname}.pdb > temp.p
	cat ${fname}.pdb > temp1
	while [ -s temp.p ]
	do
	  cat temp1 > temp.p
	  ~/Programs/naccess2.1.1/naccess temp.p -w
	  grep "^ATOM" temp.asa > temp1
	  grep " HOH " temp.asa | perl -e 'while(<>){@a=split;if($a[-2] == 0.0) {print;}}' >> temp1
	  
	  diff temp.asa temp1 > temp.p
	done
	mv temp1 ${fname}.q0
done < $1