#!/bin/perl

#Perl script to compare restraints to a list of ones to fix. If 
#the restraint matches, it is replaces by the one on the list.
#If the rst on the adjusted list has a bin column set to 'rm', the 
#restraint is removed from the list

#Melanie Nelson
#6/2/99

require "getopt.pl";

if ($#ARGV != 3){
	$prg_name = $0;
	$prg_name = `basename $prg_name`;
	chomp ($prg_name);
	die<<EODIE;
This script reads a DIANA format restraint list and compares it to
a list of restraints whose bins have been manually adjusted because of
spin diffusion, overlap, etc. This list of restraints to fix should
also be in diana format. If a restraint in the main list matches
one in the adjusted list, the one in the main list is replaced by
the one in the adjusted list. If the restraint in the adjusted
list has its bin column set to rm, the restraint is removed
from the final main list.

DIANA restraint list format:
 24 SER  HN     61 VAL  HA      3.50
 28 LEU  HN     26 GLU- HN      4.50
 31 LEU  HN     29 LYS+ HN      4.50
 36 GLY  HN     40 LEU  HN      4.50
 70 VAL  HN     70 VAL  HB      3.50

adjusted restraint list format (with one restraint flagged to 
be removed):
 24 SER  HN     61 VAL  HA      6.00
 28 LEU  HN     26 GLU- HN      6.00
 31 LEU  HN     29 LYS+ HN      rm
 36 GLY  HN     40 LEU  HN      6.00
 70 VAL  HN     70 VAL  HB      4.50

Usage: $prg_name -r rst_list -f fix_list [>! output]
EODIE
}

#get arguments from the command line
&Getopt('rf');
$rst_list = $opt_r;
$fix_list = $opt_f;

#read list of adjusted restraints into an array for matching
open (FIXLIST, $fix_list) ||
	die ("Could not open list of adjusted restraints, $fix_list\n");

$x = 0;
while (<FIXLIST>){
	next if(/^\s*#/);
	next if(/^\s*$/);
	chomp;

#for printing later
	$store_rst[$x] = $_;

	($resnum1[$x], $resname1[$x], $atm1[$x], $resnum2[$x], $resname2[$x], 
	$atm2[$x], $bin[$x]) = split;

	$x++;

}

#now go through the main restraint file, printing either the
#original line, or the matching line from the adjusted restraint
#list

open (RSTLIST, $rst_list) ||
	die("Could not open main restraint list, $rst_list\n");

while(<RSTLIST>){
	next if(/^\s*#/);
	next if(/^\s*$/);
	chomp;

#for easy printing, store original line
#will be printed unless we match something later
	$print_line = $_;

#printing is on by default-- only turned off if indicated by
#the line in the adjusted restraint list file
	$print_flag = 1;

	($resnum1, $resname1, $atm1, $resnum2, $resname2, $atm2, $bin) = split;

#do the matching-- can assume that if residue numbers match, the
#residue names will match, too
#if bin column (last column) in line from adjusted list is 'rm', 
#flag this restraint not to be printed in the final list
	for ($n = 0; $n <= $#store_rst; $n++){
		if (($resnum1 eq $resnum1[$n] && $atm1 eq $atm1[$n] &&
			$resnum2 eq $resnum2[$n] && $atm2 eq $atm2[$n]) ||
			($resnum1 eq $resnum2[$n] && $atm1 eq $atm2[$n] &&
			$resnum2 eq $resnum1[$n] && $atm2 eq $atm1[$n])){
			if ($bin[$n] =~ 'rm'){
				$print_flag = 0;
			} else {
				$print_line = $store_rst[$n];
			}
		}
	}

	if ($print_flag != 0){
		print "$print_line\n";
	}

}