#!/usr/bin/perl
$NUM_OF_MOLECULES=6;


chkargs();

my $arr_res_active_passive=&get_imput_res();
my $air_file=$ARGV[0];

&fill_segid();

&make_air_file( $arr_res_active_passive, $air_file);


print "DONE!!\n";
END;
1;

sub chkargs
{
	if(scalar(@ARGV)== 0)
	{
		print "Usage:\n $0 filename for the AIR generated file\n";
		exit(1);
	}
}

sub make_air_file
{
	my $arr_res_active_passive = $_[0];
	my $air_file = $_[1];
	
	my $i=0;
	my $j=0;
	my $ki=0;
	my $kj=0;
	my $kk=0;
	
	my $ctrl=0;
	
	open AIRFILE, ">", $air_file or die "Can not write file $air_file\n$!\n";
	
	for($i=0;$i<$NUM_OF_MOLECULES;$i++)
	{
		print AIRFILE "!\n! HADDOCK AIR restraints for molecule $SEGID[$i]\n!\n";
		for($j=0 ; $j<scalar(@{$$arr_res_active_passive[$i][0]}) ; $j++ )
		{
			$ctrl=0;
			print AIRFILE "!\nassign ( resid ".$$arr_res_active_passive[$i][0][$j]." and segid ".$SEGID[$i].")\n       (\n";
			#print "!\nassign ( resid ".$$arr_res_active_passive[$i][0][$j]." and segid ".$SEGID[$i].")\n       (\n";
			for($ki=0;$ki < $NUM_OF_MOLECULES;$ki++)
			{
				if($ki == $i)
				{
					next;
				}
				for($kj=0;$kj < scalar(@{$$arr_res_active_passive[$ki][0]}) ; $kj++)
				{
					if($ctrl)
					{
						print AIRFILE "     or\n";
						#print  "     or\n";
					}

					print AIRFILE "        ( resid ".$$arr_res_active_passive[$ki][0][$kj]." and segid ".$SEGID[$ki].")\n";
					#print "        ( resid ".$$arr_res_active_passive[$ki][0][$kj]." and segid ".$SEGID[$ki].")\n";
					$ctrl=1;
				}
				for($kj=0;$kj < scalar(@{$$arr_res_active_passive[$ki][1]}) ; $kj++)
				{
					print AIRFILE "     or\n";
					print AIRFILE "        ( resid ".$$arr_res_active_passive[$ki][1][$kj]." and segid ".$SEGID[$ki].")\n";
					#print "     or\n";
					#print "        ( resid ".$$arr_res_active_passive[$ki][1][$kj]." and segid ".$SEGID[$ki].")\n";
				}
				
			}
			print AIRFILE "       )  2.0 2.0 0.0\n";
			#print "       )  2.0 2.0 0.0\n";

		}
	}

	
	
	close AIRFILE;
	
}

sub fill_segid
{
	$SEGID[0]="A";
	$SEGID[1]="B";
	$SEGID[2]="C";
	$SEGID[3]="D";
	$SEGID[4]="E";
	$SEGID[5]="F";
}

sub get_imput_res
{

	my $i=0;
	my @arr_res_active_passive;
	my $input;
	
	print "Enter residues separated by the character SPACE (\' \') or the character COMMA (\',\')\n".
	      "Press enter for those molecules you do not want to provide residues\n".
	      "WARNING: all non digit caracters will be eliminated from the numbers you enter\n\n";





	for($i=0;$i<$NUM_OF_MOLECULES;$i++)
	{
		print "ACTIVE Residues for molecule $i:\n";
		$input=<STDIN>;
		chomp $input ;
		if($input ne undef)
		{
			$input=&clean_residuelist($input);
			@{$arr_res_active_passive[$i][0]}=split /\s+/,$input;
#			print "@{$arr_res_active_passive[$i][0]}\n";
		}
		print "PASSIVE Residues for molecule $i:\n";
		$input=<STDIN>;
		chomp $input ;
		if($input ne undef)
		{
			$input=&clean_residuelist($input);
			@{$arr_res_active_passive[$i][1]}=split /\s+/,$input;
#			print "@{$arr_res_active_passive[$i][1]}\n";
		}
	}
	
	return \@arr_res_active_passive;
	
}
sub clean_residuelist
{
	my $str=$_[0];
	
	$str=~s/\,/\ /g;
	#print "2- ".$str."\n";
	$str=~s/\s+/\ /g;
	#print "3- ".$str."\n";
	$str=~s/[^\d\ ]//g;
	#@arr=split '\ ',$str;
	#print "4- "."@arr"."\n";

	return $str;
}