P:\test>perl -MO=Deparse 376142-dl.pl >376142.pl
376142-dl.pl syntax OK

##</code><code>##

if ($line =~ 
	/$atomid.*\s*\w+\s+$resid\s+$atomidmatch.* \w+\s+$residmatch\s+\d\./ 
 or $line =~ 
 	/$atomidmatch.*\s*\w+\s+$residmatch\s+$atomid.* \w+\s+$resid\s+\d\./) {
	print OUTFILE "array2[$el]\n";
	last;
}

##</code><code>##

sub outputIf {
	my( $line, $atomid, $atomidmatch, 
	     $residmatch, $resid, $array2_el, $outfile) = @_;
	
	if ($line =~ 
	 	/$atomid.*\s*\w+\s+$resid\s+$atomidmatch.* \w+\s+$residmatch\s+\d\./ 
	 or $line =~ 
	 	/$atomidmatch.*\s*\w+\s+$residmatch\s+$atomid.* \w+\s+$resid\s+\d\./
	) {
		print $outfile "array2_el\n";
		return 1;
	}
	return 0;
}

##</code><code>##

last if outputIf( $line, $atomid, $atomidmatch, $1, $2, $array2[$el], \*OUTFILE );

##</code><code>##

if ($array2[$el + 10] =~ /resid (\d+) and name (H\w+\d*).?\)/ 
and $array2[$el     ] =~ /resid (\d+) and name (H\w+\d*).?\)/) {
	$resid = $1;
	$atomid = $2;
	if ($array2[$el + 10] =~ /resid (\d+) and name (H\w+\d*).\n?\)/) {
		$residmatch = $1;
		$atomidmatch = $2;
	}
	die "Can't open $distfil\ne" unless open DISTFILE, "$distfile";
	while (defined($_ = <DISTFILE>)) {
		$line = $_;
		last if outputIf( $line, $atomid, 
			$atomidmatch, $residmatch, $resid, $array2[$el] );

		if ($array2[$el + 11] =~ /resid (\d+) and name(H\w+\d*).?\)/) {
			last if outputIf( $line, $atomid, 
				$atomidmatch, $1, $2, $array2[$el] );
		}
		elsif ($array2[$el + 12] =~ /resid (\d+) and name(H\w+\d*).?\)/) {
			last if outputIf( $line, $atomid, 
				$atomidmatch, $1, $2, $array2[$el] );
		}
		elsif ($array2[$el + 13] =~ /resid (\d+) and name(H\w+\d*).?\)/) {
			last if outputIf( $line, $atomid, 
				$atomidmatch, $1, $2, $array2[$el] );
		}
		elsif ($array2[$el + 14] =~ /resid (\d+) and name(H\w+\d*).?\)/) {
			last if outputIf( $line, $atomid, 
				$atomidmatch, $1, $2, $array2[$el] );
		}
		elsif ($array2[$el + 15] =~ /resid (\d+) and name(H\w+\d*).?\)/) {
			last if outputIf( $line, $atomid, 
				$atomidmatch, $1, $2, $array2[$el] );
		}
	}
}

##</code><code>##

@array2 = <KATFILE>;
chomp @array2;

foreach $el ( 0 .. @array2 ) {
	next if whileif( \@array2, $el, 10, $distfile, $outfile );
	next if whileIf( \@array2, $el, 11, $distfile, $outfile );
	next if whileIf( \@array2, $el, 12, $distfile, $outfile );
	next if whileIf( \@array2, $el, 13, $distfile, $outfile );
	next if whileIf( \@array2, $el, 14, $distfile, $outfile );
	next if whileIf( \@array2, $el, 15, $distfile, $outfile );
    print OUTFILE "$array2[$el]\n";
}


##</code><code>##

sub whileIf {
	my( $arrayRef, $el, $offset, $distfile, $outfile ) = @_;
	
	if ($array2[$el + $offset] =~ /resid (\d+) and name (H\w+\d*).?\)/ 
	and $array2[$el     ] =~ /resid (\d+) and name (H\w+\d*).?\)/) {
		$resid = $1;
		$atomid = $2;
		
		die "Can't open $distfil\ne" unless open DISTFILE, "$distfile";

WHILELOOP:		
		while( defined( $line = <DISTFILE> ) ) {
			for my $offset2 ( 0 .. 5 ) {
				last WHILELOOP 
					if $array2[$el + $offset] =~ 
						/resid (\d+) and name (H\w+\d*).\n?\)/
			    	and outputIf( $line, $atomid, $atomidmatch, 
			    		$1, $2, $array2[$el], $outfile )				 ;
			}
		}
		return 1;
	}
	return 0;
}

##</code><code>##

$katfile = '/remote/belgarath/tpukala/pegasus/xplor/signif/25jun2.kat2';
$outfile = 'temp.kat';
die "Can't open $outfile" unless open OUTFILE, ">$outfile";
die "Can't open $katfile" unless open KATFILE, "$katfile";
@array = <KATFILE>;
chomp @array;
$numelements = @array;
@arraylist = 0 .. $numelements;
foreach $el (@arraylist) {
    if ($array[$el] =~ /^\)$/ and $array[$el + 1] =~ /^\($/) {
        print OUTFILE ")\n*\n*\n*\n*\n*\n*\n*\n";
    }
    elsif ($array[$el] =~ /assign/ and $array[$el + 1] =~ /^\($/) {
        print OUTFILE "assign\n*\n*\n*\n*\n*\n*\n*\n*\n*\n*\n";
    }
    else {
        print OUTFILE "$array[$el]\n";
    }
}
close KATFILE;
close OUTFILE;
$distfile = "/remote/belgarath/tpukala/pegasus/xplor/signif/25jun/rnk_2\n5jun_signif_.dst";
$katfile = '/remote/belgarath/tpukala/pegasus/xplor/signif/temp.kat';
$outfile = 'temp2.kat';
die "Can't open $outfile" unless open OUTFILE, ">$outfile";
die "Can't open $katfile" unless open KATFILE, "$katfile";
@array2 = <KATFILE>;
chomp @array2;

foreach $el ( 0 .. @array2 ) {
    whileif( \@array2, $el, $_, $distfile, \*OUTFILE ) and next for 10 .. 15;
    print OUTFILE "$array2[$el]\n";
}

close KATFILE;
close OUTFILE;
$katfile = '/remote/belgarath/tpukala/pegasus/xplor/signif/temp2.kat';
$outfile = 'half.kat';
die "Can't open $outfile" unless open OUTFILE, ">$outfile";
die "Can't open $katfile" unless open KATFILE, "$katfile";
@array3 = <KATFILE>;
chomp @array3;
$numelements3 = @array3;
@arraylist3 = 0 .. $numelements3;
foreach $el (@arraylist3) {
    if ($array3[$el] =~ /^\*$/) {
        ();
    }
    elsif ($array3[$el] eq $array3[$el + 1]) {
        ();
    }
    else {
        print OUTFILE "$array3[$el]\n";
    }
}

## Exit main program
exit;

sub outputIf {
	my( $line, $atomid, $atomidmatch, $residmatch, 
		$resid, $array2_el, $outfile ) = @_;
	
	if ($line =~ 
		/$atomid.*\s*\w+\s+$resid\s+$atomidmatch.* \w+\s+$residmatch\s+\d\./ 
	 or $line =~ 
	 	/$atomidmatch.*\s*\w+\s+$residmatch\s+$atomid.* \w+\s+$resid\s+\d\./
	) {
		print $outfile "array2_el\n";
		return 1;
	}
	return 0;
}

sub whileIf {
	my( $arrayRef, $el, $offset, $distfile, $outfile ) = @_;
	
	if ($array2[$el + $offset] =~ /resid (\d+) and name (H\w+\d*).?\)/ 
	and $array2[$el     ] =~ /resid (\d+) and name (H\w+\d*).?\)/) {
		$resid = $1;
		$atomid = $2;
		
		die "Can't open $distfil\ne" unless open DISTFILE, "$distfile";

WHILELOOP:		
		while( defined( $line = <DISTFILE> ) ) {
			for my $offset2 ( 0 .. 5 ) {
				last WHILELOOP 
					if $array2[$el + $offset] =~ 
						/resid (\d+) and name (H\w+\d*).\n?\)/
			    	and outputIf( $line, $atomid, $atomidmatch, 
			    		$1, $2, $array2[$el], $outfile )				 ;
			}
		}
		return 1;
	}
	return 0;
}