for my $i ( 0 .. $natms{$f1}-1 ) {

    my $xyz = @{$coord{$f1}[$i]};
    my $rad = pop @xyz;

    for my $j ( 0 .. $natms{$f2}-1 ) {
# use map to compute the x,y,z diffs just once each:
        my @difs = map { $xyz[$_] - $coord{$f2}[$j][$_] } ( 0, 1, 2 );
        my $dist = sqrt( $difs[0] * $difs[0] +
                         $difs[1] * $difs[1] +
                         $difs[2] * $difs[2] );
        my $rsum = $rad + $coord{$f2}[$j][3];
        if ( $dist < $rsum ) {
            print TXT "Overlap for $atmnb{$f1}[$i] and $atmnb{$f2}[$j]\n";
        }
        else {
            print PDB $input{$f1}[$i];
        }
    }
}