#HETATM 1562 O HOH 189 48.728 50.544 -16.104 
my $num = qr{-?\d+\.\d+};
my $coordinate = qr{\s+($num)\s+($num)\s+($num)\s*$};

sub get_coordinates_for {
    my $filename = shift;
    my @coordinates = ();

    if (open $FH,  $filename) {
        my $linecounter = 0;
        while (my $line = <$FH>) {
            $linecounter++;
            if ($line =~ m{$coordinate}) {
                my ($x , $y , $z) = ($1 , $2 , $3);
                push @coordinates , [$x , $y , $z];
            }
            else {
                warn "[$filename : $linecounter] invalid lineformat!\n
+";
            }
        }
        close $FH;
    }
    else {
        die "failed to open $filename for reading($!)\n";
    }
    return \@coordinates;
}

my $file1 = shift @ARGV;
my $file2 = shift @ARGV;
my $coordinates1_ref = get_coordinates_for($file1);
my $coordinates2_ref = get_coordinates_for($file2);

# calculate the results:
foreach my $coordinate1 ( @$coordinates1_ref ) {
    my ($x , $y , $z) = @$coordinate1;
    foreach my $coordinate2 (@$coordinates2_ref) {
        my ($a , $b , $c) = @$coordinate2;
        my $distance = sqrt( ($x-$a)**2 + ($y-$b)**2 + ($z-$c)**2 );
        print "distance ($x,$y,$z) to ($a,$b,$c) = $distance\n";
    }
}

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In reply to Re: substr in nested foreach loop by rminner
in thread substr in nested foreach loop by sarani

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