#!/usr/bin/perl -w


$num = 0;
$count = 0;

while (<>) {  

# Find x, y, z coordinates and store in separate arrays

    if ($_ =~ /^ATOM/) {
        @line = $_ =~ m/^(.....).(.....).(....).(...)..(....)....(........)(........)(........)/;
        
        $x = $line[5];
        $arrayx[$num] = $x;
                         
        $y = $line[6];
        $arrayy[$num] = $y;
        
        $z = $line[7];
        $arrayz[$num] = $z;
        
        ++$num;        
    }    

# Count number of atoms
    
    if ($_ =~ /^ATOM/) {
        ++$count;
    }
}

# Calculate distance between all atom coordinates

foreach $i (0..$count) {

    foreach $j ($i + 1..$count) {
    
    $dist = sqrt(
            ($arrayx[$i] - $arrayx[$j])**2 +
            ($arrayy[$i] - $arrayy[$j])**2 +
            ($arrayz[$i] - $arrayz[$j])**2
        );
    
    print "$dist\n";
    
    }
}