Re: Calc distance between atoms in pdb file

Here's a somewhat simpler and more idiomatic version of your code that does the same thing that may help you. Ask about anything you do not understand:

#!/usr/bin/perl -w
use strict;

my( @arrayx, @arrayy, @arrayz );

while (<>) {
# Find x, y, z coordinates and store in separate arrays

    if ($_ =~ /^ATOM/) {
        my @line = $_ =~ m/^(.....).(.....).(....).(...)..(....)....(.
+.......)(........)(........)/;

        ## using push mean you don't have to count because ...
        push @arrayx, $line[5];
        push @arrayy, $line[6];
        push @arrayz, $line[7];
    }

}
close *ARGV; ## prevent confusing error message suffixes

# Calculate distance between all atom coordinates
## ... $#xxx gives you the highest index in array @xxx

foreach my $i ( 0 .. $#arrayx ) { 

    foreach my $j ( $i + 1 .. $#arrayx ) {

        my $dist = sqrt(
                ($arrayx[$i] - $arrayx[$j])**2 +
                ($arrayy[$i] - $arrayy[$j])**2 +
                ($arrayz[$i] - $arrayz[$j])**2
            );

        ## Adding $i and $j to your output will let you know what that
+ output is.
        print "$i <> $j : $dist\n";

    }
}
[download]

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Comment on Re: Calc distance between atoms in pdb file Download Code

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Re^2: Calc distance between atoms in pdb file by Anonymous Monk on Nov 14, 2016 at 11:06 UTC
I'm getting an error of `uSE OF UNINITIALIZED VALUE IN SUBTRACTION AT LINE 47` `foreach my $i ( 0 .. 1520) { foreach my $j ( $i + 1 .. 1520 ) { my $dist = sqrt( ($arrayx[$i] - $arrayx[$j])2 + ($arrayy[$i] - $arrayy[$j])2 + ($arrayz[$i] - $arrayz[$j])**2 ); ## Adding $i and $j to your output will let you know what that print "$i <> $j : $dist\n"; } } exit 0;` [download]	[reply] [d/l] [select]
Re^3: Calc distance between atoms in pdb file by soonix (Chancellor) on Nov 14, 2016 at 11:17 UTC
Where do the `1520` come from? Obviously not from the originally posted code.	[reply] [d/l]
Re^4: Calc distance between atoms in pdb file by Anonymous Monk on Nov 14, 2016 at 15:57 UTC
I took the value to $count-1 ... that is where 1520 came from	[reply]
Re^2: Calc distance between atoms in pdb file by Anonymous Monk on Nov 14, 2016 at 15:58 UTC
I'm Still getting Use of uninitialized value in subtraction	[reply]