Hi all! I'm new to Perl and I'm trying to use it to renumber the entries of a pdb file (sample below)

ATOM 9 H5T THY C 1 107.274 35.359 -9.821 0.00 0.00 N1 H

ATOM 10 O5' THY C 1 107.686 36.230 -9.553 1.00 0.00 N1 O

ATOM 11 C5' THY C 1 108.813 35.973 -8.710 1.00 0.00 N1 C

ATOM 12 H5' THY C 1 109.513 35.493 -9.239 0.00 0.00 N1 H

ATOM 13 H5'' THY C 1 108.495 35.550 -7.861 0.00 0.00 N1 H

ATOM 14 N1 THY C 1 107.956 38.157 -5.232 1.00 0.00 N1 N

ATOM 15 C6 THY C 1 107.862 39.006 -4.149 1.00 0.00 N1 C

ATOM 16 H6 THY C 1 108.479 39.755 -3.910 0.00 0.00 N1 H

ATOM 17 C2 THY C 1 107.024 37.166 -5.449 1.00 0.00 N1 C

ATOM 18 O2 THY C 1 107.071 36.398 -6.397 1.00 0.00 N1 O

ATOM 19 N3 THY C 1 106.027 37.104 -4.506 1.00 0.00 N1 N

So I want to renumber the entries in the second column (next to ATOM), starting them all sequentially from 1. This is what I've written so far: 
#/bin/perl/

use strict;
use warnings;

my $pdb;

my $line;
my @columns;

open $pdb, '<', "structure.pdb" or die $!;

#match string and select column
my $string = "ATOM"; # match for ATOM
my @nth_column;
my $n = 1; # select 2nd column

while ($line = <$pdb>) {
  if ($line =~ $string) {
  chomp $line;
  @columns = split /\s+/, $line;
  push @nth_column, $columns[$n];
  #for testing:
  print "$columns[$n] \n";
  }
}

[download]

So I am printing the correct column but I'm having a bit of a brain fart because I can't figure out how to actually do the renumbering? Would I match for a digit using regex and then introduce a counter? Does that sound reasonable?

Thanks in advance!!

In reply to renumber entries in column? by aria

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