It's just a simple one-liner 

#!/usr/bin/perl

# http://perlmonks.org/?node_id=1128822

use strict;
use warnings;

$_ = <<END; # input
1 H 35
1 C 22
2 H 20
2 C 30

A  1  HB2 MET 1
A  2  CA  MET 1
A  3  HA  ASP 2
A  4  CA  ASP 2
END

=output wanted
1  MET  HB2 35
1  MET  CA  22
2  ASP  HA  20
2  ASP  CA  30
=cut

print "$1  $5  $4 $3\n" while /^(\S+)\s+(\w)\s+(\S+)(?=.*\n\n.*^\S+\s+
+\S+\s+(\2..)\s+(\S+)\s+\1)/gms;

[download]

:)

In reply to Re: Match two files using regex by Anonymous Monk
in thread Match two files using regex by chemshifts

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