in reply to Question on REGEXP

My preferred way to escape a special regex character, e.g the alternation(|) character, is to use a character class:

use strict;
use warnings;
use 5.014;  

my $pattern =<<'END_OF_PATTERN';
    1QJ8:A    #These characters, followed by...
    [|]       #a literal pipe, followed by...
    PDBID     #these characters, folllowed by...
    [|]       #a literal pipe, followed by...
    CHAIN     #this word
END_OF_PATTERN

my $str = '1QJ8:A...PDBID....CHAIN...1QJ8:A|PDBID|CHAIN';
my @matches =  $str =~ /$pattern/gxms;

say "@matches";

--output:--
1QJ8:A|PDBID|CHAIN

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