#!/usr/bin/perl
use strict;
use warnings;

my $list = <<LIST;
PF10417.3
PF11001.3
PF05.3
LIST

my @domains1 = ('PF05.3',     'PF11001.3', 'PF00389.24', 'PF10417.3');
my @domains2 = ('PF01',       'PF02',      'PF11001.3',  'PF00389');
my @domains3 = ('PF00389.24', 'PF05.3',    'PF01',       'PF00389');
my %neighbours;

for my $domain (\@domains1, \@domains2, \@domains3) {
    for my $idx (0 .. $#$domain) {
        my @near = grep {$_ >= 0 && $_ <= $#$domain} $idx - 1, $idx + 1;
        push @{$neighbours{$domain->[$idx]}}, map {$domain->[$_]} @near;
    }
}

open my $inList, '<', \$list or die "cannot open 'domainlist'becuase:$!";

while (defined (my $domain = <$inList>)) {
    chomp $domain;

    print "Domain $domain has neighbours: @{$neighbours{$domain}}\n";
}