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foreach my $ref (keys %$self){
   next unless $self->{$ref}{'chain'} = 1;
   # process chain 1 atoms 
}

foreach my $ref (keys %$data){
   next unless $data->{$ref}->type eq 'ATOM';
...
foreach my $ref (keys %{$self->{1}}) {
   # process chain 1 atoms
}