As I just wrote elsewhere, regexps are not a good tool for parsing XML. There may be comments, <!CDATA ... ]> sections, escaped data, newlines and other whitespace at unexpected places, ...

use strict;
use XML::Parser;

my $parser = new XML::Parser(
    Handlers => {
        Start => sub {
            my ($expat,$tag,%attr) = @_;
            print $attr{'molecule_idref'}, "\n" if %attr and exists $a
+ttr{'molecule_idref'};
        }
    }
);

$parser->parse(\*DATA);

__DATA__
<root>
<foo molecule_idref="123">fgdfg</foo>
<bar molecule_idref="456">fgd
 <foo other="74" molecule_idref="789">fgdfg</foo>
fg</bar>
some text about how to write things containing molecule_idref="666".
<baz molecule_idref="987"/>
</root>
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