Chemistry::File::MDLMol - MDL molfile reader/writer


    use Chemistry::File::MDLMol;

    # read a molecule
    my $mol = Chemistry::Mol->read('myfile.mol');

    # write a molecule

    # use a molecule as a query for substructure matching
    use Chemistry::Pattern;
    use Chemistry::Ring;

    my $patt = Chemistry::Pattern->read('query.mol');
    if ($patt->match($mol)) {
        print "it matches!\n";


MDL Molfile (V2000) reader/writer.

This module automatically registers the 'mdl' format with Chemistry::Mol.

The first three lines of the molfile are stored as $mol->name, $mol->attr("mdlmol/line2"), and $mol->attr("mdlmol/comment").

This version only reads and writes some of the information available in a molfile: it reads coordinates, atom and bond types, charges, isotopes, radicals, and atom lists. It does not read other things such as stereochemistry, 3d properties, etc.

This module is part of the PerlMol project,

Query properties

The MDL molfile format supports query properties such as atom lists, and special bond types such as "single or double", "single or aromatic", "double or aromatic", "ring bond", or "any". These properties are supported by this module in conjunction with Chemistry::Pattern. However, support for query properies is currently read-only, and the other properties listed in the specification are not supported yet.

So that atom and bond objects can use these special query options, the conditions are represented as Perl subroutines. The generated code can be read from the 'mdlmol/test_sub' attribute:


This may be useful for debugging, such as when an atom doesn't seem to match as expected.

Aromatic Queries

To be able to search for aromatic substructures are represented by Kekule structures, molfiles that are read as patterns (with Chemistry::Pattern-read) are aromatized automatically by using the Chemistry::Ring module. The default bond test from Chemistry::Pattern::Bond is overriden by one that checks the aromaticity in addition to the bond order. The test is,

    $patt->aromatic ?  $bond->aromatic 
        : (!$bond->aromatic && $patt->order == $bond->order);

That is, aromatic pattern bonds match aromatic bonds, and aliphatic pattern bonds match aliphatic bonds with the same bond order.




The MDL file format specification. or Arthur Dalby et al., J. Chem. Inf. Comput. Sci, 1992, 32, 244-255.


Ivan Tubert-Brohman <>


Copyright (c) 2009 Ivan Tubert-Brohman. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.