Ivan Tubert-Brohman


Chemistry::File::SMARTS - SMARTS chemical substructure pattern linear notation parser


    use Chemistry::File::SMARTS;

    # this string matches an oxygen next to an atom with three 
    # neighbors, one of which is a hydrogen, and a positive charge
    my $smarts = 'O[D3H+]'; 

    # parse a SMARTS string and compile it into a
    # Chemistry::Pattern object
    my $patt = Chemistry::Pattern->parse("$smarts", format => 'smarts');

    # find matches of the pattern in a Chemistry::Mol object $mol
    my $mol = Chemistry::Mol->read("myfile.mol");
    while ($patt->match($mol)) {
        print "pattern matches atoms: ", $patt->atom_map, "\n"

    # NOTE: if the SMARTS pattern relies on aromaticity or ring
    # properties, you have to make sure that the target 
    # molecule is "aromatized" first:
    my $smarts = 'c:a';
    my $patt = Chemistry::Pattern->parse("$smarts", format => 'smarts');
    use Chemistry::Ring 'aromatize_mol';
    aromatize_mol($mol);  # <--- AROMATIZE!!!
    while ($patt->match($mol)) {
        print "pattern matches atoms: ", $patt->atom_map, "\n"

    # Note that "atom mapping numbers" end up as $atom->name
    my $patt = Chemistry::Pattern->parse("[C:7][C:8]", format => 'smarts');
    print $patt->atoms(1)->name;    # prints 7


This module parse a SMARTS (SMiles ARbitrary Target Specification) string, generating a Chemistry::Pattern object. It is a file I/O driver for the PerlMol toolkit; it's not called directly but by means of the Chemistry::Pattern->parse class method.

For a detailed description of the SMARTS language, see http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html. Note that this module doesn't implement the full language, as detailed under CAVEATS.

This module is part of the PerlMol project, http://www.perlmol.org/.


The following features are not implemented yet:

chirality: @, @@
component-level gruouping

That is, the difference between these three cases:


The so-called parser is very lenient, so if you give it something that's not quite reasonable it will ignore it or interpret it in a strange way without warning.

As shown in the synopsis, you have to make sure that the molecule is "aromatized" if you want to apply to it a pattern that relies on aromaticity or ring properties.




Chemistry::Pattern, Chemistry::Mol, Chemistry::File, Chemistry::File::SMILES.

For more information about SMARTS, see the SMARTS Theory Manual at http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html


Ivan Tubert-Brohman <itub@cpan.org>


Copyright (c) 2005 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.