NAME

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

SYNOPSIS

           use Chemistry::File::MDLMol;

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

           # write a molecule
           $mol->write("myfile.mol");

           # use a molecule as a query for substructure matching
           use Chemistry::Pattern;
           use Chemistry::Ring;
           Chemistry::Ring::aromatize_mol($mol);

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

DESCRIPTION

       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, <https://github.com/perlmol>.

   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 properties 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:

           $atom->attr('mdlmol/test_sub');
           $bond->attr('mdlmol/test_sub');

       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 overridden 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.

SOURCE CODE REPOSITORY

       <https://github.com/perlmol/Chemistry-File-MDLMol>

SEE ALSO

       Chemistry::Mol

       The MDL file format specification.
       <https://discover.3ds.com/ctfile-documentation-request-form#_ga=2.229779804.1581205944.1643725102-a2d5f010-6f4c-11ec-a2da-e3641d195888>,
       <https://discover.3ds.com/sites/default/files/2020-08/biovia_ctfileformats_2020.pdf>,
       <https://web.archive.org/web/20070927033700/http://www.mdl.com/downloads/public/ctfile/ctfile.pdf>,
       or Arthur Dalby et al., J. Chem. Inf. Comput. Sci, 1992, 32, 244-255.
       <https://doi.org/10.1021/ci00007a012>.

AUTHOR

       Ivan Tubert-Brohman <itub@cpan.org>

COPYRIGHT

       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.