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MDLMol(3)	      User Contributed Perl Documentation	     MDLMol(3)

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 coordinats, atom and	bond types, charges, radicals,
       and atom	lists. It does not read	other things such as stereochemistry,
       3d properties, isotopes,	etc.

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

   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:

	   $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 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.

VERSION
       0.21

SEE ALSO
       Chemistry::Mol

       The MDL file format specification.
       <http://www.mdl.com/downloads/public/ctfile/ctfile.pdf> or Arthur Dalby
       et al., J. Chem.	Inf. Comput. Sci, 1992,	32, 244-255.

       The PerlMol website <http://www.perlmol.org/>

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.

perl v5.32.0			  2009-05-10			     MDLMol(3)

NAME | SYNOPSIS | DESCRIPTION | VERSION | SEE ALSO | AUTHOR | COPYRIGHT

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