NAME

Chemistry::File::SMILES - SMILES linear notation parser/writer

SYNOPSYS

#!/usr/bin/perl
use Chemistry::File::SMILES;

# parse a SMILES string
my $s = 'C1CC1(=O)[O-]';
my $mol = Chemistry::Mol->parse($s, format => 'smiles');

# print a SMILES string
print $mol->print(format => 'smiles');

DESCRIPTION

This module parses a SMILES (Simplified Molecular Input Line Entry Specification) string. This is a File I/O driver for the PerlMol project. http://www.perlmol.org/. It registers the 'smiles' format with Chemistry::Mol.

This parser interprets anything after whitespace as the molecule's name; for example, when the following SMILES string is parsed, $mol->name will be set to "Methyl chloride":

CCl	 Methyl chloride

The name is not included by default on output. However, if the name option is defined, the name will be included after the SMILES string, separated by a tab.

print $mol->print(format => 'smiles', name => 1);

CAVEATS

Branches that start before an atom, such as (OC)C, which should be equivalent to C(CO) and COC, according to some variants of the SMILES specification. Many other tools don't implement this rule either.

Not yet available: Proper handling of aromatic atoms; unique (canonical) SMILES output.

VERSION

0.31

SEE ALSO

Chemistry::Mol, Chemistry::File

The SMILES Home Page at http://www.daylight.com/dayhtml/smiles/ The Daylight Theory Manual at http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html

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

AUTHOR

Ivan Tubert <itub@cpan.org>

COPYRIGHT

Copyright (c) 2004 Ivan Tubert. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.