NAME

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

SYNOPSYS

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

    # parse a SLN string for benzene
    my $s = 'C[1]H:CH:CH:CH:CH:CH@1';
    my $mol = Chemistry::Mol->parse($s, format => 'sln');

    # print a SLN string
    print $mol->print(format => 'sln');

    # print a unique (canonical) SLN string
    print $mol->print(format => 'sln', unique => 1);

    # parse a multiline SLN file
    my @mols = Chemistry::Mol->read("file.sln", format => 'sln');

    # write a multiline SLN file
    Chemistry::Mol->write("file.sln", mols => [@mols]);


DESCRIPTION

This module parses a SLN (Sybyl Line Notation) string. This is a File I/O driver for the PerlMol project. http://www.perlmol.org/. It registers the 'sln' format with Chemistry::Mol, and recognizes filenames ending in '.sln'.

Optional attributes for atoms, bonds, and molecules are stored as $atom->attr("sln/attr"), $bond->attr("sln/attr"), and $mol->attr("sln/attr"), respectively. Boolean attributes are stored with a value of 'TRUE'. That's the way boolean attributes are recognized when writing, so that they can be written in the shortened form.

    $sln_attr->{backbone} = 1;
    # would be ouput as "C[backbone=1]"

    $sln_attr->{backbone} = 'TRUE';
    # would be ouput as "C[backbone]"

Also note that attribute names are normalized to lowercase on reading.

OPTIONS

The following options are available when reading:

  • kekulize
  • Assign bond orders for unsatisfied valences or for aromatic bonds. For example, benzene read as C[1]H:CH:CH:CH:CH:CH@1 will be converted internally to something like C[1]H=CHCH=CHCH=CH@1. This is needed if another format or module expects a Kekule representation without an aromatic bond type.

The following options are available when writing:

  • mols
  • If this option points to an array of molecules, these molecules will be written, one per line, as in the example in the SYNOPSYS.

  • aromatic
  • Detect aromaticity before writing. This will ensure that aromatic bond types are used instead of alternate single and double bonds.

  • unique
  • Canonicalize before writing, and produce a unique strucure. NOTE: this option does not guarantee a unique representation for molecules with bracketed attributes.

  • name
  • Include the name of the molecule ($mol->name) in the output string.

  • coord3d, coords
  • Include the 3D coordinates of every atom in the molecule in the output string. coord3d and coords may be used interchangeably.

  • attr
  • Output the atom, bond, and molecule attributes found in $mol->attr("sln/attr"), etc.

CAVEATS

This version does not implement the full SLN specification. It supports simple structures and some attributes, but it does not support any of the following:

  • Macro atoms
  • Pattern matching options
  • Markush structures
  • 2D Coordinates

The SLN specification is vague on several points, and I don't have a reference implementation available, so I had to make several arbitrary decisions. Also, this version of this module has not been tested exhaustively, so please report any bugs that you find.

If the parser doesn't understand a string, it only says "syntax error", which may not be very helpful.

VERSION

0.11

SEE ALSO

Chemistry::Mol, Chemistry::File, Chemistry::File::SMILES

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

Ash, S.; Cline, M. A.; Homer, R. W.; Hurst, T.; Smith, G. B., SYBYL Line Notation (SLN): A Versatile Language for Chemical Structure Representation. J. Chem. Inf. Comput. Sci; 1997; 37(1); 71-79. DOI: 10.1021/ci960109j (http://dx.doi.org/10.1021/ci960109j)

AUTHOR

Ivan Tubert-Brohman <itub@cpan.org>

COPYRIGHT

Copyright (c) 2004 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.