NAME

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

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

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

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

SEE ALSO

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

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