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=head1 OPTIONS

The following options are available when reading:

=over

=item 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.

=back

The following options are available when writing:

=over

=item 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.

=item aromatic

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

=item unique

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

=item name

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

=item coord3d, coords

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

=item attr

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

=back

=head1 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:

=over

=item Macro atoms

=item Pattern matching options

=item Markush structures

=item 2D Coordinates

=back

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.

=cut

# INITIALIZATION
Chemistry::Mol->register_format('sln');
my $Parser = Chemistry::File::SLN::Parser->new;

sub name_is {
    my ($self, $name) = @_;
    $name =~ /\.sln$/i;
}

sub file_is {
    $_[0]->name_is($_[1]);
}

sub parse_string {
    my ($self, $string, %opts) = @_;

    my (@lines) = split /(?:\n|\r\n?)/, $string;
    my @mols;
    for my $line (@lines) {
        my $mol = $self->parse_single_line($line, %opts);
        return $mol unless wantarray;
        push @mols, $mol;
    }
    @mols;
}

sub parse_single_line {
    my ($self, $string, %opts) = @_;

    my $mol_class = $opts{mol_class} || "Chemistry::Mol";


    # call the actual yapp-generated parser
    my $tree = $Parser->run($string) or return;
    #use Data::Dumper; print Dumper $tree;

    my $mol = $mol_class->new;
    my @nodes = @{$tree->{chain}};
    my %closures;
    my $last_atom;
    my @stack;