Scroll to navigation

Chemistry::OpenSMILES::Parser(3pm) User Contributed Perl Documentation Chemistry::OpenSMILES::Parser(3pm)

NAME

Chemistry::OpenSMILES::Parser - OpenSMILES format reader

SYNOPSIS

    use Chemistry::OpenSMILES::Parser;
    my $parser = Chemistry::OpenSMILES::Parser->new;
    my @moieties = $parser->parse( 'C#C.c1ccccc1' );
    $\ = "\n";
    for my $moiety (@moieties) {
        #  $moiety is a Graph::Undirected object
        print scalar $moiety->vertices;
        print scalar $moiety->edges;
    }

DESCRIPTION

"Chemistry::OpenSMILES::Parser" is OpenSMILES format reader.

METHODS

"parse( $smiles, \%options )"

Parses a SMILES string and returns an array of disconnected molecular entities as separate instances of Graph::Undirected. Their interpretation is described in detail in Chemistry::OpenSMILES.

Options

parse() accepts the following options for key-value pairs in an anonymous hash for its second parameter:

"max_hydrogen_count_digits"
In OpenSMILES specification the number of attached hydrogen atoms for atoms in square brackets is limited to 9. IUPAC SMILES+ has increased this number to 99. With the value of "max_hydrogen_count_digits" the parser can be instructed to allow other than 1 digit for attached hydrogen count.
"raw"
With "raw" set to anything evaluating to true, the parser will not convert neither implicit nor explicit hydrogen atoms in square brackets to atom hashes of their own. Moreover, it will not attempt to unify the representations of chirality. It should be noted, though, that many of subroutines of Chemistry::OpenSMILES expect non-raw data structures, thus processing raw output may produce distorted results. In particular, write_SMILES() calls from Chemistry::OpenSMILES::Writer have to be instructed to expect raw data structure: 

    write_SMILES( \@moieties, { raw => 1 } );

This option is now deprecated and may be removed in upcoming versions.

CAVEATS

Deprecated charge notations ("--" and "++") are supported.

OpenSMILES specification mandates a strict order of ring bonds and branches:

    branched_atom ::= atom ringbond* branch*

Chemistry::OpenSMILES::Parser supports both the mandated, and inverted structure, where ring bonds follow branch descriptions.

Whitespace is not supported yet. SMILES descriptors must be cleaned of it before attempting reading with Chemistry::OpenSMILES::Parser.

The derivation of implicit hydrogen counts for aromatic atoms is not unambiguously defined in the OpenSMILES specification. Thus only aromatic carbon is accounted for as if having valence of 3.

Chiral atoms with three neighbours are interpreted as having a lone pair of electrons one of its chiral neighbours. The lone pair is always understood as being the second in the order of neighbour enumeration, except when the atom with the lone pair starts a chain. In that case lone pair is the first.

AUTHORS

Andrius Merkys, <merkys@cpan.org>

2025-09-01 perl v5.40.1