SemanticWeb-Schema/lib/SemanticWeb/Schema/MolecularEntity.pm
use utf8;
package SemanticWeb::Schema::MolecularEntity;
# ABSTRACT: Any constitutionally or isotopically distinct atom
use v5.14;
use Moo;
extends qw/ SemanticWeb::Schema::BioChemEntity /;
use MooX::JSON_LD 'MolecularEntity';
use Ref::Util qw/ is_plain_hashref /;
# RECOMMEND PREREQ: Ref::Util::XS
use namespace::autoclean;
our $VERSION = 'v23.0.0';
has chemical_role => (
is => 'rw',
predicate => '_has_chemical_role',
json_ld => 'chemicalRole',
);
has in_ch_i => (
is => 'rw',
predicate => '_has_in_ch_i',
json_ld => 'inChI',
);
has in_ch_i_key => (
is => 'rw',
predicate => '_has_in_ch_i_key',
json_ld => 'inChIKey',
);
has iupac_name => (
is => 'rw',
predicate => '_has_iupac_name',
json_ld => 'iupacName',
);
has molecular_formula => (
is => 'rw',
predicate => '_has_molecular_formula',
json_ld => 'molecularFormula',
);
has molecular_weight => (
is => 'rw',
predicate => '_has_molecular_weight',
json_ld => 'molecularWeight',
);
has monoisotopic_molecular_weight => (
is => 'rw',
predicate => '_has_monoisotopic_molecular_weight',
json_ld => 'monoisotopicMolecularWeight',
);
has potential_use => (
is => 'rw',
predicate => '_has_potential_use',
json_ld => 'potentialUse',
);
has smiles => (
is => 'rw',
predicate => '_has_smiles',
json_ld => 'smiles',
);
1;
__END__
=pod
=encoding UTF-8
=head1 NAME
SemanticWeb::Schema::MolecularEntity - Any constitutionally or isotopically distinct atom
=head1 VERSION
version v23.0.0
=head1 DESCRIPTION
Any constitutionally or isotopically distinct atom, molecule, ion, ion
pair, radical, radical ion, complex, conformer etc., identifiable as a
separately distinguishable entity.
=head1 ATTRIBUTES
=head2 C<chemical_role>
C<chemicalRole>
A role played by the BioChemEntity within a chemical context.
A chemical_role should be one of the following types:
=over
=item C<InstanceOf['SemanticWeb::Schema::DefinedTerm']>
=back
=head2 C<_has_chemical_role>
A predicate for the L</chemical_role> attribute.
=head2 C<in_ch_i>
C<inChI>
Non-proprietary identifier for molecular entity that can be used in printed
and electronic data sources thus enabling easier linking of diverse data
compilations.
A in_ch_i should be one of the following types:
=over
=item C<Str>
=back
=head2 C<_has_in_ch_i>
A predicate for the L</in_ch_i> attribute.
=head2 C<in_ch_i_key>
C<inChIKey>
InChIKey is a hashed version of the full InChI (using the SHA-256
algorithm).
A in_ch_i_key should be one of the following types:
=over
=item C<Str>
=back
=head2 C<_has_in_ch_i_key>
A predicate for the L</in_ch_i_key> attribute.
=head2 C<iupac_name>
C<iupacName>
Systematic method of naming chemical compounds as recommended by the
International Union of Pure and Applied Chemistry (IUPAC).
A iupac_name should be one of the following types:
=over
=item C<Str>
=back
=head2 C<_has_iupac_name>
A predicate for the L</iupac_name> attribute.
=head2 C<molecular_formula>
C<molecularFormula>
The empirical formula is the simplest whole number ratio of all the atoms
in a molecule.
A molecular_formula should be one of the following types:
=over
=item C<Str>
=back
=head2 C<_has_molecular_formula>
A predicate for the L</molecular_formula> attribute.
=head2 C<molecular_weight>
C<molecularWeight>
This is the molecular weight of the entity being described, not of the
parent. Units should be included in the form '<Number> <unit>',
for example '12 amu' or as '<QuantitativeValue>.
A molecular_weight should be one of the following types:
=over
=item C<InstanceOf['SemanticWeb::Schema::QuantitativeValue']>
=item C<Str>
=back
=head2 C<_has_molecular_weight>
A predicate for the L</molecular_weight> attribute.
=head2 C<monoisotopic_molecular_weight>
C<monoisotopicMolecularWeight>
The monoisotopic mass is the sum of the masses of the atoms in a molecule
using the unbound, ground-state, rest mass of the principal (most abundant)
isotope for each element instead of the isotopic average mass. Please
include the units in the form '<Number> <unit>', for example
'770.230488 g/mol' or as '<QuantitativeValue>.
A monoisotopic_molecular_weight should be one of the following types:
=over
=item C<InstanceOf['SemanticWeb::Schema::QuantitativeValue']>
=item C<Str>
=back
=head2 C<_has_monoisotopic_molecular_weight>
A predicate for the L</monoisotopic_molecular_weight> attribute.
=head2 C<potential_use>
C<potentialUse>
Intended use of the BioChemEntity by humans.
A potential_use should be one of the following types:
=over
=item C<InstanceOf['SemanticWeb::Schema::DefinedTerm']>
=back
=head2 C<_has_potential_use>
A predicate for the L</potential_use> attribute.
=head2 C<smiles>
A specification in form of a line notation for describing the structure of
chemical species using short ASCII strings. Double bond stereochemistry \
indicators may need to be escaped in the string in formats where the
backslash is an escape character.
A smiles should be one of the following types:
=over
=item C<Str>
=back
=head2 C<_has_smiles>
A predicate for the L</smiles> attribute.
=head1 SEE ALSO
L<SemanticWeb::Schema::BioChemEntity>
=head1 SOURCE
The development version is on github at L<https://github.com/robrwo/SemanticWeb-Schema>
and may be cloned from L<git://github.com/robrwo/SemanticWeb-Schema.git>
=head1 BUGS
Please report any bugs or feature requests on the bugtracker website
L<https://github.com/robrwo/SemanticWeb-Schema/issues>
When submitting a bug or request, please include a test-file or a
patch to an existing test-file that illustrates the bug or desired
feature.
=head1 AUTHOR
Robert Rothenberg <rrwo@cpan.org>
=head1 COPYRIGHT AND LICENSE
This software is Copyright (c) 2018-2023 by Robert Rothenberg.
This is free software, licensed under:
The Artistic License 2.0 (GPL Compatible)
=cut