Skip to content

Slot: smiles string (smiles_string)

A string encoding of a molecular graph, no chiral or isotopic information. There are usually a large number of valid SMILES which represent a given structure. For example, CCO, OCC and C(O)C all specify the structure of ethanol.

URI: chemrof:smiles_string Alias: smiles_string

Inheritance

Applicable Classes

Name Description Modifies Slot
Macromolecule A large molecule, such as a polymer, lipid, or macrocycle no
SmallMolecule A molecule characterized by availability in small-molecule databases no
Molecule A chemical entity that consists of two or more atoms where all atoms are conn... no
MolecularCation A polyatomic ion that is positive no
RacemicMixture a chemical compound that has equal amounts of left- and right-handed enantiom... no
ChemicalEntity A discrete structure that is one or more atoms that can be described by a che... no
NaturalProduct no
Atom A chemical entity consisting of exactly one atomic nucleus and the electron(s... no
ChemicalSalt a chemical compound consisting of an ionic assembly of cations and anions no
Protein A macromolecule composed of one or more polypeptide chains of amino acids tha... no
MonoatomicIon An atom type that has a charge no
FullySpecifiedAtom An atom type that has atomic number, charge, and neutron number stated (equiv... no
Nuclide an atomic species characterized by the specific constitution of its nucleus no
MolecularComplex A molecular complex is a chemical complex composed of at least one weakly int... no
MolecularSubsequence no
SequenceInterval a chain of connected monomers in a linear polymer - for example, a sub-region... no
Isobar Isobars are atoms (nuclides) of different chemical elements that have the sam... no
ChemicalElement generic form of an atom, with unspecified neutron or charge no
Ester An ester is a chemical compound derived from an acid (organic or inorganic) i... no
DNASequenceInterval no
PartiallySpecifiedAtom An atom type that only has a subset of properties (has atomic number, charge,... no
Stereoisomer no
ChemicalMixture A polyatomic entity that consists of two or more parts that are weakly bound,... no
ImpreciseChemicalMixture A macroscopic polyatomic entity that consists of multiple chemical entities w... no
MolecularSpecies A molecule in which the units are identical no
NetUnchargedMolecule A molecule that has no net charge no
Radionuclide an atom that has excess nuclear energy, making it unstable no
AtomCation A monoatomic ion that is positive, e no
NucleotideSequenceInterval no
Homopolymer a polymer with a single type of repeating unit no
Glycan A macromolecule consisting of a large number of monosaccharides linked glycos... no
MolecularAnion A polyatomic ion that is negative no
Zwitterion A molecule that has both a positive and negative charges but is net neutral no
Copolymer a polymer with a more than one type of repeating unit no
RNASequenceInterval no
MolecularComponent A proper part of a molecule that is larger than an atom no
Monomer no
PolyatomicEntity Any chemical entity consisting of more than one atom no
Peptide no
PreciseChemicalMixture A polyatomic entity that consists of two or more parts that are weakly bound,... no
SupramolecularPolymer polymeric arrays of monomeric units that are connected by reversible and high... no
AtomAnion A monoatomic ion that is negative no
PolymerPart no
MonomolecularPolymer A macromolecule composed of repeating subunits no
PolyatomicIon A molecule that has a net charge no
FunctionalGroup no
NeutralMolecule A molecule that has no net charge and is not a zwitterion no
Enantiomer one of two stereoisomers of a chiral molecule that are mirror images no
NonSpeciesMolecule A molecule in which the units are not identical no
UnchargedAtom An atom type that has no charge no
MoleculeByChargeState A molecule that has a charge state specified no
AminoAcidSequenceInterval no
Allotrope A molecule consisting of atoms of the same element no
AtomIonicForm an atom type in which only charge state is specified, designated by the eleme... no
Isotope A specific subtype of an atom with a specified neutron number no
ChemicalGroup no
Moiety a named part of a molecule no

Properties

Comments

  • a problematic set of structures to describe using SMILES notation is those which cannot be easily described using molecular graphs (see “Limitations of molecular graph representations” section), such as organometallic compounds and ionic salts.

Identifier and Mapping Information

Annotations

property value
owl AnnotationAssertion

Schema Source

  • from schema: https://w3id.org/chemrof

Mappings

Mapping Type Mapped Value
self chemrof:smiles_string
native chemrof:smiles_string
exact CHEMINF:000018

LinkML Source

name: smiles_string
annotations:
  owl:
    tag: owl
    value: AnnotationAssertion
description: A string encoding of a molecular graph, no chiral or isotopic information.
  There are usually a large number of valid SMILES which represent a given structure.
  For example, CCO, OCC and C(O)C all specify the structure of ethanol.
title: smiles string
comments:
- a problematic set of structures to describe using SMILES notation is those which
  cannot be easily described using molecular graphs (see “Limitations of molecular
  graph representations” section), such as organometallic compounds and ionic salts.
from_schema: https://w3id.org/chemrof
exact_mappings:
- CHEMINF:000018
rank: 1000
is_a: chemical_formula
domain: ChemicalEntity
alias: smiles_string
domain_of:
- ChemicalEntity
range: ChemicalEncoding