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

Schema Source

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

Mappings

Mapping Type Mapped Value
self chemrof:smiles_string
native chemrof:smiles_string

LinkML Source

name: smiles_string
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
rank: 1000
is_a: chemical_formula
domain: ChemicalEntity
alias: smiles_string
domain_of:
- ChemicalEntity
range: ChemicalEncoding