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