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