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 |
|---|---|---|
| Peptide | no | |
| Isotope | A specific subtype of an atom with a specified neutron number | no |
| NucleotideSequenceInterval | no | |
| Protein | A macromolecule composed of one or more polypeptide chains of amino acids tha... | no |
| PolymerPart | no | |
| ChemicalMixture | A polyatomic entity that consists of two or more parts that are weakly bound,... | no |
| MonomolecularPolymer | A macromolecule composed of repeating subunits | no |
| Homopolymer | a polymer with a single type of repeating unit | no |
| MolecularSpecies | A molecule in which the units are identical | no |
| PartiallySpecifiedAtom | An atom type that only has a subset of properties (has atomic number, charge,... | no |
| SmallMolecule | A molecule characterized by availability in small-molecule databases | no |
| MolecularAnion | A polyatomic ion that is negative | no |
| FunctionalGroup | no | |
| AtomCation | A monoatomic ion that is positive, e | no |
| MolecularCation | A polyatomic ion that is positive | no |
| Macromolecule | A large molecule, such as a polymer, lipid, or macrocycle | no |
| UnchargedAtom | An atom type that has no charge | no |
| ChemicalSalt | a chemical compound consisting of an ionic assembly of cations and anions | no |
| PolyatomicEntity | Any chemical entity consisting of more than one atom | no |
| ChemicalElement | generic form of an atom, with unspecified neutron or charge | no |
| Glycan | A macromolecule consisting of a large number of monosaccharides linked glycos... | no |
| Copolymer | a polymer with a more than one type of repeating unit | no |
| PolyatomicIon | A molecule that has a net charge | no |
| ChemicalEntity | A discrete structure that is one or more atoms that can be described by a che... | no |
| Ester | An ester is a chemical compound derived from an acid (organic or inorganic) i... | no |
| SupramolecularPolymer | polymeric arrays of monomeric units that are connected by reversible and high... | no |
| Stereoisomer | no | |
| PreciseChemicalMixture | A polyatomic entity that consists of two or more parts that are weakly bound,... | no |
| AtomIonicForm | an atom type in which only charge state is specified, designated by the eleme... | no |
| Nuclide | an atomic species characterized by the specific constitution of its nucleus | no |
| Molecule | A chemical entity that consists of two or more atoms where all atoms are conn... | no |
| Zwitterion | A molecule that has both a positive and negative charges but is net neutral | 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 |
| Enantiomer | one of two stereoisomers of a chiral molecule that are mirror images | no |
| Moiety | a named part of a molecule | no |
| NeutralMolecule | A molecule that has no net charge and is not a zwitterion | no |
| NaturalProduct | no | |
| SequenceInterval | a chain of connected monomers in a linear polymer - for example, a sub-region... | no |
| MolecularComponent | A proper part of a molecule that is larger than an atom | no |
| NonSpeciesMolecule | A molecule in which the units are not identical | no |
| Isobar | Isobars are atoms (nuclides) of different chemical elements that have the sam... | no |
| MoleculeByChargeState | A molecule that has a charge state specified | no |
| RacemicMixture | a chemical compound that has equal amounts of left- and right-handed enantiom... | no |
| ImpreciseChemicalMixture | A macroscopic polyatomic entity that consists of multiple chemical entities w... | no |
| DNASequenceInterval | no | |
| MolecularComplex | A molecular complex is a chemical complex composed of at least one weakly int... | no |
| Monomer | no | |
| Atom | A chemical entity consisting of exactly one atomic nucleus and the electron(s... | no |
| RNASequenceInterval | no | |
| Radionuclide | an atom that has excess nuclear energy, making it unstable | no |
| MolecularSubsequence | no | |
| Allotrope | A molecule consisting of atoms of the same element | no |
| ChemicalGroup | no | |
| AtomAnion | A monoatomic ion that is negative | no |
| AminoAcidSequenceInterval | no | |
| NetUnchargedMolecule | A molecule that has no net 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 |
| exact | CHEMINF:000018 |
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
exact_mappings:
- CHEMINF:000018
rank: 1000
is_a: chemical_formula
domain: ChemicalEntity
alias: smiles_string
domain_of:
- ChemicalEntity
range: ChemicalEncoding