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