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