Class: atomic bond (AtomicBond)

_A connection between two atoms. Note this is the reified form of 'atomically connected to'. _

 classDiagram
    class AtomicBond
      OwlClass <|-- AtomicBond
      ChemicalRelationship <|-- AtomicBond

      AtomicBond : bond_angle

      AtomicBond : bond_energy

      AtomicBond : bond_length

      AtomicBond : bond_length_in_angstroms

      AtomicBond : bond_order

      AtomicBond : bond_type

          AtomicBond --> BondTypeEnum : bond_type

      AtomicBond : object

          AtomicBond --> AtomOccurrence : object

      AtomicBond : owl_subclass_of

          AtomicBond --> OwlClass : owl_subclass_of

      AtomicBond : subject

          AtomicBond --> AtomOccurrence : subject

      AtomicBond : torsional_angle

Inheritance

ChemicalRelationship [ OwlClass]
- AtomicBond [ OwlClass]

Slots

Name	Cardinality and Range	Description	Inheritance
subject	0..1 AtomOccurrence		direct
object	0..1 AtomOccurrence		direct
bond_type	0..1 BondTypeEnum		direct
bond_order	0..1 Integer	the number of electron pairs (bonds) between a pair of atoms	direct
bond_length	0..1 Float	the average distance between nuclei of two bonded atoms in a molecule	direct
bond_energy	0..1 Float	the measure of bond strength in a chemical bond	direct
bond_length_in_angstroms	0..1 Float	the average distance between nuclei of two bonded atoms in a molecule	direct
bond_angle	0..1 Float		direct
torsional_angle	0..1 Float		direct
owl_subclass_of	0..1 OwlClass	Holds between C and P if C owl:subClassOf P	OwlClass

Usages

used by	used in	type	used
SmallMolecule	has_bonds	range	AtomicBond
Macromolecule	has_bonds	range	AtomicBond
Peptide	has_bonds	range	AtomicBond
Protein	has_bonds	range	AtomicBond
Glycan	has_bonds	range	AtomicBond
MonomolecularPolymer	has_bonds	range	AtomicBond
Copolymer	has_bonds	range	AtomicBond
Homopolymer	has_bonds	range	AtomicBond
Molecule	has_bonds	range	AtomicBond
NaturalProduct	has_bonds	range	AtomicBond
MolecularSpecies	has_bonds	range	AtomicBond
NonSpeciesMolecule	has_bonds	range	AtomicBond
MoleculeByChargeState	has_bonds	range	AtomicBond
PolyatomicIon	has_bonds	range	AtomicBond
MolecularCation	has_bonds	range	AtomicBond
MolecularAnion	has_bonds	range	AtomicBond
NetUnchargedMolecule	has_bonds	range	AtomicBond
Zwitterion	has_bonds	range	AtomicBond
NeutralMolecule	has_bonds	range	AtomicBond
AtomicBond	bond_order	domain	AtomicBond
AtomicBond	bond_length	domain	AtomicBond
Ester	has_bonds	range	AtomicBond
Stereoisomer	has_bonds	range	AtomicBond
Enantiomer	has_bonds	range	AtomicBond
Allotrope	has_bonds	range	AtomicBond

Aliases

bond
chemical bond

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/chemrof

Mappings

Mapping Type	Mapped Value
self	gc:Bond
native	chemrof:AtomicBond
undefined	CHEMINF:000063

LinkML Source

Direct

name: AtomicBond
description: 'A connection between two atoms. Note this is the reified form of ''atomically
  connected to''. '
title: atomic bond
from_schema: https://w3id.org/chemrof
aliases:
- bond
- chemical bond
mappings:
- CHEMINF:000063
is_a: ChemicalRelationship
mixins:
- OwlClass
attributes:
  subject:
    name: subject
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain_of:
    - AtomicBond
    range: AtomOccurrence
  object:
    name: object
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain_of:
    - AtomicBond
    range: AtomOccurrence
  bond_type:
    name: bond_type
    from_schema: https://w3id.org/chemrof
    domain_of:
    - AtomicBond
    range: BondTypeEnum
  bond_order:
    name: bond_order
    description: the number of electron pairs (bonds) between a pair of atoms
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain: AtomicBond
    domain_of:
    - AtomicBond
    range: integer
  bond_length:
    name: bond_length
    description: the average distance between nuclei of two bonded atoms in a molecule
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain: AtomicBond
    domain_of:
    - AtomicBond
    range: float
  bond_energy:
    name: bond_energy
    description: the measure of bond strength in a chemical bond.
    from_schema: https://w3id.org/chemrof
    aliases:
    - average bond enthalpy
    - mean bond enthalpy
    rank: 1000
    domain_of:
    - AtomicBond
    range: float
  bond_length_in_angstroms:
    name: bond_length_in_angstroms
    description: the average distance between nuclei of two bonded atoms in a molecule.
      It is a transferable property of a bond between atoms of fixed types, relatively
      independent of the rest of the molecule.
    from_schema: https://w3id.org/chemrof
    domain_of:
    - AtomicBond
    range: float
  bond_angle:
    name: bond_angle
    from_schema: https://w3id.org/chemrof
    domain_of:
    - AtomicBond
    range: float
  torsional_angle:
    name: torsional_angle
    from_schema: https://w3id.org/chemrof
    domain_of:
    - AtomicBond
    range: float
class_uri: gc:Bond

Induced

name: AtomicBond
description: 'A connection between two atoms. Note this is the reified form of ''atomically
  connected to''. '
title: atomic bond
from_schema: https://w3id.org/chemrof
aliases:
- bond
- chemical bond
mappings:
- CHEMINF:000063
is_a: ChemicalRelationship
mixins:
- OwlClass
attributes:
  subject:
    name: subject
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: subject
    owner: AtomicBond
    domain_of:
    - AtomicBond
    range: AtomOccurrence
  object:
    name: object
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: object
    owner: AtomicBond
    domain_of:
    - AtomicBond
    range: AtomOccurrence
  bond_type:
    name: bond_type
    from_schema: https://w3id.org/chemrof
    alias: bond_type
    owner: AtomicBond
    domain_of:
    - AtomicBond
    range: BondTypeEnum
  bond_order:
    name: bond_order
    description: the number of electron pairs (bonds) between a pair of atoms
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain: AtomicBond
    alias: bond_order
    owner: AtomicBond
    domain_of:
    - AtomicBond
    range: integer
  bond_length:
    name: bond_length
    description: the average distance between nuclei of two bonded atoms in a molecule
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain: AtomicBond
    alias: bond_length
    owner: AtomicBond
    domain_of:
    - AtomicBond
    range: float
  bond_energy:
    name: bond_energy
    description: the measure of bond strength in a chemical bond.
    from_schema: https://w3id.org/chemrof
    aliases:
    - average bond enthalpy
    - mean bond enthalpy
    rank: 1000
    alias: bond_energy
    owner: AtomicBond
    domain_of:
    - AtomicBond
    range: float
  bond_length_in_angstroms:
    name: bond_length_in_angstroms
    description: the average distance between nuclei of two bonded atoms in a molecule.
      It is a transferable property of a bond between atoms of fixed types, relatively
      independent of the rest of the molecule.
    from_schema: https://w3id.org/chemrof
    alias: bond_length_in_angstroms
    owner: AtomicBond
    domain_of:
    - AtomicBond
    range: float
  bond_angle:
    name: bond_angle
    from_schema: https://w3id.org/chemrof
    alias: bond_angle
    owner: AtomicBond
    domain_of:
    - AtomicBond
    range: float
  torsional_angle:
    name: torsional_angle
    from_schema: https://w3id.org/chemrof
    alias: torsional_angle
    owner: AtomicBond
    domain_of:
    - AtomicBond
    range: float
  owl_subclass_of:
    name: owl_subclass_of
    description: 'Holds between C and P if C owl:subClassOf P. Note that in this model,
      most classes are metaclasses (see ''owl class''), where these metaclasses may
      represent *groupings* or specific countable elements or species. We provide
      two different sub-properties of subclass of for two cases: (1) subtype_of, which
      connects grouping classes (e.g. alkane is_a hydrocarbon; alpha-amino-acid is_a
      amino-acid), (2) classified_by, which connects a specific element to a grouping
      class (e.g. methane is_a hydrocarbon; iron is_a metal; serine is_a amino-acid)'
    title: owl subclass of
    from_schema: https://w3id.org/chemrof
    aliases:
    - is a
    exact_mappings:
    - rdfs:subClassOf
    narrow_mappings:
    - bo:family
    rank: 1000
    is_a: classification_relationship
    mixin: true
    domain: OwlClass
    alias: owl_subclass_of
    owner: AtomicBond
    domain_of:
    - OwlClass
    range: OwlClass
class_uri: gc:Bond