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Class: atomic bond (AtomicBond)

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

URI: gc:Bond

 classDiagram
    class AtomicBond
    click AtomicBond href "../AtomicBond"
      OwlClass <|-- AtomicBond
        click OwlClass href "../OwlClass"
      ChemicalRelationship <|-- AtomicBond
        click ChemicalRelationship href "../ChemicalRelationship"

      AtomicBond : bond_angle

      AtomicBond : bond_energy

      AtomicBond : bond_length

      AtomicBond : bond_length_in_angstroms

      AtomicBond : bond_order

      AtomicBond : bond_type




    AtomicBond --> "0..1" BondTypeEnum : bond_type
    click BondTypeEnum href "../BondTypeEnum"


      AtomicBond : object




    AtomicBond --> "0..1" AtomOccurrence : object
    click AtomOccurrence href "../AtomOccurrence"


      AtomicBond : owl_subclass_of




    AtomicBond --> "0..1" OwlClass : owl_subclass_of
    click OwlClass href "../OwlClass"


      AtomicBond : subject




    AtomicBond --> "0..1" AtomOccurrence : subject
    click AtomOccurrence href "../AtomOccurrence"


      AtomicBond : torsional_angle

Inheritance

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