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
- 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
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