Class: ConformationalEnsemble

Ensemble of conformational states for a protein

classDiagram class ConformationalEnsemble click ConformationalEnsemble href "../ConformationalEnsemble/" NamedThing <|-- ConformationalEnsemble click NamedThing href "../NamedThing/" ConformationalEnsemble : clustering_method ConformationalEnsemble : conformational_states ConformationalEnsemble --> "*" ConformationalState : conformational_states click ConformationalState href "../ConformationalState/" ConformationalEnsemble : description ConformationalEnsemble : energy_landscape ConformationalEnsemble : id ConformationalEnsemble : principal_motions ConformationalEnsemble : protein_id ConformationalEnsemble : rmsd_threshold ConformationalEnsemble : title ConformationalEnsemble : transition_pathways

Inheritance

NamedThing
- ConformationalEnsemble

Slots

Name	Cardinality and Range	Description	Inheritance
protein_id	1 String	UniProt accession	direct
conformational_states	* ConformationalState	Individual conformational states	direct
clustering_method	0..1 String	Method used for conformational clustering	direct
rmsd_threshold	0..1 Float	RMSD threshold for clustering (Angstroms)	direct
transition_pathways	0..1 String	Description of transition pathways between states	direct
energy_landscape	0..1 String	Description of the energy landscape	direct
principal_motions	* String	Description of principal motions	direct
id	1 Uriorcurie	Globally unique identifier as an IRI or CURIE for machine processing and exte...	NamedThing
title	0..1 String		NamedThing
description	0..1 String		NamedThing

Usages

used by	used in	type	used
Sample	conformational_ensemble	range	ConformationalEnsemble
AggregatedProteinView	conformational_ensemble	range	ConformationalEnsemble

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/lambda-ber-schema/

Mappings

Mapping Type	Mapped Value
self	lambdaber:ConformationalEnsemble
native	lambdaber:ConformationalEnsemble

LinkML Source

Direct

name: ConformationalEnsemble
description: Ensemble of conformational states for a protein
from_schema: https://w3id.org/lambda-ber-schema/
is_a: NamedThing
attributes:
  protein_id:
    name: protein_id
    description: UniProt accession
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    domain_of:
    - ProteinAnnotation
    - ConformationalEnsemble
    required: true
  conformational_states:
    name: conformational_states
    description: Individual conformational states
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ConformationalEnsemble
    range: ConformationalState
    multivalued: true
    inlined: true
    inlined_as_list: true
  clustering_method:
    name: clustering_method
    description: Method used for conformational clustering
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ConformationalEnsemble
  rmsd_threshold:
    name: rmsd_threshold
    description: RMSD threshold for clustering (Angstroms)
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ConformationalEnsemble
    range: float
    unit:
      ucum_code: Angstrom
  transition_pathways:
    name: transition_pathways
    description: Description of transition pathways between states
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ConformationalEnsemble
  energy_landscape:
    name: energy_landscape
    description: Description of the energy landscape
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ConformationalEnsemble
  principal_motions:
    name: principal_motions
    description: Description of principal motions
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    domain_of:
    - ConformationalEnsemble
    multivalued: true

Induced

name: ConformationalEnsemble
description: Ensemble of conformational states for a protein
from_schema: https://w3id.org/lambda-ber-schema/
is_a: NamedThing
attributes:
  protein_id:
    name: protein_id
    description: UniProt accession
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    alias: protein_id
    owner: ConformationalEnsemble
    domain_of:
    - ProteinAnnotation
    - ConformationalEnsemble
    range: string
    required: true
  conformational_states:
    name: conformational_states
    description: Individual conformational states
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: conformational_states
    owner: ConformationalEnsemble
    domain_of:
    - ConformationalEnsemble
    range: ConformationalState
    multivalued: true
    inlined: true
    inlined_as_list: true
  clustering_method:
    name: clustering_method
    description: Method used for conformational clustering
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: clustering_method
    owner: ConformationalEnsemble
    domain_of:
    - ConformationalEnsemble
    range: string
  rmsd_threshold:
    name: rmsd_threshold
    description: RMSD threshold for clustering (Angstroms)
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: rmsd_threshold
    owner: ConformationalEnsemble
    domain_of:
    - ConformationalEnsemble
    range: float
    unit:
      ucum_code: Angstrom
  transition_pathways:
    name: transition_pathways
    description: Description of transition pathways between states
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: transition_pathways
    owner: ConformationalEnsemble
    domain_of:
    - ConformationalEnsemble
    range: string
  energy_landscape:
    name: energy_landscape
    description: Description of the energy landscape
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: energy_landscape
    owner: ConformationalEnsemble
    domain_of:
    - ConformationalEnsemble
    range: string
  principal_motions:
    name: principal_motions
    description: Description of principal motions
    from_schema: https://w3id.org/lambda-ber-schema/functional_annotation
    rank: 1000
    alias: principal_motions
    owner: ConformationalEnsemble
    domain_of:
    - ConformationalEnsemble
    range: string
    multivalued: true
  id:
    name: id
    description: Globally unique identifier as an IRI or CURIE for machine processing
      and external references. Used for linking data across systems and semantic web
      integration.
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    identifier: true
    alias: id
    owner: ConformationalEnsemble
    domain_of:
    - NamedThing
    range: uriorcurie
    required: true
  title:
    name: title
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    slot_uri: dcterms:title
    alias: title
    owner: ConformationalEnsemble
    domain_of:
    - NamedThing
    range: string
  description:
    name: description
    from_schema: https://w3id.org/lambda-ber-schema/
    rank: 1000
    alias: description
    owner: ConformationalEnsemble
    domain_of:
    - NamedThing
    - AttributeGroup
    range: string