Class: Particles¶

Particle information included in the topology.

URI: https://CCPBioSim.ac.uk/biosim-schema/Particles

         classDiagram
    class Particles
    click Particles href "../../classes/Particles/"
      Particles : coarse_grained
        
      Particles : fixed_charges
        
      Particles : masses
        
      Particles : resolution
        
          
    
        
        
        Particles --> "0..1" ModelResolution : resolution
        click ModelResolution href "../../enums/ModelResolution/"
    

        
      Particles : system_charge
        
          
    
        
        
        Particles --> "0..1" ChargeQuantity : system_charge
        click ChargeQuantity href "../../classes/ChargeQuantity/"

Slots¶

Name	Cardinality and Range	Description	Inheritance
masses	0..1 boolean	Are masses present in the topology?	direct
fixed_charges	0..1 boolean	Are fixed charges on atoms included in the topology?	direct
system_charge	0..1 ChargeQuantity	Total electrostatic charge of the system given by the elementary charge (e)	direct
coarse_grained	0..1 boolean	Are atoms coarse-grained?	direct
resolution	0..1 ModelResolution	Resolution of simulated system	direct

Usages¶

used by	used in	type	used
TopologyMetadata	particles	range	Particles

Identifier and Mapping Information¶

Schema Source¶

from schema: https://CCPBioSim.ac.uk/biosim-schema/

Mappings¶

Mapping Type	Mapped Value
self	https://CCPBioSim.ac.uk/biosim-schema/Particles
native	https://CCPBioSim.ac.uk/biosim-schema/Particles

LinkML Source¶

Direct¶

name: Particles
description: Particle information included in the topology.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
slots:
- masses
- fixed_charges
- system_charge
- coarse_grained
- resolution

Induced¶

name: Particles
description: Particle information included in the topology.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
attributes:
  masses:
    name: masses
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: toptrajparser
          key: masses
    description: Are masses present in the topology?
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Particles
    domain_of:
    - Particles
    range: boolean
  fixed_charges:
    name: fixed_charges
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: toptrajparser
          key: fixed_charges
    description: Are fixed charges on atoms included in the topology?
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Particles
    domain_of:
    - Particles
    range: boolean
  system_charge:
    name: system_charge
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: toptrajparser
          key: system_charge
          unit: e
    description: Total electrostatic charge of the system given by the elementary
      charge (e).
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Particles
    domain_of:
    - Particles
    range: ChargeQuantity
    pattern: ^[+-]?\d+(\.\d+)?$
  coarse_grained:
    name: coarse_grained
    description: Are atoms coarse-grained?
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Particles
    domain_of:
    - Particles
    range: boolean
  resolution:
    name: resolution
    description: Resolution of simulated system.
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Particles
    domain_of:
    - Particles
    range: ModelResolution