Class: Trajectories

Information in trajectory files.

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

         classDiagram
    class Trajectories
    click Trajectories href "../../classes/Trajectories/"
      Trajectories : energies
        
      Trajectories : forces
        
      Trajectories : frame_count
        
      Trajectories : polarizable_charges
        
      Trajectories : positions
        
      Trajectories : replica
        
      Trajectories : velocities
        
      Trajectories : water
        
      
    

Slots

Name	Cardinality and Range	Description	Inheritance
positions	0..1 boolean	Are per-frame positions included in the trajectory?	direct
forces	0..1 boolean	Are per-frame forces included in the trajectory?	direct
velocities	0..1 boolean	Are per-frame velocities included in the trajectory?	direct
polarizable_charges	0..1 boolean	Are per-frame polarizable charges included in the trajectory?	direct
energies	0..1 boolean	Are per-frame energies included in the trajectory?	direct
water	0..1 boolean	Are water molecules included in the trajectory?	direct
replica	0..1 boolean	Is this trajectory a replica of another provided trajectory?	direct
frame_count	0..1 integer	Total number of snapshots that make up a trajectory	direct

Usages

used by	used in	type	used
TrajectoryMetadata	trajectory_output	range	Trajectories

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/Trajectories
native	https://CCPBioSim.ac.uk/biosim-schema/Trajectories

LinkML Source

Direct

name: Trajectories
description: Information in trajectory files.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
slots:
- positions
- forces
- velocities
- polarizable_charges
- energies
- water
- replica
- frame_count

Induced

name: Trajectories
description: Information in trajectory files.
from_schema: https://CCPBioSim.ac.uk/biosim-schema/
attributes:
  positions:
    name: positions
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: toptrajparser
          key: positions
    description: Are per-frame positions included in the trajectory?
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Trajectories
    domain_of:
    - Trajectories
    range: boolean
  forces:
    name: forces
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: toptrajparser
          key: forces
    description: Are per-frame forces included in the trajectory?
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Trajectories
    domain_of:
    - Trajectories
    range: boolean
  velocities:
    name: velocities
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: toptrajparser
          key: velocities
    description: Are per-frame velocities included in the trajectory?
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Trajectories
    domain_of:
    - Trajectories
    range: boolean
  polarizable_charges:
    name: polarizable_charges
    description: Are per-frame polarizable charges included in the trajectory?
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Trajectories
    domain_of:
    - Trajectories
    range: boolean
  energies:
    name: energies
    description: Are per-frame energies included in the trajectory?
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Trajectories
    domain_of:
    - Trajectories
    range: boolean
  water:
    name: water
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: toptrajparser
          key: water
    description: Are water molecules included in the trajectory?
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Trajectories
    domain_of:
    - Trajectories
    range: boolean
  replica:
    name: replica
    description: Is this trajectory a replica of another provided trajectory?
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Trajectories
    domain_of:
    - Trajectories
    range: boolean
  frame_count:
    name: frame_count
    annotations:
      engine_mapping:
        tag: engine_mapping
        value:
        - engine: toptrajparser
          key: frame_count
    description: Total number of snapshots that make up a trajectory.
    examples:
    - value: '1'
    from_schema: https://CCPBioSim.ac.uk/biosim-schema/
    rank: 1000
    owner: Trajectories
    domain_of:
    - Trajectories
    range: integer
    minimum_value: 0