# BioSim CZ vocabulary: File Semantic Type
#
# Curated subset of molecular data format concepts aligned with MOLSIM.
# MOLSIM parent class: MOLSIM_001085 (molecular data format)

# molsim: MOLSIM_002065
- id: parameter_file
  title:
    en: Parameter File
  help:
    en: File that specifies simulation control variables, algorithmic settings, and thermodynamic conditions (e.g., GROMACS .mdp, AMBER mdin).

- id: run_input
  title:
    en: Run Input
  help:
    en: Prepared or executable simulation input that bundles the information needed to start a run, such as processed parameters, topology, coordinates, and engine-specific settings (e.g., GROMACS .tpr). Not explicitly defined in MOLSIM; mapped to the vocabulary as a curated term.

# molsim: MOLSIM_001091
- id: topology
  title:
    en: Topology
  help:
    en: File that defines the constituent atoms of a molecular system, their connectivity, and associated force field parameters (e.g., .top, .prmtop, .psf).

# molsim: MOLSIM_001088
- id: structure
  title:
    en: Structure
  help:
    en: File that describes the three-dimensional arrangement of atoms in a molecule (e.g., .gro, .pdb, .crd, .inpcrd).

# molsim: MOLSIM_001090
- id: trajectory
  title:
    en: Trajectory
  help:
    en: File that stores the history of atomic positions (and optionally velocities or forces) recorded during a simulation (e.g., .xtc, .trr, .nc, .dcd).

# molsim: MOLSIM_000441
- id: state
  title:
    en: State / Restart
  help:
    en: File that stores a complete snapshot of a simulation state sufficient to resume the run (e.g., .cpt, .rst, .rst7).

# molsim: MOLSIM_000439
- id: log
  title:
    en: Log
  help:
    en: File that records the progress, settings, and key information generated during a simulation run (e.g., .log, .out, .std).

- id: energy_data
  title:
    en: Energy Data
  help:
    en: File that stores energy and related time-series data produced during a simulation (e.g., GROMACS .edr, AMBER .ene). Not explicitly defined in MOLSIM; mapped to the vocabulary as a curated term.

- id: other
  title:
    en: Other
  help:
    en: File type not covered by the categories above.
