CLI Usage

The command line intentionally stays thin and delegates directly to the Python API.

Root command

mltsa --version

MD commands

The dedicated MD CLI is available as mltsa-md. The root command also supports mltsa md ... as a shortcut.

Label trajectories

mltsa-md label ^
  --h5 md_dataset.h5 ^
  --experiment labels ^
  --topology topology.pdb ^
  --trajectory traj_0001.dcd ^
  --trajectory traj_0002.dcd ^
  --rule sum_distances ^
  --selection-pair "index 10" "index 220" ^
  --lower-threshold 0.4 ^
  --upper-threshold 0.8 ^
  --window-size 25

Build a feature set

mltsa-md build ^
  --h5 md_dataset.h5 ^
  --feature-set closest ^
  --feature-type closest_residue_distances ^
  --label-experiment labels

Run analysis

mltsa-md analyze ^
  --h5 md_dataset.h5 ^
  --feature-set closest ^
  --model random_forest ^
  --explain native ^
  --results-h5 md_results.h5 ^
  --experiment rf_native

Keyword arguments

The build and analyze commands support repeated KEY=VALUE options for model or explanation parameters where appropriate.