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Command-Line Interface

← Back to README · Documentation index

MolForge ships a CLI. Invoke it either as the installed molforge command or as a module:

molforge --help
python -m molforge.cli --help    # equivalent

Both the CLI and any future UI assemble a ForgeParams through a single shared core, molforge.cli.builder.build_params, so validation, type coercion, and step routing behave identically everywhere. See Pipeline Configuration for the parameters this builds, and the Python API for the equivalent programmatic entry point.

molforge run

molforge run <input> [--config FILE] [--steps a,b,c] [--set step.param=value ...] [--output DIR] [--batch]
  • input: one or more ChEMBL IDs, CSV files, or other data sources.
  • --config, -c: YAML/JSON configuration file to seed the pipeline.
  • --steps: comma-separated step list (overrides the config's steps).
  • --set: repeatable parameter override. Use key=value for a top-level ForgeParams field, or dotted step.param=value to target a step. Values are coerced to the target field's type.
  • --output, -o: output root directory.
  • --batch, -b: process every input in batch mode.
  • --quiet, -q: suppress progress messages.

--steps and --set overrides are applied on top of any --config.

# Single ChEMBL target with the standard pipeline
molforge run CHEMBL234

# Override steps and a couple of parameters inline
molforge run CHEMBL234 --steps source,chembl,curate,confs \
    --set confs.backend=openeye --set chembl.standard_type=Ki --set chembl.standard_units=nM

# Seed from a config file, then tweak
molforge run CHEMBL2971 --config demo/jak2_ic50.yaml --set confs.max_confs=50

# Batch processing
molforge run CHEMBL234 CHEMBL279 CHEMBL280 --batch

molforge init

molforge init [--interactive] [--template NAME] [--output FILE]

Generates a configuration file. With --interactive (or by default in an interactive terminal when no --template is given), it launches a questionary-based wizard. Otherwise it copies a static template.

Available templates: api, basic, conformers, distributions, full.

molforge init                                       # interactive wizard
molforge init --template full --output my_config.yaml
molforge init --template conformers

molforge info

molforge info [actors|backends|<step>|examples|version]
  • actors: list all registered actors (core and plugin).
  • backends: show backend options (filter with --actor <step>).
  • <step> (e.g. confs): describe that step's parameters — name, type, default, choices, and docstring — via live introspection.
  • examples: print usage examples.
  • version (default): show the MolForge version.
molforge info actors
molforge info confs                # describe the confs step's parameters
molforge info backends --actor confs
molforge --diagram                 # print the architecture diagram

molforge validate

molforge validate <config>

Loads and validates a configuration file, reporting the resolved pipeline steps.

molforge validate demo/jak2_ic50.yaml

See the example run for a complete config file and the output a molforge run produces.