First CLI Run

This tutorial walks through a first successful psma run from a CSV file using the command-line interface.

Goal

By the end of the tutorial you will:

  • run the PSMA workflow from the CLI

  • write the standard artifact set to disk

  • know which arguments are required for a SMILES-based run

Prerequisites

  • the package is installed with its runtime dependencies

  • your input file is a CSV

  • the CSV contains:

    • an endpoint column

    • a SMILES column

Example command

pixi run psma run docs/_data/solubility_NCATS-sol.csv \
  --output-dir .tmp/ncats_sol_cli \
  --y-col low_solubility \
  --label-threshold 0.5 \
  --label-direction ge \
  --similarity-method rdkit_morgan_tanimoto \
  --smiles-col canonical_smiles \
  --split-method random

What the command does

The CLI reads the CSV, validates the required columns for the selected similarity backend, computes the PSMA surface, and writes the standard artifacts to --output-dir.

Expected outputs

After a successful run, the output directory should contain:

  • train_coords.csv

  • test_coords.csv

  • predictions_test.csv

  • surface_grid.npz

  • params.json

  • metrics.json

Next steps