submission-validator

Validate CAPRI (Critical Assessment of PRedicted Interactions) docking submission PDB files.

See CHECKS.md for the list of validation checks.

Install

We recommend using uv

uv venv .venv --python-3.14
source .venv/bin/activate
uv pip install -e ".[dev]"

Usage

submission-validator <path-to-pdb-file>

Each check prints a ✅/❌ line. Failing checks also show a short message explaining what went wrong.

Fix common format issues

Pass --fix <output> to apply pdb_tidy (from pdb-tools) to the input file, write the cleaned version to <output>, and re-validate automatically:

submission-validator input.pdb --fix fixed.pdb

Web app (browser)

The validator also runs entirely in the browser via Pyodide — no server required, no data leaves your machine.

Prerequisites: Node.js ≥ 20 on PATH.

Start the dev server:

source .venv/bin/activate
cd web && npm install && npm run dev

npm run dev builds a wheel from the local Python package then starts the Vite dev server. Open the URL printed in the terminal.

Production build:

cd web
npm run build   # outputs to web/dist/

The web/dist/ directory is a self-contained static site. The GitHub Actions workflow (.github/workflows/pages.yml) deploys it to GitHub Pages automatically on every push to main.

The web UI mirrors the CLI: it shows a per-check overview with pass/fail status and error details, and — when validation fails — offers a Try to fix button that runs pdb_tidy in-browser and lets you download the repaired file if the fix succeeds.