# HADDOCK3 Documentation

Sphinx source for the docs published on GitHub Pages.

- `docs/pages/` — hand-authored content, tracked in git.
- `docs/src/` — generated by `sphinx-apidoc` + `build_defaults_rst.py`. Not tracked, rebuilt every time.
- `docs/titles.yaml` — page titles for `docs/src/` content.
- `docs/figs/` — images used by `docs/pages/`.

## Build

```bash
pip install -e '.[dev,docs]'
cd docs
make html
open ../haddock3-docs/pages/index.html
```

`make html` runs `sphinx-apidoc` + `sphinx-build` (see `docs/Makefile`), same as CI.
`make linkcheck` checks for broken links.

## Docstrings

Napoleon (`docs/conf.py`) supports NumPy and Google style. NumPy style example:

```python
def identify_unknown_hetatms(pdb_file: FilePath) -> list[str]:
    """Return residue names in a PDB that are not in the supported residues.

    Parameters
    ----------
    pdb_file : FilePath
        Path to the PDB file to inspect.

    Returns
    -------
    list[str]
        Unique residue names not found in the supported residues set.
    """
```