Changelog

Version 3.1.3

Released: 2026

  • Documentation rewrite for ReadTheDocs publication

  • Both HalogenGroups and PFASGroups entry points documented

  • All code examples updated to current API (ResultsModel pattern)

  • CLI reference page added

  • API reference pages updated with autodoc

Version 3.2.0

New features:

  • ``get_compiled_HalogenGroups()``: Returns compiled HalogenGroup instances (compute=True groups only), suitable for extending with custom groups and passing directly to parse_smiles() or generate_fingerprint(). The older get_HalogenGroups() continues to return raw JSON dicts.

    from HalogenGroups import get_compiled_HalogenGroups, HalogenGroup, parse_smiles

groups = get_compiled_HalogenGroups()
groups.append(HalogenGroup(
    group_id=200, name="my_custom_group",
    smarts="[CX4](F)(F)(F)",
    category="Custom",
    is_PFAS=True,
))
results = parse_smiles(["FC(F)(F)C(F)(F)F"], halogen_groups=groups)

API changes:

  • generate_fingerprint return value is now a 2-D numpy.ndarray of shape (n_molecules, n_groups) instead of a Python list.

Version 3.1.0

New features:

  • Multi-halogen fingerprinting: generate_fingerprint() and to_fingerprint() now accept a halogens parameter. Multiple halogens produce horizontally-stacked vectors (116 × n_halogens columns).

  • Saturation filter: saturation parameter ('saturated' | 'unsaturated' | None) for both parsing and fingerprinting.

  • Corrected group-selection indexing: selections resolve by canonical group IDs rather than list positions.

  • ``ResultsFingerprint`` metadata: halogens and saturation stored in the object and shown in __repr__ / summary().

Version 2.2.4

New features:

  • ResultsFingerprint class with group selection, multiple encoding modes (binary / count / max_component), PCA, t-SNE, UMAP, and KL divergence.

  • Database persistence: to_sql() / from_sql() for ResultsFingerprint and ResultsModel (SQLite and PostgreSQL via SQLAlchemy).

  • 100+ new unit tests.

Version 2.2.3

New features:

  • ResultsModel container: wraps parse_smiles / parse_mols output with helpers show(), summarise(), table(), and to_dataframe().

  • Extended visualisation utilities (plot_pfasgroups).

  • Updated PFAS group definitions to 116 groups.

Version 2.0

  • Complete rewrite of the SMARTS-based matcher.

  • New JSON-based group definition format.

  • Regulatory PFAS definition support (OECD, REACH, OPPT, UK EA, PFASSTRUCTv5).

  • CLI entry points halogengroups / pfasgroups added.