orthonym.data.natural_products

Note

Internal API. Names and behaviour may change between releases.

Natural product scaffold data and derivative lookup tables.

Provides pre-canonicalized SMILES for natural product scaffolds (for substructure matching) and exact derivative names (for direct lookup). All SMILES keys are already in RDKit canonical form – no runtime canonicalization is needed.

Also provides IUPAC atom numbering maps for steroid scaffolds, enabling decoration enumeration (hydroxy, ketone, unsaturation) on scaffold atoms.

orthonym.data.natural_products.GENERAL_ONLY_NATURAL_PRODUCTS: Dict[str, str] = {'CC12CCC(CC1=O)C2(C)C': 'camphor'}

Canonical SMILES -> name for derivatives withdrawn from the PIN path.

orthonym.data.natural_products.get_natural_product_name(canonical_smiles)

Look up exact natural product derivative name by canonical SMILES.

Parameters:

canonical_smiles (str) – RDKit canonical SMILES string.

Returns:

The retained/trivial name if found and PIN-admissible, otherwise None.

Return type:

str | None

orthonym.data.natural_products.get_carotene_parent_name(mol)

Retained carotene parent name for mol by exact InChIKey, or None.

Stereo-exact: only the all-E fundamental parent matches; a Z-isomer or a modified carotenoid returns None and is named systematically (fail-closed). The Greek name is OPSIN-round-trip gated by the caller, so a mismatch can never ship.

orthonym.data.natural_products.get_scaffold_patterns()

Return pre-compiled RDKit Mol objects keyed by canonical SMILES.

Returns:

Dict mapping canonical SMILES to compiled RDKit Mol objects.

Return type:

dict

orthonym.data.natural_products.get_steroid_numbering(scaffold_smiles)

Get IUPAC numbering map for a steroid scaffold.

Parameters:

scaffold_smiles (str) – Canonical SMILES of the scaffold.

Returns:

Dict mapping query atom index to IUPAC locant, or None if not found.

Return type:

Dict[int, int] | None

orthonym.data.natural_products.get_scaffold_numbering(scaffold_smiles)

Get IUPAC numbering map for any scaffold (steroid or alkaloid).

Checks steroid maps first, then alkaloid maps.

Parameters:

scaffold_smiles (str) – Canonical SMILES of the scaffold.

Returns:

Dict mapping query atom index to IUPAC locant, or None if not found.

Return type:

Dict[int, int] | None