orthonym.rules.nitriles#

Note

Internal API. Names and behaviour may change between releases.

Nitrile naming rules for IUPAC nomenclature.

Nitrile naming follows these patterns: - Chain-terminal nitriles: stem + ‘nitrile’ (acetonitrile, propanenitrile) - Ring-attached nitriles: parent + ‘carbonitrile’ (cyclohexanecarbonitrile)

The nitrile carbon (C of -C#N) IS counted in the chain length.

Based on IUPAC 2013 Blue Book.

orthonym.rules.nitriles.is_ring_attached_nitrile(mol, nitrile_atoms)#

Check if a nitrile group is directly attached to a ring.

A ring-attached nitrile is one where the nitrile carbon (C of -C#N) is directly bonded to a ring carbon. These use the -carbonitrile suffix.

Parameters:

  • mol – RDKit Mol object

  • nitrile_atoms (tuple) – Atom indices from nitrile SMARTS match [CX2]#[NX1] where index 0 is the carbon

Returns:

True if the nitrile carbon is attached to a ring atom

Return type:

bool

orthonym.rules.nitriles.get_nitrile_parent_chain(mol, nitrile_atoms, principal_chain=None)#

Get the parent chain for a chain-terminal nitrile.

For chain-terminal nitriles, the chain includes the nitrile carbon. The nitrile carbon is ALWAYS position 1 (terminal).

Parameters:

  • mol – RDKit Mol object

  • nitrile_atoms (tuple) – Atom indices from nitrile SMARTS match

  • principal_chain (List[int] | None) – Optional pre-computed principal chain

Returns:

List of atom indices representing the parent chain The nitrile carbon will be at index 0 (position 1 in naming)

Return type:

List[int]

orthonym.rules.nitriles.get_ring_parent_name(mol, ring_atoms)#

Get the parent name for a ring attached to a nitrile.

Parameters:

  • mol – RDKit Mol object

  • ring_atoms (tuple) – Atom indices of the ring

Returns:

Ring parent name (e.g., “cyclohexane”, “cyclopentane”)

Return type:

str

orthonym.rules.nitriles.name_nitrile(mol, nitrile_atoms, parent_name=None, chain_length=None, is_ring=None)#

Generate IUPAC name for a nitrile compound.

Parameters:

  • mol – RDKit Mol object

  • nitrile_atoms (tuple) – Atom indices from nitrile SMARTS match

  • parent_name (str | None) – Optional ring parent name (e.g., “cyclohexane”)

  • chain_length (int | None) – Optional chain length (if known)

  • is_ring (bool | None) – Optional flag if nitrile is ring-attached

Returns:

IUPAC name for the nitrile (e.g., “propanenitrile”, “cyclohexanecarbonitrile”)

Return type:

str

orthonym.rules.nitriles.get_nitrile_locant(nitrile_atoms, atom_to_locant)#

Get the locant for a nitrile group.

For chain-terminal nitriles, the locant is always 1 (implicit). For nitriles as prefixes (cyano-), we need the chain position.

Parameters:

  • nitrile_atoms (tuple) – Atom indices from nitrile SMARTS match

  • atom_to_locant (dict) – Mapping from atom index to chain locant

Returns:

Locant position or None if not on chain

Return type:

int | None