`orthonym.rules.tricyclo`#

Note

Internal API. Names and behaviour may change between releases.

Tricyclo compound naming according to IUPAC 2013 nomenclature.

Implements tricyclo[x.y.z.a^b,c] descriptor generation for bridged tricyclic hydrocarbons.

IUPAC Reference: Blue Book 2013, (Tricyclic bridged ring systems)

The tricyclo descriptor format is: - tricyclo[a.b.c.d^e,f]alkane

where: - a, b are the two branches of the main ring (atoms between main bridgeheads) - c is the main bridge (first additional bridge) - d^e,f describes the secondary bridge: d atoms, connecting positions e and f

Examples: - Adamantane: tricyclo[3.3.1.1^3,7]decane

Main ring: 6 atoms, split 3.3

Main bridge: 1 atom

Secondary bridge: 1 atom connecting positions 3 and 7

Numbering rules: 1. Start at one main bridgehead (position 1) 2. Number along the longer branch of main ring 3. Continue to second bridgehead 4. Number back along shorter branch 5. Number main bridge 6. Number secondary bridges (from higher-numbered bridgehead)

orthonym.rules.tricyclo.is_tricyclo_system(mol)#

Check if molecule is a tricyclo (3-ring bridged) system.

Parameters:: mol – RDKit Mol object
Returns:: True if molecule has exactly 3 rings
Return type:: bool

orthonym.rules.tricyclo.generate_tricyclo_descriptor(mol)#

Generate the tricyclo[a.b.c.d^e,f] descriptor for a molecule.

Parameters:: mol – RDKit Mol object
Returns:: Descriptor string like “tricyclo[3.3.1.1^3,7]”, or None
Return type:: str | None

Examples

>>> mol = Chem.MolFromSmiles('C1C2CC3CC1CC(C2)C3') # adamantane
>>> generate_tricyclo_descriptor(mol)
'tricyclo[3.3.1.1^3,7]'

orthonym.rules.tricyclo.get_tricyclo_numbering(mol)#

Generate IUPAC numbering for a tricyclo system.

Numbering rules: 1. Start at one main bridgehead (position 1) 2. Number along longer branch of main ring to other bridgehead 3. Number back along shorter branch toward position 1 4. Number main bridge atoms 5. Number secondary bridge atoms

Parameters:: mol – RDKit Mol object
Returns:: Dict mapping atom_idx -> IUPAC locant (1-indexed), or None
Return type:: Dict[int, int] | None

orthonym.rules.tricyclo.name_tricyclo_system(mol)#

Generate the full IUPAC name for a tricyclo system.

Parameters:: mol – RDKit Mol object
Returns:: Full IUPAC name like “tricyclo[3.3.1.1^3,7]decane”, or None
Return type:: str | None

Examples

>>> mol = Chem.MolFromSmiles('C1C2CC3CC1CC(C2)C3') # adamantane
>>> name_tricyclo_system(mol)
'tricyclo[3.3.1.1^3,7]decane'

orthonym.rules.tricyclo.get_retained_tricyclo_name(canonical_smiles)#

Look up retained name for a tricyclo compound.

Parameters:: canonical_smiles (str) – Canonical SMILES string
Returns:: Retained name if found, None otherwise
Return type:: str | None

orthonym.rules.tricyclo.is_retained_tricyclo(canonical_smiles)#

Check if a SMILES has a retained tricyclo name.

orthonym.rules.tricyclo.generate_polycyclo_descriptor(mol)#

Generate descriptor for any bridged polycyclic system.

Handles bicyclo, tricyclo, tetracyclo, etc.

Parameters:: mol – RDKit Mol object
Returns:: Descriptor string or None
Return type:: str | None

orthonym.rules.tricyclo.name_polycyclo_system(mol)#

Generate IUPAC name for any bridged polycyclic system.

Routes to appropriate naming function based on ring count.

Parameters:: mol – RDKit Mol object
Returns:: IUPAC name or None
Return type:: str | None

orthonym.rules.tricyclo.name_polycyclo_with_functional_groups(mol)#

Name a polycyclic system that also has functional groups.

This handles cases like the diterpenoid where we have: - Hexacyclo ring system - Multiple ester groups - Lactone ring

Parameters:: mol – RDKit Mol object
Returns:: IUPAC name combining polycyclic parent with functional group suffixes
Return type:: str | None

orthonym.rules.tricyclo#

`orthonym.rules.tricyclo`#