`orthonym.rules.salts`#

Note

Internal API. Names and behaviour may change between releases.

Salt and zwitterion naming rules per IUPAC 2013.

Handles naming of: - Salts: Compositional nomenclature (cation + anion as separate words) - Zwitterions: Internal ion pairs with combined suffixes

IUPAC 2013 References: -: Anion nomenclature -: Cation nomenclature -: Zwitterion nomenclature

Key naming patterns: - Salts: “cation anion” format (sodium acetate, ammonium chloride) - Zwitterions: base name with ionic suffixes (2-azaniumylacetate) - Multiple ions: alphabetized cations before alphabetized anions - Stoichiometry: multiplicative prefixes for repeated ions (diacetate)

orthonym.rules.salts.name_salt(mol, style='pin', *, general_fallback=False, general_fallback_unverified=False, allow_aromatic_general=False)#

Name a salt using compositional nomenclature.

Format: cation_name + space + anion_name Example: “sodium acetate”, “ammonium chloride”

Also handles: - Neutral organic fragments with inorganic counter-ions (Drug.HCl pattern) - H+ fragments merged with anions for hydroacid salt naming - Partial salts with “hydrogen” prefix (sodium hydrogen fumarate)

For multiple cations/anions, order alphabetically. For stoichiometry > 1, use multiplier prefixes.

Parameters:

mol – RDKit Mol object (contains disconnected fragments)
style (str) – ‘pin’ for preferred names

Returns:

Salt name as “cation anion” (separate words)

Return type:

str

Example

>>> mol = Chem.MolFromSmiles('[Na+].[O-]C(C)=O')
>>> name_salt(mol)
'sodium acetate'

orthonym.rules.salts.name_zwitterion(mol, style='pin')#

Name a zwitterionic compound.

IUPAC rules: - Anionic centers get lower locants (higher seniority) - Cationic suffixes cited BEFORE anionic suffixes - Format: base-name-cation_suffix-anion_suffix

Common zwitterions: - Amino acid zwitterions: glycine = 2-ammonioacetate (PIN) or glycine (trivial)

Parameters:

mol – RDKit Mol object with internal positive and negative charges
style (str) – ‘pin’ for preferred names

Returns:

Zwitterion IUPAC name

Return type:

str

Example

>>> mol = Chem.MolFromSmiles('C[N+](C)(C)CC(=O)[O-]')
>>> name_zwitterion(mol)
'(trimethylazaniumyl)acetate'

orthonym.rules.salts.is_salt(mol)#

Check if a molecule is a salt (has separate cation and anion fragments).

Parameters:: mol – RDKit Mol object
Returns:: True if molecule is a salt
Return type:: bool

Example

>>> mol = Chem.MolFromSmiles('[Na+].[Cl-]')
>>> is_salt(mol)
True

orthonym.rules.salts.is_zwitterion(mol)#

Check if a molecule is a zwitterion (internal + and - charges).

Parameters:: mol – RDKit Mol object
Returns:: True if molecule is a zwitterion
Return type:: bool

Example

>>> mol = Chem.MolFromSmiles('[NH3+]CC([O-])=O')
>>> is_zwitterion(mol)
True

orthonym.rules.salts#

`orthonym.rules.salts`#