orthonym.rules.amides#

Note

Internal API. Names and behaviour may change between releases.

Amide naming rules for IUPAC nomenclature.

Amide naming follows these patterns: - Primary amides: stem + ‘amide’ (acetamide, propanamide) - Secondary amides: N-substituent + stem + ‘amide’ (N-methylacetamide) - Tertiary amides: N,N-disubstituent + stem + ‘amide’ (N,N-dimethylacetamide) - Ring-attached amides: parent + ‘carboxamide’ (cyclohexanecarboxamide)

Based on IUPAC 2013 Blue Book.

orthonym.rules.amides.get_amide_type(mol, amide_atoms)#

Determine if an amide is primary, secondary, or tertiary.

The amide nitrogen determines the type: - Primary: -C(=O)NH2 (N has 2 hydrogens) - Secondary: -C(=O)NHR (N has 1 hydrogen, 1 substituent) - Tertiary: -C(=O)NR2 (N has 0 hydrogens, 2 substituents)

Parameters:

  • mol – RDKit Mol object

  • amide_atoms (tuple) – Atom indices from amide SMARTS match

Returns:

“primary”, “secondary”, or “tertiary”

Return type:

str

orthonym.rules.amides.get_n_substituents(mol, amide_atoms)#

Get substituents attached to the amide nitrogen.

For secondary/tertiary amides, find the carbon substituents attached to nitrogen (not the carbonyl carbon).

Parameters:

  • mol – RDKit Mol object

  • amide_atoms (tuple) – Atom indices from amide SMARTS match

Returns:

List of dicts – [{“atoms”: [atom_indices], “name”: “methyl”},…]

Return type:

List[Dict]

orthonym.rules.amides.format_n_substitution(substituents)#

Format N-substituents as IUPAC prefix.

Rules: - Single substituent: “N-methyl” - Two identical: “N,N-dimethyl” - Two different: “N-ethyl-N-methyl” (alphabetized)

Parameters:

substituents (List[Dict]) – List of dicts from get_n_substituents

Returns:

Formatted N-substitution prefix (e.g., “N-methyl”, “N,N-dimethyl”), or None if any substituent name is a refusal sentinel (M2 Task 3 splice guard, below) – never a string containing the sentinel.

Return type:

str | None

orthonym.rules.amides.is_ring_attached_amide(mol, amide_atoms)#

Check if an amide is attached to a ring.

A ring-attached amide has its carbonyl carbon directly bonded to a ring carbon. These use -carboxamide suffix.

Parameters:

  • mol – RDKit Mol object

  • amide_atoms (tuple) – Atom indices from amide SMARTS match

Returns:

True if the amide is ring-attached

Return type:

bool

orthonym.rules.amides.get_amide_chain_length(mol, amide_atoms)#

Get the chain length for an amide (including carbonyl carbon).

Works for regular amides (=O) and a phase chalcogen amides (=S thioamide / =Se selenoamide / =Te telluroamide) per +.

The chain length determines the parent name: - 1: formamide / methanethioamide / methaneselenoamide - 2: acetamide / ethanethioamide / ethaneselenoamide - 3: propanamide / propanethioamide / propaneselenoamide etc.

Parameters:

  • mol – RDKit Mol object

  • amide_atoms (tuple) – Atom indices from amide SMARTS match

Returns:

Chain length (number of carbons in parent chain)

Return type:

int

orthonym.rules.amides.get_amide_parent_name(chain_length, is_ring=False, suffix_form='amide')#

Get the parent amide name based on chain length and suffix form.

Parameters:

  • chain_length (int) – Number of carbons in parent chain

  • is_ring (bool) – If True, use -carboxamide form

  • suffix_form (str) –

    One of “amide”, “thioamide”, “selenoamide”, “telluroamide”

    • functional replacement). For chalcogen forms

    the IUPAC PIN preserves the parent-stem terminal ‘e’ (e.g., ‘propanethioamide’) because the suffix starts with a consonant.

Returns:

Parent amide name (e.g., “formamide”, “acetamide”, “propanamide”, “ethanethioamide”, “propaneselenoamide”).

Return type:

str

class orthonym.rules.amides.RingAmideParts(ring_hydride, suffix, retained, n_substituents)#

Bases: object

The structural parts of a ring carboxamide name (branch review fixes).

ring_hydride (‘cyclohexane’) and suffix (‘carboxamide’, ‘carbothioamide’) for a saturated cycloalkane, or the retained benzamide; n_substituents as get_n_substituents returns them (empty for a primary amide). A composer assembles the name from these parts – never by cutting an emitted name apart.

ring_hydride#
suffix#
retained#
n_substituents#
parent_word(suffix_locant=False)#

The parent word. suffix_locant: a ring prefix is cited as well, so the suffix keeps its locant, the Blue Book “… then all locants must be cited”): ‘cyclohexane-1-carboxamide’; alone it is omitted

(c),:2891): ‘cyclohexanecarboxamide’. The retained ‘benzamide’

numbers its carbonyl-bearing carbon 1 and cites no suffix locant.

orthonym.rules.amides.ring_amide_parts(mol, amide_atoms, suffix_form='amide')#

RingAmideParts for a ring-attached amide name_amide can spell, else None (see name_amide).

orthonym.rules.amides.name_amide(mol, amide_atoms, suffix_form='amide')#

Generate IUPAC name for an amide compound.

Handles: - Primary amides: acetamide - Secondary amides: N-methylacetamide - Tertiary amides: N,N-dimethylacetamide; dimethylformamide (a formamide with the same group on both N-H cites no N locants) - Ring-attached amides: cyclohexanecarboxamide - a phase chalcogen amides (suffix_form=”thioamide”/”selenoamide”/”telluroamide”):

ethanethioamide, N-methylpropaneselenoamide, etc.

Parameters:

  • mol – RDKit Mol object

  • amide_atoms (tuple) – Atom indices from amide SMARTS match

  • suffix_form (str) – PIN suffix variant — “amide” (default) or chalcogen analog (“thioamide” / “selenoamide” / “telluroamide”, per.

Returns:

IUPAC name for the amide

Return type:

str | None

orthonym.rules.amides.name_chain_diamide(mol, all_amide_matches, chain, atom_to_locant)#

Name an acyclic chain diamide with optional N-substituents (D3).

Handles the mixed primary + N-substituted (and symmetric primary / symmetric secondary) acyclic diamide class per BB (parent = {stem}anediamide) and (N-substituents cited as N{locant} prefixes where the locant is the chain-carbon locant of the amide carbonyl; identical substituents on both ends give the N1,N4-di... form).

Fail-closed: returns None (so the caller falls through to the existing polyfunctional / general_acyclic path unchanged) whenever any precondition is not met, or any N-substituent cannot be named.

Parameters:

  • mol – RDKit Mol object.

  • all_amide_matches (List[tuple]) – list of amide SMARTS match tuples (primary and/or secondary), carbonyl carbon at tuple index 0.

  • chain (List[int]) – the principal chain atom-index list (the diamide backbone).

  • atom_to_locant (Dict[int, int]) – mapping from chain atom index -> locant.

Returns:

The PIN name string, or None (fail-closed).

Return type:

str | None