orthonym.assembly.acyl_amido_polyacid#

Note

Internal API. Names and behaviour may change between releases.

The amido prefix of an acyl branch that carries a second carboxylic acid (Asp, Glu).

method (1) (the Blue Book-32998) writes -NH-CO-R as the amide name with

its final ‘e’ changed to ‘o’. acyl_amido_prefix_from_branch gets there by naming the ACID HO-CO-R and turning ‘…oic acid’ into ‘…amido’; for an acyl whose R holds another COOH that acid is a diacid (‘2-aminobutanedioic acid’), one amido prefix cannot be read off it (acid_name_to_amido_prefix declines on purpose), and the whole peptide was declined at the default tier. The Blue Book spells such an acyl with the second acid as ‘carboxy’ on the chain that ends at the amide carbon: “Substituent groups with the free valence on a nitrogen atom” (:54456), -HN-CO-[CH2]2-CH(NH2)-COOH is ‘4-amino-4-carboxybutanamido’ (:54470).

The acyl namer already writes that form when the acyl hangs on a carbon: -CO-CH(NH2)-CH2-COOH on a carbon is ‘(2S)-2-amino-3-carboxypropanoyl’. So the amide nitrogen is replaced by a carbon in a COPY of the molecule (atom indices are kept), the acyl atoms are named there, and the ‘…oyl’ word becomes ‘…amido’. Three checks keep the stand-in honest:

  • the copy changes one atom, so the CIP labels of every stereocentre of the acyl are computed on both molecules by the project’s CIP path (assign_stereochemistry) and must agree, otherwise the descriptors in the name would not be the original’s;

  • the name must end in ‘oyl’ and cite ‘carboxy’ (the shape this module exists for);

  • the acyl name’s non-PIN status carries to the prefix (record_derived_non_pin_fragment), as record_prefix_from_acid_status does on the ordinary route;

  • when the caller asked for a verified prefix, the amide R-CO-NH2 the prefix stands for (’…amide’) must read back from OPSIN as that amide on the full InChIKey, as fragment_acid_name_verified demands of the acid name on the ordinary route.

orthonym.assembly.acyl_amido_polyacid.polyacid_acyl_amido_prefix(mol, n_idx, carbonyl_c, sub_atoms, verify=False)#

The bare amido prefix of the N-attached acyl branch sub_atoms when its acyl holds a second free COOH (‘2-amino-3-carboxypropanamido’), else None (fail closed).

sub_atoms is the ENTIRE substituent (the amide N plus the acyl); verify asks for the OPSIN full-InChIKey read-back of the amide the prefix stands for.