Fixup - component grouping in recursive smarts
fixup failing unit test
Don’t thrown an error for low-charge values when deterring electron contribution.
Don’t set geometric configuration for aromatic bonds.
Ignore aromatic information when converting atoms and bonds.
If the InChI generation provided a warning this is also okay…
Separate auxinfo generation from the numbers and allow options to be provided.
Obtain numbering required by Universal SMILES.
Deprecating the canonical labeller and the prime numbers utility.
Much faster generation of initial invariants, these don’t distinguish all cases but can easily be substituted for better (more expensive) values later. Using the adjacency list representation to avoid using the AtomContainer results in nearly a 80x speed improvement. This also provides correct values - the previous invariants were mixing partial / formal charges and missing explicit hydrogens from the H count. The new values are also picky and complain at unset values - there have been many bug reports with non-canonical SMILES due to missing hydrogens. Also adding the primes to the class for internal use.
A utility for ranking indicies by a seperate array of values. The ranking is built around a sorting procedure with the comparisson baked in.
Including invariant refinement in Canon.