tidy up imports and stray variable from debuging.
Beam will now auto-suppress hydrogen counts (library update in a few commits).
Circumvent CDK quirks of leaving nulls around.
Configuration options in the SMILES generator. We now use a different canon procedure which will require updates to tests.
General SMILES tests are no longer canonical (should not change with canon changes), those which are canonical test for equivalence and did not need changing.
Resolving regressions in cdk-fragment.
More concise name for creating SMILES strings (most common op) the reaction smiles has a name to avoid using overloading. Existing names still work for downstream usage but are deprecated.
Rename arbitrary to generic - correct description.
Latest version of beam includes performance improvements, custom sort operations (required for Universal SMILES), ability to resonate a structure and generate a canonical kekule representation (i.e. avoid aromatic SMILES), minor bug fixes.
Access SMILES output order.
Ensure canonical SMILES have the same kekule representation.
Obtain the InChI canonical numbering via reflection, the cdk-inchi module must be present to generate SMILES but is not a dependency of the ‘cdk-smiles’ module.
Correct hydrogen labelling and additional transformations when generating absolute SMILES.
Preliminary tests show we don’t want to pass aromatic flags to InChI. Perhaps this should now be the default as SMILES are kekulised on load.
Testing absolute SMILES on some molecules with stereo-chemistry.
The old API method didn’t throw and exception - this is reverted so existing code doesn’t need to be updated.
The aromatic option when generating InChI’s is on a singleton and should be reset.
Ring connectivity is now alway set - it is invariant and useful to have when resting ring membership (logical).
Generate aromatic SMILES for unit test.