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InformaticsMatters / squonk

Squonk platform and computational notebook
Apache License 2.0
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Allow to generate Kekule forms of molecules #119

Open tdudgeon opened 4 years ago

tdudgeon commented 4 years ago

This was requested by Sygnature. The Convert molecule format cell can be used for this.

tdudgeon commented 4 years ago

Initial work complete. An extra option of smiles-kekule was added to the Convert molecule format cell. But this was a lot more complex than it seems as the cell was broken, and handling bad molecules took some care. Further verification is needed. In particular it appears that CDK does not automatically generate atom type or implict H info and this method was added to handle this: https://github.com/InformaticsMatters/squonk/blob/119_support_for_kekulization/components/cdk-lib/src/main/groovy/org/squonk/cdk/io/CDKMoleculeIOUtils.java#L226-L229

tdudgeon commented 4 years ago

It might also be good to add a smiles-aromatic format as well, but there are complications of which aromaticity model is wanted.