Bob Hanson

This depends upon the dependency libraries. They all need to have source available. Image processing has been experimented with and worked in preliminary tests. Could be a fine project.

I agree. V3000 allows for dative and coordinate bonds. Whether you call these "zero order" or not, is up to you. [ https://depth-first.com/articles/2021/11/17/ten-reasons-to-adopt-the-v3000-molfile-format/ ] But bonding in general adds significant...

I agree with Antanas. My thought on aromaticity is that -- particularly with associated 3D structures, as we in this case -- standard Kekulé bonding is preferable. Aromaticity is not...

I would prefer a more succinct format. Why duplicate "site" a zillion times? Maybe just array of arrays. Suggest array of [index1, index2, type] Where type is reserved for future...

Yes, sorry, I was on my phone and, ah, still in bed... Meant to follow that with: "That said, the more use of associative arrays, the more easily extended this...

IMHO: 1. SMILES are fundamentally valuable with or without canonicalization. 2. To the extent that a SMILES is valuable depends upon the context. 3. One context is structure matching. 4....

I'd like to refresh this discussion with another aspect of uncertainty. Recent work in Jmol relating to finding space groups, identifying Wyckoff positions, and carrying out proper packing depends critically...

Sorry, that was in org.scijava.handle.DataHandleService I hacked this by changing org.scijava.plugin.WrapperService. : default PT create(final D data) { final PT instance = find(data); if (instance != null) instance.set(data); if (instance...

Somehow I missed this. Apologies. Looking at https://github.com/google/j2cl/blob/master/docs/limitations.md From what I can see, j2cl probably has a lot of limitations. No reflection, for one thing. Probably no dynamic class loading,...

OK, after looking at j2cl, I would say this: I think the answer is that there are missing pieces of Java in both. The transpiling is probably along similar lines...