John Mayfield

Overall patch looks good and with a few minor changes am happy to merge it in. The biggest blockers are the cdk-data as a dependency and too many public methods....

> @johnmay, Thank you for your comments! > > cdk-data is now out of the non-test scope again and I have implemented some of your suggestions. > > About the...

We should add an ``isMetaloid()`` to the Elements class. ``isCharged()`` is a bit wobbly IMO due to resonance/tautomers. 

Aromatic bonds in molfiles are query features and so you get back a query molecule (or at least one with query bonds) when you try to read it. MDL never...

Please also note RDKit it not the arbiter of what is “correct” behaviour - in this case MDL/Symyx/Accelerys/BIOVIA define how molfiles should be read.

Yes everything's out of sync, If you have a patch I can review apply otherwise you'll have to wait for my plan to rewrite both readers on a common base....

WIP #916, that branch is relatively stable there will even been an to mimick the RDKit semantics which are quite different to everyone else. See also - SmirksQuirks : https://nextmovesoftware.com/talks/Mayfield_SmirksQuirks_AcsFall_2023.pdf

Well there are no coordinates so up/down bonds are meaningless, I mean I'm not sure how you would expect it to guess what you meant by giving it two UP...

Oh on the main branch you can actually do this which is much cleaner: ```java IChemObjectBuilder builder = SilentChemObjectBuilder.getInstance(); IAtomContainer isomer = builder.newAtomContainer(); isomer.newAtom(IAtom.C, 0); isomer.newAtom(IAtom.Cl, 0); isomer.newAtom(IAtom.Br, 0); isomer.newAtom(IAtom.I,...

> NullPointerException: A carrier was undefined Got a link to your code? I feel like with have https://en.wikipedia.org/wiki/XY_problem. > But in most cases, many "focuses" have no saturated bonds during...