I've been working with the satChecker some part of this week. And
today I think I got i working, at least all the molecules that I have
tested work (including the horribly one that I think Cristopher
mailed, i.e the one that has the SMILES:
What i does is this:
First it see if it can find a solution where all atoms are saturated,
if not it settles with the solution with most saturated atoms. If so
it makes an notice in the log (as a warning).
I don't know if you want to look at the code, but I attach the files
so you can if you want to.
Egon has reviewed Klas' patch and add new explicit atom types to owl. I have checked these changes and signed off as well as add some additional unit tests for the BondManipulator.
(me) Signed off Egon's commits: https://github.com/johnmay/cdk/tree/421-14x-betterAtomTypes