#541 single/double bond order and better atom types

Rajarshi Guha
master (162)
John May


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


  • Rajarshi, your independent, second review please.

  • John May
    John May

    Just adding incase it gets missed but someone from Bioclipse pointed out the cdk.module was wrong.
    Looks like it should be valencycheck not valency (unless the module making handles this).


  • Rajarshi Guha
    Rajarshi Guha

    Looks good to me

  • Rajarshi, thanx!

    Are you going to sign them off and push them to the repos?

  • Since some of these patches change too much to my taste, it is pushed to master.