#541 single/double bond order and better atom types

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


  • Egon Willighagen

    Rajarshi, your independent, second review please.

  • John May

    John May - 2012-09-23

    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 - 2012-09-24

    Looks good to me

  • Egon Willighagen

    Rajarshi, thanx!

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

  • Egon Willighagen

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


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