From: SourceForge.net <no...@so...> - 2012-10-07 14:12:53
|
Patches item #3568970, was opened at 2012-09-18 07:57 Message generated for change (Comment added) made by egonw You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3568970&group_id=20024 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. >Category: master >Group: Accepted >Status: Closed >Resolution: Accepted Priority: 5 Private: No Submitted By: John May (jwmay) Assigned to: Rajarshi Guha (rajarshi) Summary: single/double bond order and better atom types Initial Comment: Hi, 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: c1ccc(C[C@@H](C(N[C@H](Cc2c3ccccc3[nH]c2)C(N[C@@H](CCCN)C(N[C@@H](Cc2ccc(cc2)O)C(N[C@H](C(N[C@@H] ). =) 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. /Klas 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 ---------------------------------------------------------------------- >Comment By: Egon Willighagen (egonw) Date: 2012-10-07 07:12 Message: Since some of these patches change too much to my taste, it is pushed to master. ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2012-09-24 06:13 Message: Rajarshi, thanx! Are you going to sign them off and push them to the repos? ---------------------------------------------------------------------- Comment By: Rajarshi Guha (rajarshi) Date: 2012-09-24 06:05 Message: Looks good to me ---------------------------------------------------------------------- Comment By: John May (jwmay) Date: 2012-09-23 10:15 Message: 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). J ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2012-09-23 08:40 Message: Rajarshi, your independent, second review please. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3568970&group_id=20024 |