On Tuesday 29 May 2007, Stefan Kuhn wrote: > On Tuesday 29 May 2007 12:39, Andreas Schüller wrote: > > I've filed the HydrogenAdder problem with carbocations as a bug report. > > And I made a test case for it.
Even better! :) Now, the test is interesting... it uses the default HydrogenAdder, which uses the SaturationChecker in the background, which uses the structgen atom type list, which does NOT contain charged atom types :) So, make sure to move the test to HydrogenAdder2Test. Yes, I know this is rather unintuitive! It's historical, nothing logic about this. Here's the deal: CDK has three custom atom type lists: - structgen: only for uncharged species, with hybridization information - valency: with charged atoms, but without hybridization info - hybridization: with charged, with hybrid info The first is used/useful in combination with structure generation. The second was later added to support charged molecules. The last was even added later than that, for help of the SMILES parser, which sometimes hydrogen counts can only be derived using hybridization information from the SMILES string. Basically, the first should be a subset of the second, which is a subset of the third. Historically, at least. I will add information to the JavaDoc of the HydrogenAdder about how to get a 'proper' HydrogenAdder right now. If you wonder why the default in the HAdder never was made the third atom type list, you might consider that that might very well break things. In other words, binary compatibility. Egon PS. only after seeing the test, I got an idea what might be going wrong in the problem reported... it might not be the define solution to the problem, but writing a JUnit test at least got the ball rolling... -- [EMAIL PROTECTED] Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
