If I remember correctly the Murcko framework code in the CDK is broken. I have been working on an updated package for fragmentation but, of course, the real world slows things down ...
On Sep 30, 2010, at 7:31 AM, Pascal Muller wrote: > Hi, > > >> Each of the components should only do the minimal promised work, >> which gives maximum >> flexibility in wiring things together as you like them. >> In your example, you would always need to do aromaticity detection >> (using some >> CDKHueckelAromaticityDetector.java or so) to do the detection >> before doing the Murcko stuff. >> The reasoning in this case, (...) > > Ok, I think I understand... > But do you agree that the Murcko framework should retain the bond > order? I.e., that a benzene should not be a cyclohexane in the > frameworks? Correct - aromaticity should be retained > > And should, or not, the framework retain all cycles? Correct > And is intended that the nitrogen keeps the charge in the framework? > (I don't know what the behaviour should be in this case...) I'd say yes ---------------------------------------------------- Rajarshi Guha | NIH Chemical Genomics Center http://www.rguha.net | http://ncgc.nih.gov ---------------------------------------------------- Build a system that even a fool can use and only a fool will want to use it. ------------------------------------------------------------------------------ Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
