Indeed, the simplest definition of a molecular scaffold obtained by removing all *terminal chain* is really trivial to obtain, and no need of ringsearch or chain detection to do so, a simple recursive method is far enough.
I currently have this implementation in my program, along with framework definition (= scaffold but no matters of atom types). I may also implement other definition of molecular scaffold in the future (eg. ring assemblies, ring system), defined in the paper you pointed among others if I remember well, and which are a little more difficult to implement I think. Once validated and documented, if you are interested I could give you a CDK pluggable version of them... Cheers ;) Quoting Christoph Steinbeck <[email protected]>: > Not that I would be aware of, but it would be really good and actually > easy to do. > The definition of a scaffold from the Waldmann article on the > Scaffold-Tree would be something worth implementing and the CDK > ringsearch and chain-detection routines would help. > > I haven't got time to do it, though :-) > > Cheers, > > Chris > > Vincent Le Guilloux wrote: >> Hello, >> >> Is there any class/methods that could generate a scaffold from a >> given molecule? >> >> By scaffold, I mean any existing definition of it (Murcko, ring >> assemblies, ring system...) >> >> Just asking so I don't code something already existing :) currently >> I haven't found such method/class in the test >> repository/documentation... >> >> And just a question for my curiosity: in the feature list of the >> cdk is indicated " active site detection " in protein structures. >> Could you tell me a few words about that ? Just what (existing?) >> algorithm do you use, and if there is a publication :) >> >> Thanks in advance. >> Best regards ;) >> > > -- > Dr. Christoph Steinbeck > Head of Chemoinformatics and Metabolism > European Bioinformatics Institute (EBI) > Wellcome Trust Genome Campus > Hinxton, Cambridge CB10 1SD UK > Phone +44 1223 49 2640 > > What is man but that lofty spirit - that sense of enterprise. > ... Kirk, "I, Mudd," stardate 4513.3.. -- Vincent Le Guilloux Phd Student - ICOA - UMR CNRS 6005 Div. of chemoinformatic and molecular modeling. University of Orléans Phone: ++33 2 38 49 45 77 Fax : ++33 2 38 41 72 81 ------------------------------------------------------------------------------ The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your production scanning environment may not be a perfect world - but thanks to Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700 Series Scanner you'll get full speed at 300 dpi even with all image processing features enabled. http://p.sf.net/sfu/kodak-com _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
