On Nov 27, richard apodaca wrote: > I have a group of molecules, some of which contain a > common substructure. I want to display the molecules > with common substructures using the same orientation > for each. How can I do this in CDK? > > I had a look at Kabsch Alignment: > > http://cdk.sourceforge.net/api/org/openscience/cdk/geometry/alignment/KabschAlignment.html > > but I'm not sure it's what I'm looking for. If not, > does CDK have the capability I described? >
You are on the right path. See sample 2 in the KabschAlignment's javadoc. I've not done it myself, but I would do it as follows: 1. use UniversalIsomorphismTester to find the maximal common substructure between two molecules 2. for both molecules identify atoms that belong to the common substructure (i.e. set up atom arrays a1 and a2 in the sample 2). Again, the UniversalIsomorphismTester can be used here. 3. use KabschAlignment for the alignement 4. use some 3D visualization tool for the display. Jmol perhaps? Best wishes, Sulev ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
