On Thursday 04 January 2007 14:38, Daniel Gottstein wrote: > > You should run the RebondTool [1] prior to adding hydrogens. This tool > > requires vanderwaals radii to be assigned to the atoms, so the full use > > looks like this:
<snip> > > (taken from cdk.test.graph.rebond.RebondToolTest). > thank you for your help, but I'm sorry to say that I still have a problem. > I don't really understand the parameters that are needed to instantiate the > RebondTool. > > The Koders-example uses: > RebondTool rebonder = new RebondTool(2.0, 0.5, 0.5) > > But a molecule such as 1FJS.pdb will probably need different values (or > maybe not?). > > I found a setup that works quite well but I don't know if it is reasonable. > > RebondTool rebonder = new RebondTool(1.4, 0.83, 0.83); I think this is reasonable. <snip> > the results are: > before h2add: > 2475 > after h2add: > 5061 > > whereas pymol results are: > before: 2475 > after: 5062 That looks quite acceptable. Happy with that? > I do have an additional problem. How can I write a new PDBFile and create > the contents with Outputstream? I don't quite know how to make use of the > PDBWriter class yet. Well, the PDBWriter is really only suitable for small molecules, and does not save most of the PDBPolymer content, that is, about strands, the sequence etc. At least, not at this moment... It does save all the atoms with coordinates, but no bonds at this moment. Patching it to support writing bonds should be trivial. Egon -- [EMAIL PROTECTED] Cologne University Bioinformatics Center (CUBIC) Blog: http://chem-bla-ics.blogspot.com/ GPG: 1024D/D6336BA6 ------------------------------------------------------------------------- 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
