You should take a look at the program Reduce from the Richardson lab at Duke, it adds protons and is written in C++. It will take a pdb and without requiring modification or formating add protons to it. Versions exist for Linux, Windows, MacOS X, Irix, and Sun-SPARC, and the source code is available as well. It can be used as a plug-in program, just call out to it with whatever options are required, then get back the protenated pdb.
Information and references (including algorithms published in JMB) at http://kinemage.biochem.duke.edu/software/reduce.php Note: not a member of the Richardson lab, but a (program using) collaborator. S. Endo-Streeter On Wednesday 06 December 2006 08:55, d.gottst...@gmx.de wrote: > Hello everybody, > > I'm currently working on a java project in which, after loading a pdb-file, > I need to add Hydrogens to the molecules. Since Pymol has an implemented > method for this problem, I'd be interested in the algorithm used, so I can > reimplement it in java. Does anybody know if there is a publication, where > I can find it? Another approach I am following is the usage of the CDK > package, but I'm not really sure how to apply it to my problem and how good > the method works. I'd be thankful for any help I can get ;). > > greetings, Danrik -- ______________________________________ Stuart T. Endo-Streeter Structural Biology and Biophysics Dept. Biochemistry LSRC C266 Duke University 919-681-1668 stuart.endostree...@duke.edu
