Actually, the easiest way is to use JmolViewer.getProperty(null, "chainInfo", "")
This returns a HashTable with entry "models" that is a Vector. Each models element is a HashTable with entry "chains", which is a Vector. Each chains element is a Hashtable "residues", which is a Vector of the groups in the chain, each element again a HashTable. The "atomInfo1" entry of that HashTable is a String that will give you the three-letter code for the group. Thus: models Vector[1] chains Vector[1] residues Vector[46] atomInfo2 "[THR]1:A.CG2 #7" atomInfo1 "[THR]1:A.N #1" _apt2 6 _apt1 0 groupID 17 seqCode "1" visibilityFlags 0 groupIndex 0 , atomInfo2 "[THR]2:A.CG2 #14" atomInfo1 "[THR]2:A.N #8" _apt2 13 _apt1 7 groupID 17 seqCode "2" visibilityFlags 0 groupIndex 1 , etc... Alternatively you can get the group name from the groupID entry (an Integer) using Group.getGroupName((short)groupID) I realize it's not trivial to drill down to that groupID level. But it can be done. Just be careful with your parentheses. Bob Charles Musgui wrote: > Hello, > > I would like to know how I can interact with a protein model loaded > within JMol. To be more precise, here is what I'd like to do, directly > using the JMol API: > 1. get the protein model, then get the Chain IDs contained in the > model (I suppose here I handle a protein 3D structure) > 2. get a particular Chain using its ID, > 3. given the chain, get its protein sequence > > I've tried to understand the JMol API and I've found the package > "org.jmol.modelsetbio", but I've failed to figure out how to retrieve > a "BioModel" out of the JMolViewer. > > Thanks for your help, > Charles > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Microsoft >Defy all challenges. Microsoft(R) Visual Studio 2008. >http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >------------------------------------------------------------------------ > >_______________________________________________ >Jmol-developers mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-developers > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
