Hi Fabian, Miguel, Today, I've uploaded two patches that might interest you. Both deal with crystal support in Jmol-HEAD.
The first is in jmol.adapters.CdkJmolModelAdapter (1.22->1.23) which interfaces CDK with Jmol's rendering engine... I've implemented the getCrystalCellIterator() method, hopefully correct... but looks ok. It uses a CrystalCellIterator to loop over the unit cell axis, a,b and c. Miguel, the result is that it only shows these three axis... how should I make it complete the full unit cell box? The second patch is in cdk.io.VASPReader, which was yet unimplemented... Fabian, some time ago you asked about ABINIT in CDK... I hope this VASP reader could help you get an idea of how that would look like in CDK... I've basically copied the VASP code in Jmol, so it should be straight forward to see what changes I had to make... Note that is has not been fully succesful yet... if you open the VASP file in Jmol-HEAD you'll see that there is something wrong with the coordinates... Haven't figured out yet why it is so... I've tried to interpret the coordinates in the VASP as fractional... and tried to use both cartesian *and* fractional in the CDK objects... both with the same result... Have to figure out why this is so... Also, it is not yet possible to store symmetry operations for a spacegroup, neither is it possible to define the crystal box yet in Jmol-HEAD... I'll work on this later... But I think it would be best to keep the crystal box stuff on the Jmol side... I think this bit as part of the rendering process... but the space group symmetry operations (-x, y+0.5, z etc) should go into CDK's Crystal class... I need also to make to helper class that converts the Crystal into a P1 crystal, thus applying the given symmetry operations... As Peter noted, this should take into account symmetry operations that lead to atoms at the same coordinates... and I was thinking to use the Bspt code for this, Miguel, can the Bspt code be used in a dynamic process? I.e. can I add atoms to the tree while using it at the same time? Ok, enough for now. Egon Egon -- PhD Molecular Representation in Chemometrics Laboratory of Analytical Chemistry http://www-cac.sci.kun.nl/people/egonw.html ------------------------------------------------------- This SF.net email sponsored by: Enterprise Linux Forum Conference & Expo The Event For Linux Datacenter Solutions & Strategies in The Enterprise Linux in the Boardroom; in the Front Office; & in the Server Room http://www.enterpriselinuxforum.com _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
