> in any case, what file formats does Jmol plan to support? Tim, The following is a collection of random statements about the current status of Jmol/CDK file support and integration:
The development version of Jmol has an interface called the 'JmolModelAdapter'. This interface separates the file IO from Jmol data structures that are used for Display. The idea is to allow one to run Jmol on top of any Java molecular modeling package. Currently there are two implementations, the CdkJmolModelAdapter and the SimpleModelAdapter. The Jmol beta test code that you have been running is using the 'SimpleModelAdapter' which only supports .xyz, .mol, and .pdb files. It is not using CDK. The currently released version of Jmol support 15 or 20 file formats. mmCIF is one of them. However, in some cases it only reads out a subset of the data out of the files. For example, the CDK/Jmol code for .pdb files only read the ATOM and HETATM records. There are some performance problems with CDK io. Again taking .pdb as an example, reading hemoglobin takes over 8 seconds on my Linux box. (The simple model adapter takes .75 seconds) I have not taken a look at the CDK code for mmCIF, but I suspect it will have the same issues. In addition, there is an overall problem of size. Including CDK in the JmolApplet makes the size go from +/- 320K to +/- 700K. I have tried to come up with a clean mechanism to split out the CDK file support into a separate .jar file that would be downloaded only if needed, but to date have not been terribly successful. We need to get these issues worked out, but recently I have been focusing on other functionality within Jmol. Miguel ------------------------------------------------------- This SF.net email is sponsored by: IBM Linux Tutorials. Become an expert in LINUX or just sharpen your skills. Sign up for IBM's Free Linux Tutorials. Learn everything from the bash shell to sys admin. Click now! http://ads.osdn.com/?ad_id=1278&alloc_id=3371&op=click _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
