Jmol 10.x.23 reads Spartan PC binary .spartan files. These files contain molecular orbitals as well as dipole and vibration information.
If both MOs and vibrational modes are present, the first model (frame 1) holds the MOs (isosurface mo 1, isosurface mo 2, etc.), and the second - n-the models are one per vibration. A reasonable cutoff appears to be about 0.008. I'm not exactly sure how this correlates to relative probability. One idea I haven't implemented but could would be to color these based on occupancy -- different default colors for occupied vs unoccupied. Enjoy! Bob Hanson See http://www.stolaf.edu/people/hansonr/jmol/test/proto/new.htm Bob Bob Hanson wrote: >OK, I think the method is so simple, I should implement a binary >compound document file reader. It's only about six methods and two short >data structures. So here's the idea: > >Resolver.java: > >Check for the 8-byte "magic number" that the file starts with -- I'm >doing this already. If it is found, open the compound document and read >the directory. The presence of a document called "Property Archive" >will indicate this is a Spartan file. > >Read the two documents Archive and Property Archive into a string >buffer, close the file, and pass that string buffer on to the >SpartanReader, which is already set to read the archive this way. > > > this was not necessary. It was cleaner to treat the compound documents like gzip files and preprocess them in FileManager. >I imagine a very small class, "CompoundDocument", that you pass an input >stream to, and it does the rest. > > > CompoundDocument is now a class of Viewer, accompanying FileManager there. >Q: What's the easiest way to read binary from our "buffered reader" we >are setting up now? > > > Easiest way I found was to treat it as a DataInputStream. I also experimented with RandomAccessFile, and that worked nicely, especially since it has seek(), but I got caught by the fact that Java applets must stream -- no random access. So that bit of code is there, but it's commented out. It appears to be fast enough. >Q: Can you read binary from a buffered reader by wrapping it some way or >another? > > DataInputStream works nicely, with a bit of littleEndian --> bigEndian conversions. >Q: Totally different, better approach? > > > There is probably a more efficient way of doing this. But part of the trick is that one must read randomly, I think. There's no guarantee that the file sectors will be in any order whatsoever. Bob >Bob > > > > > >------------------------------------------------------------------------- >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >_______________________________________________ >Jmol-developers mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-developers > > ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
