On Oct 21, 2004, at 12:25 AM, Miguel wrote:
We'd actually have to come up with a way in which each reader can come up with a 'good' AtomSetName for each AtomSet. I guess the energy or vibrational frequency would be good starts for that.
Yes
Q: Do these atomSets have both a vibrational frequency and an energy?
Yes. A vibrational analysis is done for a single particular nuclear arrangement which an electronic energy for the stationary system. The vibrations are energies above that electronic ground state associated with the fact that a molecule always vibrates.
And I think you are right that we should change from ModelReader to AtomSetCollectionReader.
Done. Which means I had to remove ModelReader.java and add AtomSetCollectionReader.java.
Correct.
I noticed that there are still quite a few variables and classes that still have the name Model in them. I did not touch those...
OK ... we should try to get those cleaned up tomorrow.
Well, I was wondering since the class names that are still in the org/jmol/adapter directory are:
CdkModelAdapter, ModelAdapter, ModelResolver, SmarterModelAdapter.
changing the Model to AtomSetCollection, would make some of them pretty long. (I recall downloading a java project in my OS 9 days and getting in trouble because the filenames where too long...)
In some cases, the variable names in the Readers could indeed refer to a single structural model and therefor really a single AtomSet.
Oops, I accidentally deleted the old file before I added the new one. But it caught it soon enough that the repository was without it for only a few minutes. I hope I didn't mess anybody up...
From the cvs command line you delete files and add files ... but in fact
they are only 'tagged' for deletion/addition. It doesn't actually happen
until you 'check in'
The idea is that you can rearrange things and get everything worked out,
then *commit* in an atomic transaction ... like a real database :-)
Otherwise, it would be unacceptable for group project development.
So I didn't do it exactly in an atomic fashion. Within BBEdit you can Add and Commit a file to put it in the repository, but to remove one you need to do a Remove and a Commit Parent Folder (of Commit Folder on the repository as a whole) to really have it removed from the repository. In retrospect that actually makes sense (like some many other things do :-)
Ren�
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