Hi Miguel,
you are fast!
On Oct 21, 2004, at 1:56 PM, Miguel wrote:
Miguel & Rene wrote:
Or am I missing something here?
I think so :-)
Actually, I think everything you had was good.
Great.
Maybe we should keep an instance of it in the SmarterModelAdapter class?
I did commit what I did, so you can see it.
OK, I will take a look.
I may make some changes and check them in ... so you should refrain from
making any more mods until I send you another email.
I checked in a bunch of changes:
ModelResolver.java -> Resolver.java ModelAdapter.java -> JmolAdapter.java SmarterModelAdapter.java -> SmarterJmolAdapter.java CdkModelAdapter.java -> CdkJmolAdapter.java FrameExporetModelAdapter.java -> FrameExportJmolAdapter.java
In JmolAdapter.java:
- all uses of the word "model" are gone from methods and variables
- we now have getAtomSetCount(), getAtomSetNumber(), getAtomSetName(),
and getAtomSetProperties()
Properties, so some time in the future you want me to put a java.util.Properties atomSetProperties field in the AtomSetCollection?
I'll hold off on that until I have some of the AtomSetName stuff going.
These are generally not implemented.
References to "Model" in the AtomIterator have been renamed to AtomSet.
Within the org.jmol.adapter.smarter package I did not change most of the
variable names that contain 'model' ... that is your job.
OK. But I assume that you I should stay away from the Atom.modelNumber?
I am no longer working on these files and you can work on them.
OK. I checked them out.
Finally, I uncovered something that is important.
The AtomSetCollection class does not have support for atomSetCount. We *must* add this. But it may require touching several Reader implementations ... so I need to think about the best way to do it.
Indeed. I was wondering whether we'd need to use an addAtomSet method, but since we really do not have an AtomSet class, that would be confusing.
Maybe a protected int newAtomSet() method which would increase the atomSetCount and return it. This atomSetCount could/should then be used for the atom.modelNumber (or really atomSetNumber) in the atoms added/duplicated.
What bothers me, is that we can not really enforce that the atomSetCount is indeed the number used for associating both the atoms and the atomSetName for a particular AtomSet. If the AtomSet were a class, we could. I think...
On the other hand, are there readers that want or need to have direct control over the atomSetNumber used for an AtomSet's atoms? The computational chemistry ones would not, but maybe some of the other ones that I am not too familiar with, may (e.g., Cml or Pdb ones).
Ren�
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