Miguel,
I added the AtomSetProperties array and methods for it to the AtomSetCollection. I also added some methods to the AtomSetCollection to deal with them.
I think they work.
I only implemented dealing with them (i.e., setting them) in the GaussianReader.
Once we have this more stable, I can start modifying the other readers to retain more information about the AtomSets read.
I noticed that it may be tricky to copy a Properties when you clone an AtomSet, which I really think we should consider, otherwise the name 'clone' is a bit misleading (since at the moment it really only clones the Atoms that are associated with that AtomSet).
Another thing I was wondering. We have a cloneFirstAtomSet and a cloneLastAtomSet. These would only play a role in the computational chemistry files, so if we are not discarding previously read atoms any more, one should only use the cloneLastAtomSet (since the first atom set may not have the same geometry as the one that the frequencies are for). I'll look into that when I start working on those file readers...
Ren�
On Oct 29, 2004, at 4:42 PM, Miguel wrote:
I did look at the code a bit and saw some comments about getAtomSetCount not been implemented. It looks to me like you did,
I think that it is implemented at the wrapper layer, but the individual readers are not implementing it. But maybe I have forgotten ... maybe I implemented all of it.
but
I have a question about why you did it differently than how the other
atomsetCollection fields (like fileHader, collectionName etc.) are
accessed from the SmarterJmolAdapter. You return the value by calling a
get method, as opposed to directly accessing the field. Show we do it
one way or another or do you feel that mixing the approaches up is
fine?
Don't know. I don't think it matters that much. If you want to change it
then you can.
Miguel
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