Thanks, Miguel,
The scheme below was just for discussion purposes. I just wanted to
know if I had summarized the issues. I see that I forgot Shape Labels.
Anything else? Oh, some translucency, I think.
Basically, I just want to get a handle on what all the objects are and
how their state is described -- if we really wanted to make a
snapshot, what that would consist of. A snapshot might be relatively
opaque to the user, or it might be in human-readable form if space is
not an issue. Or there could be a condensed and an expanded form.
I'm just brainstorming here. Trying to think of an alternative to a
straight script history. Not suggesting at all that it be "exposed".
Rather, just getting a handle on the underlying structure.
I have some ideas that generally condense the BitSet idea, but I have
to think about them some more before I suggest anything.
Bob
Miguel wrote:
I've made a list of the objects I see as pertinent to the
discussion of taking a snapshot of the state of the model.
Just for general interest; I may be missing one thing or
another. The trick would be to somehow encode the critical
information without taking up too much space.
[i] is over frame.atomCount
[j] is over frame.bondCount
"mad" stands for "milliAngstromDiameter"
I do not think that mads should be exposed to the outside. They are for
internal use. Outside users should receive doubles.
"colix" stands for "color index"
colixes should definitely not be exposed to outside users. Outside users
should receive int RGB values OR java.awt.Color objects.
atoms[i]
|
----madAtom
----colixAtom
----translucent
bonds[j]
|
----- order
----- mad
----- colix
shapes
|
----- stars
|
----mads[i]
----colixes[i]
|
----- vectors
|
----mads[i]
----colixes[i]
|
----- dots
|
----dotsConvexMaps[i]
----colixesConvex[i]
----tori[]
----cavities[]
|
----- balls (selector for atoms)
|
----- sticks (selectors for bonds)
|
----hsticks
----sssticks
|
----- sasurface
|
----surfaces[]
|
----- mps (Model-Chain-Polymer-Shape)
|
| includes backbone, cartoon,
meshribbons, ribbons, rockets, strands, trace
|
----mpsmodels[].mpspolymers[].monomers[].mads[]
----mpsmodels[].mpspolymers[].monomers[].colix[]
----mpsmodels[].mpspolymers[].monomers[].translucent[]
|
----- echo (there are only three)
|
----toptext
----middletext
----bottomtext
|
----- hover (there is only one)
|
----atomIndex
----colixBackground
----colixForeground
----font3d
----labelFormat
|
----- measures (up to 16 sets)
|
----Measurement[16]
|
----- SelectionIndependentShape
|
----axes
----bbcage
----uccage
----frank
----polyhedra[]
----meshCollection
|
----isosurface[]
|
----pmesh[]
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Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr
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