Egon,
Right. "AtomSetCollection" is just an Object as far as Jmol is concerned. It
can be any CDK class you want it to be, as long as your Adapter can read it.
It is opened and processed entirely within the Adapter class. What you would
need to do is patch in some additional information in the form of hashtables
(htParams and the Info objects). As long as you aren't doing anything with
symmetry, it should be pretty straightforward.
I've moved all the code that relates to this into ModelLoader.java -- just
walk your way through that looking for necessary. Primarily you need to
create some HashMaps:
Map<String, Object> info =
adapter.getAtomSetCollectionAuxiliaryInfo(atomSetCollection);
Map<String, Object> modelAuxiliaryInfo =
adapter.getAtomSetAuxiliaryInfo(atomSetCollection, i);
These are now required.
Bob
On Sat, Jan 15, 2011 at 3:04 AM, Egon Willighagen <
[email protected]> wrote:
> On Fri, Jan 14, 2011 at 10:54 PM, Robert Hanson <[email protected]>
> wrote:
> > I see, so you need the intermediate stage, not the actual model. one
> problem
> > was that "openClientFile" was a misnomer -- clearly the actual file by
> then
> > is long closed.
>
> Indeed.
>
> > Where are you getting the AtomSetCollection from?
>
> Well, right now, from nothing much, but we hope to change that again.
> There used to be a bridge between the CDK data model and Jmol... that
> is, there was a CDK implementation of AtomSetCollection. This allowed
> CDK data to be directly visualized in Jmol...
>
> But due to other priorities, I never got around to updating that
> bridge for more recent Jmol releases, up to the point that this now no
> longer seems possible...
>
> Right now, I have commented out the code in Bioclipse, but will need
> to check if this breaks anything in the upcoming 2.6 release. I will
> report soon.
>
> We also want to split how we handle various chemical types: small
> molecules, protein, crystals... I think I'll do that first. That would
> also simplify any resurrection of that old functionality...
>
> Egon
>
> --
> Dr E.L. Willighagen
> Postdoctoral Researcher
> Institutet för miljömedicin
> Karolinska Institutet
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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