On Wed, 2006-11-22 at 23:35 +0100, Egon Willighagen wrote:
> On Wednesday 22 November 2006 23:28, Rajarshi Guha wrote:
> > On Wed, 2006-11-22 at 23:13 +0100, Egon Willighagen wrote:
> > > On Wednesday 22 November 2006 15:20, Rajarshi Guha wrote:
> > > > On Wed, 2006-11-22 at 09:24 +0100, Egon Willighagen wrote:
> > > > > Ah, better use the version in Bioclipse SVN. trunk/bc_jmol
> > > >
> > > > The link above does go to the Bioclipse SVN
> > >
> > > So, does it work for you?
> >
> > No. My previous mail explained the problem.
> >
> > It appears that AtomIterator has a single constructor that takes an
> > IChemModel (or IChemFile?).
> >
> > There is no constructor that takes an IAtomContainer
>
> Ah, indeed. Sorry for being so absent.
>
> Um, yeah, you need to wrap it into a IChemFile. for example, using this code:
>
> MoleculeSet moleculeSet = new MoleculeSet();
> moleculeSet.addMolecule(mol);
> ChemModel model = new ChemModel();
> model.setMoleculeSet(moleculeSet);
> ChemSequence sequence = new ChemSequence();
> sequence.addChemModel(model);
> ChemFile chemFile = new ChemFile();
> chemFile.addChemSequence(sequence);
Aah, thanks. However when I send in a ChemFile object I get the
following error:
Exception in thread "main" java.lang.NullPointerException
at org.jmol.viewer.ModelManager.setShapeProperty(ModelManager.java:380)
at org.jmol.viewer.Viewer.setShapeProperty(Viewer.java:2683)
at org.jmol.viewer.Frame.doAutobond(Frame.java:1479)
at org.jmol.viewer.Frame.initializeModel(Frame.java:368)
at org.jmol.viewer.Frame.<init>(Frame.java:214)
at org.jmol.viewer.ModelManager.setClientFile(ModelManager.java:87)
at org.jmol.viewer.Viewer.openClientFile(Viewer.java:1238)
Is this because I'm using the SVN version of Jmol? When I try and open
the file that I'm using my code with the CLI Jmol it opens and displays
fine
-------------------------------------------------------------------
Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
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A sine curve goes off to infinity, or at least the end
of the blackboard.
-- Prof. Steiner
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