[Jmol-developers] [ jmol-Bugs-3168380 ] 12.1.xx prereleases not reading multi-model CIFs

[SourceForge.net <no...@so...>]

Bugs item #3168380, was opened at 2011-01-30 16:03
Message generated for change (Comment added) made by hansonr
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3168380&group_id=23629

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: File Input/Output
Group: None
Status: Open
>Resolution: Fixed
Priority: 5
Private: No
Submitted By: Simon Westrip (publcif)
Assigned to: Bob Hanson (hansonr)
Summary: 12.1.xx prereleases not reading multi-model CIFs

Initial Comment:
Current prerelease versions are failing to read CIFs that contain more than one structure:

java.lang.NullPointerException
        at org.jmol.adapter.readers.cifpdb.CifReader.createBonds(Unknown Source)
        at org.jmol.adapter.readers.cifpdb.CifReader.setBondingAndMolecules(Unknown Source)
        at org.jmol.adapter.readers.cifpdb.CifReader.applySymmetryAndSetTrajectory(Unknown Source)
        at org.jmol.adapter.readers.cifpdb.CifReader.initializeReader(Unknown Source)
        at org.jmol.adapter.smarter.AtomSetCollectionReader.readData(Unknown Source)
        at org.jmol.adapter.smarter.SmarterJmolAdapter.getAtomSetCollection(Unknown Source)
        at org.jmol.viewer.FileManager$FileReader.run(Unknown Source)
        at org.jmol.viewer.FileManager.createAtomSetCollectionFromFile(Unknown Source)
        at org.jmol.viewer.Viewer.getAtomSetCollection(Unknown Source)
        at org.jmol.viewer.Viewer.loadModelFromFile(Unknown Source)
        at org.jmol.script.ScriptEvaluator.load(Unknown Source)
        at org.jmol.script.ScriptEvaluator.instructionDispatchLoop(Unknown Source)
        at org.jmol.script.ScriptEvaluator.evaluateCompiledScript(Unknown Source)
        at org.jmol.viewer.Viewer.evalStringWaitStatus(Unknown Source)
        at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runScript(Unknown Source)
        at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.runNextScript(Unknown Source)
        at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(Unknown Source)
        at java.lang.Thread.run(Unknown Source)


----------------------------------------------------------------------

>Comment By: Bob Hanson (hansonr)
Date: 2011-01-31 06:33

Message:
OK, I found it. Affects 12.1 only, not 12.0. Fixed for Jmol 12.1.33 --- see
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip

----------------------------------------------------------------------

Comment By: Bob Hanson (hansonr)
Date: 2011-01-30 22:17

Message:
I'll need an example file; the ones I have work fine.

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3168380&group_id=23629