Bugs item #1192487, was opened at 2005-04-29 17:32
Message generated for change (Comment added) made by nicove
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>Category: File Input/Output
Group: CVS
>Status: Closed
>Resolution: Fixed
Priority: 5
Submitted By: Nicolas (nicove)
Assigned to: Nobody/Anonymous (nobody)
Summary: NullPointerException in Monomer.scanForOffsets
Initial Comment:
I already posted the problem in the Jmol developers list.
I don't know what to do for this problem.
The file causing problem is in Jmol-web:
fah/projects/p2003.xyz.gz
FileManager.openFile(../fah/projects/p2003.xyz.gz)
SmarterJmolAdapter:The Resolver thinks:FoldingXyz
openFile(../fah/projects/p2003.xyz.gz) 2804 ms
Exception in thread "Thread-14"
java.lang.NullPointerException
at org.jmol.viewer.Monomer.scanForOffsets
(Monomer.java:81)
at
org.jmol.viewer.AminoMonomer.validateAndAllocate
(AminoMonomer.java:46)
at
org.jmol.viewer.Frame.distinguishAndPropogateGroup
(Frame.java:434)
at org.jmol.viewer.Frame.finalizeGroupBuild
(Frame.java:374)
at org.jmol.viewer.Frame.<init>
(Frame.java:192)
at org.jmol.viewer.ModelManager.setClientFile
(ModelManager.java:73)
at org.jmol.viewer.Viewer.openClientFile
(Viewer.java:1026)
at org.jmol.viewer.Viewer.getOpenFileError1
(Viewer.java:999)
at org.jmol.viewer.Viewer.getOpenFileError
(Viewer.java:984)
at org.jmol.viewer.Eval.load(Eval.java:1651)
at
org.jmol.viewer.Eval.instructionDispatchLoop
(Eval.java:351)
at org.jmol.viewer.Eval.run(Eval.java:291)
at java.lang.Thread.run(Unknown Source)
----------------------------------------------------------------------
>Comment By: Nicolas (nicove)
Date: 2006-03-26 22:16
Message:
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Apparently, it has been fixed (the 3 files are working with
the SVN version). I am closing the tracker item.
----------------------------------------------------------------------
Comment By: Miguel (migueljmol)
Date: 2006-03-26 22:06
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Q: What is the status on this?
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Comment By: Nicolas (nicove)
Date: 2006-03-09 17:53
Message:
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The goal of the foldingxyz reader is to be able to read
files produced by the [EMAIL PROTECTED] client (cf.
http://folding.stanford.edu/ ), so changing the files is not
an option.
Is it needed to assign atomNames in the reader ?
I don't know what rule is used to name the atoms.
----------------------------------------------------------------------
Comment By: Bob Hanson (hansonr)
Date: 2006-03-09 16:58
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The problem is as follows:
1) the FAH files have PDB-like atom IDs, and the foldingxyz
reader is assigning them as atomNames.
2) Jmol uses atomNames to identify important atoms, such as
the alpha carbon or the amide nitrogen. It needs to do this
in order to draw cartoons, find hygrogen bonds, and such. In
doing so, it assigns to them offsets based on number of
records from the first atom oouf each group.
3) Jmol is scanning the atom list for these special atom
IDs, which are supposed to be localized.
4) Because the file isn't organized anywhere close to how a
PDB file is organized, and the offsets are being set to too
high numbers. The biggest "spread" allowed is 254 records (a
byte).
5) In this file, for example, atom 2049 is the first atom
labeled "C", the carbonyl carbon. But the "group" starts at
atom 1 with "N".
I think you have to decide what you want: do you want the
foldingxyz reader to read and save atom names and thus
allow for RasMol rendering? If so, then put these files in
correct order. If not, don't assign atom names to them.
Alternatively, we can provide a simple property that you can
have the foldingxyz reader set when group looking is
inappropriate.
I'm going to check in code that simply flags these errors
and sends a message to the console but doesn't fully abort
the file load.
-Bob Hanson
----------------------------------------------------------------------
Comment By: Nicolas (nicove)
Date: 2006-03-09 07:24
Message:
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I have it on other files, same execption.
The files are in Jmol-web/source/docs/fah/projects, it's
p1485.xyz.gz, p1486.xyz.gz.
I don't understand what's the problem :(
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