Bob
I have emptied both the Java cache in my PC and the browser cache (IE11 with
java plugin), and get
exactly the same behaviour from the Jmol_S applet. I get the same error
message if I try
label %[cipRule]
and no labels are produced. Normal default atom labelling works as usual, so
the error seems to be in the
chirality stuff.
If I use the JSmol applet, I get a different behaviour in IE11. I get a
message box saying
RangeError: Argument list too large to apply
This message comes up twice. After OKing it for the second time, the
chirality labels appear only on the
rule 1a atoms.
A following
label %[cipRule]
command then works straightaway, but still labels only the rule 1a atoms.
If, after refresh, I give the two commands in the opposite order, I still get
the two error messages on the
first command, and no error messages on the second. The labelling each does
is the same for each,
whatever the order.
JSmol in Firefox in the PC gives a bit more explicit error message:
RangeError: arguments array passed to Function.prototype.apply is too large
Otherwise its behaviour is the same as in IE11.
Jmol_S in Firefox with Java plugin fails in the same way as IE11 with Java,
either using
Firefox in the PC or Firefox in Linux.
JSMol in Firefox in Linux works fine, as does JSMol in Chrome in the PC.
I guess that you may have used one of these for your tests.
As for Jmol.jar as an application in Linux, I was able to get some more
information from the
Java Jmol Console.
It seems to show that the cache had been emptied, twice, and that loading of
the model was normal.
When I gave the
label %[chirality]
command, the Java Jmol Console then showed a considerably more explicit error
message series, which
I send as a DOS text attachment.
As I said yesterday, no labels were produced.
Bruce
From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: 08 June 2017 04:35
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Jmol 14.18.1
You will have to clear your cache.
On Wed, Jun 7, 2017 at 11:43 AM, Bruce Tattershall
<bruce.tattersh...@newcastle.ac.uk<mailto:bruce.tattersh...@newcastle.ac.uk>>
wrote:
Sorry Bob, but this version fails to do any chirality labelling for me, for
either of my two models which you
looked at yesterday.
The following is copied from the Jmol Script Console:
label %[chirality]
script ERROR: java.lang.AbstractMethodError:
org.jmol.modelset.Atom.getEdges()[Lorg/jmol/util/SimpleEdge;
org.jmol.shape.Labels set label
Bruce
From: Robert Hanson [mailto:hans...@stolaf.edu<mailto:hans...@stolaf.edu>]
Sent: 07 June 2017 14:15
To: jmol-users@lists.sourceforge.net<mailto:jmol-users@lists.sourceforge.net>
Subject: [Jmol-users] Jmol 14.18.1
Jmol.___JmolVersion="14.18.1" // 2017.06.06
Jmol-14.18.1-binary.zip (69.8
MB)<https://sourceforge.net/projects/jmol/files/latest/download?source=files>
new feature: WRITE SDF writes > <.... user data
-- can be set using MODEL PROPERTY "molData" x where x is an associative
array
-- can be read using _M.molData
new feature: associativeArray.pop() -- clears associativeArray
new feature: assArray1.push(assArray2) -- adds all key/value entries in
assArray2 to assArray1.
new feature: assArray1 + assArray2 -- adds all key/value entries into a new
associative array. (Complements a1 - a2)
bug fix: CIP misses Rule 4b cases where a branching atom has R or S chirality.
-- see test_bt_P4.mol and test_bt_O3.mol (BH64.65 and BH64.66)
-- see AY236.179 (3D structure was diasteriomer, so I missed that)
bug fix: WRITE MOL should not generate > <JMOL_PARTIAL_CHARGES> because it is
not SDF format
bug fix: WRITE SDF should generate > <JMOL_PARTIAL_CHARGES> with a trailing
space
bug fix: (SMILES) targetString.find("SMILES",patternString) will fail for
.[C@H]2 (new group and attached to a connection number)
bug fix: SHOW CHEMICAL SMILES fails when logLevel is set > 4
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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
vwr handling error condition: java.lang.AbstractMethodError:
org.jmol.modelset.Atom.getEdges()[Lorg/jmol/util/SimpleEdge;
java.lang.AbstractMethodError:
org.jmol.modelset.Atom.getEdges()[Lorg/jmol/util/SimpleEdge;
at org.jmol.symmetry.CIPChirality.addSmallRings(CIPChirality.java:790)
at org.jmol.symmetry.CIPChirality.getSmallRings(CIPChirality.java:771)
at
org.jmol.symmetry.CIPChirality.getChiralityForAtoms(CIPChirality.java:468)
at
org.jmol.symmetry.Symmetry.calculateCIPChiralityForAtoms(Symmetry.java:777)
at
org.jmol.modelset.ModelSet.calculateChiralityForAtoms(ModelSet.java:4118)
at
org.jmol.modelset.ModelSet.getAtomCIPChiralityCode(ModelSet.java:4108)
at org.jmol.modelset.Atom.getCIPChirality(Atom.java:1416)
at org.jmol.modelset.Atom.atomPropertyString(Atom.java:1365)
at
org.jmol.modelset.LabelToken.appendAtomTokenValue(LabelToken.java:632)
at
org.jmol.modelset.LabelToken.formatLabelAtomArray(LabelToken.java:275)
at org.jmol.shape.Labels.setLabel(Labels.java:474)
at org.jmol.shape.Labels.setProperty(Labels.java:166)
at
org.jmol.viewer.ShapeManager.setShapePropertyBs(ShapeManager.java:202)
at org.jmol.viewer.ShapeManager.setLabel(ShapeManager.java:192)
at org.jmol.script.ScriptEval.cmdLabel(ScriptEval.java:4163)
at org.jmol.script.ScriptEval.processShapeCommand(ScriptEval.java:2689)
at org.jmol.script.ScriptEval.processCommand(ScriptEval.java:2266)
at org.jmol.script.ScriptEval.commandLoop(ScriptEval.java:2251)
at org.jmol.script.ScriptEval.dispatchCommands(ScriptEval.java:2114)
at org.jmol.script.ScriptEval.executeCommands(ScriptEval.java:417)
at
org.jmol.script.ScriptEval.evaluateCompiledScript(ScriptEval.java:403)
at
org.jmol.script.ScriptManager.evalStringWaitStatusQueued(ScriptManager.java:362)
at org.jmol.viewer.Viewer.evalStringWaitStatusQueued(Viewer.java:3850)
at
org.jmol.script.ScriptQueueThread.runNextScript(ScriptQueueThread.java:111)
at org.jmol.script.ScriptQueueThread.run1(ScriptQueueThread.java:78)
at org.jmol.thread.JmolThread.run(JmolThread.java:105)
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