Feature Requests item #1878094, was opened at 2008-01-23 07:19
Message generated for change (Comment added) made by hansonr
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Category: New IO Format
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Rene Kanters (rkanters)
Assigned to: Bob Hanson (hansonr)
Summary: Spartan spinput format
Initial Comment:
Hi,
I was wondering whether it is possible to start supporting the Spartan spinput
format (which can be created in the windows version of Spartan).
It seems very similar to the Odyssey format and in my cases where I have
molecules that have a positive charge and S = 1, I have the line 1 2 in the
file. If I change this to a 0 1, which is what triggers the resolver to
conclude that it is an Odyssey file, the file is read properly.
I noticed the email this morning to force load to interpret a file as a cif
(where the resolved tripped up), and was wondering whether it maybe possible to
resolve this problem/feature request in a similar way too?
Thanks,
René
Just in case somebody is wondering I'll include a spinput file with this request
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>Comment By: Bob Hanson (hansonr)
Date: 2008-02-05 11:10
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try updating again, and do a clean build.
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Comment By: Rene Kanters (rkanters)
Date: 2008-02-05 10:54
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Hi,
I just did an update in Eclipse to get the latest modifications, but when
I run Jmol I now get the following message:
ffa185198:~/Projects/Eclipse/Jmol-datafiles/spinput rkanters$ jmol
splash_image=jar:file:/Users/rkanters/Projects/Eclipse/Jmol/build/Jmol.jar!/org/openscience/jmol/images/Jmol_splash.jpg
history file is /Users/rkanters/.jmol/history
using Smarter Model Adapter
(C) 2007 Jmol Development
Jmol Version 11.5.4 2007-12-20 00:37
java.vendor:Apple Computer, Inc.
java.version:1.5.0_13
os.name:Mac OS X
memory:4.3/6.0
appletId:
uncaught exception: java.lang.NoSuchMethodError:
org.jmol.g3d.Graphics3D.getFont3D(I)Lorg/jmol/g3d/Font3D;
java.lang.NoSuchMethodError:
org.jmol.g3d.Graphics3D.getFont3D(I)Lorg/jmol/g3d/Font3D;
at org.jmol.shape.Measures.initShape(Unknown Source)
at org.jmol.shape.Shape.initializeShape(Unknown Source)
at org.jmol.modelset.ModelSet.allocateShape(Unknown Source)
at org.jmol.modelset.ModelSet.loadShape(Unknown Source)
at org.jmol.modelset.ModelLoader.finalizeShapes(Unknown Source)
at org.jmol.modelset.ModelLoader.initializeModelSet(Unknown
Source)
at org.jmol.modelset.ModelLoader.<init>(Unknown Source)
at org.jmol.viewer.ModelManager.zap(Unknown Source)
at org.jmol.viewer.Viewer.zap(Unknown Source)
at org.jmol.viewer.Viewer.setAppletContext(Unknown Source)
at org.openscience.jmol.app.Jmol.<init>(Unknown Source)
at org.openscience.jmol.app.Jmol.<init>(Unknown Source)
at org.openscience.jmol.app.Jmol.getJmol(Unknown Source)
at org.openscience.jmol.app.Jmol.main(Unknown Source)
Exception in thread "main" java.lang.NullPointerException
at org.openscience.jmol.app.Jmol.main(Unknown Source)
so something got broken.
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Comment By: Bob Hanson (hansonr)
Date: 2008-02-05 07:52
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OK, that's checked in for 11.5.4 now.
a) ignore comment lines starting with "C "
b) check to see that next line starts with " "
c) skip one line; check next line for exactly two integers -- charge and
spin
d) check next line for exactly four numbers
Please test using negatively charged species.
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Comment By: Rene Kanters (rkanters)
Date: 2008-02-03 14:49
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The line is basically contains the charge and spin multiplicity (in that
order), so the checked in modification of determining whether there are two
tokens both of which evaluate to a value larger or equal to 0 would only
work for neutral or positive charged ions (not negative ones).
I didn't dare to mess with the logic of determining the file format
because I wasn't sure what unanticipated consequences my modifications may
have on recognizing other file formats, but if it is OK to just verify that
the first value is integer and the second larger or equal to 0 the
recognition should work.
Thanks,
René
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Comment By: Bob Hanson (hansonr)
Date: 2008-02-01 22:57
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What are the options for that line? Anything else besides 0 1 and 1 2 ?
This is fixed now for 11.5.4 for those two options, which will be released
soon. If other options are possible, then you will have to force the
Odyssey reader using:
load odyssey::filename.spinput
Otherwise Jmol will think this is a MOL file.
Bob Hanson
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