User 4caaa3dd84
11-02-2009 23:14:01
Hello out there!
I just noticed (after some time of frustration), that it's impossible to copy/paste structures, which have contracted groups in it!
This said, I'm not able to paste an example here - just create a carbon chain, make on carbon atom a superatom and try to copy your carbon chain - it won't work :-(.
I assume this is a problem of cml?
thanks,
pheidrias
PS: Is there any possiblity to draw superatoms directly (e.g, drop them from a selection and put them directly to the screen like atoms)?
User 4caaa3dd84
12-02-2009 16:46:44
Hello Akos,
I think the problem results from, that I only select one atom to group it.
1.) - draw a chain of 4 cabon atoms
2.) - select the second carbon atom
3.) - group it (name it, superatom selection)
and now try to copy it --> in my case this fails and when I today wanted to open my drawing from yesterday, I got:
"Cannot read molecule 1"
with
Code: |
"java.lang.NullPointerException"
at chemaxon.struc.MoleculeGraph.setEdge(Unknown Source)
at chemaxon.struc.CGraph.insertEdge(Unknown Source)
at chemaxon.struc.sgroup.SuperatomSgroup.expand(Unknown Source)
at chemaxon.struc.Sgroup.setXState(Unknown Source)
at chemaxon.struc.Sgroup.setGUIStateRecursively(Unknown Source)
at chemaxon.struc.sgroup.SuperatomSgroup.setGUIStateRecursively(Unknown Source)
at chemaxon.struc.Molecule.setGUIContracted(Unknown Source)
at chemaxon.marvin.io.formats.cml.MrvImport.readDocument(Unknown Source)
at chemaxon.marvin.io.MRecordImporter.readDoc(Unknown Source)
at chemaxon.marvin.common.swing.modules.LoadSave.open(Unknown Source)
at chemaxon.marvin.common.swing.modules.LoadSave.run(Unknown Source)
at java.lang.Thread.run(Thread.java:636)
|
The point, why I want to groups just one atom is, that I needed a "Any Metal"-Atom. If I choose the predefined groups (from your query options etc.), they are always italic character. So I found this workaround (renaming a copper atom to "M1") very practical - not having the premonition of that my drawing will break down...
ChemAxon 990acf0dec
12-02-2009 19:56:51
Hi Guntram,
Now I could reproduce the bug, thanks for the report. We will repair it soon.
On the other hand, for your purpose I think an Alias atom is better than an S-group.
You can define an Alias atom by typing its alias (what you want to appear instead of the atom label) in the Value field of the Query tab of the Periodic Table dialog, then click on the Alias button above it, and then on the atom.
Best regards,
Akos
User 4caaa3dd84
12-02-2009 20:20:00
Hi Akos,
this is a good thing. After having done this, is there any possiblity to reach this defined alias again (instead of copy-pasting the first created one)? Like putting it into "My Templates"?
When you are going to fix the "one Atom"-problem, can you maybe also think on increasing the number of "Attachment points"? It seems to accept only 2 of them per group. But Metals do reach up to 12 (or even more?) coordinations...this would open a wide gate to the group of frustrated inorganic chemists, who never can draw even simple molecules correctly with standard drawing software!
Thanks a lot,
pheidrias
ChemAxon 5433b8e56b
29-06-2009 22:58:56
Hi Guntram,
We have made a partial fix to the "one Atom" problem before the redesign of the whole S-Group handling. You can use the fix with 2D molecules in mrv format from version 5.2.3. We inform you when the redesign is ready, and more than two "Attachment Point" are also available.
Best Regards,
Istvan