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copy/paste of contracted groups impossible?
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Guntram

Joined: 04 Feb 2009
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Link to postPosted: Thu Feb 12, 2009 12:14 amPost subject: copy/paste of contracted groups impossible? Reply with quote

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)?
Akos
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Link to postPosted: Thu Feb 12, 2009 8:26 amPost subject: Re: copy/paste of contracted groups impossible? Reply with quote

Hi Guntram,
Quote:
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 cannot imagine this, and from the above description I cannot find out what you did (what kind of superatom you defined?). I assume you either defined the group in a wrong way (I mean it did not result in an a real S-group), or something is wrong during your copy/paste action (e.g. you use Copy As with a wrong option, or you paste the structure not in Marvin), otherwise the group definition could be pasted.

Please write down step by step what did you do, and then we probably can help.
In addition, please try the following:
1. Draw a structure
2. Select the whole structure
3. Right-click -> Group
4. Choose the Superatom type, and type in a name, then select OK
5. Right-click (either on the canvas or on the structure) -> Contract
6. Select the contracted group, then push Ctrl+C
7. Push Ctrl+V then click somewhere on the canvas
8. Right-click on the pasted superatom, and select Expand
Quote:
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)?.
Yes: if you add a superatom to MyTemplates (through right-click, or drag&drop to the bottom toolbar) this can later be used as template, plus it appears in the abbreviated groups list, so if type its name on the canvas, you can put it down directly. Please note, that if you want to create substituent S-groups similar to Ph or BOC, you have to define the attachment point as well. For further details please refer to the documentation:

http://www.chemaxon.com/marvin/help/sketch/sketch-basic.html#howto-draw.sgroups


Best regards,

Akos
Guntram

Joined: 04 Feb 2009
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Link to postPosted: Thu Feb 12, 2009 5:46 pmPost subject: Reply with quote

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...
Akos
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Link to postPosted: Thu Feb 12, 2009 8:56 pmPost subject: Reply with quote

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
Guntram

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Link to postPosted: Thu Feb 12, 2009 9:20 pmPost subject: Reply with quote

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
Akos
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Link to postPosted: Fri Feb 13, 2009 2:00 pmPost subject: Reply with quote

Quote:
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"?


Yes, if you place it to MyTemplates, you can use it later. But use the right click -> Add to MyTemplates option, because for some reason with drag&drop the alias atom disappears from the template (this is a bug that we will repair soon). But the first option might also be useless for you now, because even though the alias atom is there (it appears when you place the template on the canvas), presently (due to probably the same bug) it is not displayed in the template nether on the MyTemplate toolbar, nor in the Template Library.
Quote:
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!


This feature request is already on our list, but it requires quite a big redesign in the S-groups, in the Template Library, and also in the Markush enumeration tool, so it will not come very soon (probably only in version 6.0).


Best regards,

Akos
István
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Link to postPosted: Mon Jun 29, 2009 11:58 pmPost subject: Reply with quote

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

Guntram

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Link to postPosted: Tue Jun 30, 2009 10:48 amPost subject: Reply with quote

This is good news!


Thank you!

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