shortcut groups with multicenter groups?

User 870ab5b546

07-05-2013 15:16:13

I'd like to make a Cp shortcut group.  I tried defining it this way:


Cp  *.c1cccc1 |m:0:1.2.3.4.5|   1

However, when I draw Cp→Ta on the canvas, the multicenter group is no longer present:


[Ta]*.c1cccc1 |C:1.0|

<?xml version="1.0"?>
<cml version="ChemAxon file format v5.10.0, generated by v5.11.5">
<MDocument>
<MChemicalStruct>
<molecule molID="m1">
<atomArray atomID="a1 a2" elementType="R Ta" sgroupRef="sg1 0" x2="-3.416874885559082 -0.7699999809265137" y2="1.6362500190734863 1.6362500190734863"/>
<bondArray>
<bond atomRefs2="a1 a2" convention="cxn:coord"/>
</bondArray>
<molecule id="sg1" role="SuperatomSgroup" title="Cp" molID="m2">
<atomArray atomID="a3 a4 a5 a6 a7 a8" elementType="C C C C C C" attachmentPoint="1 0 0 0 0 0" sgroupAttachmentPoint="1 0 0 0 0 0" mrvQueryProps="A: 0 0 0 0 0" x2="-2.4955112950036478 2.71037487633377 3.956261047671191 3.480374876333773 1.940374876333772 1.4644887049963522" y2="3.2725000381469727 4.582502283009115 3.6773129944787066 2.2126859593841695 2.212685959384168 3.677312994478705"/>
<bondArray>
<bond atomRefs2="a4 a5" order="A"/>
<bond atomRefs2="a5 a6" order="A"/>
<bond atomRefs2="a6 a7" order="A"/>
<bond atomRefs2="a7 a8" order="A"/>
<bond atomRefs2="a4 a8" order="A"/>
</bondArray>
</molecule>
</molecule>
</MChemicalStruct>
</MDocument>
</cml>

Is there any way I can fix this problem?  If not, can you make it a feature request?

ChemAxon d26931946c

08-05-2013 09:48:30

Hi Bob,


From 6.0 we will support cxsmiles in the import of our abbreviated group format instead of SMILES and all of it's features will be available in abbrevgroup format too. Note that the export of these groups with cxsmiles is planned to 6.1 only.


Best regeards,


Peter

User 870ab5b546

08-05-2013 19:10:34

So in Marvin 6.0 I will be able to define Cp and draw structures with it, but if I export the structures to MRV, the Cp will automatically be ungrouped.  Correct?  And this flaw will be fixed in 6.1?

ChemAxon d26931946c

09-05-2013 08:46:38

No, exporting to MRV will be fine but you will have to create the


Cp  *.c1cccc1 |m:0:1.2.3.4.5|   1

string manually, you can't create it with molconvert or save it from Marvin. From 6.1 you this will be available if the molecule is saved as Chemaxon Abbreviation.

User 870ab5b546

09-05-2013 14:42:28

Oh, that's fine, I would create it manually anyway.