Sgroup, SuperatomSgroup, SgroupAtom, ...

Do you have any documentation (other than what I can find in the API) on how to use the Sgroup, SuperatomSgroup, and SgroupAtom classes? What they are supposed to be used to represent, how they interact with one another, how to add them to or remove them from existing molecules, etc.?





And what are a DataSgroup and a MultipleSgroup?

Hi Bob,





Unfortunately, we don't have any documentation other then the APIDOC on how to use Sgroups. All the handling, adding, removing, interaction of Sgroups is quite complex, we could describe this with a tutorial-like description and with a few code examples. We will try to prepare this for Marvin 5.0.2.





The basic principle of Sgroups is to create a group from a set of atoms and bonds. The Sgroup contains a graph with atoms and bonds. You can add different attributes to this graph, in this case you will get a subtype of the Sgroup: SuperatomSgroup, MultipleSgroup, DataSgroup...


Now all the Sgroup types defined in Ctfile are implemented and we use Sgroups for more purposes, for example to represent frequency variation (RepeatingUnitSgroup), markush structures (MulticenterSgroup) and coordination compounds (MulticenterSgroup).

Quote:

And what are a DataSgroup and a MultipleSgroup?...

Multiple Sgroups are used to represent a repeating part in a structure with a shorter form.


DataSgroups are used to represent an attached data to a structure. You can try to create this in Marvin by selecting one or more atoms, and then select menu item Structure->Add->Data...


SuperatomSgroups (abbreviated groups) are used to represent a part of a structure with a text abbreviation. You can retrieve the hidden structure from the text abbreviation with the "Expand" function and hide the structure with the "Contract" function in Marvin Sketcher. The Sgroupatom is the atom that you can see in Marvin Sketcher if the SuperatomSgroup is in contrated state.





Regards,


Erika.

Hi,


I am also very interested to get a documentation how to use the Sgroups. In an earlier topic (http://www.chemaxon.com/forum/ftopic3420.html) I asked "What does the little asterisk in the amino acid templates mean" and I got the answer "The asterisk shows the attachment point for the Sgroup".





The amino acid templates changed from Marvin 4.1.13 as "normal" molecules to Marvin 5.0.0 to "Sgroup" fragments (Why has alanine one asterisk and arginine two asterisks?). And to get "normal" molecules you have to use Structure-Group-Ungroup.





By the way: The amino acid templates should be presented in another structur formula: The NCC-chain in the drawing plane and the R-group bonded with a wedge bond. So it would be easy to build a peptide chain in the so called NCC-chain-formulas. But this is another topic.





Regards, Hans-Ulrich

Hi,





please apologize, it was a mistake of me: I cannot reproduce the two asterisks at arginine.





Regards, Hans-Ulrich

Erika wrote:

Unfortunately, we don't have any documentation other then the APIDOC on how to use Sgroups. All the handling, adding, removing, interaction of Sgroups is quite complex, we could describe this with a tutorial-like description and with a few code examples. We will try to prepare this for Marvin 5.0.2.

Yes, we noticed the complexity. ;-)





We are interested in code that substitutes an R group in a Molecule with an Sgroup of our choice. The bond between R and its attached atom would be replaced by a bond between the attached atom and the attachment point of the S group.

Hi,

Quote:

The amino acid templates changed from Marvin 4.1.13 as "normal" molecules to Marvin 5.0.0 to "Sgroup" fragments. And to get "normal" molecules you have to use Structure-Group-Ungroup.

You can set the state of the Sgroup from the Groups menu in the Template Library dialog. If you set it to "Ungroup"


you will get the old behavior. The old default behavior was "Ungroup" now it's changed to "Expand".

Quote:

The amino acid templates should be presented in another structure formula:The NCC-chain in the drawing plane and the R-group bonded with a wedge bond. So it would be easy to build a peptide chain in the so called NCC-chain-formulas.

Could you send us an example for the "peptide chain in the so called NCC-chain-formulas", please?





Regards,


Erika

Hi Erika,





I posted the building of peptides in NCC formulas in the new topic "Building Peptides by Adding Amino Acids ( NCC formulas )":


http://www.chemaxon.com/forum/ftopic3526.html





Regards, Hans-Ulrich





PS: Can you transport this topic form "Structure based prediction and Chemical Terms" to "Structure editing, viewing and file formats" ? After submitting it, I found it would be better in the second topic list.