RGroupDecomposition API question

Hi,

I would like to do RGroupDecomposition. The user inputs a query scaffold with the exit vectors labelled "R1", "R2", etc. Decomposition should then only take place at the user-defined exit vectors. What parameters should I use for this setup?

Next, I would like to have the attachment points of the resulting "ligands" also labeled with R1, R2, etc, when I convert them to images.

I checked the API examples but couldn't get the ligands back with r-labels.

Any suggestions? A small code example would be helpful.

Thanks and best regards,

Daniel

I would like to do RGroupDecomposition. The user inputs a query scaffold with the exit vectors labelled "R1", "R2", etc. Decomposition should then only take place at the user-defined exit vectors. What parameters should I use for this setup?

You should call RGroupDecomposition.addHydrogens(Molecule query) for the query in the current version but this will be the default behavior in the next major release 5.3. Actually there will be 3 options: R-atoms matching heavy atom group / heavy atom group or hydrogen / heavy atom group or hydrogen or the empty set, and the first (heavy atom group) will be the default.

Next, I would like to have the attachment points of the resulting "ligands" also labeled with R1, R2, etc, when I convert them to images. I checked the API examples but couldn't get the ligands back with r-labels.

Labelling with R-atom ID (1 for R1, 2 for R2, ...) is possible in atom maps or atom labels, but the atom map is not seen when converted to image, therefore I suggest to use atom labels:
RGroupDecomposition.setAttachmentType(RGroupDecomposition.ATTACHMENT_LABEL)
Writing explicitly "R1", "R2" in the atom label is not possible but if it is needed then I can just as well add this option in the 5.3 release.

Any suggestions? A small code example would be helpful.

An example is attached:

java RGDecompTest query.mrv target1.mrv

produces 3 image files for the 3 R-ligands,

java RGDecompTest query.mrv target2.mrv

produces no hits because there is an unmatched ligand in the target.

Documentation:

http://www.chemaxon.com/jchem/doc/user/RGroupDecomposition.html

http://www.chemaxon.com/jchem/doc/guide/rgdecomp/index.html

 

API:

http://www.chemaxon.com/jchem/doc/api/chemaxon/sss/search/RGroupDecomposition.html

 

There will be changes in RGroupDecomposition in the 5.3 release.

Dear Nora,

Many thanks for all your infos.

It would be great if you could add and option for drawing explicit "R1", "R2", etc, labels to the 5.3 release.

Best regards,

Daniel

R1, R2, ... labelling mode will be included in th 5.3 release.