Issues with R1 and R2 when structures come from other tools

Hi,





just a quck note, Reactor 5.1.3.2 has issues when R-groups are imported  from





other packages (ie from PubChem). In such a case the R1 and R2 letters are a





little bit smaller (lo0ok different) and the reaction will be incomplete.














The only solution is to redraw all R1 and R2 rests.





No file to proof, but that solved my issues.














Tobias

For the reproduction, can you please attach an example file here that looks incorrect if I load it?

Hi,





I just copied that structure as SMILES





http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=24701471





and the used it to created some reaction.








I did not have the file anymore (because I fixed it). Sorry. I juste keep for





reference, I had a post with multireaction centers, so maybe Reactor and Fragmenter





got mixed up. But the issue exists (at least for me :-)








http://www.chemaxon.com/forum/ftopic4687.html








Tobias

R-atoms are not known by the SMILES standard. They are available in mol, sdf, mrv and even in the ChemAxon extended SMILES fomat, but not in standard SMILES.


But, anyway, how do you get the SMILES from the page you linked? It contains SDF export feature, but I cannot see SMILES there.

Hi,





I just copied the SDF (bottom of page) and transferred it to MSketch and then did all





the final drawing there including cop/paste to new windows. So the SDF was transferred.





Tobias

Hi Tobias,





I've checked the SDFile on the PubChem link you sent, and the problem is that it is not properly formatted: the R-groups are defined with a "*" atom having an Alias on top of it (i.e. the R1 and R2 groups are only labels). According to the CTFile format documentation (see page 40 at http://www.symyx.com/downloads/public/ctfile/ctfile.pdf) R-groups should be stored in SDFiles (RGFiles) as R# atoms, plus an additional R-group definition line (starting with "M  RGP").





This is why it does not work in Reactor, and you have to redraw the R-groups. So the issue is in PubChem.








Best regards,





Akos

Hi Akos,





thanks for checking, you are absolutely right. The mentioned file is





written as S-group instead of an R-group:


So instead of * * in the PubChem SDF file, which is according





to the S-group definition (but should be an R File). I sent the





error to the NCBI helpdesk.











  -OEChem-03310920172D


 


 24 24  0     1  0  0  0  0  0999 V2000


    5.9819    6.1973    0.0000 *   0  0  0  0  0  0  0  0  0  0  0  0


    5.0000    6.8878    0.0000 *   0  0  0  0  0  0  0  0  0  0  0  0


   10.9310    6.9069    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0


... snip





17 20  1  0  0  0  0


 17 24  1  1  0  0  0


 18 21  1  0  0  0  0


A    1


R2


A    2


R1


M  END


 





 





it should read as follow (MDL V2000 definition, created with Marvin)


which is according to the MDL R-Group definition





 





Marvin  03310917262D         





 





 24 24  0  0  0  0            999 V2000


    3.1900   -2.2842    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0


    2.1750   -1.5739    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0


    8.3062   -1.5520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0


    6.4291   -1.5562    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0


..... snip





 17 20  1  0  0  0  0


 17 24  1  1  0  0  0


 18 21  1  0  0  0  0


M  RGP  2   1   2   2   1


M  END








Tobias