reactions that fail to trigger

I have two reactions that trigger when I use the example Reactor JSP page (http://www.chemaxon.com/jchem/examples/reactor/jsp/index.jsp) but not via my java code nor the 'react' command (version 3.1.5). Can you explain this for me?





react "CC1=Cc2ccccc2NC1=O" -r bt0276_droe.mrv


react "CC1=Cc2cc(O)ccc2NC1=O" -r bt0278_droe.mrv





I can also submit my java code if you'd like.

We are investigating the problem and let you know when we know more about it.

This problem is due to an inconsistency in storing of double bond stereo data for ring bonds in various file formats. In SMILES, such bonds are stored as CT (cis-or-trans) while in MRV they are stored as C (cis). This is why our substructure search does not find a hit.





We are working on this but have no solution yet. As a workaround, you can explicitly mark the ring double bond in the MRV reaction as CT with a wiggly bond. I attach the modified reactions:

Code:

react "CC1=Cc2ccccc2NC1=O" -r bt0276.mrv CC1=Cc2cc(O)ccc2NC1=O react "CC1=Cc2cc(O)ccc2NC1=O" -r bt0278.mrv CC1=Cc2c(O)c(O)ccc2NC1=O

Remark: it is better to map the reactant explicit H atom which is removed in the reaction with a unique map.