Improper mapping values when using Map/Map Reaction

Hello,

I am having an issue with the reaction mapping while using JChem Standardizer (Version 5.6, I believe).  I am trying to map the atoms on both sides of a reaction (to be able to deduce changes.) Some files seem fine but others, like the one I have attached, end up with weird results. In the output I attached, the numbering continues from one side of the reaction to another, with the end result that every atom has its own mapping number. I'm not sure why this happens - is this a known issue with Standardizer mapping? Is there a bug, or some limit in terms of what reactions can be successfully mapped? Any guidance would be appreciated.

I have tried both the Map and Map Reaction atoms, together and separately. (To be honest though, I don't know what the difference is.)

Thank you,

Alex

Hello Alex,

The found issue is a known problem; Reactions are mapped by the automapper tool, which sometimes does not calculate map numbers well.

Therefore, we have developed a new automapper tool; This new, improved automapper will be released in version 6.0, planned for end of May.

The difference between map and map reaction is the following:

Action "Map": maps molecules, multifragmanet molecules, and reactions as well. Reactions are mapped by the automapper tool.

Action "Map Reaction":  maps only reactios (using automapper); it does not map molecules or multifragmanet molecules.

Thus, in case of reactions, both actions should result in the same output.

Also, there was a known issue in this behavior that we fixed in version 5.11.4:
"Action "Map" did not consider reactions; reaction files were mapped as multicomponent files."

Please, find attached your reaction - mapped by the new automapper tool.

Best regards,

Viktoria

Thank you for your reply Viktoria, and thank you for providing a correct file! I look forward to this update.

Would it be possible to know which algorithm the updated AutoMapper will implement? I have been doing research into various mapping algorithms and it would be beneficial for me to understand which one the tool I am using implements.

The updated automapper implements a mixed algorithm, which
applies maximum common substructure search and a custom implementation.