Reverse substructure search for reactions?

User b7aa615db3

11-09-2004 18:41:59

Substructure search can find all reactions that contain the query structure


as a portion of the target reaction. Is there support for the opposite?





For example, I would like to use the left side of a reaction as the query


and have it return all the reactions whose left side was a subset of the


query. Then, I could apply all those reactions to the query.





Attached is an example query and target that I would like to match.

ChemAxon 9c0afc9aaf

13-09-2004 13:29:49

Hi,





Currently we do not support this search method for database searches.





We plan to add superstructure search, but that is not quite what you need, since your query.rdf is not a superstructure of target.rdf, because there are no products.





However you can use our API to achieve this functionality.


Some guidelines:





- Use MolSearch to perform substructure searches


- Get the reactant from your query.rdf. This will be the target for MolSearch.


- Get the reactant(s) from the target structure (target.rdf). This will be the query for MolSearch.





You should use these methods to get the reactants:





RxnMolecule.getReactantCount()


RxnMolecule.getReactant(int x)

ChemAxon d76e6e95eb

13-09-2004 17:35:39

Would you like to use this feature in your metabolism application, Dave?

User b7aa615db3

14-09-2004 00:34:33

Gyuri wrote:
Would you like to use this feature in your metabolism application, Dave?
Yes we would. Although there are other ways to do this type of matching (as Szilard mentioned), it seems to me that the process mentioned in the original post is the most elegant. And it would be a natural extension to reaction searching.





Thanks for taking an interest in our feedback.

ChemAxon d76e6e95eb

14-09-2004 12:59:54

Just to inform you, we develop a new synthesis algorithm for Synthesizer called exhaustive algorithm (not released yet). It can be interesting for metabolism application developers. If your reaction library contains generic metabolic transformations, then the given compound(s) can be converted by all applicable transformations. This can be continued with each generated metabolite until a termination criteria (provided by you) is fulfilled.





You can try Reactor (the core engine of Synthesizer) online: http://www.jchem.com/examples/reactor/jsp/index.jsp. You will find some reaction examples there, metabolic transformations can also be described in the same format.