stoichiometry, collapsing/expanding, atom/atom mapping

[rwst]

a way to display reactions with their stoichometry

expanded or collapseable view of reactions with multiple stoichometry example: 2A + B -> C could be expaned to A + A + B -> C for atom mapping

Have JCP use CDK to guess the best mapping in reactions. The pseudo code is straightforward:

1. match all reactants against all products (the larger the common substructure, the better the match)
2. decide which reactants match against which products
3. then proceed in mapping atoms for each reactant-product pair This will leave gaps of moved atom groups. It is reported to give a surprising variety of possible maps in many reactions and the result is not easy to extract without human moderation. Therefore, it might be guided by mappings manually set by the user, possibly in a interactive manner:
4. give the above method a try
5. if fails, have user select 1 or a few atom atom mappings
6. continue with step 1.

[asad]

A robust reaction handling module would be wonderful.

You might like to try the atom atom mapping module in the ECBlast http://www.ebi.ac.uk/thornton-srv/software/rbl/

[rwst]

Thanks for the link!