Reaction Decoder Mapper

Perform Atom-Atom Mapping (AAM) using the Reaction Decoder Tool from the EBI. This node is based on the CDK version bundled within the RDT-2.2.0-SNAPSHOT-jar-with-dependencies library which was built from source after modifications to the library including:
  1. Returning the BufferedImage object
  2. Catch scaling exception on reactions without bonds
  3. Make annotator method public to allow access
No changes to the mapping algorithm have been made.

You must ensure that the reactions provided have structures in kekule form to avoid aromatisation issues.

Reaction centre image: reaction centres are highlighted in pink and neighbouring atoms in green

Reaction highlight image: the mapping of reactant to product is colour coded via the highlight


The unmapped reaction in SMILES or MDL Rxn format.

Input Ports

A table containing unmapped reactions in SMILES or RXN format.

Output Ports

Appended mapped reactions in RXN format.


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