#AAMTool
Perform Atom Atom Mapping (AAM) on a balanced biochemical reaction (supported I/O formats are SMILES/RXN) catalysed by enzymes. This tool is also used in generation AAM for EC-BLAST. The knowledge of AAM is used to reconstruct metabolic pathways, understand bond changes in a reaction and compare reactions etc.
###Please cite:
Rahman, S.A. et.al. EC-BLAST: A Tool to Automatically Search and Compare Enzyme Reactions
Nature Methods 11, 171โ174 (2014) doi:10.1038/nmeth.2803 http://www.nature.com/nmeth/journal/v11/n2/abs/nmeth.2803.html
###How To Run?
java -jar ReactionDecoder.jar -Q SMI -q "[O]=C[CH2]CH[CH3].[H][OH]>>[H][O]C[CH2]CH[CH3].[O]=C[CH2]CH[CH3]" -g -j AAM -f BOTH -m
java -jar ReactionDecoder.jar -Q RXN -q example.rxn -g -j AAM -f BOTH -m
######Note: This code is compatible to JVM 7.0+
###Key Features
--Atom Atom Mapping (AAM) on enzymatic reactions.
--SMILES/RXN files supported for I/O.
--Generate image of the mapped reaction.
--Generate reaction patterns and bond change fingerprints.
###License
The ReactionDecoder is licensed under Creative Commons (CC) license.
https://github.com/asad/AAMTool/tree/master/bin/ReactionDecoder.jar