Perform Atom Atom Mapping (AAM) on a balanced biochemical reaction.
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README.md

#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, 171–174 (2014) doi:10.1038/nmeth.2803 http://www.nature.com/nmeth/journal/v11/n2/abs/nmeth.2803.html

###How To Run?

using a reaction SMILES as an input:

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

using a reaction RXN file as an input:

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.

Source code and JAR

https://github.com/asad/ReactionDecoder