use POM.xml and mvn commands to build your project
1) mvn -DskipTests=true install (skip test)
2) mvn install (include test)
3) mvn clean (clean)
4) mvn package
5) mvn -P local clean install -DskipTests=true (fast single jar compilation, skip test)
6) mvn -P local clean install (single jar compilation with test)

public static void main(String[] args) throws CloneNotSupportedException, CDKException, AssertionError, Exception {
        final SmilesGenerator sg = new SmilesGenerator(SmiFlavor.AtomAtomMap);
        final SmilesParser smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance());

        String reactionSM = "CC(=O)C=C.CC=CC=C>>CC1CC(CC=C1)C(C)=O";
        String reactionName = "Test";

        IReaction cdkReaction = smilesParser.parseReactionSmiles(reactionSM);

        IReaction performAtomAtomMapping = performAtomAtomMapping(cdkReaction, reactionName);
        System.out.println("AAM sm: " + sg.create(performAtomAtomMapping));
    }

    /**
     *
     * @param cdkReaction
     * @param reactionName
     * @return
     * @throws InvalidSmilesException
     * @throws AssertionError
     * @throws Exception
     */
    public static IReaction performAtomAtomMapping(IReaction cdkReaction, String reactionName) throws InvalidSmilesException, AssertionError, Exception {
        cdkReaction.setID(reactionName);
        /*
         RMT for the reaction mapping
         */
        boolean forceMapping = true;//Overrides any mapping present int the reaction
        boolean generate2D = true;//2D perception of the stereo centers
        boolean generate3D = false;//2D perception of the stereo centers
        StandardizeReaction standardizeReaction = new StandardizeReaction(); //Standardize the reaction
        ReactionMechanismTool rmt = new ReactionMechanismTool(cdkReaction, forceMapping, generate2D, generate3D, standardizeReaction);
        MappingSolution s = rmt.getSelectedSolution();//Fetch the AAM Solution
        IReaction reaction = s.getReaction();//Fetch Mapped Reaction
        return reaction;
    }

Author: Syed Asad Rahman
e-mail: asad@ebi.ac.uk
c/o EMBL-European BioInformatics Institute (EBI)
WTGC, CB10 1SD Hinxton
UK

Note: The copyright of this software belongs to the author
and EMBL-European BioInformatics Institute (EBI).

java -jar ReactionDecoder.jar -Q SMI -q "CC(O)CC(=O)OC(C)CC(O)=O.O[H]>>[H]OC(=O)CC(C)O.CC(O)CC(O)=O" -g -c -j AAM -f TEXT

java -jar ReactionDecoder.jar -Q SMI -q "O=C(O)C(N)CC(=O)N.O=C(O)C(N)CS>>C(N)(CC(=O)N)C(=O)O.O=C(O)C(N)CS" -b -g -c -j AAM -f TEXT

java -jar ReactionDecoder.jar -Q SMI -q "CC(O)CC(=O)OC(C)CC(O)=O.O[H]>>[H]OC(=O)CC(C)O.CC(O)CC(O)=O" -g -c -j ANNOTATE -f XML

java -jar ReactionDecoder.jar -Q RXN -q example/ReactionDecoder_mapped.rxn  -T RXN -t example/ReactionDecoder_mapped.rxn -j COMPARE -f BOTH -u

java -jar ReactionDecoder.jar -Q RXN -q example/ReactionDecoder_mapped.rxn  -T RXN -t example/ReactionDecoder_mapped.rxn -j COMPARE -f BOTH