Introduction

Reaction Decoder Tool (RDT) v3.0.0

1. Atom Atom Mapping (AAM) Tool

2. Reaction Annotator (Extract Bond Changes, Identify & Mark Reaction Centres)

3. Reaction Comparator (Reaction Similarity based on the Bond Changes, Reaction Centres or Substructures)

Contact

Author: Dr. Syed Asad Rahman e-mail: asad.rahman@bioinceptionlabs.com

Installation

a) You could download the latest RDT release version from the github.

b) Compile the core code using maven:

use pom.xml and mvn commands to build your project
1) mvn clean compile                                  (compile only)
2) mvn clean test                                     (compile and run tests)
3) mvn clean install -DskipTests=true                 (install, skip tests)
4) mvn clean install                                  (install with tests)
5) mvn -P local clean install -DskipTests=true        (fat jar, skip tests)
6) mvn -P local clean install                         (fat jar with tests)

Atom Atom Mapping using Java API

import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.silent.SilentChemObjectBuilder;
import org.openscience.cdk.smiles.SmiFlavor;
import org.openscience.cdk.smiles.SmilesGenerator;
import org.openscience.cdk.smiles.SmilesParser;
import com.bioinceptionlabs.reactionblast.mechanism.MappingSolution;
import com.bioinceptionlabs.reactionblast.mechanism.ReactionMechanismTool;
import com.bioinceptionlabs.reactionblast.tools.StandardizeReaction;

public class Example {
    public static void main(String[] args) throws Exception {
        final SmilesGenerator sg = new SmilesGenerator(SmiFlavor.AtomAtomMap);
        final SmilesParser smilesParser = new SmilesParser(SilentChemObjectBuilder.getInstance());

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

        IReaction cdkReaction = smilesParser.parseReactionSmiles(reactionSM);

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

    public static IReaction performAtomAtomMapping(IReaction cdkReaction, String reactionName) throws Exception {
        cdkReaction.setID(reactionName);
        boolean forceMapping = true;
        boolean generate2D = true;
        boolean generate3D = false;
        boolean complexMapping = true;
        boolean acceptNoChange = false;
        StandardizeReaction standardizeReaction = new StandardizeReaction();
        ReactionMechanismTool rmt = new ReactionMechanismTool(
                cdkReaction, forceMapping, generate2D, generate3D,
                complexMapping, acceptNoChange, standardizeReaction);
        MappingSolution s = rmt.getSelectedSolution();
        return s.getReaction();
    }
}

Migrating from v2.x

The package namespace has changed from uk.ac.ebi to com.bioinceptionlabs in v3.0.0.

Maven dependency

<!-- Old (v2.x) -->
<groupId>uk.ac.ebi.rdt</groupId>

<!-- New (v3.0.0) -->
<groupId>com.bioinceptionlabs.rdt</groupId>

Import changes

Replace imports in your code:

Old (v2.x)	New (v3.0.0)
uk.ac.ebi.aamtool.*	com.bioinceptionlabs.aamtool.*
uk.ac.ebi.reactionblast.*	com.bioinceptionlabs.reactionblast.*
uk.ac.ebi.centres.*	com.bioinceptionlabs.centres.*

A simple find-and-replace of uk.ac.ebi with com.bioinceptionlabs in your import statements is sufficient. The API itself is unchanged.

License

RDT is released under the GNU Lesser General Public License (LGPL) version 3.0.

Author: Syed Asad Rahman
e-mail: asad.rahman@bioinceptionlabs.com
BioInception

Note: The copyright of this software belongs to the author
and BioInception.

How to Cite RDT?

SA Rahman, G Torrance, L Baldacci, SM Cuesta, F Fenninger, N Gopal, S Choudhary, JW May, GL Holliday, C Steinbeck and JM Thornton: Reaction Decoder Tool (RDT): Extracting Features from Chemical Reactions, Bioinformatics (2016)

doi: 10.1093/bioinformatics/btw096

Sub-commands

Perform AAM

AAM using SMILES

java -jar rdt-3.0.0-jar-with-dependencies.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

Perform AAM for Transporters

AAM using SMILES (accept mapping with no bond changes -b)

java -jar rdt-3.0.0-jar-with-dependencies.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

Annotate Reaction using SMILES

java -jar rdt-3.0.0-jar-with-dependencies.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

Compare Reactions

Compare Reactions using SMILES with precomputed AAM mappings

java -jar rdt-3.0.0-jar-with-dependencies.jar -Q RXN -q example/ReactionDecoder_mapped.rxn  -T RXN -t example/ReactionDecoder_mapped.rxn -j COMPARE -f BOTH -u

Compare Reactions using RXN files

java -jar rdt-3.0.0-jar-with-dependencies.jar -Q RXN -q example/ReactionDecoder_mapped.rxn  -T RXN -t example/ReactionDecoder_mapped.rxn -j COMPARE -f BOTH