1. Atom Atom Mapping (AAM) Tool
2. Reaction Annotator (Extract Bond Changes, Identify & Mark Reaction Centres)
3. Reaction Comparator (Reaction Similarity based on Bond Changes, Reaction Centres or Substructures)
Author: Dr. Syed Asad Rahman e-mail: [email protected] Organisation: BioInception PVT LTD
a) Download the latest RDT release from GitHub.
b) Compile 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)
import com.bioinceptionlabs.reactionblast.api.RDT;
import com.bioinceptionlabs.reactionblast.api.ReactionResult;
ReactionResult result = RDT.map("CC(=O)O.OCC>>CC(=O)OCC.O");
System.out.println("Mapped: " + result.getMappedSmiles());
System.out.println("Bond changes: " + result.getTotalBondChanges());import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.silent.SilentChemObjectBuilder;
import org.openscience.cdk.smiles.SmilesParser;
import com.bioinceptionlabs.reactionblast.mechanism.ReactionMechanismTool;
import com.bioinceptionlabs.reactionblast.tools.StandardizeReaction;
SmilesParser sp = new SmilesParser(SilentChemObjectBuilder.getInstance());
IReaction rxn = sp.parseReactionSmiles("CC(=O)C=C.CC=CC=C>>CC1CC(CC=C1)C(C)=O");
rxn.setID("DielsAlder");
ReactionMechanismTool rmt = new ReactionMechanismTool(
rxn, true, true, false, true, false, new StandardizeReaction());
System.out.println("Algorithm: " + rmt.getSelectedSolution().getAlgorithmID());RDT is released under the GNU Lesser General Public License (LGPL) version 3.0.
Author: Syed Asad Rahman
e-mail: [email protected]
BioInception PVT LTD
Note: The copyright of this software belongs to the author and BioInception PVT LTD.
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
AAM using SMILES
java -jar rdt-3.9.0-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 (accept mapping with no bond changes: -b)
java -jar rdt-3.9.0-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
java -jar rdt-3.9.0-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 using precomputed AAM mappings
java -jar rdt-3.9.0-jar-with-dependencies.jar -Q RXN -q example/ReactionDecoder_mapped.rxn -T RXN -t example/ReactionDecoder_mapped.rxn -j COMPARE -f BOTH -u
Compare using RXN files
java -jar rdt-3.9.0-jar-with-dependencies.jar -Q RXN -q example/ReactionDecoder_mapped.rxn -T RXN -t example/ReactionDecoder_mapped.rxn -j COMPARE -f BOTH