Introduction
Reaction Decoder Tool (RDT)
1. Atom Atom Mapping (AAM) Tool
2. Reaction Annotator (Extract Bond Changes, Identify & Mark Reaction Centres) and
3. Reaction Comparator (Reaction Similarity based on the Bond Changes, Reaction Centres or Substructures)
Contact
Author: Dr. Syed Asad Rahman e-mail: [email protected]
Installation
a) You could [download the latest RDT] (https://github.com/asad/ReactionDecoder/releases) release version from the github.
b) Compile the core code using maven?:
POM.xml commands
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)
Atom Atom Mapping using Java API
View mapped reaction using CDKDEPICT Tool.
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;
}
License
RDT is released under the GNU General Public License version 3.
Author: Syed Asad Rahman
e-mail: [email protected]
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).
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 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
Perform AAM for Transporters
AAM using SMILES (accept mapping with no bond changes -b)
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
Annotate Reaction using SMILES
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
Compare Reactions
Compare Reactions using SMILES with precomputed AAM mappings
java -jar ReactionDecoder.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 ReactionDecoder.jar -Q RXN -q example/ReactionDecoder_mapped.rxn -T RXN -t example/ReactionDecoder_mapped.rxn -j COMPARE -f BOTH