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)
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 install -DskipTests=true
5) mvn package
6) mvn -P local clean install (with -jar-with-dependencies)
c) Compile and bundle the code using ant?:
d) Ant Build commands
CLEAN:
ant clean
BUILD:
ant compile
DIST:
ant jar
DOC:
ant javadoc
TEST:
ant test
HELP:
ant run
Fat Jar:
ant package-for-store
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).
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 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 -j AAM -f TEXT
java -cp dist/*:lib/* aamtool.ReactionDecoder -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 -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 -j ANNOTATE -f XML
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
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