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README.md

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)

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 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

License

RDT is released under the GNU General Public License version 3.

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).

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

Subcommands

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 -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

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 -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