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#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)

=================
##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
```
Introduction
============

####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
```
`Reaction Decoder Tool (RDT)`
-----------------------------

===================
##Compare Reactions
===================
`1. Atom Atom Mapping (AAM) Tool`

####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
```
`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)`

####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
```

===================
##License
===================
Installation
============

####Reaction Decoder Tool (RDT)
```
Author: Syed Asad Rahman
e-mail: [email protected]
c/o EMBL-European BioInformatics Institute (EBI)
WTGC, CB10 1SD Hinxton
UK
`a)` You could [download the latest RDT] (https://github.com/asad/ReactionDecoder/releases) release version from the github.

Note: The copyright of this software belongs to the author
and EMBL-European BioInformatics Institute (EBI).
```

===================
##Citation
===================

####Reference
```
Rahman, S.A. et.al.(2016) Reaction Decoder Tool (RTD):
Extracting Features from Chemical Reactions (submitted)
```
`b)` Compile the code using `ant`?:

=================
##How To Compile the code?
=================
####Ant Build
`Ant Build` commands

```
CLEAN:
@@ -83,3 +37,66 @@ Fat Jar:
ant package-for-store
```


Licence
=======

`RDT` is released under the [GNU General Public License version 3](http://www.gnu.org/licenses/gpl.html).

```
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`


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
```
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a) CDK 1.5.12 supported
b) Code cleaned and optimised

-----------------------
Changes (22/03/2016)
-----------------------
a) Old Atom Rank (Index) reported


-----------------------
TO DO
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