RDT

Change Logs
changes.txt
(09/11/2016)

a) Cli 1.3 added
b) Bug fixed for -u option in COMPARE function
c) Do not print atom index for pre mapped reactions
d) Aromatic bond writing commented
e) Reaction SMILES in Kekulé format.

RTD1.4 with CDK 1.5.13

Major changes:
a) Unbalanced reaction- Molecular rearrangement reactions mapping bug fixed.
b) CDK 1.5.13 lib added

changes.txt

RDT v1.3

changes.txt

This release reports index mapping between old and new atom ranks.

Two functions added in the Reactor class
a)getInputRankLabelledAtomsReactant()
b)getInputRankLabelledAtomsProduct()

For example:

INPUT REACTION
O.C1(CC=CCC1)S>>CCCC(CC(O)S)[H]

SELECTED AAM MAPPING
[SH:1][CH:2]1[CH2:3][CH:4]=[CH:5][CH2:6][CH2:7]1.[OH2:8]>>[SH:1][CH:2]([OH:8])[CH2:7][CH:6]([CH2:5][CH2:4][CH3:3])[H:9]

REACTANT ATOM RANK OLD<->NEW

{1=8, 2=2, 3=3, 4=4, 5=5, 6=6, 7=7, 8=1}

PRODUCT ATOM RANK OLD<->NEW

{1=5, 2=7, 3=6, 4=2, 5=3, 6=4, 7=8, 8=9, 9=1}

Reaction Decoder Tool (RDT)

Reaction Decoder Tool (RDT)

Atom Atom Mapping (AAM) Tool, Reaction Annotator and Comparator

---

How To Compile the code?

Ant Build

CLEAN:
  ant clean
BUILD:
  ant compile
DIST:
  ant jar
DOC:
  ant javadoc
TEST:
  ant test
HELP:
  ant run
Fat Jar:
 ant package-for-store

---

Perform AAM

a) 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

b) 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

a) Compare Reactions using SMILES with precomputed AAM mappings

java -jar ReactionDecoder.jar -Q SMI -q -Q RXN -q example/ReactionDecoder_mapped.rxn  -T RXN -t example/ReactionDecoder_mapped.rxn -j COMPARE -f BOTH -u

b) 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

changes.txt

Reaction Decoder Tool (RDT)

Reaction Decoder Tool (RDT)

Atom Atom Mapping (AAM) Tool, Reaction Annotator and Comparator

---

How To Compile the code?

Ant Build

CLEAN:
  ant clean
BUILD:
  ant compile
DIST:
  ant jar
DOC:
  ant javadoc
TEST:
  ant test
HELP:
  ant run

---

Perform AAM

a) 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

b) 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

a) Compare Reactions using SMILES with precomputed AAM mappings

java -jar ReactionDecoder.jar -Q SMI -q -Q RXN -q example/ReactionDecoder_mapped.rxn  -T RXN -t example/ReactionDecoder_mapped.rxn -j COMPARE -f BOTH -u

b) 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

Reaction Decoder Tool (RDT)- v1.0

Reaction Decoder Tool (RDT)

Atom Atom Mapping (AAM) Tool, Reaction Annotator and Comparator

Perform AAM

a) 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

b) 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

a) Compare Reactions using SMILES with precomputed AAM mappings

java -jar ReactionDecoder.jar -Q SMI -q -Q RXN -q example/ReactionDecoder_mapped.rxn  -T RXN -t example/ReactionDecoder_mapped.rxn -j COMPARE -f BOTH -u

b) 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

Reaction Decoder Tool (RDT)

Reaction Decoder Tool (RDT)

Atom Atom Mapping (AAM) Tool, Reaction Annotator and Comparator

Perform AAM

a) 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

b) 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

a) Compare Reactions using SMILES with precomputed AAM mappings

java -jar ReactionDecoder.jar -Q SMI -q -Q RXN -q example/ReactionDecoder_mapped.rxn  -T RXN -t example/ReactionDecoder_mapped.rxn -j COMPARE -f BOTH -u

b) 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