This is a new version of the Reaction Decoder Tool (RDTool). In this version, some bugs were fixed, code speed was improved, and the main focus was done on Atom-to-Atom mapping. Also, the tool supports now an opportunity to call only one mapping method and to apply it to an RDF file. The previous version was taken from ReactionDecoder (or RDTool) author: Syed Asad Rahman https://github.com/asad repository: https://github.com/asad/ReactionDecoder
Alexandre Varnek (varnek@unistra.fr)
Timur Madzhidov (tmadzhidov@gmail.com)
Rail Suleymanov (rail.suleymanov@gmail.com)
Arkadii Lin (arkadiyl18@gmail.com)
Natalia Duybankova (NDyubank@its.jnj.com)
Ramil Nugmanov (nougmanoff@hotmail.com)
Timur Madzhidov (tmadzhidov@gmail.com)
Alexandre Varnek (varnek@unistra.fr)
Joerg Wegner (jwegner@its.jnj.com)
Copyright 2020, MaDeSmart, Machine Design of Small Molecules by AI VLAIO project HBC.2018.2287
Kazan Federal University, Russia
University of Strasbourg, France
University of Linz, Austria
University of Leuven, Belgium
Janssen Pharmaceutica N.V., Beerse, Belgium
Rail Suleymanov, Arcadia, St. Petersburg, Russia
-j, job type (MAPPING/CONSENSUS)
-rdf_id, reaction id field (for RDF format)
-i, input file
-o, output directory
-fmt, format (RDF/SMI), optional, default = RDF
-t, optional; if specified, defines maximum number of seconds a substructures enumeration will run for
-min, skip MIN algorithm, default = false
-max, skip MAX algorithm, default = false
-mixture, skip MIXTURE algorithm, default = false
Example: java -jar release/aam-utils.jar -j MAPPING -i first_10.rdf -o first_10_results -rdf_id Reaction_ID
-i, list of input files in RDF format, separated with semicolon
-o, output file in RDF format
-ignore_tfc, ignore "total_fragment_changes" metric
Example: java -jar release/aam-utils.jar -j CONSENSUS -i "first_10_results/MIN_reactions.rdf;first_10_results/MAX_reactions.rdf" -o first_10_results/consensus.rdf
- cdk: 2.3
- commons-cli: 1.4
- jgrapht-core: 1.1