/kegg-reaction-graph-mapper

Extracts reaction graph .mol files from standard KEGG .mol files

Primary LanguagePython

kegg-reaction-graph-mapper

A tool to extract reaction graph .mol files from standard KEGG dataset .mol files. This implementation was originally done by Markus Heinonen. Please refer to "Heinonen, M. and Lappalainen, S. and Mielikäinen, T. and Rousu, J. Computing Atom Mappings for Biochemical Reactions without Subgraph Isomoprhism. J. Comp. Biol. 2011, 18:43-58)".

Contents

  • atommapper
  • build.sh
  • extract-reactiongraphs.py
  • feature-generator
  • reaction-list
  • README.md - This readme

Usage

Prerequisites

  • python
  • java

** Build **

The script build.sh compiles everything, namely the the atommapper written in Java.

** Run **

The package uses KEGG .mol files as input and computes reaction graph .mol files as mentionend in ("Efficient Path Kernels for Reaction Function Prediction" - M Heinonen, N Välimäki, V Mäkinen, J Rousu - 2012). A script is contained to run all steps automatically: extract-reactiongraphs.py [-h] -k KEGGPATH [-v]. The results will be stored in the results directory.

Here are the same steps if run manually:

  1. reaction-list: Create KEGG reaction listing with python reaction-list/extract-reactions.py -k KEGGPATH > RESULTS/kegg-reactions.txt.
  2. feature-generator: Create atom features from KEGG mol files using python generator2011.py KEGGPATH/mol/* -k all --output-dir RESULTS/mol-features/. The optional parameter k specifies the context size, default is all. There are other optional parameters for this script.
  3. atommapper: Create reactiongraph mol files with atommapper: java Mapper2000 -rgraphs -moldir KEGGPATH/mol/ -featdir RESULTS/mol-features/ -reacfile RESULTS/kegg-reactions.txt -output RESULTS/reaction-graphs. There are further optional parameters for this script.

License and Copyright

Copyright (c) 2011 Markus Heinonen, Sampsa Lappalainen, Taneli Mielikäinen, and Juho Rousu.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.