Standard reaction Gibbs energy estimation for biochemical reactions
Python Jupyter Notebook Matlab
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README.md

component-contribution

Standard reaction Gibbs energy estimation for biochemical reactions

Requirements (for the python version):

  • python == 2.7
  • numpy >= 1.6.2
  • scipy >= 0.14
  • python-openbabel >= 2.3.2
  • ChemAxon's Marvin >= 5.11

Requirements (for the MATLAB version):

  • Matlab >= 7
  • python == 2.7
  • numpy >= 1.14.0
  • scipy >= 1.0.0
  • pandas >= 0.23.0
  • Open-Babel >= 2.3.1 ('babel' must be in PATH, including python bindings)
  • ChemAxon's Marvin >= 5.11 ('cxcalc' must be in PATH)

For more information on the method behind component-contribution, please view our open access paper:

Noor E, Haraldsdóttir HS, Milo R, Fleming RMT (2013) Consistent Estimation of Gibbs Energy Using Component Contributions, PLoS Comput Biol 9:e1003098, DOI: 10.1371/journal.pcbi.1003098

Please, quote this paper if you publish work that uses component-contribution.

Description of files in /data

  • compounds.tsv - table of all KEGG compounds, their name and InChI (used only in Matlab code)
  • fixed_mapping.tsv - table mapping some KEGG compound IDs to BiGG IDs (overriding the InChI-based mapping)
  • formation_energies_transformed.tsv - table of biochemical formation energies (used for training CC)
  • kegg_additions.tsv - table of compounds that are missing from KEGG together with their InChI
  • kegg_compounds.json.gz - JSON of all KEGG compounds including their InChI and names
  • redox.tsv - table of reduction potentials (used for training CC)
  • TECRDB.tsv - table of K'eq values from the NIST database (http://xpdb.nist.gov/enzyme_thermodynamics/)

Installing on Windows

  1. install Anaconda 5.1 for Windows (recommended python 3.6 version)
  2. install the openbabel package
  1. optional: install "Marvin Suite" by ChemAxon
  • Marvin is only required for adding structures of new compounds that are not in the KEGG database
  • instructions
  • add cxcalc.bat to PATH
  • you will need to get a license to use ChemAxon (it is free for academic use)

Installing on Ubuntu

  1. as root: apt install openbabel
  2. as root: pip install -r requirements.txt
  3. optional: install "Marvin Suite" by ChemAxon
  • Marvin is only required for adding structures of new compounds that are not in the KEGG database
  • instructions
  • add cxcalc to PATH, e.g. using a symbolic link from /usr/bin/cxcalc
  • you will need to get a license to use ChemAxon (it is free for academic use)