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
• oct2py >= 3.1 (dependent on Octave)
• Open-Babel >= 2.3.1
• ChemAxon's Marvin >= 5.11

Requirements (for the MATLAB version):

• Matlab >= 7
• python == 2.7
• numpy >= 1.6.2
• scipy >= 0.14
• 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 32-bit python2.7

• recommended version Winpython
• you must install the 32-bit version since OpenBabel is not compiled for 64-bit windows
• make sure to register the python interpreter before installing openbabel python bindings
• add python.exe to PATH: instructions

2. install OpenBabel (version 2.3.2)

• instructions
• installer

3. install OpenBabel python (version 1.8) bindings

• instructions
• installer

4. optional: install Octave

• Not required for the Matlab version of component-contribution
• instructions
• there is no need to use "pip" to install oct2py as it is already part of winpython
• installer
• add octave.exe to PATH

5. 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-get install openbabel octave
2. as root: pip install -U numpy scipy oct2py
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)