These are chat archives for opencobra/cobrapy

Aug 2017
Bhushan Dhamale
Aug 10 2017 05:12

Thanks a lot @cdiener :smiley:

@BhushanDhamale you would need dynamic FBA for that. @pstjohn and @matthiaskoenig are the experts on that :smile:

Peter St. John
Aug 10 2017 20:50
How would people feel about a degree of reduction function for metabolites? “$\gamma$ Value: the degree of reduction of a molecule, describes the electron content of a chemical compound based on the biological frame of reference where water, CO2, protons, NH4+, and SO4 2 have a $\gamma$= 0."
Here’s a quick example of what the function might look like
def calc_degree_of_reduction(met):
    """C. Smolke, The metabolic pathway engineering handbook: tools and applications (2009)."""
    elements = {'C': 0, 'H': 0, 'O': 0, 'N': 0, 'S': 0}
    charge = met.charge if met.charge else 0
    return (
        4 * elements['C'] + 
        1 * elements['H'] + 
       -2 * elements['O'] +
       -3 * elements['N'] +
        6 * elements['S'] +
       -1 * charge)
I’d probably want it to live as Metabolite.dor, or in a cobra.util function if that was too prominent
Henning Redestig
Aug 10 2017 23:03
I don't have anything against that if useful, but have been thinking that it would be nice with a Metabolite.compound property which was e.g. inchikey and given that, it would be easy to get the power of rdkit for this type of calculations
Peter St. John
Aug 10 2017 23:38
that would be cool, especially if you could ultimately build in some sort of thermodynamic functionality.
DOR is pretty basic, we wouldn’t need anything outside of Metabolite.elements and Metabolite.charge. In looking at actual fermentation data it’s really useful — but I suppose i’m mainly using the model at that point as a repo of chemical ID’s and formulas.
I will say that rdkit wouldn’t play nice as a required dependency, it’s not pip installable.