Python functions for determining the chemical formulae and molecular weights of macromolecules in genome-scale metabolic models.
Please see the following paper for more details:
Siu H. J. Chan, Jingyi Cai, Lin Wang, Margaret N. Simons-Senftle, Costas D. Maranas (2017) Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models, Bioinformatics, 33(22), 3603–3609.
Link
Require Cobrapy(>=0.15.1). See the help files for documentation.
Main object: biomassmw.
It is initialized with a cobra model. Use the following two methods to calculate chemical formulae or the range for biomass MW:
.compute_met_form: Compute the chemical formulas of the unknown metabolites given the formulas for a set of known metabolites using a set of reactions..compute_met_range: Compute the minimum and maximum possible MW of the target metabolite.