MATLAB and 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; Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models, Bioinformatics, btx453
MATLAB functions (
MatlabCobraToolbox/ Require COBRA Toolbox)
Compute the chemical formulas of the unknown metabolites given the formulas for a set of known metabolites using a set of reactions.
Similar to computeFormulasFillMets but return the minimum and maximum possible MW of the target metabolite.
For converting chemical formulas into a matrix and checking the elemental balance of reactions
For manually checking the feasibility of CPLEX solutions
For converting a matrix into chemical formulas
For calculating molecular weights
For conveniently setting CPLEX parameters in Matlab
Python functions (
PythonCobrapy/ Require Cobrapy)
It is initialized with a cobra model. Use the following two methods to calculate chemical formulae or the range for biomass MW:
.computeMetForm: Compute the chemical formulas of the unknown metabolites given the formulas for a set of known metabolites using a set of reactions.
.computeMetRange: Compute the minimum and maximum possible MW of the target metabolite.