rxnfit documentation

Current version: 0.3.0, release: 20260314

Overviews

“rxnfit” is a Python module that builds ordinary differential equations (ODEs) for reaction kinetics from elementary reaction formulas and rate constants given in CSV format, and computes concentration time courses numerically.

• When all rate constants are known, the time evolution of each species’ concentration is obtained by numerical integration of the ODEs (e.g. with scipy.integrate.solve_ivp).

• When some rate constants are unknown, they can be estimated by fitting the ODE solution to experimental concentration time-course data (e.g. with scipy.optimize.minimize).

• A rate constant may be given as an expression in other rate constants (e.g. k₂ = 2·k₁), or as a function of time t via an override CSV.

Project Link : https://github.com/PEJpOhno/rxnfit

Tutorial : in preparation

How to cite : Ohno, M. rxnfit. GitHub. https://github.com/PEJpOhno/rxnfit (2023).

This module and its accompanying documentation were developed with the support of Cursor’s AI-assisted tools.