Controlling parameters from command line

For controlling the parameters e.g. from a commandline, this can be done by parsing the commandline arguments such as here:

github.com/mcellteam/mcell_tests/blob/afcdd35493f979e6f8edeef4e2b0b4bd5ce4d42b/tests/pymcell4/2700_concentration_based_rxn_rate/model.py#L33

one can then also override parameters when loading a BNGL file:

github.com/mcellteam/mcell_tests/blob/master/tests/pymcell4_positive/2010_bng_parameter_override/model.py#L17


And when the python files generated by CellBlender are used as a basis for a model along with customization
(https://mcell.org/tutorials/scripting/customization.html), there is a customization function that can be used, an example here:

github.com/mcellteam/mcell_tests/blob/afcdd35493f979e6f8edeef4e2b0b4bd5ce4[…]4/hybrid_circadian_clock/mcell4_particle_based/customization.py

This only sets SEED but can set other parameters, this is how the dictionary parameter_overrides is used later when module parameters is imported:

github.com/mcellteam/mcell_tests/blob/afcdd35493f979e6f8edeef4e2b0b4bd5ce4[…]ell4/hybrid_circadian_clock/mcell4_particle_based/parameters.py