Make MW>0 check optional

KarrLab / wc_sim

A multi-algorithmic simulator for whole-cell models

MIT License

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Make MW>0 check optional #25

Closed artgoldberg closed 5 years ago

artgoldberg commented 6 years ago

These changes are needed for a proper fix: Add a command line argument: change wc_sim/wc_sim/multialgorithm/main.py Pass the argument to the simulator: wc_sim/wc_sim/multialgorithm/simulation.py Pass argument to the model check code in _prepare() Modify model checking code in: wc_lang/wc_lang/prepare.py Don’t call ‘verify_species_types’

jonrkarr commented 5 years ago

Done

wc_lang now allows Species.molecular_weight = 0 (negative molecular weights are not allowed). This needed to happen anyway to represent things such as UV radiation (which damages DNA) which have no mass (ignoring the equivalence of mass and energy).
I think this issue is resolved by the change to wc_lang and no change to wc_sim is neeeded.

Todo

Arthur, review this issue is satisfactorily addressed.