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EnzymeML / PyEnzyme

🧬 - Data management and modeling framework based on EnzymeML.
BSD 2-Clause "Simplified" License
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Initial concentration of Reactant not stored in XML if init_conc=0.0 #12

Closed jmrohwer closed 3 years ago

jmrohwer commented 3 years ago

When a new reactant is created with

enzmldoc.addReactant(Reactant(
                    name = ...,
                    vessel = ...,
                    init_conc = 0.0,
                    substanceunits = ...,
                    ...
):

the initial concentration is not stored in the XML when the value is zero (the init_conc key is completely absent from the XML), it is however stored when the value is non zero.

This creates a problem for simulation tools (e.g. PySCeS) wanting to simulate the kinetic model, because the initial concentration is loaded as NaN instead of zero.

JR-1991 commented 3 years ago

Thanks, the issue has been fixed in commit 173d93f7b1efb87d6700dcef28130001ed42a76b.