First, a little background on why you're seeing this behavior. SBML does not indicate whether a particular reaction follows mass action kinetics. And SimBiology needs to support more general reaction rates and kinetic laws. So SimBiology simply imports SBML reactions by recreating the specifed math as written. And this is the first time I personally have heard anyone request the product to handle this. I don't think we'd want to do the analysis required for this by default, since it could slow down the import of large models. But maybe we could make it an option for import. I'll log this in our database of enhancement requests.
In the mean time, I would probably update the reactions programmatically. To figure out which parameters are used with which reaction, I would take advantage of findUsages. Here's some prototype code to do that, in case it's helpful. (But please note that I have not thoroughly tested it, so use it at your own risk.)
model = sbmlimport('lotka.xml');
% Find all parameters in the model
parameters = sbioselect(model, 'Type', 'parameter');
% See how each parameter is used.
for paramIndex = 1:numel(parameters)
parameter = parameters(paramIndex);
[~, usageTable] = findUsages(parameter);
% Update any reaction that uses this parameter in its rate.
reactions = usageTable.Component(usageTable.Property == "ReactionRate");
for reactionIndex = 1:numel(reactions)
reaction = reactions(reactionIndex);
oldRate = reaction.ReactionRate;
kineticLaw = reaction.KineticLaw;
if isempty(kineticLaw)
% Add a kinetic law
kineticLaw = addkineticlaw(reaction, 'MassAction');
else
% Update the existing kinetic law to mass action
kineticLaw.KineticLawName = 'MassAction';
end
kineticLaw.ParameterVariableNames = parameter.Name;
newRate = reaction.ReactionRate;
if ~strcmp(oldRate, newRate)
warning("Reaction rate for reaction %s changed from %s to %s.", ...
reaction.Name, oldRate, newRate);
end
end
end
