Re: [SOSlib-discuss] equivalent to observablesArray ?[Scanned]

[Eric F. <efe...@ph...>]

Hi Rainer,

Sorry for this late reply, I was away. Thanks a lot for these info.
These suggestions look good to me (in particular
ODEModel_getVariableIndexFromSBase).

Eric 

> -----Original Message-----
> From: Rainer Machne [mailto:ra...@tb...] 
> Sent: 30 October 2008 14:52
> To: Eric Fernandez
> Subject: Re: [SOSlib-discuss] equivalent to observablesArray 
> ?[Scanned]
> 
> Eric Fernandez wrote:
> > Hi,
> > 
> > I shall answer to myself. What I want is returned by:
> > 
> > for ( int i = 0; i != Model_getNumSpecies(om->m); i++ )
> 
> Hi Eric,
> 
> We should probably introduce an interface function for om->m.
> This SBML model, btw, is exactly the model from the input file.
> 
> I have jsut added to CVS two new functions:
> 
> 	const Model_t *ODEModel_getInputSBMLl(om)
> 
> returns the pointer om->m, i.e. the input SBML. And
> 
> 	const Model_t *ODEModel_getODESBMLl(om)
> 
> returns the pointer om->simple, which is an internally 
> produced SBML model where all reactions have been replaced by 
> SBML rate rules.
> 
> 
> >     {
> >       Species_t *species = Model_getSpecies(om->m, i);
> >       cout << Species_getId(species) << " ";
> >     }
> > 
> > (the same way the observables were built before).
> > 
> 
> 
> Just a warning for potential other readers:
> 
> Above code to get the Species from the input SBML model is not really 
> relevant for getting values from the derived ODE model or the 
> integrator:
> The order of species, parameters, rules and reactions in the 
> input SBML 
> DOES NOT correspond to the order of 1) ODE variables, 2) assigned 
> variables, 3) constants in odeModel (om->names) and cvodeData 
> (data->values). There is no direct mapping between SBML and 
> ODE models.
> 
> The way to interface variables/parameters of the derived ODE 
> Model is as 
> follows:
> 
> 1) Get a variableIndex_t from the ODEModel, each by the function
> 
> 
> variableIndex_t *ODEModel_getVariableIndex (odeModel_t *om, 
> const char 
> *symbol)
> 
> To map this from the SBML model, you could set the string in above 
> function:
> 	symbol = Species_getId(species)
> 
> There are however various other functions to retrieve 
> specific variables 
> from the ODE model. Now, that i am writing this, maybe we can 
> introduce 
> simple convenience functions, which allow to get the 
> variableIndex just 
> via SBML species, parameter, compartment or reaction pointers, e.g.:
> 
> 	ODEModel_getVariableIndexFromSBase
> 
> Interested? It is rather trivial though.
> 
> 2) Use this variableIndex to get the current values from the 
> integrator by
> 
> IntegratorInstance_getVariableValue(integratorInstance_t *engine, 
> variableIndex_t *vi)
> 
> 
> I guess you know that, but maybe it's helpful for others.
> 
> Rainer