void SBML_sim::loadSBML(SBMLDocument * doc)
{
if (!doc || doc->getNumErrors() > 0)
{
}
else
{
Model * model = doc->getModel();
ListOfParameters * params = model->getListOfParameters();
ListOfReactions * reacs = model->getListOfReactions();
ListOfSpecies * species = model->getListOfSpecies();
ListOfSpeciesTypes * types = model->getListOfSpeciesTypes();
ListOfEvents * events = model->getListOfEvents();
ListOfRules * rules = model->getListOfRules();
vector<string> assignmentEquations, rateEquations, eventTriggers;
vector< vector<string> > eventResponses;
if (events)
for (int i=0; i < events->size(); ++i)
{
Event * e = events->get(i);
eventTriggers.push_back( SBML_formulaToString( e->getTrigger()->getMath() ) );
ListOfEventAssignments * eventAssn = e->getListOfEventAssignments();
vector<string> responses;
string s;
for (int j=0; j < eventAssn->size(); ++j)
{
s = eventAssn->get(j)->getVariable();
s.append("=");
s.append( SBML_formulaToString( eventAssn->get(j)->getMath() ) );
responses.push_back(s);
}
eventResponses.push_back( responses );
}
if (rules)
for (int i=0; i < rules->size(); ++i)
{
Rule * r = rules->get(i);
if (r->isAssignment())
{
AssignmentRule * ar = (AssignmentRule*)r;
assignmentVariables.push_back(ar->getVariable());
assignmentValues.push_back(1.0);
assignmentEquations.push_back(ar->getFormula());
}
}
if (species)
for (int i=0; i < species->size(); ++i)
if (!species->get(i)->getConstant() && !species->get(i)->getBoundaryCondition())
{
variableNames.push_back(species->get(i)->getId());
if (species->get(i)->isSetInitialAmount())
variableValues.push_back(species->get(i)->getInitialAmount());
else
if (species->get(i)->isSetInitialConcentration())
variableValues.push_back(species->get(i)->getInitialConcentration());
else
variableValues.push_back(0.0);
}
else
{
parameterNames.push_back(species->get(i)->getId());
if (species->get(i)->isSetInitialAmount())
parameterValues.push_back(species->get(i)->getInitialAmount());
else
if (species->get(i)->isSetInitialConcentration())
parameterValues.push_back(species->get(i)->getInitialConcentration());
else
parameterValues.push_back(0.0);
}
if (params)
for (int i=0; i < params->size(); ++i)
{
parameterNames.push_back(params->get(i)->getId());
parameterValues.push_back(params->get(i)->getValue());
}
int numReacs = 0;
if (reacs)
numReacs = reacs->size();
stoichiometryMatrix = new double[ numReacs * variableNames.size() ];
for (int i=0; i < numReacs; ++i)
{
Reaction * r = reacs->get(i);
reactionNames.push_back(r->getId());
rateEquations.push_back(r->getKineticLaw()->getFormula());
ListOfSpeciesReferences * reactants = r->getListOfReactants(),
* products = r->getListOfProducts();
for (int j=0; j < variableNames.size(); ++j)
{
stoichiometryMatrix[ j*numReacs + i ] = 0.0;
for (int k=0; k < reactants->size(); ++k)
if (reactants->get(k) && reactants->get(k)->getSpecies() == variableNames[j])
stoichiometryMatrix[ j*numReacs + i ] -= 1.0;
//stoichiometryMatrix[ j*numReacs + i ] -= SpeciesReference_getStoichiometry(reactants->get(k));
for (int k=0; k < products->size(); ++k)
if (products->get(k) && products->get(k)->getSpecies() == variableNames[j])
stoichiometryMatrix[ j*numReacs + i ] += 1.0;
//stoichiometryMatrix[ j*numReacs + i ] += SpeciesReference_getStoichiometry(reactants->get(k));
}
}
for (int i=0; i < rateEquations.size(); ++i)
{
mu::Parser p;
addSBMLFunctions(p);
p.SetExpr(rateEquations[i]);
for (int j=0; j < variableNames.size(); ++j)
p.DefineVar("time",&(this->time));
for (int j=0; j < variableNames.size(); ++j)
p.DefineVar("Time",&(this->time));
for (int j=0; j < variableNames.size(); ++j)
p.DefineVar(variableNames[j],&variableValues[j]);
for (int j=0; j < parameterNames.size(); ++j)
p.DefineVar(parameterNames[j],¶meterValues[j]);
for (int j=0; j < assignmentVariables.size(); ++j)
p.DefineVar(assignmentVariables[j],&assignmentValues[j]);
p.SetVarFactory(muparser_add_variable, (void*)this);
try
{
p.Eval();
rateEqns.push_back(p);
}
catch(...)
{
//reactionNames.clear();
//rateEqns.clear();
break;
}
}
for (int i=0; i < assignmentEquations.size(); ++i)
{
mu::Parser p;
addSBMLFunctions(p);
p.SetExpr(assignmentEquations[i]);
for (int j=0; j < variableNames.size(); ++j)
p.DefineVar(variableNames[j],&variableValues[j]);
for (int j=0; j < parameterNames.size(); ++j)
p.DefineVar(parameterNames[j],¶meterValues[j]);
for (int j=0; j < assignmentVariables.size(); ++j)
p.DefineVar(assignmentVariables[j],&assignmentValues[j]);
//p.SetVarFactory(muparser_add_variable, (void*)this);
try
{
p.Eval();
assignmentEqns.push_back(p);
}
catch(...)
{
std::cout << assignmentEquations[i] << std::endl;
//assignmentVariables.clear();
//assignmentEqns.clear();
break;
}
}
for (int i=0; i < eventTriggers.size(); ++i)
{
mu::Parser p;
addSBMLFunctions(p);
p.SetExpr(eventTriggers[i]);
for (int j=0; j < variableNames.size(); ++j)
p.DefineVar("time",&(this->time));
for (int j=0; j < variableNames.size(); ++j)
p.DefineVar("Time",&(this->time));
for (int j=0; j < variableNames.size(); ++j)
p.DefineVar(variableNames[j],&variableValues[j]);
for (int j=0; j < parameterNames.size(); ++j)
p.DefineVar(parameterNames[j],¶meterValues[j]);
for (int j=0; j < assignmentVariables.size(); ++j)
p.DefineVar(assignmentVariables[j],&assignmentValues[j]);
try
{
p.Eval();
//resposes for the trigger
vector<mu::Parser> responses;
for (int j=0; j < eventResponses[i].size(); ++j)
{
mu::Parser p;
addSBMLFunctions(p);
p.SetExpr(eventResponses[i][j]);
try
{
p.Eval();
responses.push_back(p);
}
catch(...) {}
}
if (responses.size() > 0)
{
triggerEqns.push_back(p);
responseEqns.push_back(responses);
}
}
catch(...)
{
//assignmentVariables.clear();
//assignmentEqns.clear();
break;
}
}
//delete params;
//delete reacs;
}
}
/* Give this reaction links to all species involved in it,
and give those species links to this reaction.
*/
void DSBReaction::doublyLink(QMap<QString, DSBSpecies*> map)
{
ListOfSpeciesReferences *lsr;
SimpleSpeciesReference *ssr;
unsigned int N;
QString specId;
// "reactants", or inputs
lsr = m_sbmlReaction->getListOfReactants();
N = lsr->size();
for (unsigned int i = 0; i < N; i++)
{
ssr = lsr->get(i);
specId = QString(ssr->getSpecies().c_str());
if (!map.contains(specId))
{
// TODO: Report error. Reaction is referring to a species that
// was not declared in the SBML list of species.
qDebug() << "map does not contain species id " << specId;
}
else
{
DSBSpecies *dsbspec = map.value(specId);
m_inputs.append(dsbspec);
dsbspec->addReactionEntered(this);
}
}
// "products", or outputs
lsr = m_sbmlReaction->getListOfProducts();
N = lsr->size();
for (unsigned int i = 0; i < N; i++)
{
ssr = lsr->get(i);
specId = QString(ssr->getSpecies().c_str());
if (!map.contains(specId))
{
// TODO: Report error. Reaction is referring to a species that
// was not declared in the SBML list of species.
qDebug() << "map does not contain species id " << specId;
}
else
{
DSBSpecies *dsbspec = map.value(specId);
m_outputs.append(dsbspec);
dsbspec->addReactionExited(this);
}
}
// modifiers (e.g. catalysts)
lsr = m_sbmlReaction->getListOfModifiers();
N = lsr->size();
for (unsigned int i = 0; i < N; i++)
{
ssr = lsr->get(i);
specId = QString(ssr->getSpecies().c_str());
if (!map.contains(specId))
{
// TODO: Report error. Reaction is referring to a species that
// was not declared in the SBML list of species.
qDebug() << "map does not contain species id " << specId;
}
else
{
DSBSpecies *dsbspec = map.value(specId);
m_modifiers.append(dsbspec);
dsbspec->addReactionModified(this);
}
}
}