Пример #1
0
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],&parameterValues[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],&parameterValues[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],&parameterValues[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;
	}
}
Пример #2
0
/* 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);
        }
    }
}