/// <summary>
/// Brings the model to steady state or throws an exception if it cant
/// </summary>
/// <param name="verifyConcentrations">if true, the floating species concentration will be checked</param>
/// <param name="cutoff">the value considered as close enough to steady state</param>
/// <param name="retries">number of tries</param>
/// <returns></returns>
private double BringToSteadyStateOrThrow(int retries = 20, bool verifyConcentrations = false, double cutoff = 10E-5)
{
double steadyStateValue = 1;
bool fndSteadyState = false;
int simCount = 1;
while (!fndSteadyState && simCount < retries)
{
rr.reset();
try
{
for (int k = 0; k < simCount; k++)
{
rr.simulate();
}
steadyStateValue = rr.steadyState();
}
catch (SBWException)
{
//simCount++;
}
if (steadyStateValue < cutoff)
{
fndSteadyState = true;
if (verifyConcentrations)
{
double[] ststSpeciesValues = rr.getFloatingSpeciesConcentrations();
for (int i = 0; i < ststSpeciesValues.Length; i++)
{
if (ststSpeciesValues[i] < 0)
{
fndSteadyState = false;
simCount++;
break;
}
}
}
}
else
{
simCount++;
}
}
if (simCount == retries)
{
var ae = new BifException("Error in sbwBifGAOptimize",
"Model has not reached steady state!!!");
throw ae;
}
return(steadyStateValue);
}
private void cmdSteadyState_Click(object sender, EventArgs e)
{
thread.QueueItem(() =>
{
if (m_sSBML != null)
{
if (m_sSBML.Length > 0)
{
try
{
if (sim == null)
{
sim = new RoadRunner();
}
sim.loadSBML(m_sSBML);
sim.simulate();
double steadyState = sim.steadyState();
if (
MessageBox.Show(
"Found steady state with sums of squares: " + steadyState +
". Do you want to use this state to be used?", "Steady state calculated",
MessageBoxButtons.YesNo, MessageBoxIcon.Question) != DialogResult.Yes)
{
return;
}
sim.simulate();
ArrayList floatingSpeciesNames = sim.getFloatingSpeciesNames();
double[] speciesConcentrations1 = sim.getFloatingSpeciesConcentrations();
ArrayList boundarySpeciesNames = sim.getBoundarySpeciesNames();
double[] speciesConcentrations2 = sim.getBoundarySpeciesConcentrations();
ArrayList parameterTupleList = sim.getAllGlobalParameterTupleList();
NOM.loadSBML(m_sSBML);
for (int index = 0; index < floatingSpeciesNames.Count; ++index)
{
NOM.setValue((string)floatingSpeciesNames[index], speciesConcentrations1[index]);
}
for (int index = 0; index < boundarySpeciesNames.Count; ++index)
{
NOM.setValue((string)boundarySpeciesNames[index], speciesConcentrations2[index]);
}
foreach (ArrayList arrayList in parameterTupleList)
{
NOM.setValue((string)arrayList[0], (double)arrayList[1]);
}
m_sSBML = NOM.getSBML();
loadSBML(m_sSBML);
return;
}
catch (Exception ex)
{
MessageBox.Show("Could not compute steady state due to: " + ex.Message,
"Steady state could not be computed ...", MessageBoxButtons.OK, MessageBoxIcon.Hand);
return;
}
}
}
MessageBox.Show("There is no model to analyze. Load a model first.", "No Model loaded",
MessageBoxButtons.OK, MessageBoxIcon.Hand);
});
}
