public ReactionLinkCommand(SpeciesReference speciesReference, Reaction reaction, LinkType linkType, bool adding)
{
this.speciesReference = speciesReference;
this.reaction = reaction;
this.linkType = linkType;
this.adding = adding;
}
public ComponentLinkCommand(SpeciesReference speciesReference, ComponentBase component, int linkNumber, ComponentLinkType linkType, bool adding)
{
this.speciesReference = speciesReference;
this.component = component;
this.linkNumber = linkNumber;
this.linkType = linkType;
this.adding = adding;
}
public void Setup(Experiment experiment, Simulation simulation, string speciesName)
{
// ********* INITIAL SETUP
// Hopf model
MuCell.Model.SBML.Reader.SBMLReader s = new MuCell.Model.SBML.Reader.SBMLReader("../../UnitTests/smallest.Hopf.xml");
// Cell definition 1
MuCell.Model.CellDefinition celldef1 = new MuCell.Model.CellDefinition("celldef1");
celldef1.addSBMLModel(s.model);
// Create a NEW model
MuCell.Model.SBML.Model model = new MuCell.Model.SBML.Model();
MuCell.Model.SBML.Species species1 = new MuCell.Model.SBML.Species();
MuCell.Model.SBML.Species species2 = new MuCell.Model.SBML.Species();
model.listOfSpecies = new List<MuCell.Model.SBML.Species>();
model.listOfSpecies.Add(species1);
model.listOfSpecies.Add(species2);
// Set some values for species1
species1.ID = speciesName;
species1.InitialAmount = 4.0d;
// Set some values for species2
species2.ID = "Y";
species2.InitialAmount = 0.1d;
model.AddId(speciesName, species1);
model.AddId("Y", species2);
// Set up the reaction
MuCell.Model.SBML.Reaction reaction1 = new MuCell.Model.SBML.Reaction("reaction1");
model.listOfReactions = new List<MuCell.Model.SBML.Reaction>();
model.listOfReactions.Add(reaction1);
// Set up the kinetic law
reaction1.KineticLaw = new MuCell.Model.SBML.KineticLaw(model);
reaction1.KineticLaw.Formula = speciesName.Replace(' ', '_')+"*2";
// set up the species reference for the reactants
MuCell.Model.SBML.SpeciesReference ref1 = new MuCell.Model.SBML.SpeciesReference(species1, 1);
// set up the species references for the products
MuCell.Model.SBML.SpeciesReference ref2 = new MuCell.Model.SBML.SpeciesReference(species1, 0.75);
MuCell.Model.SBML.SpeciesReference ref3 = new MuCell.Model.SBML.SpeciesReference(species2, 2);
// Add the references
reaction1.Reactants.Add(ref1);
reaction1.Products.Add(ref2);
reaction1.Products.Add(ref3);
// set up the cell definition
MuCell.Model.CellDefinition celldef2 = new MuCell.Model.CellDefinition("celldef2");
celldef2.addSBMLModel(model);
// instantiat the environment
MuCell.Model.Vector3 size = new MuCell.Model.Vector3(1, 1, 1);
MuCell.Model.Environment environment = new MuCell.Model.Environment(size);
// Cells
List<MuCell.Model.CellInstance> cells = new List<MuCell.Model.CellInstance>();
// Create 10 cells of celldef1 and 20 cells of celldef2
for(int i=0;i<10;i++){
int a = ((i+2)%3)+1;
int b = (i%3)+1;
int c = ((i+1)%3)+1;
CellInstance cell11 = celldef1.createCell();
cells.Add(cell11);
environment.AddCellToGroup(a, cell11);
CellInstance cell21 = celldef2.createCell();
CellInstance cell22 = celldef2.createCell();
cells.Add(cell21);
cells.Add(cell22);
environment.AddCellToGroup(b, cell21);
environment.AddCellToGroup(c, cell22);
}
// StateSnapshot for intial state
MuCell.Model.StateSnapshot initialState = new MuCell.Model.StateSnapshot(cells);
initialState.SimulationEnvironment = environment;
// Parameters
MuCell.Model.SimulationParameters parameters = new MuCell.Model.SimulationParameters();
parameters.InitialState = initialState;
parameters.SimulationLength = 0.01001d;
parameters.SnapshotInterval = 1;
parameters.StepTime = 0.01001d;
parameters.SolverMethod = MuCell.Model.Solver.SolverMethods.RungeKutta;
// Simulation
simulation.Parameters = parameters;
// Experiment
experiment.addCellDefinition(celldef1);
experiment.addCellDefinition(celldef2);
experiment.addSimulation(simulation);
// Start simulation
simulation.StartSimulation();
this.models = new List<MuCell.Model.SBML.Model>();
this.models.Add(s.model);
this.models.Add(model);
}
public void SpeciesReferenceElement(Hashtable attrs)
{
String speciesId;
Species species;
try
{
speciesId = (String)attrs["species"];
species = (Species)this.model.findObject(speciesId);
// find out if it is a list of reactants or products
if (((String)elementStack.Pop()) == "listOfReactants")
{
SpeciesReference speciesRef;
List<SpeciesReference> reactantsList = (List<SpeciesReference>)elementStack.Peek();
if (attrs.ContainsKey("stoichiometry"))
{
speciesRef = new SpeciesReference(species,
(double)(double.Parse((String)attrs["stoichiometry"])));
}
else
{
speciesRef = new SpeciesReference(species);
}
reactantsList.Add(speciesRef);
elementStack.Push("listOfReactants");
}
else
// list of products instead
{
SpeciesReference speciesRef;
List<SpeciesReference> productsList = (List<SpeciesReference>)elementStack.Peek();
if (attrs.ContainsKey("stoichiometry"))
{
speciesRef = new SpeciesReference(species,
(double)(double.Parse((String)attrs["stoichiometry"])));
}
else
{
speciesRef = new SpeciesReference(species);
}
productsList.Add(speciesRef);
elementStack.Push("listOfProducts");
}
}
catch (ArgumentNullException e)
{
Console.WriteLine("speciesReference element missing required attribute 'species'");
throw (e);
}
}
