public ReactionLinkCommand(SpeciesReference speciesReference, Reaction reaction, LinkType linkType, bool adding) { this.speciesReference = speciesReference; this.reaction = reaction; this.linkType = linkType; this.adding = adding; }
public ParameterCommand(Parameter parameter, Reaction parentReaction, Model.SBML.Model model) { this.parameter = parameter; this.parentReaction = parentReaction; this.model = model; }
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 ReactionElement(Hashtable attrs) { Reaction reaction = new Reaction(attrs); if (reaction.ID != null) { this.model.AddId(reaction.ID, reaction); } Boolean fast = false; Boolean reversible = true; if (attrs.ContainsKey("fast")) fast = Boolean.Parse((String)attrs["fast"]); if (attrs.ContainsKey("reversible")) reversible = Boolean.Parse((String)attrs["reversible"]); reaction.AddProperties(fast, reversible); this.model.listOfReactions.Add(reaction); elementStack.Push(reaction); }
public ReactionCommand(Reaction reaction, bool adding, Model.SBML.Model model) { this.reaction = reaction; this.adding = adding; this.model = model; }
public ModifierLinkCommand(ModifierSpeciesReference modifierReference, Reaction reaction, bool adding) { this.modifierReference = modifierReference; this.reaction = reaction; this.adding = adding; }