static void Main()
{
Debug.Assert(CRootContainer.getRoot() != null);
// create a new datamodel
CDataModel dataModel = CRootContainer.addDatamodel();
Debug.Assert(CRootContainer.getDatamodelList().size() == 1);
// get the model from the datamodel
CModel model = dataModel.getModel();
Debug.Assert(model != null);
// set the units for the model
// we want seconds as the time unit
// microliter as the volume units
// and nanomole as the substance units
model.setTimeUnit(CUnit.s);
model.setVolumeUnit(CUnit.microl);
model.setQuantityUnit(CUnit.nMol);
// we have to keep a set of all the initial values that are changed during
// the model building process
// They are needed after the model has been built to make sure all initial
// values are set to the correct initial value
ObjectStdVector changedObjects = new ObjectStdVector();
// create a compartment with the name cell and an initial volume of 5.0
// microliter
CCompartment compartment = model.createCompartment("cell", 5.0);
CDataObject obj = compartment.getInitialValueReference();
Debug.Assert(obj != null);
changedObjects.Add(obj);
Debug.Assert(compartment != null);
Debug.Assert(model.getCompartments().size() == 1);
// create a new metabolite with the name glucose and an inital
// concentration of 10 nanomol
// the metabolite belongs to the compartment we created and is is to be
// fixed
CMetab glucose = model.createMetabolite("glucose", compartment.getObjectName(), 10.0, CModelEntity.Status_FIXED);
obj = glucose.getInitialValueReference();
Debug.Assert(obj != null);
changedObjects.Add(obj);
Debug.Assert(glucose != null);
Debug.Assert(model.getMetabolites().size() == 1);
// create a second metabolite called glucose-6-phosphate with an initial
// concentration of 0. This metabolite is to be changed by reactions
CMetab g6p = model.createMetabolite("glucose-6-phosphate", compartment.getObjectName(), 0.0, CModelEntity.Status_REACTIONS);
Debug.Assert(g6p != null);
obj = g6p.getInitialValueReference();
Debug.Assert(obj != null);
changedObjects.Add(obj);
Debug.Assert(model.getMetabolites().size() == 2);
// another metabolite for ATP, also fixed
CMetab atp = model.createMetabolite("ATP", compartment.getObjectName(), 10.0, CModelEntity.Status_FIXED);
Debug.Assert(atp != null);
obj = atp.getInitialValueReference();
Debug.Assert(obj != null);
changedObjects.Add(obj);
Debug.Assert(model.getMetabolites().size() == 3);
// and one for ADP
CMetab adp = model.createMetabolite("ADP", compartment.getObjectName(), 0.0, CModelEntity.Status_REACTIONS);
Debug.Assert(adp != null);
obj = adp.getInitialValueReference();
Debug.Assert(obj != null);
changedObjects.Add(obj);
Debug.Assert(model.getMetabolites().size() == 4);
// now we create a reaction
CReaction reaction = model.createReaction("hexokinase");
Debug.Assert(reaction != null);
Debug.Assert(model.getReactions().size() == 1);
// hexokinase converts glucose and ATP to glucose-6-phosphate and ADP
// we can set these on the chemical equation of the reaction
CChemEq chemEq = reaction.getChemEq();
// glucose is a substrate with stoichiometry 1
chemEq.addMetabolite(glucose.getKey(), 1.0, CChemEq.SUBSTRATE);
// ATP is a substrate with stoichiometry 1
chemEq.addMetabolite(atp.getKey(), 1.0, CChemEq.SUBSTRATE);
// glucose-6-phosphate is a product with stoichiometry 1
chemEq.addMetabolite(g6p.getKey(), 1.0, CChemEq.PRODUCT);
// ADP is a product with stoichiometry 1
chemEq.addMetabolite(adp.getKey(), 1.0, CChemEq.PRODUCT);
Debug.Assert(chemEq.getSubstrates().size() == 2);
Debug.Assert(chemEq.getProducts().size() == 2);
// this reaction is to be irreversible
reaction.setReversible(false);
Debug.Assert(reaction.isReversible() == false);
// now we ned to set a kinetic law on the reaction
// maybe constant flux would be OK
// we need to get the function from the function database
CFunctionDB funDB = CRootContainer.getFunctionList();
Debug.Assert(funDB != null);
// it should be in the list of suitable functions
// lets get all suitable functions for an irreversible reaction with 2 substrates
// and 2 products
CFunctionStdVector suitableFunctions = funDB.suitableFunctions(2, 2, COPASI.TriFalse);
Debug.Assert((suitableFunctions.Count > 0));
int i, iMax = (int)suitableFunctions.Count;
for (i = 0; i < iMax; ++i)
{
// we just assume that the only suitable function with Constant in
// it's name is the one we want
if (suitableFunctions[i].getObjectName().IndexOf("Constant") != -1)
{
break;
}
}
if (i != iMax)
{
// we set the function
// the method should be smart enough to associate the reaction entities
// with the correct function parameters
reaction.setFunction(suitableFunctions[i]);
Debug.Assert(reaction.getFunction() != null);
// constant flux has only one function parameter
Debug.Assert(reaction.getFunctionParameters().size() == 1);
// so there should be only one entry in the parameter mapping as well
Debug.Assert(reaction.getParameterCNs().Count == 1);
CCopasiParameterGroup parameterGroup = reaction.getParameters();
Debug.Assert(parameterGroup.size() == 1);
CCopasiParameter parameter = parameterGroup.getParameter(0);
// make sure the parameter is a local parameter
Debug.Assert(reaction.isLocalParameter(parameter.getObjectName()));
// now we set the value of the parameter to 0.5
Debug.Assert(parameter.getType() == CCopasiParameter.Type_DOUBLE);
parameter.setDblValue(0.5);
obj = parameter.getValueReference();
Debug.Assert(obj != null);
changedObjects.Add(obj);
}
else
{
System.Console.Error.WriteLine("Error. Could not find a kinetic law that conatins the term \"Constant\".");
System.Environment.Exit(1);
}
// now we also create a separate reaction for the backwards reaction and
// set the kinetic law to irreversible mass action
// now we create a reaction
reaction = model.createReaction("hexokinase-backwards");
Debug.Assert(reaction != null);
Debug.Assert(model.getReactions().size() == 2);
chemEq = reaction.getChemEq();
// glucose is a product with stoichiometry 1
chemEq.addMetabolite(glucose.getKey(), 1.0, CChemEq.PRODUCT);
// ATP is a product with stoichiometry 1
chemEq.addMetabolite(atp.getKey(), 1.0, CChemEq.PRODUCT);
// glucose-6-phosphate is a substrate with stoichiometry 1
chemEq.addMetabolite(g6p.getKey(), 1.0, CChemEq.SUBSTRATE);
// ADP is a substrate with stoichiometry 1
chemEq.addMetabolite(adp.getKey(), 1.0, CChemEq.SUBSTRATE);
Debug.Assert(chemEq.getSubstrates().size() == 2);
Debug.Assert(chemEq.getProducts().size() == 2);
// this reaction is to be irreversible
reaction.setReversible(false);
Debug.Assert(reaction.isReversible() == false);
// now we ned to set a kinetic law on the reaction
CFunction massAction = (CFunction)funDB.findFunction("Mass action (irreversible)");
Debug.Assert(massAction != null);
// we set the function
// the method should be smart enough to associate the reaction entities
// with the correct function parameters
reaction.setFunction(massAction);
Debug.Assert(reaction.getFunction() != null);
Debug.Assert(reaction.getFunctionParameters().size() == 2);
// so there should be two entries in the parameter mapping as well
Debug.Assert(reaction.getParameterCNs().Count == 2);
// mass action is a special case since the parameter mappings for the
// substrates (and products) are in a vector
// Let us create a global parameter that is determined by an assignment
// and that is used as the rate constant of the mass action kinetics
// it gets the name rateConstant and an initial value of 1.56
CModelValue modelValue = model.createModelValue("rateConstant", 1.56);
Debug.Assert(modelValue != null);
obj = modelValue.getInitialValueReference();
Debug.Assert(obj != null);
changedObjects.Add(obj);
Debug.Assert(model.getModelValues().size() == 1);
// set the status to assignment
modelValue.setStatus(CModelEntity.Status_ASSIGNMENT);
// the assignment does not have to make sense
modelValue.setExpression("1.0 / 4.0 + 2.0");
// now we have to adjust the parameter mapping in the reaction so
// that the kinetic law uses the global parameter we just created instead
// of the local one that is created by default
// The first parameter is the one for the rate constant, so we point it to
// the key of out model value
reaction.setParameterObject(0, modelValue);
// now we have to set the parameter mapping for the substrates
reaction.addParameterObject("substrate", g6p);
reaction.addParameterObject("substrate", adp);
// finally compile the model
// compile needs to be done before updating all initial values for
// the model with the refresh sequence
model.compileIfNecessary();
// now that we are done building the model, we have to make sure all
// initial values are updated according to their dependencies
model.updateInitialValues(changedObjects);
// save the model to a COPASI file
// we save to a file named example1.cps
// and we want to overwrite any existing file with the same name
// Default tasks are automatically generated and will always appear in cps
// file unless they are explicitley deleted before saving.
dataModel.saveModel("example1.cps", true);
// export the model to an SBML file
// we save to a file named example1.xml, we want to overwrite any
// existing file with the same name and we want SBML L2V3
try
{
dataModel.exportSBML("example1.xml", true, 2, 3);
}
catch
{
System.Console.Error.WriteLine("Error. Exporting the model to SBML failed.");
}
}
static void Main(string[] args)
{
Debug.Assert(CRootContainer.getRoot() != null);
// create a new datamodel
CDataModel dataModel = CRootContainer.addDatamodel();
Debug.Assert(CRootContainer.getDatamodelList().size() == 1);
// the only argument to the main routine should be the name of an SBML file
if (args.Length == 1)
{
string filename = args[0];
try
{
// load the model
dataModel.importSBML(filename);
}
catch
{
System.Console.Error.WriteLine("Error while importing the model from file named \"" + filename + "\".");
System.Environment.Exit(1);
}
CModel model = dataModel.getModel();
Debug.Assert(model != null);
// create a report with the correct filename and all the species against
// time.
CReportDefinitionVector reports = dataModel.getReportDefinitionList();
// create a new report definition object
CReportDefinition report = reports.createReportDefinition("Report", "Output for timecourse");
// set the task type for the report definition to timecourse
report.setTaskType(CTaskEnum.Task_timeCourse);
// we don't want a table
report.setIsTable(false);
// the entries in the output should be seperated by a ", "
report.setSeparator(new CCopasiReportSeparator(", "));
// we need a handle to the header and the body
// the header will display the ids of the metabolites and "time" for
// the first column
// the body will contain the actual timecourse data
ReportItemVector header = report.getHeaderAddr();
ReportItemVector body = report.getBodyAddr();
body.Add(new CRegisteredCommonName(model.getObject(new CCommonName("Reference=Time")).getCN().getString()));
body.Add(new CRegisteredCommonName(report.getSeparator().getCN().getString()));
header.Add(new CRegisteredCommonName(new CDataString("time").getCN().getString()));
header.Add(new CRegisteredCommonName(report.getSeparator().getCN().getString()));
uint i, iMax = (uint)model.getMetabolites().size();
for (i = 0; i < iMax; ++i)
{
CMetab metab = model.getMetabolite(i);
Debug.Assert(metab != null);
// we don't want output for FIXED metabolites right now
if (metab.getStatus() != CModelEntity.Status_FIXED)
{
// we want the concentration oin the output
// alternatively, we could use "Reference=Amount" to get the
// particle number
body.Add(new CRegisteredCommonName(metab.getObject(new CCommonName("Reference=Concentration")).getCN().getString()));
// add the corresponding id to the header
header.Add(new CRegisteredCommonName(new CDataString(metab.getSBMLId()).getCN().getString()));
// after each entry, we need a seperator
if (i != iMax - 1)
{
body.Add(new CRegisteredCommonName(report.getSeparator().getCN().getString()));
header.Add(new CRegisteredCommonName(report.getSeparator().getCN().getString()));
}
}
}
// get the trajectory task object
CTrajectoryTask trajectoryTask = (CTrajectoryTask)dataModel.getTask("Time-Course");
// run a deterministic time course
trajectoryTask.setMethodType(CTaskEnum.Method_deterministic);
// pass a pointer of the model to the problem
trajectoryTask.getProblem().setModel(dataModel.getModel());
// actiavate the task so that it will be run when the model is saved
// and passed to CopasiSE
trajectoryTask.setScheduled(true);
// set the report for the task
trajectoryTask.getReport().setReportDefinition(report);
// set the output filename
trajectoryTask.getReport().setTarget("example3.txt");
// don't append output if the file exists, but overwrite the file
trajectoryTask.getReport().setAppend(false);
// get the problem for the task to set some parameters
CTrajectoryProblem problem = (CTrajectoryProblem)trajectoryTask.getProblem();
// simulate 100 steps
problem.setStepNumber(100);
// start at time 0
dataModel.getModel().setInitialTime(0.0);
// simulate a duration of 10 time units
problem.setDuration(10);
// tell the problem to actually generate time series data
problem.setTimeSeriesRequested(true);
// set some parameters for the LSODA method through the method
CTrajectoryMethod method = (CTrajectoryMethod)trajectoryTask.getMethod();
CCopasiParameter parameter = method.getParameter("Absolute Tolerance");
Debug.Assert(parameter != null);
Debug.Assert(parameter.getType() == CCopasiParameter.Type_DOUBLE);
parameter.setDblValue(1.0e-12);
bool result = true;
try
{
// now we run the actual trajectory
result = trajectoryTask.processWithOutputFlags(true, (int)CCopasiTask.ONLY_TIME_SERIES);
}
catch
{
System.Console.Error.WriteLine("Error. Running the time course simulation failed.");
String lastErrors = trajectoryTask.getProcessError();
// check if there are additional error messages
if (!string.IsNullOrEmpty(lastErrors))
{
// print the messages in chronological order
System.Console.Error.WriteLine(lastErrors);
}
System.Environment.Exit(1);
}
if (result == false)
{
System.Console.Error.WriteLine("An error occured while running the time course simulation.");
String lastErrors = trajectoryTask.getProcessError();
// check if there are additional error messages
if (!string.IsNullOrEmpty(lastErrors))
{
// print the messages in chronological order
System.Console.Error.WriteLine(lastErrors);
}
System.Environment.Exit(1);
}
// look at the timeseries
CTimeSeries timeSeries = trajectoryTask.getTimeSeries();
// we simulated 100 steps, including the initial state, this should be
// 101 step in the timeseries
Debug.Assert(timeSeries.getRecordedSteps() == 101);
System.Console.WriteLine("The time series consists of " + System.Convert.ToString(timeSeries.getRecordedSteps()) + ".");
System.Console.WriteLine("Each step contains " + System.Convert.ToString(timeSeries.getNumVariables()) + " variables.");
System.Console.WriteLine("The final state is: ");
iMax = (uint)timeSeries.getNumVariables();
uint lastIndex = (uint)timeSeries.getRecordedSteps() - 1;
for (i = 0; i < iMax; ++i)
{
// here we get the particle number (at least for the species)
// the unit of the other variables may not be particle numbers
// the concentration data can be acquired with getConcentrationData
System.Console.WriteLine(timeSeries.getTitle(i) + ": " + System.Convert.ToString(timeSeries.getData(lastIndex, i)));
}
}
else
{
System.Console.Error.WriteLine("Usage: example3 SBMLFILE");
System.Environment.Exit(1);
}
}
/// <summary>
/// Updates a reaction.
/// </summary>
/// <param name="reaction">COPASI Reaction.</param>
/// <param name="reagents">Reagents.</param>
/// <param name="products">Products.</param>
/// <param name="rate">Rate.</param>
public void UpdateReaction(CReaction reaction, MoleculeSpecies[] reagents, MoleculeSpecies[] products, double rate)
{
// we can set these on the chemical equation of the reaction
CChemEq chemEq = reaction.getChemEq();
// remove all existing metabolites
chemEq.getSubstrates().clear();
chemEq.getProducts().clear();
// add substrates
CMetab[] substrates = GetMetabs(reagents);
foreach (CMetab item in substrates)
{
// add substrate with stoichiometry 1
chemEq.addMetabolite(item.getKey(), 1.0, CChemEq.SUBSTRATE);
}
// add products
CMetab[] metabProducts = GetMetabs(products);
foreach (CMetab item in metabProducts)
{
// add product with stoichiometry 1
chemEq.addMetabolite(item.getKey(), 1.0, CChemEq.PRODUCT);
}
// this reaction is to be irreversible
reaction.setReversible(false);
// now we ned to set a kinetic law on the reaction
// maybe constant flux would be OK
// we need to get the function from the function database
CFunctionDB funDB = CCopasiRootContainer.getFunctionList();
// it should be in the list of suitable functions
// lets get all suitable functions for an irreversible reaction with x substrates
// and y products
CFunctionStdVector suitableFunctions = funDB.suitableFunctions((uint)substrates.Length, (uint)products.Length, COPASI.TriFalse);
CFunction function = null;
for (int i = 0; i < suitableFunctions.Count; i++)
{
// we just assume that the only suitable function with mass action in
// it's name is the one we want
if (suitableFunctions[i].getObjectName().ToLower().Contains("mass action"))
{
function = suitableFunctions[i];
break;
}
}
if (function != null)
{
reaction.setFunction(function);
CCopasiParameterGroup parameterGroup = reaction.getParameters();
CCopasiParameter parameter = parameterGroup.getParameter(0);
// make sure the parameter is a local parameter
System.Diagnostics.Debug.Assert(reaction.isLocalParameter(parameter.getObjectName()));
// now we set the value of the parameter to 0.5
System.Diagnostics.Debug.Assert(parameter.getType() == CCopasiParameter.DOUBLE);
parameter.setDblValue(rate);
CCopasiObject obj = parameter.getValueReference();
changedObjects.Add(obj);
//reaction.getParameterMappings().Clear();
foreach (var substrate in substrates)
{
reaction.addParameterMapping("substrate", substrate.getKey());
}
}
else
{
throw new System.Exception("Error. Could not find a kinetic law that conatins the term \"mass action\".");
}
}
