public void TestSBML_Species()
{
SBMLReader reader = new SBMLReader();
SBMLDocument document = reader.readSBML(TestConstant.SBML_Oscillation);
SBML_Model model = new SBML_Model(document.getModel());
SBML_Compartment sc = new SBML_Compartment(model);
SBML_Species species = new SBML_Species(model);
// getConstant
SpeciesStruct ss = new SpeciesStruct();
int i = species.getConstant(ss);
Assert.AreEqual(0, i, "getConstant returns unexpected value.");
ss.Constant = true;
i = species.getConstant(ss);
Assert.AreEqual(1, i, "getConstant returns unexpected value.");
model.Level = 1;
i = species.getConstant(ss);
Assert.AreEqual(0, i, "getConstant returns unexpected value.");
ss.BoundaryCondition = true;
i = species.getConstant(ss);
Assert.AreEqual(1, i, "getConstant returns unexpected value.");
try
{
model.Level = 0;
i = species.getConstant(ss);
}
catch (Exception)
{
}
// getSpeciesValue
double d = species.getSpeciesValue(ss);
Assert.AreEqual(0.0, d, "getSpeciesValue returns unexpected value.");
model.Level = 2;
ss.InitialAmount = double.NaN;
ss.Compartment = "cell";
d = species.getSpeciesValue(ss);
Assert.AreEqual(0.0, d, "getSpeciesValue returns unexpected value.");
try
{
ss.InitialConcentration = double.NaN;
d = species.getSpeciesValue(ss);
}
catch (Exception)
{
}
// getSpeciesID
ss.ID = "Test1";
string id = species.getSpeciesID(ss);
Assert.AreEqual("/cell:Test1", id, "getSpeciesID returns unexpected value.");
try
{
model.Level = 1;
ss.Name = "Test2";
id = species.getSpeciesID(ss);
}
catch (Exception)
{
}
try
{
model.Level = 0;
id = species.getSpeciesID(ss);
}
catch (Exception)
{
}
try
{
model.Level = 2;
ss.Compartment = "";
id = species.getSpeciesID(ss);
}
catch (Exception)
{
}
}
/// <summary>
///
/// </summary>
/// <param name="filename"></param>
public static EcellModel Convert(string filename)
{
if (!File.Exists(filename))
throw new EcellException(string.Format(MessageResources.ErrFindFile, filename));
string sbml = File.ReadAllText(filename);
SBMLReader reader = new SBMLReader();
SBMLDocument document = reader.readSBMLFromString(sbml);
Model model = document.getModel();
if (model == null)
{
throw new EcellException(string.Format("{0} has no model.", filename));
}
SBML_Model theModel = new SBML_Model(model);
SBML_Compartment theCompartment = new SBML_Compartment(theModel);
SBML_Parameter theParameter = new SBML_Parameter( theModel );
SBML_Species theSpecies = new SBML_Species( theModel );
SBML_Rule theRule = new SBML_Rule( theModel );
SBML_Reaction theReaction = new SBML_Reaction(theModel);
SBML_Event theEvent = new SBML_Event(theModel);
document.Dispose();
//Eml eml = new Eml(null);
string modelId = Path.GetFileNameWithoutExtension(filename);
EcellModel modelObject = (EcellModel)EcellObject.CreateObject(modelId, "", Constants.xpathModel, "", new List<EcellData>());
// Set Layer
List<EcellLayer> layers = new List<EcellLayer>();
layers.Add(new EcellLayer(SbmlConstant.GlobalParameters, true));
modelObject.Layers = layers;
//
// Set Stepper.
//
EcellObject stepper = EcellObject.CreateObject(modelId, "DE", EcellObject.STEPPER, "FixedODE1Stepper", new List<EcellData>());
modelObject.Children.Add(stepper);
//
// Set Compartment ( System ).
//
EcellSystem rootSystem = (EcellSystem)EcellObject.CreateObject(modelId, "/", EcellObject.SYSTEM, EcellObject.SYSTEM, new List<EcellData>());
rootSystem.SetEcellValue("StepperID", new EcellValue("DE"));
rootSystem.SetEcellValue("Name", new EcellValue("Default"));
modelObject.Children.Add(rootSystem);
EcellSystem system = rootSystem;
foreach (CompartmentStruct aCompartment in theModel.CompartmentList)
{
// getPath
string aPath = "";
if ( theModel.Level == 1 )
aPath = theModel.getPath( aCompartment.Name );
else if ( theModel.Level == 2 )
aPath = theModel.getPath( aCompartment.ID );
// setFullID
if( aPath != "/" )
{
system = (EcellSystem)EcellObject.CreateObject(modelId, aPath, EcellObject.SYSTEM, EcellObject.SYSTEM, new List<EcellData>());
modelObject.Children.Add(system);
}
// setStepper
system.SetEcellValue("StepperID", new EcellValue("DE"));
// setName( default = [] )
if (theModel.Level == 2)
if (aCompartment.Name != "")
system.SetEcellValue("Name", new EcellValue(aCompartment.Name));
// setDimensions( default = 3 )
EcellObject dimension = EcellObject.CreateObject(modelId, aPath + ":Dimensions", EcellObject.VARIABLE, EcellObject.VARIABLE, new List<EcellData>());
dimension.SetEcellValue("Value", new EcellValue((int)aCompartment.SpatialDimension));
system.Children.Add(dimension);
// setSIZE
EcellObject size = EcellObject.CreateObject(modelId, aPath + ":SIZE", EcellObject.VARIABLE, EcellObject.VARIABLE, new List<EcellData>());
size.SetEcellValue("Value", new EcellValue((double)theCompartment.getCompartmentSize(aCompartment)));
system.Children.Add(size);
}
// Set GlobalParameter ( Variable )
if ( theModel.ParameterList.Count > 0)
{
foreach(ParameterStruct aParameter in theModel.ParameterList)
{
// setFullID
string parameterKey = theParameter.getParameterID( aParameter );
EcellObject parameter = EcellObject.CreateObject(modelId, parameterKey, EcellObject.VARIABLE, EcellObject.VARIABLE, new List<EcellData>());
// Set Layer
parameter.Layer = SbmlConstant.GlobalParameters;
// setName
if ( aParameter.Name != "" )
parameter.SetEcellValue("Name", new EcellValue(aParameter.Name));
// setValue
parameter.SetEcellValue("Value", new EcellValue(aParameter.Value));
// setFixed ( default = 1 )
if ( aParameter.Constant)
parameter.SetEcellValue("Fixed", new EcellValue(1));
// set to system.
rootSystem.Children.Add(parameter);
}
}
// Set Species ( Variable )
foreach(SpeciesStruct aSpecies in theModel.SpeciesList)
{
// Create
string aSpeciesID = theSpecies.getSpeciesID( aSpecies );
EcellObject variable = EcellObject.CreateObject(modelId, aSpeciesID, EcellObject.VARIABLE, EcellObject.VARIABLE, new List<EcellData>());
// setName
if( theModel.Level == 2 )
if ( aSpecies.Name != "" )
variable.SetEcellValue("Name", new EcellValue(aSpecies.Name));
// setValue
variable.SetEcellValue("Value", new EcellValue(theSpecies.getSpeciesValue( aSpecies )));
// setFixed
variable.SetEcellValue("Fixed", new EcellValue(theSpecies.getConstant( aSpecies )));
// add
modelObject.AddEntity(variable);
}
// Set Rule ( Process )
if ( theModel.RuleList.Count > 0)
{
// make Rule System
string aSystemKey = "/SBMLRule";
system = (EcellSystem)EcellObject.CreateObject(modelId, aSystemKey, EcellObject.SYSTEM, EcellObject.SYSTEM, new List<EcellData>());
system.SetEcellValue("Name", new EcellValue("System for SBML Rule"));
system.SetEcellValue("StepperID", new EcellValue("DE"));
modelObject.Children.Add(system);
foreach(RuleStruct aRule in theModel.RuleList)
{
theRule.initialize();
// setFullID
string aRuleID = theRule.getRuleID();
EcellObject process = EcellObject.CreateObject(modelId, aRuleID, EcellObject.PROCESS, EcellObject.PROCESS, new List<EcellData>());
modelObject.AddEntity(process);
// Algebraic Rule
if ( aRule.RuleType == libsbml.libsbml.SBML_ALGEBRAIC_RULE )
{
process.Classname = "ExpressionAlgebraicProcess";
}
// Assignment Rule
else if (aRule.RuleType == libsbml.libsbml.SBML_ASSIGNMENT_RULE ||
aRule.RuleType == libsbml.libsbml.SBML_SPECIES_CONCENTRATION_RULE ||
aRule.RuleType == libsbml.libsbml.SBML_COMPARTMENT_VOLUME_RULE ||
aRule.RuleType == libsbml.libsbml.SBML_PARAMETER_RULE)
{
process.Classname = "ExpressionAssignmentProcess";
int aVariableType = theRule.getVariableType( aRule.Variable );
if (aVariableType == libsbml.libsbml.SBML_SPECIES)
theRule.setSpeciesToVariableReference( aRule.Variable, 1 );
else if (aVariableType == libsbml.libsbml.SBML_PARAMETER)
theRule.setParameterToVariableReference( aRule.Variable, 1 );
else if (aVariableType == libsbml.libsbml.SBML_COMPARTMENT)
theRule.setCompartmentToVariableReference( aRule.Variable, 1 );
else
throw new EcellException("Variable type must be Species, Parameter, or Compartment");
}
// Rate Rule
else if (aRule.RuleType == libsbml.libsbml.SBML_RATE_RULE)
{
process.Classname = "ExpressionFluxProcess";
int aVariableType = theRule.getVariableType( aRule.Variable );
if (aVariableType == libsbml.libsbml.SBML_SPECIES)
theRule.setSpeciesToVariableReference( aRule.Variable, 1 );
else if (aVariableType == libsbml.libsbml.SBML_PARAMETER)
theRule.setParameterToVariableReference( aRule.Variable, 1 );
else if (aVariableType == libsbml.libsbml.SBML_COMPARTMENT)
theRule.setCompartmentToVariableReference( aRule.Variable, 1 );
else
throw new EcellException("Variable type must be Species, Parameter, or Compartment");
}
else
throw new EcellException(" The type of Rule must be Algebraic, Assignment or Rate Rule");
// convert SBML formula to E-Cell formula
string convertedFormula = theRule.convertRuleFormula( aRule.Formula );
// set Expression Property
process.SetEcellValue("Expression", new EcellValue(convertedFormula));
// setVariableReferenceList
process.SetEcellValue("VariableReferenceList", new EcellValue(theRule.GetVariableReferenceList()));
}
}
// Set Reaction ( Process )
foreach(ReactionStruct aReaction in theModel.ReactionList)
{
theReaction.initialize();
// setFullID
string aReactionID = theReaction.getReactionID( aReaction );
EcellProcess process = (EcellProcess)EcellObject.CreateObject(modelId, aReactionID, EcellObject.PROCESS, "ExpressionFluxProcess", new List<EcellData>());
// setName
if ( theModel.Level == 2 )
if( aReaction.Name != "" )
process.SetEcellValue("Name",new EcellValue(aReaction.Name));
// setSubstrate
foreach(ReactantStruct aSubstrate in aReaction.Reactants)
{
string name = "S" + theReaction.SubstrateNumber.ToString();
string aSubstrateID = theModel.getSpeciesReferenceID( aSubstrate.Species );
if ( aSubstrateID == null )
throw new EcellException("Species "+aSubstrate.Species+" not found");
if ( aSubstrate.Denominator != 1 )
throw new EcellException("Stoichiometry Error : E-Cell System can't set a floating Stoichiometry");
int coefficient = -1 * theReaction.getStoichiometry(aSubstrate.Species, aSubstrate.Stoichiometry );
VariableReferenceStruct aSubstrateList = new VariableReferenceStruct(name, "Variable:" + aSubstrateID, coefficient);
theReaction.VariableReferenceList.Add( aSubstrateList );
theReaction.SubstrateNumber = theReaction.SubstrateNumber + 1;
}
// setProduct
foreach(ProductStruct aProduct in aReaction.Products)
{
string name = 'P' + theReaction.ProductNumber.ToString();
string aProductID = theModel.getSpeciesReferenceID( aProduct.Species );
if ( aProductID == "" )
throw new EcellException("Species "+aProduct.Species+" not found");
if ( aProduct.Denominator != 1 )
throw new EcellException("Stoichiometry Error : E-Cell System can't set a floating Stoichiometry");
int coefficient = 1 * theReaction.getStoichiometry(aProduct.Species, aProduct.Stoichiometry );
VariableReferenceStruct aProductList = new VariableReferenceStruct(name, "Variable:" + aProductID, coefficient);
theReaction.VariableReferenceList.Add( aProductList );
theReaction.ProductNumber = theReaction.ProductNumber + 1;
}
// setCatalyst
foreach(string aModifier in aReaction.Modifiers)
{
string name = "C" + theReaction.ModifierNumber.ToString();
string aModifierID = theModel.getSpeciesReferenceID( aModifier );
if ( aModifierID == "" )
throw new EcellException("Species "+aModifier+" not found");
VariableReferenceStruct aModifierList = new VariableReferenceStruct(name, "Variable:" + aModifierID, 0);
theReaction.VariableReferenceList.Add( aModifierList );
theReaction.ModifierNumber = theReaction.ModifierNumber + 1;
}
// setProperty
foreach(KineticLawStruct kineticLaw in aReaction.KineticLaws)
{
foreach(ParameterStruct aParameter in kineticLaw.Parameters)
{
if (theModel.Level == 1)
process.SetEcellValue(aParameter.Name, new EcellValue(aParameter.Value));
else if (theModel.Level == 2)
process.SetEcellValue(aParameter.ID, new EcellValue(aParameter.Value));
}
// set "Expression" Property
// convert SBML format formula to E-Cell format formula
if( kineticLaw.Formula != "" )
{
string anExpression = theReaction.convertKineticLawFormula( kineticLaw.Formula );
// set Expression Property for ExpressionFluxProcess
process.SetEcellValue("Expression", new EcellValue(anExpression));
// setVariableReferenceList
process.SetEcellValue("VariableReferenceList", new EcellValue(theReaction.GetVariableReferenceList()));
}
}
// Set Parent System.
string sysKey = process.ParentSystemID;
foreach (EcellReference er in process.ReferenceList)
{
if (er.Coefficient == -1)
sysKey = er.Key.Split(':')[0];
}
foreach (EcellReference er in process.ReferenceList)
{
if (er.Coefficient == 1)
sysKey = er.Key.Split(':')[0];
}
process.Key = sysKey + ":" + process.LocalID;
// Update EntityPath.
foreach (EcellData data in process.Value)
{
data.EntityPath = process.FullID + ":" + data.Name;
}
modelObject.AddEntity(process);
}
return modelObject;
}
public void TestSBML_Rule()
{
SBMLReader reader = new SBMLReader();
SBMLDocument document = reader.readSBML(TestConstant.SBML_BIOMD0000000003);
Model sbmlModel = document.getModel();
SBML_Model model = new SBML_Model(sbmlModel);
SBML_Compartment sc = new SBML_Compartment(model);
SBML_Species species = new SBML_Species(model);
SBML_Rule rule = new SBML_Rule(model);
}