/// <summary>
/// [ ReactionStruct ]
/// [[ Id , Name , [ KineticLawStruct ] , Reversible , Fast , [ ReactantStruct ] , [ ProductStruct ] , [ ModifierSpecies ] ]]
/// </summary>
/// <param name="aSBMLmodel"></param>
/// <returns></returns>
public static List<ReactionStruct> getReaction(Model aSBMLmodel)
{
List<ReactionStruct> list = new List<ReactionStruct>();
ListOfReactions reactions = aSBMLmodel.getListOfReactions();
for (int i = 0; i < reactions.size(); i++ )
{
Reaction aReaction = aSBMLmodel.getReaction(i);
string anId = aReaction.getId();
string aName =aReaction.getName();
//----------KineticLaw----------------------------------
List<KineticLawStruct> ListOfKineticLaw = new List<KineticLawStruct>();
if( aReaction.isSetKineticLaw())
{
KineticLaw aKineticLaw = aReaction.getKineticLaw();
if( aKineticLaw != null)
{
string aFormula_KL;
if( aKineticLaw.isSetFormula())
aFormula_KL = aKineticLaw.getFormula();
else
aFormula_KL = "";
List<string> aString_KL = new List<string>();
if (aSBMLmodel.getLevel() == 1)
{
aString_KL.Add( "" );
}
else
{
if (aKineticLaw.isSetMath())
{
ASTNode anASTNode_KL = aKineticLaw.getMath();
aString_KL.Add( libsbml.libsbml.formulaToString( anASTNode_KL ) );
}
else
aString_KL.Add( "" );
}
string aTimeUnit_KL = aKineticLaw.getTimeUnits();
string aSubstanceUnit_KL = aKineticLaw.getSubstanceUnits();
List<ParameterStruct> listOfParameters = new List<ParameterStruct>();
ListOfParameters parameters = aKineticLaw.getListOfParameters();
for (int j = 0; j < parameters.size(); j++ )
{
Parameter aParameter = aKineticLaw.getParameter(j);
if (aParameter == null)
continue;
string anId_KL_P = aParameter.getId();
string aName_KL_P = aParameter.getName();
double aValue_KL_P = aParameter.getValue();
string aUnit_KL_P = aParameter.getUnits();
bool aConstant_KL_P = aParameter.getConstant();
ParameterStruct parameter = new ParameterStruct(
anId_KL_P,
aName_KL_P,
aValue_KL_P,
aUnit_KL_P,
aConstant_KL_P);
listOfParameters.Add( parameter );
}
XMLNode anExpressionAnnotation = aKineticLaw.getAnnotation();
KineticLawStruct kineticLaw = new KineticLawStruct(
aFormula_KL,
aString_KL,
aTimeUnit_KL,
aSubstanceUnit_KL,
listOfParameters,
anExpressionAnnotation );
ListOfKineticLaw.Add(kineticLaw);
}
}
bool aReversible = aReaction.getReversible();
bool aFast = aReaction.getFast();
//----------Reactants----------------------------------
List<ReactantStruct> ListOfReactants = new List<ReactantStruct>();
ListOfSpeciesReferences reactants = aReaction.getListOfReactants();
for (int k = 0; k < reactants.size(); k++ )
{
SpeciesReference aSpeciesReference = aReaction.getReactant(k);
string aSpecies_R = aSpeciesReference.getSpecies();
int aStoichiometry_R = (int)aSpeciesReference.getStoichiometry();
string aString_R = GetStoichiometryMath(aSpeciesReference);
int aDenominator_R = aSpeciesReference.getDenominator();
ReactantStruct reactant = new ReactantStruct(
aSpecies_R,
aStoichiometry_R,
aString_R,
aDenominator_R);
ListOfReactants.Add( reactant );
}
//----------Products----------------------------------
List<ProductStruct> ListOfProducts = new List<ProductStruct>();
ListOfSpeciesReferences products = aReaction.getListOfProducts();
long max = products.size();
for (int l = 0; l < max; l++)
{
SpeciesReference aSpeciesReference = aReaction.getProduct(l);
string aSpecies_P = aSpeciesReference.getSpecies();
double aStoichiometry_P = aSpeciesReference.getStoichiometry();
string aString_P = GetStoichiometryMath(aSpeciesReference);
int aDenominator_P = aSpeciesReference.getDenominator();
ProductStruct product = new ProductStruct(
aSpecies_P,
aStoichiometry_P,
aString_P,
aDenominator_P);
ListOfProducts.Add( product );
}
//----------Modifiers----------------------------------
List<string> ListOfModifiers = new List<string>();
ListOfSpeciesReferences modifiers = aReaction.getListOfModifiers();
for (long l = 0; l < modifiers.size(); l++ )
{
ModifierSpeciesReference aSpeciesReference = aReaction.getModifier(l);
string aSpecies_M = aSpeciesReference.getSpecies();
ListOfModifiers.Add( aSpecies_M );
}
ReactionStruct reaction = new ReactionStruct(
anId,
aName,
ListOfKineticLaw,
aReversible,
aFast,
ListOfReactants,
ListOfProducts,
ListOfModifiers );
list.Add(reaction);
}
return list;
}
public void TestConstructorOfStructs()
{
//
CompartmentStruct c = new CompartmentStruct(
"ID",
"Name",
0,
0.0,
0.0,
"Unit",
"Parent",
false);
//
EventStruct e = new EventStruct(
"ID",
"Name",
"Trigger",
"delay",
"TimeUnit",
new List<EventAssignmentStruct>());
//
EventAssignmentStruct ea = new EventAssignmentStruct(
"Variable",
"Formula");
//
FunctionDefinitionStruct fd = new FunctionDefinitionStruct(
"ID",
"Name",
"Formula");
//
ParameterStruct p = new ParameterStruct(
"ID",
"Name",
0.0,
"Unit",
false);
//
ReactionStruct r = new ReactionStruct(
"ID",
"Name",
new List<KineticLawStruct>(),
false,
false,
new List<ReactantStruct>(),
new List<ProductStruct>(),
new List<string>());
//
KineticLawStruct k = new KineticLawStruct(
"Formula",
new List<string>(),
"TimeUnit",
"Substance",
new List<ParameterStruct>(),
null);
//
ReactantStruct rs = new ReactantStruct(
"Species",
0,
"Formula",
0);
//
ProductStruct ps = new ProductStruct(
"Species",
0.0,
"Formula",
0);
//
RuleStruct rule = new RuleStruct(
0,
"Formula",
"Variable");
//
SpeciesStruct s = new SpeciesStruct(
"ID",
"Name",
"Parent",
0.0,
0.0,
"Substance",
"Spatial",
"Unit",
false,
false,
0,
false);
//
UnitDefinitionStruct ud = new UnitDefinitionStruct(
"ID",
"Name",
new List<UnitStruct>());
//
UnitStruct u = new UnitStruct(
"Kind",
0,
0,
0.0,
0.0);
//
VariableReferenceStruct v = new VariableReferenceStruct(
"Name",
"Variable",
0);
//
InitialAssignmentStruct i = new InitialAssignmentStruct(
"Name",
0.0);
}