public createReactant ( ) : SpeciesReference | ||
Résultat | SpeciesReference |
public void test_Model_createReactant() { Model m = new Model(2,2); Reaction p = m.createReaction(); SpeciesReference sr = m.createReactant(); assertTrue( p.getNumReactants() == 1 ); assertTrue( (sr).getLevel() == 2 ); assertTrue( (sr).getVersion() == 2 ); m = null; }
public void test_SpeciesReference_Reactant_parent_create_model() { Model m = new Model(2,4); Reaction r = m.createReaction(); SpeciesReference sr = m.createReactant(); ListOf lo = r.getListOfReactants(); assertTrue( lo == r.getReactant(0).getParentSBMLObject() ); assertTrue( lo == sr.getParentSBMLObject() ); assertTrue( r == lo.getParentSBMLObject() ); }
public void test_create_l1v1_units() { SBMLDocument d; Model m; Compartment c; KineticLaw kl; Parameter p; Reaction r; Species s; SpeciesReference sr; Unit u; UnitDefinition ud; d = new SBMLDocument(); m = new Model(2,4); d.setModel(m); ud = m.createUnitDefinition(); ud.setName( "substance"); u = m.createUnit(); u.setKind(libsbml.UNIT_KIND_MOLE); u.setScale(-3); ud = m.createUnitDefinition(); ud.setName( "mls"); u = m.createUnit(); u.setKind(libsbml.UNIT_KIND_MOLE); u.setScale(-3); u = m.createUnit(); u.setKind(libsbml.UNIT_KIND_LITER); u.setExponent(-1); u = m.createUnit(); u.setKind(libsbml.UNIT_KIND_SECOND); u.setExponent(-1); c = m.createCompartment(); c.setName( "cell"); s = m.createSpecies(); s.setName( "x0"); s.setCompartment( "cell"); s.setInitialAmount(1); s = m.createSpecies(); s.setName( "x1"); s.setCompartment( "cell"); s.setInitialAmount(1); s = m.createSpecies(); s.setName( "s1"); s.setCompartment( "cell"); s.setInitialAmount(1); s = m.createSpecies(); s.setName( "s2"); s.setCompartment( "cell"); s.setInitialAmount(1); p = m.createParameter(); p.setName( "vm"); p.setUnits( "mls"); p.setValue(2); p = m.createParameter(); p.setName( "km"); p.setValue(2); r = m.createReaction(); r.setName( "v1"); sr = m.createReactant(); sr.setSpecies( "x0"); sr = m.createProduct(); sr.setSpecies( "s1"); kl = m.createKineticLaw(); kl.setFormula( "(vm * s1)/(km + s1)"); r = m.createReaction(); r.setName( "v2"); sr = m.createReactant(); sr.setSpecies( "s1"); sr = m.createProduct(); sr.setSpecies( "s2"); kl = m.createKineticLaw(); kl.setFormula( "(vm * s2)/(km + s2)"); r = m.createReaction(); r.setName( "v3"); sr = m.createReactant(); sr.setSpecies( "s2"); sr = m.createProduct(); sr.setSpecies( "x1"); kl = m.createKineticLaw(); kl.setFormula( "(vm * s1)/(km + s1)"); d = null; }
private static void createReaction(EcellObject anEml, Model aSBMLModel) { EcellProcess aProcess = (EcellProcess)anEml; List<EcellReference> aVariableReferenceList = aProcess.ReferenceList; string anExpression = aProcess.Expression; // ------------------ // make Rule object // ------------------ if ( anEml.ParentSystemID == "/SBMLRule" ) { // get Process Class anExpression = convertExpression( anExpression, aVariableReferenceList, aProcess.ParentSystemID); if( aProcess.Classname == ProcessConstants.ExpressionAlgebraicProcess ) { // create AlgebraicRule object AlgebraicRule anAlgebraicRule = aSBMLModel.createAlgebraicRule(); // set AlgebraicRule Formula anAlgebraicRule.setFormula( anExpression ); } else if( aProcess.Classname == ProcessConstants.ExpressionAssignmentProcess ) { foreach(EcellReference aVariableReference in aVariableReferenceList) { if ( aVariableReference.Coefficient != 0 ) { // create AssignmentRule object AssignmentRule anAssignmentRule =aSBMLModel.createAssignmentRule(); // set AssignmentRule Formula anAssignmentRule.setFormula( aVariableReference.Coefficient.ToString() + "* ( " + anExpression + ")" ); string aVariableID = getVariableReferenceId( aVariableReference.FullID, aProcess.ParentSystemID ); anAssignmentRule.setVariable( aVariableID ); } } } else if( aProcess.Classname == ProcessConstants.ExpressionFluxProcess ) { foreach(EcellReference aVariableReference in aVariableReferenceList) { if ( aVariableReference.Coefficient != 0 ) { // create AssignmentRule object RateRule aRateRule = aSBMLModel.createRateRule(); // set AssignmentRule Formula aRateRule.setFormula( aVariableReference.Coefficient + "* ( " + anExpression + ")" ); string aVariableID = getVariableReferenceId( aVariableReference.FullID, aProcess.ParentSystemID ); aRateRule.setVariable( aVariableID ); } } } else { throw new EcellException("The type of Process must be Algebraic, Assignment, Flux Processes: " + aProcess.Key); } } // ---------------------- // make Reaction object // ---------------------- else { // create Parameter object Reaction aReaction = aSBMLModel.createReaction(); // create KineticLaw Object KineticLaw aKineticLaw = aSBMLModel.createKineticLaw(); // set Reaction ID if (aSBMLModel.getLevel() == 1) aReaction.setName( anEml.LocalID ); if (aSBMLModel.getLevel() == 2) aReaction.setId( anEml.LocalID ); foreach(EcellData aProperty in anEml.Value) { if (!aProperty.Loadable) continue; string aFullPN = aProcess.FullID + ":" + aProperty.Name; // set Name property ( Name ) if ( aProperty.Name == "Name" ) { // set Reaction Name if (aSBMLModel.getLevel() == 1) { } else if (aSBMLModel.getLevel() == 2) aReaction.setName( (string)aProperty.Value ); } // set Expression property ( KineticLaw Formula ) else if ( aProperty.Name == "Expression") { // convert Expression of the ECELL format to // SBML kineticLaw formula // setExpressionAnnotation( aKineticLaw, anExpression ); bool aDelayFlag = false; anExpression = convertExpression(anExpression, aVariableReferenceList, aProcess.ParentSystemID); // get Current System Id string CompartmentOfReaction = ""; foreach (EcellReference aVariableReference in aVariableReferenceList) { if (aVariableReference.Coefficient == 0) continue; CompartmentOfReaction = getCompartmentID(aVariableReference.FullID, aProcess.ParentSystemID); } // set KineticLaw Formula if ( aDelayFlag == false ) aKineticLaw.setFormula( anExpression ); else { ASTNode anASTNode = libsbml.libsbml.parseFormula( anExpression ); anASTNode = setDelayType( anASTNode ); aKineticLaw.setMath( anASTNode ); } } // set VariableReference property ( SpeciesReference ) else if ( aProperty.Name == "VariableReferenceList" ) { // make a flag. Because SBML model is defined // both Product and Reactant. This flag is required // in order to judge whether the Product and the // Reactant are defined. bool aReactantFlag = false; bool aProductFlag = false; foreach(EcellReference aVariableReference in aVariableReferenceList) { // -------------------------------- // add Reactants to Reaction object // -------------------------------- if ( aVariableReference.Coefficient < 0 ) { // change the Reactant Flag aReactantFlag = true; // create Reactant object SpeciesReference aReactant = aSBMLModel.createReactant(); // set Species Id to Reactant object string aSpeciesReferenceId = getVariableReferenceId ( aVariableReference.FullID, aProcess.ParentSystemID ); aReactant.setSpecies( aSpeciesReferenceId ); // set Stoichiometry aReactant.setStoichiometry( -aVariableReference.Coefficient ); } // ------------------------------- // add Products to Reaction object // ------------------------------- else if ( aVariableReference.Coefficient > 0 ) { // change the Product Flag aProductFlag = true; // create Product object SpeciesReference aProduct = aSBMLModel.createProduct(); // set Species Id string aSpeciesReferenceId = getVariableReferenceId ( aVariableReference.FullID, aProcess.ParentSystemID ); aProduct.setSpecies( aSpeciesReferenceId ); // set Stoichiometry aProduct.setStoichiometry( aVariableReference.Coefficient ); } // -------------------------------- // add Modifiers to Reaction object // -------------------------------- else { // create Modifier object ModifierSpeciesReference aModifier = aSBMLModel.createModifier(); // set Species Id to Modifier object string aVariableReferenceId = getVariableReferenceId( aVariableReference.FullID, aProcess.ParentSystemID ); aModifier.setSpecies( aVariableReferenceId ); } } // set EmptySet Species, because if it didn"t define, // Reactant or Product can not be defined. //if (!aReactantFlag) //{ // // create Reactant object // SpeciesReference aReactant = aSBMLModel.createReactant(); // // set Species Id to Reactant object // aReactant.setSpecies("EmptySet"); // // set Stoichiometry // aReactant.setStoichiometry(0); //} //else if (!aProductFlag) //{ // // create Product object // SpeciesReference aProduct = aSBMLModel.createProduct(); // // set Species Id // aProduct.setSpecies("EmptySet"); // // set Stoichiometry // aProduct.setStoichiometry(0); //} } // These properties are not defined in SBML Lv2 else if ( aProperty.Name == "Priority" || aProperty.Name == "Activity" || aProperty.Name == "IsContinuous" || aProperty.Name == "StepperID" || aProperty.Name == "FireMethod" || aProperty.Name == "InitializeMethod" ) { continue; } else { // create Parameter Object (Local) Parameter aParameter = aSBMLModel.createKineticLawParameter(); // set Parameter ID aParameter.setId( aProperty.Name ); // set Parameter Value aParameter.setValue((double)aProperty.Value); } } // add KineticLaw Object to Reaction Object aReaction.setKineticLaw( aKineticLaw ); } }
public void test_SpeciesReference_Reactant_ancestor_create_model() { Model m = new Model(2,4); Reaction r = m.createReaction(); SpeciesReference sr = m.createReactant(); ListOf lo = r.getListOfReactants(); assertTrue( sr.getAncestorOfType(libsbml.SBML_REACTION) == r ); assertTrue( sr.getAncestorOfType(libsbml.SBML_LIST_OF) == lo ); assertTrue( sr.getAncestorOfType(libsbml.SBML_MODEL) == m ); assertTrue( sr.getAncestorOfType(libsbml.SBML_DOCUMENT) == null ); assertTrue( sr.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null ); SpeciesReference obj = r.getReactant(0); assertTrue( obj.getAncestorOfType(libsbml.SBML_REACTION) == r ); assertTrue( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo ); assertTrue( obj.getAncestorOfType(libsbml.SBML_MODEL) == m ); assertTrue( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == null ); assertTrue( obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == null ); }