22 #include "utilities.hpp"
54 CPPUNIT_ASSERT(pModel != NULL);
56 CPPUNIT_ASSERT(pModel->getVolumeUnitEnum() ==
CModel::ml);
57 CPPUNIT_ASSERT(pModel->getTimeUnitEnum() ==
CModel::s);
58 CPPUNIT_ASSERT(pModel->getCompartments().size() == 1);
59 const CCompartment* pCompartment = pModel->getCompartments()[0];
60 CPPUNIT_ASSERT(pCompartment != NULL);
62 CPPUNIT_ASSERT(pModel->getMetabolites().size() == 2);
63 CMetab* pA = pModel->getMetabolites()[0];
64 CPPUNIT_ASSERT(pA != NULL);
66 const CMetab* pB = pModel->getMetabolites()[1];
67 CPPUNIT_ASSERT(pB != NULL);
69 CPPUNIT_ASSERT(pModel->getModelValues().size() == 1);
70 const CModelValue* pModelValue = pModel->getModelValues()[0];
71 CPPUNIT_ASSERT(pModelValue != NULL);
73 CPPUNIT_ASSERT(pModelValue->getInitialExpression() !=
"");
74 const CExpression* pExpr = pModelValue->getInitialExpressionPtr();
75 CPPUNIT_ASSERT(pExpr != NULL);
78 CPPUNIT_ASSERT(pNode != NULL);
80 CPPUNIT_ASSERT(pObjectNode != NULL);
82 CPPUNIT_ASSERT(!objectCN.empty());
83 std::vector<CCopasiContainer*> listOfContainers;
84 listOfContainers.push_back(pModel);
86 CPPUNIT_ASSERT(pObject != NULL);
88 CPPUNIT_ASSERT(pObject->
getObjectName() == std::string(
"InitialConcentration"));
91 CPPUNIT_ASSERT(pModel->getReactions().size() == 2);
92 const CReaction* pReaction1 = pModel->getReactions()[0];
93 CPPUNIT_ASSERT(pReaction1 != NULL);
94 CPPUNIT_ASSERT(pReaction1->isReversible() ==
false);
96 const CFunction* pKineticFunction = pReaction1->getFunction();
97 CPPUNIT_ASSERT(pKineticFunction != NULL);
99 CPPUNIT_ASSERT(pMassAction != NULL);
100 const CChemEq* pChemEq = &pReaction1->getChemEq();
101 CPPUNIT_ASSERT(pChemEq != NULL);
105 CPPUNIT_ASSERT(pElement != NULL);
106 CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
107 CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
111 const CReaction* pReaction2 = pModel->getReactions()[1];
112 CPPUNIT_ASSERT(pReaction2 != NULL);
113 CPPUNIT_ASSERT(pReaction2->isReversible() ==
false);
115 pKineticFunction = pReaction2->getFunction();
116 CPPUNIT_ASSERT(pKineticFunction != NULL);
117 CPPUNIT_ASSERT(pKineticFunction->getObjectName() == std::string(
"Henri-Michaelis-Menten (irreversible)"));
119 pChemEq = &pReaction2->getChemEq();
120 CPPUNIT_ASSERT(pChemEq != NULL);
121 CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
122 CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
123 pElement = pChemEq->getSubstrates()[0];
124 CPPUNIT_ASSERT(pElement != NULL);
125 CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
126 CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
127 CPPUNIT_ASSERT(pChemEq->getProducts().size() == 1);
128 pElement = pChemEq->getProducts()[0];
129 CPPUNIT_ASSERT(pElement != NULL);
130 CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
131 CPPUNIT_ASSERT(pElement->getMetabolite() == pB);
132 CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
133 const std::vector<std::vector<std::string> > parameterMappings = pReaction2->getParameterMappings();
134 CPPUNIT_ASSERT(parameterMappings.size() == 3);
135 CPPUNIT_ASSERT(parameterMappings[0].size() == 1);
136 const std::string parameterKey = parameterMappings[0][0];
137 CPPUNIT_ASSERT(parameterKey == pA->getKey());
141 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
142 "<sbml xmlns=\"http://www.sbml.org/sbml/level2/version3\" level=\"2\" version=\"3\">\n"
144 " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
145 " <p>Model with fixed compartment volume, two species with hasOnlySubstanceUnits flag set to false. The units are set to ml and item. There is an initial assignment for the global parameter that contains a reference to species A.</p>\n"
146 " <p>The imported model should contain an initial assignment for the global parameter that consists of the reference to the initial concentration of species A. The species references in the reactions should be imported unmodified.</p>\n"
149 " <model id=\"Model_1\" name=\"New Model\">\n"
150 " <listOfFunctionDefinitions>\n"
151 " <functionDefinition id=\"function_1\" name=\"Henri-Michaelis-Menten (irreversible)\">\n"
152 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
155 " <ci> substrate </ci>\n"
168 " <ci> substrate </ci>\n"
173 " <ci> substrate </ci>\n"
178 " </functionDefinition>\n"
179 " </listOfFunctionDefinitions>\n"
180 " <listOfUnitDefinitions>\n"
181 " <unitDefinition id=\"volume\">\n"
183 " <unit kind=\"litre\" scale=\"-3\"/>\n"
185 " </unitDefinition>\n"
186 " <unitDefinition id=\"substance\">\n"
188 " <unit kind=\"item\"/>\n"
190 " </unitDefinition>\n"
191 " </listOfUnitDefinitions>\n"
192 " <listOfCompartments>\n"
193 " <compartment id=\"compartment_1\" name=\"compartment\" size=\"1\"/>\n"
194 " </listOfCompartments>\n"
196 " <species id=\"species_1\" name=\"A\" compartment=\"compartment_1\" initialConcentration=\"1\"/>\n"
197 " <species id=\"species_2\" name=\"B\" compartment=\"compartment_1\" initialConcentration=\"1\"/>\n"
198 " </listOfSpecies>\n"
199 " <listOfParameters>\n"
200 " <parameter id=\"parameter_1\" name=\"K\" value=\"0\" constant=\"true\"/>\n"
201 " </listOfParameters>\n"
202 " <listOfInitialAssignments>\n"
203 " <initialAssignment symbol=\"parameter_1\">\n"
204 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
205 " <ci> species_1 </ci>\n"
207 " </initialAssignment>\n"
208 " </listOfInitialAssignments>\n"
209 " <listOfReactions>\n"
210 " <reaction id=\"reaction_1\" name=\"reaction_0\" reversible=\"false\">\n"
211 " <listOfReactants>\n"
212 " <speciesReference species=\"species_1\"/>\n"
213 " </listOfReactants>\n"
215 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
218 " <ci> compartment_1 </ci>\n"
220 " <ci> species_1 </ci>\n"
223 " <listOfParameters>\n"
224 " <parameter id=\"k1\" value=\"0.1\"/>\n"
225 " </listOfParameters>\n"
228 " <reaction id=\"reaction_2\" name=\"reaction_1\" reversible=\"false\">\n"
229 " <listOfReactants>\n"
230 " <speciesReference species=\"species_1\"/>\n"
231 " </listOfReactants>\n"
232 " <listOfProducts>\n"
233 " <speciesReference species=\"species_2\"/>\n"
234 " </listOfProducts>\n"
236 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
239 " <ci> compartment_1 </ci>\n"
241 " <ci> function_1 </ci>\n"
242 " <ci> species_1 </ci>\n"
248 " <listOfParameters>\n"
249 " <parameter id=\"Km\" value=\"0.1\"/>\n"
250 " <parameter id=\"V\" value=\"0.1\"/>\n"
251 " </listOfParameters>\n"
254 " </listOfReactions>\n"
Header file of class CExpression.
size_t getCompartmentNumber() const
Header file of class CModelEntity and CModelValue.
const std::string & getObjectName() const
virtual size_t size() const
const CRegisteredObjectName & getObjectCN() const
const CCopasiVector< CChemEqElement > & getProducts() const
const CCopasiVector< CChemEqElement > & getSubstrates() const
static CCopasiDataModel * addDatamodel()
const CCopasiVector< CChemEqElement > & getModifiers() const
void test_hasOnlySubstanceUnits()
static CCopasiDataModel * pCOPASIDATAMODEL
bool importSBMLFromString(const std::string &sbmlDocumentText, CProcessReport *pImportHandler=NULL, const bool &deleteOldData=true)
The class for handling a chemical kinetic function.
static void init(int argc, char *argv[], const bool &withGui=false)
static const char * MODEL_STRING
CCopasiObject * ObjectFromName(const std::vector< CCopasiContainer * > &listOfContainer, const CCopasiObjectName &CN) const
CCopasiContainer * getObjectParent() const