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(
"InitialParticleNumber"));
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);
101 CPPUNIT_ASSERT(pMassAction == NULL);
102 const CChemEq* pChemEq = &pReaction1->getChemEq();
103 CPPUNIT_ASSERT(pChemEq != NULL);
107 CPPUNIT_ASSERT(pElement != NULL);
108 CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
109 CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
113 const CReaction* pReaction2 = pModel->getReactions()[1];
114 CPPUNIT_ASSERT(pReaction2 != NULL);
115 CPPUNIT_ASSERT(pReaction2->isReversible() ==
false);
117 pKineticFunction = pReaction2->getFunction();
118 CPPUNIT_ASSERT(pKineticFunction != NULL);
119 CPPUNIT_ASSERT(pKineticFunction->getObjectName() == std::string(
"Henri-Michaelis-Menten (irreversible)"));
121 pChemEq = &pReaction2->getChemEq();
122 CPPUNIT_ASSERT(pChemEq != NULL);
123 CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
124 CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
125 pElement = pChemEq->getSubstrates()[0];
126 CPPUNIT_ASSERT(pElement != NULL);
127 CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
128 CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
129 CPPUNIT_ASSERT(pChemEq->getProducts().size() == 1);
130 pElement = pChemEq->getProducts()[0];
131 CPPUNIT_ASSERT(pElement != NULL);
132 CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
133 CPPUNIT_ASSERT(pElement->getMetabolite() == pB);
134 CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
135 const std::vector<std::vector<std::string> > parameterMappings = pReaction2->getParameterMappings();
136 CPPUNIT_ASSERT(parameterMappings.size() == 3);
137 CPPUNIT_ASSERT(parameterMappings[0].size() == 1);
138 const std::string parameterKey = parameterMappings[0][0];
139 CPPUNIT_ASSERT(parameterKey == pA->getKey());
143 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
144 "<sbml xmlns=\"http://www.sbml.org/sbml/level2/version3\" level=\"2\" version=\"3\">\n"
145 " <model id=\"Model_1\" name=\"New Model\">\n"
147 " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
148 " <p>Model with fixed compartment volume, two species with hasOnlySubstanceUnits flag set to true. 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"
149 " <p>The imported model should contain an initial assignment for the global parameter that consists of the reference to the particle number of species A. The species references in the reactions should be imported multiplied by the volume.</p>\n"
152 " <listOfFunctionDefinitions>\n"
153 " <functionDefinition id=\"function_1\" name=\"Henri-Michaelis-Menten (irreversible)\">\n"
154 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
157 " <ci> substrate </ci>\n"
170 " <ci> substrate </ci>\n"
175 " <ci> substrate </ci>\n"
180 " </functionDefinition>\n"
181 " </listOfFunctionDefinitions>\n"
182 " <listOfUnitDefinitions>\n"
183 " <unitDefinition id=\"volume\">\n"
185 " <unit kind=\"litre\" scale=\"-3\"/>\n"
187 " </unitDefinition>\n"
188 " <unitDefinition id=\"substance\">\n"
190 " <unit kind=\"item\"/>\n"
192 " </unitDefinition>\n"
193 " </listOfUnitDefinitions>\n"
194 " <listOfCompartments>\n"
195 " <compartment id=\"compartment_1\" name=\"compartment\" size=\"1\"/>\n"
196 " </listOfCompartments>\n"
198 " <species id=\"species_1\" name=\"A\" compartment=\"compartment_1\" initialAmount=\"1\" hasOnlySubstanceUnits=\"true\"/>\n"
199 " <species id=\"species_2\" name=\"B\" compartment=\"compartment_1\" initialAmount=\"1\" hasOnlySubstanceUnits=\"true\"/>\n"
200 " </listOfSpecies>\n"
201 " <listOfParameters>\n"
202 " <parameter id=\"parameter_1\" name=\"K\" value=\"0\" constant=\"true\"/>\n"
203 " </listOfParameters>\n"
204 " <listOfInitialAssignments>\n"
205 " <initialAssignment symbol=\"parameter_1\">\n"
206 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
207 " <ci> species_1 </ci>\n"
209 " </initialAssignment>\n"
210 " </listOfInitialAssignments>\n"
211 " <listOfReactions>\n"
212 " <reaction id=\"reaction_1\" name=\"reaction_0\" reversible=\"false\">\n"
213 " <listOfReactants>\n"
214 " <speciesReference species=\"species_1\"/>\n"
215 " </listOfReactants>\n"
217 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
221 " <ci> species_1 </ci>\n"
224 " <listOfParameters>\n"
225 " <parameter id=\"k1\" value=\"0.1\"/>\n"
226 " </listOfParameters>\n"
229 " <reaction id=\"reaction_2\" name=\"reaction_1\" reversible=\"false\">\n"
230 " <listOfReactants>\n"
231 " <speciesReference species=\"species_1\"/>\n"
232 " </listOfReactants>\n"
233 " <listOfProducts>\n"
234 " <speciesReference species=\"species_2\"/>\n"
235 " </listOfProducts>\n"
237 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
240 " <ci> compartment_1 </ci>\n"
242 " <ci> function_1 </ci>\n"
245 " <ci> species_1 </ci>\n"
246 " <ci> compartment_1 </ci>\n"
253 " <listOfParameters>\n"
254 " <parameter id=\"Km\" value=\"0.1\"/>\n"
255 " <parameter id=\"V\" value=\"0.1\"/>\n"
256 " </listOfParameters>\n"
259 " </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
void test_hasOnlySubstanceUnits()
static const char * MODEL_STRING
const CCopasiVector< CChemEqElement > & getProducts() const
const CCopasiVector< CChemEqElement > & getSubstrates() const
static CCopasiDataModel * addDatamodel()
const CCopasiVector< CChemEqElement > & getModifiers() const
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)
CCopasiObject * ObjectFromName(const std::vector< CCopasiContainer * > &listOfContainer, const CCopasiObjectName &CN) const
CCopasiContainer * getObjectParent() const
static CCopasiDataModel * pCOPASIDATAMODEL