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() == 2);
71 const CModelValue* pFactor = pModel->getModelValues()[1];
72 CPPUNIT_ASSERT(pFactor != NULL);
74 CPPUNIT_ASSERT(fabs((pFactor->getInitialValue() - pModel->getQuantity2NumberFactor()) / pModel->getQuantity2NumberFactor()) < 1e-3);
75 const CModelValue* pModelValue = pModel->getModelValues()[0];
76 CPPUNIT_ASSERT(pModelValue != NULL);
81 CPPUNIT_ASSERT(pNode != NULL);
83 CPPUNIT_ASSERT(pOperatorNode != NULL);
86 CPPUNIT_ASSERT(pObjectNode != NULL);
88 CPPUNIT_ASSERT(!objectCN.empty());
89 std::vector<CCopasiContainer*> listOfContainers;
90 listOfContainers.push_back(pModel);
92 CPPUNIT_ASSERT(pObject != NULL);
94 CPPUNIT_ASSERT(pObject->
getObjectName() == std::string(
"ParticleNumber"));
97 CPPUNIT_ASSERT(pObjectNode != NULL);
98 objectCN = pObjectNode->getObjectCN();
99 CPPUNIT_ASSERT(!objectCN.empty());
101 CPPUNIT_ASSERT(pObject != NULL);
102 CPPUNIT_ASSERT(pObject->isReference() ==
true);
103 CPPUNIT_ASSERT(pObject->getObjectName() == std::string(
"Value"));
104 CPPUNIT_ASSERT(pObject->getObjectParent() == pFactor);
106 CPPUNIT_ASSERT(pModel->getReactions().size() == 2);
107 const CReaction* pReaction1 = pModel->getReactions()[0];
108 CPPUNIT_ASSERT(pReaction1 != NULL);
109 CPPUNIT_ASSERT(pReaction1->isReversible() ==
false);
111 const CFunction* pKineticFunction = pReaction1->getFunction();
112 CPPUNIT_ASSERT(pKineticFunction != NULL);
116 CPPUNIT_ASSERT(pMassAction == NULL);
117 const CChemEq* pChemEq = &pReaction1->getChemEq();
118 CPPUNIT_ASSERT(pChemEq != NULL);
122 CPPUNIT_ASSERT(pElement != NULL);
123 CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
124 CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
128 const CReaction* pReaction2 = pModel->getReactions()[1];
129 CPPUNIT_ASSERT(pReaction2 != NULL);
130 CPPUNIT_ASSERT(pReaction2->isReversible() ==
false);
132 pKineticFunction = pReaction2->getFunction();
133 CPPUNIT_ASSERT(pKineticFunction != NULL);
134 CPPUNIT_ASSERT(pKineticFunction->getObjectName() == std::string(
"Henri-Michaelis-Menten (irreversible)"));
136 pChemEq = &pReaction2->getChemEq();
137 CPPUNIT_ASSERT(pChemEq != NULL);
138 CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
139 CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
140 pElement = pChemEq->getSubstrates()[0];
141 CPPUNIT_ASSERT(pElement != NULL);
142 CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
143 CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
144 CPPUNIT_ASSERT(pChemEq->getProducts().size() == 1);
145 pElement = pChemEq->getProducts()[0];
146 CPPUNIT_ASSERT(pElement != NULL);
147 CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
148 CPPUNIT_ASSERT(pElement->getMetabolite() == pB);
149 CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
150 const std::vector<std::vector<std::string> > parameterMappings = pReaction2->getParameterMappings();
151 CPPUNIT_ASSERT(parameterMappings.size() == 3);
152 CPPUNIT_ASSERT(parameterMappings[0].size() == 1);
153 const std::string parameterKey = parameterMappings[0][0];
154 CPPUNIT_ASSERT(parameterKey == pA->getKey());
158 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
159 "<sbml xmlns=\"http://www.sbml.org/sbml/level2/version3\" level=\"2\" version=\"3\">\n"
160 " <model id=\"Model_1\" name=\"New Model\">\n"
162 " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
163 " <p>Model with fixed compartment volume, two species with hasOnlySubstanceUnits flag set to true. The units are set to ml and microMol. There is an assignment rule for the global parameter that contains a reference to species A.</p>\n"
164 " <p>The imported model should contain an assignment for the global parameter that consists of the reference to the particle number of species A divided by a constant (6.023e17). The species references in the reactions should be imported multiplied by the volume.</p>\n"
167 " <listOfFunctionDefinitions>\n"
168 " <functionDefinition id=\"function_1\" name=\"Henri-Michaelis-Menten (irreversible)\">\n"
169 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
172 " <ci> substrate </ci>\n"
185 " <ci> substrate </ci>\n"
190 " <ci> substrate </ci>\n"
195 " </functionDefinition>\n"
196 " </listOfFunctionDefinitions>\n"
197 " <listOfUnitDefinitions>\n"
198 " <unitDefinition id=\"volume\">\n"
200 " <unit kind=\"litre\" scale=\"-3\"/>\n"
202 " </unitDefinition>\n"
203 " <unitDefinition id=\"substance\">\n"
205 " <unit kind=\"mole\" scale=\"-6\"/>\n"
207 " </unitDefinition>\n"
208 " </listOfUnitDefinitions>\n"
209 " <listOfCompartments>\n"
210 " <compartment id=\"compartment_1\" name=\"compartment\" size=\"1\"/>\n"
211 " </listOfCompartments>\n"
213 " <species id=\"species_1\" name=\"A\" compartment=\"compartment_1\" initialAmount=\"1\" hasOnlySubstanceUnits=\"true\"/>\n"
214 " <species id=\"species_2\" name=\"B\" compartment=\"compartment_1\" initialAmount=\"1\" hasOnlySubstanceUnits=\"true\"/>\n"
215 " </listOfSpecies>\n"
216 " <listOfParameters>\n"
217 " <parameter id=\"parameter_1\" name=\"K\" value=\"0\" constant=\"false\"/>\n"
218 " </listOfParameters>\n"
220 " <assignmentRule variable=\"parameter_1\">\n"
221 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
222 " <ci> species_1 </ci>\n"
224 " </assignmentRule>\n"
226 " <listOfReactions>\n"
227 " <reaction id=\"reaction_1\" name=\"reaction_0\" reversible=\"false\">\n"
228 " <listOfReactants>\n"
229 " <speciesReference species=\"species_1\"/>\n"
230 " </listOfReactants>\n"
232 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
236 " <ci> species_1 </ci>\n"
239 " <listOfParameters>\n"
240 " <parameter id=\"k1\" value=\"0.1\"/>\n"
241 " </listOfParameters>\n"
244 " <reaction id=\"reaction_2\" name=\"reaction_1\" reversible=\"false\">\n"
245 " <listOfReactants>\n"
246 " <speciesReference species=\"species_1\"/>\n"
247 " </listOfReactants>\n"
248 " <listOfProducts>\n"
249 " <speciesReference species=\"species_2\"/>\n"
250 " </listOfProducts>\n"
252 " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
255 " <ci> compartment_1 </ci>\n"
257 " <ci> function_1 </ci>\n"
260 " <ci> species_1 </ci>\n"
261 " <ci> compartment_1 </ci>\n"
268 " <listOfParameters>\n"
269 " <parameter id=\"Km\" value=\"0.1\"/>\n"
270 " <parameter id=\"V\" value=\"0.1\"/>\n"
271 " </listOfParameters>\n"
274 " </listOfReactions>\n"
const CExpression * getExpressionPtr() const
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
static CCopasiDataModel * pCOPASIDATAMODEL
const Type & getType() const
void test_hasOnlySubstanceUnits()
const CCopasiVector< CChemEqElement > & getProducts() const
static const char * MODEL_STRING
const CCopasiVector< CChemEqElement > & getSubstrates() const
static CCopasiDataModel * addDatamodel()
static Type subType(const Type &type)
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)
const CModelEntity::Status & getStatus() const
CCopasiNode< Data > * getChild()
CCopasiObject * ObjectFromName(const std::vector< CCopasiContainer * > &listOfContainer, const CCopasiObjectName &CN) const
CCopasiContainer * getObjectParent() const