COPASI API  4.16.103
test000035.cpp
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1 // Begin CVS Header
2 // $Source: /Volumes/Home/Users/shoops/cvs/copasi_dev/copasi/sbml/unittests/test000035.cpp,v $
3 // $Revision: 1.8 $
4 // $Name: $
5 // $Author: gauges $
6 // $Date: 2010/03/11 11:52:00 $
7 // End CVS Header
8 
9 // Copyright (C) 2010 by Pedro Mendes, Virginia Tech Intellectual
10 // Properties, Inc., University of Heidelberg, and The University
11 // of Manchester.
12 // All rights reserved.
13 
14 // Copyright (C) 2008 by Pedro Mendes, Virginia Tech Intellectual
15 // Properties, Inc., EML Research, gGmbH, University of Heidelberg,
16 // and The University of Manchester.
17 // All rights reserved.
18 
19 #include "test000035.h"
20 
21 #include <sstream>
22 #include "utilities.hpp"
24 #include "copasi/model/CModel.h"
25 #include "copasi/model/CMetab.h"
28 #include "copasi/model/CReaction.h"
31 
33 
34 CCopasiDataModel* test000035::pCOPASIDATAMODEL = NULL;
35 
37 {
38  // Create the root container.
39  CCopasiRootContainer::init(0, NULL, false);
40  // Create the global data model.
42 }
43 
45 {
47 }
48 
50 {
51  CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
52  CPPUNIT_ASSERT(pDataModel->importSBMLFromString(MODEL_STRING));
53  CModel* pModel = pDataModel->getModel();
54  CPPUNIT_ASSERT(pModel != NULL);
55  CPPUNIT_ASSERT(pModel->getQuantityUnitEnum() == CModel::mMol);
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);
61  CPPUNIT_ASSERT(pCompartment->getStatus() == CModelEntity::FIXED);
62  CPPUNIT_ASSERT(pModel->getMetabolites().size() == 2);
63  CMetab* pA = pModel->getMetabolites()[0];
64  CPPUNIT_ASSERT(pA != NULL);
65  CPPUNIT_ASSERT(pA->getStatus() == CModelEntity::REACTIONS);
66  const CMetab* pB = pModel->getMetabolites()[1];
67  CPPUNIT_ASSERT(pB != NULL);
68  CPPUNIT_ASSERT(pB->getStatus() == CModelEntity::REACTIONS);
69  CPPUNIT_ASSERT(pModel->getModelValues().size() == 1);
70  const CModelValue* pModelValue = pModel->getModelValues()[0];
71  CPPUNIT_ASSERT(pModelValue != NULL);
72  CPPUNIT_ASSERT(pModelValue->getStatus() == CModelEntity::FIXED);
73  CPPUNIT_ASSERT(pModelValue->getInitialExpression() != "");
74  const CExpression* pExpr = pModelValue->getInitialExpressionPtr();
75  CPPUNIT_ASSERT(pExpr != NULL);
76  // check the expression
77  const CEvaluationNode* pNode = pExpr->getRoot();
78  CPPUNIT_ASSERT(pNode != NULL);
79  const CEvaluationNodeObject* pObjectNode = dynamic_cast<const CEvaluationNodeObject*>(pNode);
80  CPPUNIT_ASSERT(pObjectNode != NULL);
81  CCopasiObjectName objectCN = pObjectNode->getObjectCN();
82  CPPUNIT_ASSERT(!objectCN.empty());
83  std::vector<CCopasiContainer*> listOfContainers;
84  listOfContainers.push_back(pModel);
85  const CCopasiObject* pObject = pCOPASIDATAMODEL->ObjectFromName(listOfContainers, objectCN);
86  CPPUNIT_ASSERT(pObject != NULL);
87  CPPUNIT_ASSERT(pObject->isReference() == true);
88  CPPUNIT_ASSERT(pObject->getObjectName() == std::string("InitialConcentration"));
89  CPPUNIT_ASSERT(pObject->getObjectParent() == pA);
90  CPPUNIT_ASSERT(pModel->getReactions().size() == 2);
91  const CReaction* pReaction1 = pModel->getReactions()[0];
92  CPPUNIT_ASSERT(pReaction1 != NULL);
93  CPPUNIT_ASSERT(pReaction1->isReversible() == false);
94  // check the kinetic law
95  const CFunction* pKineticFunction = pReaction1->getFunction();
96  CPPUNIT_ASSERT(pKineticFunction != NULL);
97  const CMassAction* pMassAction = dynamic_cast<const CMassAction*>(pKineticFunction);
98  CPPUNIT_ASSERT(pMassAction != NULL);
99  const CChemEq* pChemEq = &pReaction1->getChemEq();
100  CPPUNIT_ASSERT(pChemEq != NULL);
101  CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
102  CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
103  const CChemEqElement* pElement = pChemEq->getSubstrates()[0];
104  CPPUNIT_ASSERT(pElement != NULL);
105  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
106  CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
107  CPPUNIT_ASSERT(pChemEq->getProducts().size() == 0);
108  CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
109 
110  const CReaction* pReaction2 = pModel->getReactions()[1];
111  CPPUNIT_ASSERT(pReaction2 != NULL);
112  CPPUNIT_ASSERT(pReaction2->isReversible() == false);
113  // check the kinetic law
114  pKineticFunction = pReaction2->getFunction();
115  CPPUNIT_ASSERT(pKineticFunction != NULL);
116  CPPUNIT_ASSERT(pKineticFunction->getObjectName() == std::string("Henri-Michaelis-Menten (irreversible)"));
117  // check the function parameters one should be the reference to the substrate
118  pChemEq = &pReaction2->getChemEq();
119  CPPUNIT_ASSERT(pChemEq != NULL);
120  CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
121  CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
122  pElement = pChemEq->getSubstrates()[0];
123  CPPUNIT_ASSERT(pElement != NULL);
124  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
125  CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
126  CPPUNIT_ASSERT(pChemEq->getProducts().size() == 1);
127  pElement = pChemEq->getProducts()[0];
128  CPPUNIT_ASSERT(pElement != NULL);
129  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
130  CPPUNIT_ASSERT(pElement->getMetabolite() == pB);
131  CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
132  const std::vector<std::vector<std::string> > parameterMappings = pReaction2->getParameterMappings();
133  CPPUNIT_ASSERT(parameterMappings.size() == 3);
134  CPPUNIT_ASSERT(parameterMappings[0].size() == 1);
135  const std::string parameterKey = parameterMappings[0][0];
136  CPPUNIT_ASSERT(parameterKey == pA->getKey());
137 }
138 
139 const char* test000035::MODEL_STRING =
140  "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
141  "<sbml xmlns=\"http://www.sbml.org/sbml/level2/version3\" level=\"2\" version=\"3\">\n"
142  " <notes>\n"
143  " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
144  " <p>Model with fixed compartment volume, two species with hasOnlySubstanceUnits flag set to false. The units are set to ml and mMol. There is an initial assignment for the global parameter that contains a reference to species A.</p>\n"
145  " <p>The imported model should contain an initial assignment for the global parameter that consists of the reference to the initial concentration species A. The species references in the reactions should be imported unmodified.</p>\n"
146  " </body>\n"
147  " </notes>\n"
148  " <model id=\"Model_1\" name=\"New Model\">\n"
149  " <listOfFunctionDefinitions>\n"
150  " <functionDefinition id=\"function_1\" name=\"Henri-Michaelis-Menten (irreversible)\">\n"
151  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
152  " <lambda>\n"
153  " <bvar>\n"
154  " <ci> substrate </ci>\n"
155  " </bvar>\n"
156  " <bvar>\n"
157  " <ci> Km </ci>\n"
158  " </bvar>\n"
159  " <bvar>\n"
160  " <ci> V </ci>\n"
161  " </bvar>\n"
162  " <apply>\n"
163  " <divide/>\n"
164  " <apply>\n"
165  " <times/>\n"
166  " <ci> V </ci>\n"
167  " <ci> substrate </ci>\n"
168  " </apply>\n"
169  " <apply>\n"
170  " <plus/>\n"
171  " <ci> Km </ci>\n"
172  " <ci> substrate </ci>\n"
173  " </apply>\n"
174  " </apply>\n"
175  " </lambda>\n"
176  " </math>\n"
177  " </functionDefinition>\n"
178  " </listOfFunctionDefinitions>\n"
179  " <listOfUnitDefinitions>\n"
180  " <unitDefinition id=\"volume\">\n"
181  " <listOfUnits>\n"
182  " <unit kind=\"litre\" scale=\"-3\"/>\n"
183  " </listOfUnits>\n"
184  " </unitDefinition>\n"
185  " <unitDefinition id=\"substance\">\n"
186  " <listOfUnits>\n"
187  " <unit kind=\"mole\" scale=\"-3\"/>\n"
188  " </listOfUnits>\n"
189  " </unitDefinition>\n"
190  " </listOfUnitDefinitions>\n"
191  " <listOfCompartments>\n"
192  " <compartment id=\"compartment_1\" name=\"compartment\" size=\"1\"/>\n"
193  " </listOfCompartments>\n"
194  " <listOfSpecies>\n"
195  " <species id=\"species_1\" name=\"A\" compartment=\"compartment_1\" initialConcentration=\"1\"/>\n"
196  " <species id=\"species_2\" name=\"B\" compartment=\"compartment_1\" initialConcentration=\"1\"/>\n"
197  " </listOfSpecies>\n"
198  " <listOfParameters>\n"
199  " <parameter id=\"parameter_1\" name=\"K\" value=\"0\" constant=\"true\"/>\n"
200  " </listOfParameters>\n"
201  " <listOfInitialAssignments>\n"
202  " <initialAssignment symbol=\"parameter_1\">\n"
203  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
204  " <ci> species_1 </ci>\n"
205  " </math>\n"
206  " </initialAssignment>\n"
207  " </listOfInitialAssignments>\n"
208  " <listOfReactions>\n"
209  " <reaction id=\"reaction_1\" name=\"reaction_0\" reversible=\"false\">\n"
210  " <listOfReactants>\n"
211  " <speciesReference species=\"species_1\"/>\n"
212  " </listOfReactants>\n"
213  " <kineticLaw>\n"
214  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
215  " <apply>\n"
216  " <times/>\n"
217  " <ci> compartment_1 </ci>\n"
218  " <ci> k1 </ci>\n"
219  " <ci> species_1 </ci>\n"
220  " </apply>\n"
221  " </math>\n"
222  " <listOfParameters>\n"
223  " <parameter id=\"k1\" value=\"0.1\"/>\n"
224  " </listOfParameters>\n"
225  " </kineticLaw>\n"
226  " </reaction>\n"
227  " <reaction id=\"reaction_2\" name=\"reaction_1\" reversible=\"false\">\n"
228  " <listOfReactants>\n"
229  " <speciesReference species=\"species_1\"/>\n"
230  " </listOfReactants>\n"
231  " <listOfProducts>\n"
232  " <speciesReference species=\"species_2\"/>\n"
233  " </listOfProducts>\n"
234  " <kineticLaw>\n"
235  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
236  " <apply>\n"
237  " <times/>\n"
238  " <ci> compartment_1 </ci>\n"
239  " <apply>\n"
240  " <ci> function_1 </ci>\n"
241  " <ci> species_1 </ci>\n"
242  " <ci> Km </ci>\n"
243  " <ci> V </ci>\n"
244  " </apply>\n"
245  " </apply>\n"
246  " </math>\n"
247  " <listOfParameters>\n"
248  " <parameter id=\"Km\" value=\"0.1\"/>\n"
249  " <parameter id=\"V\" value=\"0.1\"/>\n"
250  " </listOfParameters>\n"
251  " </kineticLaw>\n"
252  " </reaction>\n"
253  " </listOfReactions>\n"
254  " </model>\n"
255  "</sbml>\n"
256  ;
Header file of class CExpression.
size_t getCompartmentNumber() const
Definition: CChemEq.cpp:110
Header file of class CModelEntity and CModelValue.
void test_hasOnlySubstanceUnits()
Definition: test000035.cpp:49
const std::string & getObjectName() const
virtual size_t size() const
const CRegisteredObjectName & getObjectCN() const
void setUp()
Definition: test000035.cpp:36
Definition: CMetab.h:178
const CCopasiVector< CChemEqElement > & getProducts() const
Definition: CChemEq.cpp:63
bool isReference() const
static const char * MODEL_STRING
Definition: test000035.h:31
const CCopasiVector< CChemEqElement > & getSubstrates() const
Definition: CChemEq.cpp:60
static CCopasiDataModel * addDatamodel()
const CCopasiVector< CChemEqElement > & getModifiers() const
Definition: CChemEq.cpp:66
bool importSBMLFromString(const std::string &sbmlDocumentText, CProcessReport *pImportHandler=NULL, const bool &deleteOldData=true)
The class for handling a chemical kinetic function.
Definition: CFunction.h:29
static void init(int argc, char *argv[], const bool &withGui=false)
Definition: CModel.h:50
void tearDown()
Definition: test000035.cpp:44
CCopasiObject * ObjectFromName(const std::vector< CCopasiContainer * > &listOfContainer, const CCopasiObjectName &CN) const
static CCopasiDataModel * pCOPASIDATAMODEL
Definition: test000035.h:32
CCopasiContainer * getObjectParent() const