COPASI API  4.16.103
test000024.cpp
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1 // Begin CVS Header
2 // $Source: /Volumes/Home/Users/shoops/cvs/copasi_dev/copasi/sbml/unittests/test000024.cpp,v $
3 // $Revision: 1.9 $
4 // $Name: $
5 // $Author: bergmann $
6 // $Date: 2012/04/20 09:23:41 $
7 // End CVS Header
8 
9 // Copyright (C) 2012 - 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 "test000024.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* test000024::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::number);
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::ASSIGNMENT);
73  const CExpression* pExpr = pModelValue->getExpressionPtr();
74  // check the expression
75  const CEvaluationNode* pNode = pExpr->getRoot();
76  CPPUNIT_ASSERT(pNode != NULL);
77  const CEvaluationNodeObject* pObjectNode = dynamic_cast<const CEvaluationNodeObject*>(pNode);
78  CPPUNIT_ASSERT(pObjectNode != NULL);
79  CCopasiObjectName objectCN = pObjectNode->getObjectCN();
80  CPPUNIT_ASSERT(!objectCN.empty());
81  std::vector<CCopasiContainer*> listOfContainers;
82  listOfContainers.push_back(pModel);
83  const CCopasiObject* pObject = pCOPASIDATAMODEL->ObjectFromName(listOfContainers, objectCN);
84  CPPUNIT_ASSERT(pObject != NULL);
85  CPPUNIT_ASSERT(pObject->isReference() == true);
86  CPPUNIT_ASSERT(pObject->getObjectName() == std::string("ParticleNumber"));
87  CPPUNIT_ASSERT(pObject->getObjectParent() == pA);
88 
89  CPPUNIT_ASSERT(pModel->getReactions().size() == 2);
90  const CReaction* pReaction1 = pModel->getReactions()[0];
91  CPPUNIT_ASSERT(pReaction1 != NULL);
92  CPPUNIT_ASSERT(pReaction1->isReversible() == false);
93  // check the kinetic law
94  const CFunction* pKineticFunction = pReaction1->getFunction();
95  CPPUNIT_ASSERT(pKineticFunction != NULL);
96  const CMassAction* pMassAction = dynamic_cast<const CMassAction*>(pKineticFunction);
97  //FTB: this no longer is recognized as mass action reaction because of the
98  // special case of a species with hOSU
99  CPPUNIT_ASSERT(pMassAction == NULL);
100  const CChemEq* pChemEq = &pReaction1->getChemEq();
101  CPPUNIT_ASSERT(pChemEq != NULL);
102  CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
103  CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
104  const CChemEqElement* pElement = pChemEq->getSubstrates()[0];
105  CPPUNIT_ASSERT(pElement != NULL);
106  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
107  CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
108  CPPUNIT_ASSERT(pChemEq->getProducts().size() == 0);
109  CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
110  // check the reactions
111  const CReaction* pReaction2 = pModel->getReactions()[1];
112  CPPUNIT_ASSERT(pReaction2 != NULL);
113  CPPUNIT_ASSERT(pReaction2->isReversible() == false);
114  // check the kinetic law
115  pKineticFunction = pReaction2->getFunction();
116  CPPUNIT_ASSERT(pKineticFunction != NULL);
117  CPPUNIT_ASSERT(pKineticFunction->getObjectName() == std::string("Henri-Michaelis-Menten (irreversible)"));
118  // check the function parameters one should be the reference to the substrate
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());
138 }
139 
140 const char* test000024::MODEL_STRING =
141  "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
142  "<sbml xmlns=\"http://www.sbml.org/sbml/level2/version3\" level=\"2\" version=\"3\">\n"
143  " <model id=\"Model_1\" name=\"New Model\">\n"
144  " <notes>\n"
145  " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
146  " <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 assignment rule for the global parameter that contains a reference to species A.</p>\n"
147  " <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. The species references in the reactions should be imported multiplied by the volume.</p>\n"
148  " </body>\n"
149  " </notes>\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"
153  " <lambda>\n"
154  " <bvar>\n"
155  " <ci> substrate </ci>\n"
156  " </bvar>\n"
157  " <bvar>\n"
158  " <ci> Km </ci>\n"
159  " </bvar>\n"
160  " <bvar>\n"
161  " <ci> V </ci>\n"
162  " </bvar>\n"
163  " <apply>\n"
164  " <divide/>\n"
165  " <apply>\n"
166  " <times/>\n"
167  " <ci> V </ci>\n"
168  " <ci> substrate </ci>\n"
169  " </apply>\n"
170  " <apply>\n"
171  " <plus/>\n"
172  " <ci> Km </ci>\n"
173  " <ci> substrate </ci>\n"
174  " </apply>\n"
175  " </apply>\n"
176  " </lambda>\n"
177  " </math>\n"
178  " </functionDefinition>\n"
179  " </listOfFunctionDefinitions>\n"
180  " <listOfUnitDefinitions>\n"
181  " <unitDefinition id=\"volume\">\n"
182  " <listOfUnits>\n"
183  " <unit kind=\"litre\" scale=\"-3\"/>\n"
184  " </listOfUnits>\n"
185  " </unitDefinition>\n"
186  " <unitDefinition id=\"substance\">\n"
187  " <listOfUnits>\n"
188  " <unit kind=\"item\"/>\n"
189  " </listOfUnits>\n"
190  " </unitDefinition>\n"
191  " </listOfUnitDefinitions>\n"
192  " <listOfCompartments>\n"
193  " <compartment id=\"compartment_1\" name=\"compartment\" size=\"1\"/>\n"
194  " </listOfCompartments>\n"
195  " <listOfSpecies>\n"
196  " <species id=\"species_1\" name=\"A\" compartment=\"compartment_1\" initialAmount=\"1\" hasOnlySubstanceUnits=\"true\"/>\n"
197  " <species id=\"species_2\" name=\"B\" compartment=\"compartment_1\" initialAmount=\"1\" hasOnlySubstanceUnits=\"true\"/>\n"
198  " </listOfSpecies>\n"
199  " <listOfParameters>\n"
200  " <parameter id=\"parameter_1\" name=\"K\" value=\"0\" constant=\"false\"/>\n"
201  " </listOfParameters>\n"
202  " <listOfRules>\n"
203  " <assignmentRule variable=\"parameter_1\">\n"
204  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
205  " <ci> species_1 </ci>\n"
206  " </math>\n"
207  " </assignmentRule>\n"
208  " </listOfRules>\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"
214  " <kineticLaw>\n"
215  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
216  " <apply>\n"
217  " <times/>\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  " <apply>\n"
242  " <divide/>\n"
243  " <ci> species_1 </ci>\n"
244  " <ci> compartment_1 </ci>\n"
245  " </apply> \n"
246  " <ci> Km </ci>\n"
247  " <ci> V </ci>\n"
248  " </apply>\n"
249  " </apply>\n"
250  " </math>\n"
251  " <listOfParameters>\n"
252  " <parameter id=\"Km\" value=\"0.1\"/>\n"
253  " <parameter id=\"V\" value=\"0.1\"/>\n"
254  " </listOfParameters>\n"
255  " </kineticLaw>\n"
256  " </reaction>\n"
257  " </listOfReactions>\n"
258  " </model>\n"
259  "</sbml>\n"
260  ;
Header file of class CExpression.
size_t getCompartmentNumber() const
Definition: CChemEq.cpp:110
void setUp()
Definition: test000024.cpp:36
Header file of class CModelEntity and CModelValue.
static const char * MODEL_STRING
Definition: test000024.h:31
const std::string & getObjectName() const
virtual size_t size() const
const CRegisteredObjectName & getObjectCN() const
Definition: CMetab.h:178
void test_hasOnlySubstanceUnits()
Definition: test000024.cpp:49
const CCopasiVector< CChemEqElement > & getProducts() const
Definition: CChemEq.cpp:63
bool isReference() const
static CCopasiDataModel * pCOPASIDATAMODEL
Definition: test000024.h:32
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
CCopasiObject * ObjectFromName(const std::vector< CCopasiContainer * > &listOfContainer, const CCopasiObjectName &CN) const
CCopasiContainer * getObjectParent() const
void tearDown()
Definition: test000024.cpp:44