COPASI API  4.16.103
test000039.cpp
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1 // Begin CVS Header
2 // $Source: /Volumes/Home/Users/shoops/cvs/copasi_dev/copasi/sbml/unittests/test000039.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 "test000039.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* test000039::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::microMol);
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  // check the expression
76  const CEvaluationNode* pNode = pExpr->getRoot();
77  CPPUNIT_ASSERT(pNode != NULL);
78  const CEvaluationNodeObject* pObjectNode = dynamic_cast<const CEvaluationNodeObject*>(pNode);
79  CPPUNIT_ASSERT(pObjectNode != NULL);
80  CCopasiObjectName objectCN = pObjectNode->getObjectCN();
81  CPPUNIT_ASSERT(!objectCN.empty());
82  std::vector<CCopasiContainer*> listOfContainers;
83  listOfContainers.push_back(pModel);
84  const CCopasiObject* pObject = pCOPASIDATAMODEL->ObjectFromName(listOfContainers, objectCN);
85  CPPUNIT_ASSERT(pObject != NULL);
86  CPPUNIT_ASSERT(pObject->isReference() == true);
87  CPPUNIT_ASSERT(pObject->getObjectName() == std::string("InitialParticleNumber"));
88  CPPUNIT_ASSERT(pObject->getObjectParent() == pA);
89  // check reactions
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  //FTB: this no longer is recognized as mass action reaction because of the
99  // special case of a species with hOSU
100  CPPUNIT_ASSERT(pMassAction == NULL);
101  const CChemEq* pChemEq = &pReaction1->getChemEq();
102  CPPUNIT_ASSERT(pChemEq != NULL);
103  CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
104  CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
105  const CChemEqElement* pElement = pChemEq->getSubstrates()[0];
106  CPPUNIT_ASSERT(pElement != NULL);
107  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
108  CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
109  CPPUNIT_ASSERT(pChemEq->getProducts().size() == 0);
110  CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
111 
112  const CReaction* pReaction2 = pModel->getReactions()[1];
113  CPPUNIT_ASSERT(pReaction2 != NULL);
114  CPPUNIT_ASSERT(pReaction2->isReversible() == false);
115  // check the kinetic law
116  pKineticFunction = pReaction2->getFunction();
117  CPPUNIT_ASSERT(pKineticFunction != NULL);
118  CPPUNIT_ASSERT(pKineticFunction->getObjectName() == std::string("Henri-Michaelis-Menten (irreversible)"));
119  // check the function parameters one should be the reference to the substrate
120  pChemEq = &pReaction2->getChemEq();
121  CPPUNIT_ASSERT(pChemEq != NULL);
122  CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
123  CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
124  pElement = pChemEq->getSubstrates()[0];
125  CPPUNIT_ASSERT(pElement != NULL);
126  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
127  CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
128  CPPUNIT_ASSERT(pChemEq->getProducts().size() == 1);
129  pElement = pChemEq->getProducts()[0];
130  CPPUNIT_ASSERT(pElement != NULL);
131  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
132  CPPUNIT_ASSERT(pElement->getMetabolite() == pB);
133  CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
134  const std::vector<std::vector<std::string> > parameterMappings = pReaction2->getParameterMappings();
135  CPPUNIT_ASSERT(parameterMappings.size() == 3);
136  CPPUNIT_ASSERT(parameterMappings[0].size() == 1);
137  const std::string parameterKey = parameterMappings[0][0];
138  CPPUNIT_ASSERT(parameterKey == pA->getKey());
139 }
140 
141 const char* test000039::MODEL_STRING =
142  "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
143  "<sbml xmlns=\"http://www.sbml.org/sbml/level2/version3\" level=\"2\" version=\"3\">\n"
144  " <model id=\"Model_1\" name=\"New Model\">\n"
145  " <notes>\n"
146  " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
147  " <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 initial assignment for the global parameter that contains a reference to species A multiplied by a constant.</p>\n"
148  " <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"
149  " </body>\n"
150  " </notes>\n"
151  " <listOfFunctionDefinitions>\n"
152  " <functionDefinition id=\"function_1\" name=\"Henri-Michaelis-Menten (irreversible)\">\n"
153  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
154  " <lambda>\n"
155  " <bvar>\n"
156  " <ci> substrate </ci>\n"
157  " </bvar>\n"
158  " <bvar>\n"
159  " <ci> Km </ci>\n"
160  " </bvar>\n"
161  " <bvar>\n"
162  " <ci> V </ci>\n"
163  " </bvar>\n"
164  " <apply>\n"
165  " <divide/>\n"
166  " <apply>\n"
167  " <times/>\n"
168  " <ci> V </ci>\n"
169  " <ci> substrate </ci>\n"
170  " </apply>\n"
171  " <apply>\n"
172  " <plus/>\n"
173  " <ci> Km </ci>\n"
174  " <ci> substrate </ci>\n"
175  " </apply>\n"
176  " </apply>\n"
177  " </lambda>\n"
178  " </math>\n"
179  " </functionDefinition>\n"
180  " </listOfFunctionDefinitions>\n"
181  " <listOfUnitDefinitions>\n"
182  " <unitDefinition id=\"volume\">\n"
183  " <listOfUnits>\n"
184  " <unit kind=\"litre\" scale=\"-3\"/>\n"
185  " </listOfUnits>\n"
186  " </unitDefinition>\n"
187  " <unitDefinition id=\"substance\">\n"
188  " <listOfUnits>\n"
189  " <unit kind=\"mole\" scale=\"-6\"/>\n"
190  " </listOfUnits>\n"
191  " </unitDefinition>\n"
192  " </listOfUnitDefinitions>\n"
193  " <listOfCompartments>\n"
194  " <compartment id=\"compartment_1\" name=\"compartment\" size=\"1\"/>\n"
195  " </listOfCompartments>\n"
196  " <listOfSpecies>\n"
197  " <species id=\"species_1\" name=\"A\" compartment=\"compartment_1\" initialAmount=\"1\" hasOnlySubstanceUnits=\"true\"/>\n"
198  " <species id=\"species_2\" name=\"B\" compartment=\"compartment_1\" initialAmount=\"1\" hasOnlySubstanceUnits=\"true\"/>\n"
199  " </listOfSpecies>\n"
200  " <listOfParameters>\n"
201  " <parameter id=\"parameter_1\" name=\"K\" value=\"0\" constant=\"true\"/>\n"
202  " </listOfParameters>\n"
203  " <listOfInitialAssignments>\n"
204  " <initialAssignment symbol=\"parameter_1\">\n"
205  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
206  " <apply>\n"
207  " <times/>\n"
208  " <ci> species_1 </ci>\n"
209  " <cn> 6.0221415e17 </cn>\n"
210  " </apply>\n"
211  " </math>\n"
212  " </initialAssignment>\n"
213  " </listOfInitialAssignments>\n"
214  " <listOfReactions>\n"
215  " <reaction id=\"reaction_1\" name=\"reaction_0\" reversible=\"false\">\n"
216  " <listOfReactants>\n"
217  " <speciesReference species=\"species_1\"/>\n"
218  " </listOfReactants>\n"
219  " <kineticLaw>\n"
220  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
221  " <apply>\n"
222  " <times/>\n"
223  " <ci> k1 </ci>\n"
224  " <ci> species_1 </ci>\n"
225  " </apply>\n"
226  " </math>\n"
227  " <listOfParameters>\n"
228  " <parameter id=\"k1\" value=\"0.1\"/>\n"
229  " </listOfParameters>\n"
230  " </kineticLaw>\n"
231  " </reaction>\n"
232  " <reaction id=\"reaction_2\" name=\"reaction_1\" reversible=\"false\">\n"
233  " <listOfReactants>\n"
234  " <speciesReference species=\"species_1\"/>\n"
235  " </listOfReactants>\n"
236  " <listOfProducts>\n"
237  " <speciesReference species=\"species_2\"/>\n"
238  " </listOfProducts>\n"
239  " <kineticLaw>\n"
240  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
241  " <apply>\n"
242  " <times/>\n"
243  " <ci> compartment_1 </ci>\n"
244  " <apply>\n"
245  " <ci> function_1 </ci>\n"
246  " <apply>\n"
247  " <divide/>\n"
248  " <ci> species_1 </ci>\n"
249  " <ci> compartment_1 </ci>\n"
250  " </apply> \n"
251  " <ci> Km </ci>\n"
252  " <ci> V </ci>\n"
253  " </apply>\n"
254  " </apply>\n"
255  " </math>\n"
256  " <listOfParameters>\n"
257  " <parameter id=\"Km\" value=\"0.1\"/>\n"
258  " <parameter id=\"V\" value=\"0.1\"/>\n"
259  " </listOfParameters>\n"
260  " </kineticLaw>\n"
261  " </reaction>\n"
262  " </listOfReactions>\n"
263  " </model>\n"
264  "</sbml>\n"
265  ;
Header file of class CExpression.
static const char * MODEL_STRING
Definition: test000039.h:31
size_t getCompartmentNumber() const
Definition: CChemEq.cpp:110
Header file of class CModelEntity and CModelValue.
const std::string & getObjectName() const
virtual size_t size() const
const CRegisteredObjectName & getObjectCN() const
void tearDown()
Definition: test000039.cpp:44
void setUp()
Definition: test000039.cpp:36
void test_hasOnlySubstanceUnits()
Definition: test000039.cpp:49
Definition: CMetab.h:178
const CCopasiVector< CChemEqElement > & getProducts() const
Definition: CChemEq.cpp:63
bool isReference() const
const CCopasiVector< CChemEqElement > & getSubstrates() const
Definition: CChemEq.cpp:60
static CCopasiDataModel * pCOPASIDATAMODEL
Definition: test000039.h:32
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