COPASI API  4.16.103
test000027.cpp
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1 // Begin CVS Header
2 // $Source: /Volumes/Home/Users/shoops/cvs/copasi_dev/copasi/sbml/unittests/test000027.cpp,v $
3 // $Revision: 1.10 $
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 "test000027.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* test000027::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() == 2);
70  // check the kinetic law
71  const CModelValue* pFactor = pModel->getModelValues()[1];
72  CPPUNIT_ASSERT(pFactor != NULL);
73  CPPUNIT_ASSERT(pFactor->getStatus() == CModelEntity::FIXED);
74  CPPUNIT_ASSERT(fabs((pFactor->getInitialValue() - pModel->getQuantity2NumberFactor()) / pModel->getQuantity2NumberFactor()) < 1e-3);
75  const CModelValue* pModelValue = pModel->getModelValues()[0];
76  CPPUNIT_ASSERT(pModelValue != NULL);
77  CPPUNIT_ASSERT(pModelValue->getStatus() == CModelEntity::ASSIGNMENT);
78  const CExpression* pExpr = pModelValue->getExpressionPtr();
79  // check the expression
80  const CEvaluationNode* pNode = pExpr->getRoot();
81  CPPUNIT_ASSERT(pNode != NULL);
82  const CEvaluationNodeObject* pObjectNode = dynamic_cast<const CEvaluationNodeObject*>(pNode);
83  CPPUNIT_ASSERT(pObjectNode != NULL);
84  CCopasiObjectName objectCN = pObjectNode->getObjectCN();
85  CPPUNIT_ASSERT(!objectCN.empty());
86  std::vector<CCopasiContainer*> listOfContainers;
87  listOfContainers.push_back(pModel);
88  const CCopasiObject* pObject = pCOPASIDATAMODEL->ObjectFromName(listOfContainers, objectCN);
89  CPPUNIT_ASSERT(pObject != NULL);
90  CPPUNIT_ASSERT(pObject->isReference() == true);
91  CPPUNIT_ASSERT(pObject->getObjectName() == std::string("ParticleNumber"));
92  CPPUNIT_ASSERT(pObject->getObjectParent() == pA);
93 
94  CPPUNIT_ASSERT(pModel->getReactions().size() == 2);
95  const CReaction* pReaction1 = pModel->getReactions()[0];
96  CPPUNIT_ASSERT(pReaction1 != NULL);
97  CPPUNIT_ASSERT(pReaction1->isReversible() == false);
98  const CFunction* pKineticFunction = pReaction1->getFunction();
99  CPPUNIT_ASSERT(pKineticFunction != NULL);
100  const CMassAction* pMassAction = dynamic_cast<const CMassAction*>(pKineticFunction);
101  //FTB: this no longer is recognized as mass action reaction because of the
102  // special case of a species with hOSU
103  CPPUNIT_ASSERT(pMassAction == NULL);
104  const CChemEq* pChemEq = &pReaction1->getChemEq();
105  CPPUNIT_ASSERT(pChemEq != NULL);
106  CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
107  CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
108  const CChemEqElement* pElement = pChemEq->getSubstrates()[0];
109  CPPUNIT_ASSERT(pElement != NULL);
110  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
111  CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
112  CPPUNIT_ASSERT(pChemEq->getProducts().size() == 0);
113  CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
114 
115  const CReaction* pReaction2 = pModel->getReactions()[1];
116  CPPUNIT_ASSERT(pReaction2 != NULL);
117  CPPUNIT_ASSERT(pReaction2->isReversible() == false);
118  // check the kinetic law
119  pKineticFunction = pReaction2->getFunction();
120  CPPUNIT_ASSERT(pKineticFunction != NULL);
121  CPPUNIT_ASSERT(pKineticFunction->getObjectName() == std::string("Henri-Michaelis-Menten (irreversible)"));
122  // check the function parameters one should be the reference to the substrate
123  pChemEq = &pReaction2->getChemEq();
124  CPPUNIT_ASSERT(pChemEq != NULL);
125  CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
126  CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
127  pElement = pChemEq->getSubstrates()[0];
128  CPPUNIT_ASSERT(pElement != NULL);
129  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
130  CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
131  CPPUNIT_ASSERT(pChemEq->getProducts().size() == 1);
132  pElement = pChemEq->getProducts()[0];
133  CPPUNIT_ASSERT(pElement != NULL);
134  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
135  CPPUNIT_ASSERT(pElement->getMetabolite() == pB);
136  CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
137  const std::vector<std::vector<std::string> > parameterMappings = pReaction2->getParameterMappings();
138  CPPUNIT_ASSERT(parameterMappings.size() == 3);
139  CPPUNIT_ASSERT(parameterMappings[0].size() == 1);
140  const std::string parameterKey = parameterMappings[0][0];
141  CPPUNIT_ASSERT(parameterKey == pA->getKey());
142 }
143 
144 const char* test000027::MODEL_STRING =
145  "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
146  "<sbml xmlns=\"http://www.sbml.org/sbml/level2/version3\" level=\"2\" version=\"3\">\n"
147  " <model id=\"Model_1\" name=\"New Model\">\n"
148  " <notes>\n"
149  " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
150  " <p>Model with fixed compartment volume, two species with hasOnlySubstanceUnits flag set to true. The units are set to ml and mMol. There is an assignment ruile for the global parameter that contains a reference to species A multiplied by a constant parameter.</p>\n"
151  " <p>The imported model should contain an 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  " </body>\n"
153  " </notes>\n"
154  " <listOfFunctionDefinitions>\n"
155  " <functionDefinition id=\"function_1\" name=\"Henri-Michaelis-Menten (irreversible)\">\n"
156  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
157  " <lambda>\n"
158  " <bvar>\n"
159  " <ci> substrate </ci>\n"
160  " </bvar>\n"
161  " <bvar>\n"
162  " <ci> Km </ci>\n"
163  " </bvar>\n"
164  " <bvar>\n"
165  " <ci> V </ci>\n"
166  " </bvar>\n"
167  " <apply>\n"
168  " <divide/>\n"
169  " <apply>\n"
170  " <times/>\n"
171  " <ci> V </ci>\n"
172  " <ci> substrate </ci>\n"
173  " </apply>\n"
174  " <apply>\n"
175  " <plus/>\n"
176  " <ci> Km </ci>\n"
177  " <ci> substrate </ci>\n"
178  " </apply>\n"
179  " </apply>\n"
180  " </lambda>\n"
181  " </math>\n"
182  " </functionDefinition>\n"
183  " </listOfFunctionDefinitions>\n"
184  " <listOfUnitDefinitions>\n"
185  " <unitDefinition id=\"volume\">\n"
186  " <listOfUnits>\n"
187  " <unit kind=\"litre\" scale=\"-3\"/>\n"
188  " </listOfUnits>\n"
189  " </unitDefinition>\n"
190  " <unitDefinition id=\"substance\">\n"
191  " <listOfUnits>\n"
192  " <unit kind=\"mole\" scale=\"-3\"/>\n"
193  " </listOfUnits>\n"
194  " </unitDefinition>\n"
195  " </listOfUnitDefinitions>\n"
196  " <listOfCompartments>\n"
197  " <compartment id=\"compartment_1\" name=\"compartment\" size=\"1\"/>\n"
198  " </listOfCompartments>\n"
199  " <listOfSpecies>\n"
200  " <species id=\"species_1\" name=\"A\" compartment=\"compartment_1\" initialAmount=\"1\" hasOnlySubstanceUnits=\"true\"/>\n"
201  " <species id=\"species_2\" name=\"B\" compartment=\"compartment_1\" initialAmount=\"1\" hasOnlySubstanceUnits=\"true\"/>\n"
202  " </listOfSpecies>\n"
203  " <listOfParameters>\n"
204  " <parameter id=\"parameter_1\" name=\"K\" value=\"0\" constant=\"false\"/>\n"
205  " <parameter id=\"parameter_2\" name=\"F\" value=\"6.0221415e20\" constant=\"true\"/>\n"
206  " </listOfParameters>\n"
207  " <listOfRules>\n"
208  " <assignmentRule variable=\"parameter_1\">\n"
209  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
210  " <apply>\n"
211  " <times/>\n"
212  " <ci> species_1 </ci>\n"
213  " <ci> parameter_2 </ci>\n"
214  " </apply>\n"
215  " </math>\n"
216  " </assignmentRule>\n"
217  " </listOfRules>\n"
218  " <listOfReactions>\n"
219  " <reaction id=\"reaction_1\" name=\"reaction_0\" reversible=\"false\">\n"
220  " <listOfReactants>\n"
221  " <speciesReference species=\"species_1\"/>\n"
222  " </listOfReactants>\n"
223  " <kineticLaw>\n"
224  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
225  " <apply>\n"
226  " <times/>\n"
227  " <ci> k1 </ci>\n"
228  " <ci> species_1 </ci>\n"
229  " </apply>\n"
230  " </math>\n"
231  " <listOfParameters>\n"
232  " <parameter id=\"k1\" value=\"0.1\"/>\n"
233  " </listOfParameters>\n"
234  " </kineticLaw>\n"
235  " </reaction>\n"
236  " <reaction id=\"reaction_2\" name=\"reaction_1\" reversible=\"false\">\n"
237  " <listOfReactants>\n"
238  " <speciesReference species=\"species_1\"/>\n"
239  " </listOfReactants>\n"
240  " <listOfProducts>\n"
241  " <speciesReference species=\"species_2\"/>\n"
242  " </listOfProducts>\n"
243  " <kineticLaw>\n"
244  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
245  " <apply>\n"
246  " <times/>\n"
247  " <ci> compartment_1 </ci>\n"
248  " <apply>\n"
249  " <ci> function_1 </ci>\n"
250  " <apply>\n"
251  " <divide/>\n"
252  " <ci> species_1 </ci>\n"
253  " <ci> compartment_1 </ci>\n"
254  " </apply> \n"
255  " <ci> Km </ci>\n"
256  " <ci> V </ci>\n"
257  " </apply>\n"
258  " </apply>\n"
259  " </math>\n"
260  " <listOfParameters>\n"
261  " <parameter id=\"Km\" value=\"0.1\"/>\n"
262  " <parameter id=\"V\" value=\"0.1\"/>\n"
263  " </listOfParameters>\n"
264  " </kineticLaw>\n"
265  " </reaction>\n"
266  " </listOfReactions>\n"
267  " </model>\n"
268  "</sbml>\n"
269  ;
const CExpression * getExpressionPtr() const
Header file of class CExpression.
size_t getCompartmentNumber() const
Definition: CChemEq.cpp:110
Header file of class CModelEntity and CModelValue.
static CCopasiDataModel * pCOPASIDATAMODEL
Definition: test000027.h:32
const std::string & getObjectName() const
virtual size_t size() const
const CRegisteredObjectName & getObjectCN() const
Definition: CMetab.h:178
void test_hasOnlySubstanceUnits()
Definition: test000027.cpp:49
const CCopasiVector< CChemEqElement > & getProducts() const
Definition: CChemEq.cpp:63
bool isReference() const
static const char * MODEL_STRING
Definition: test000027.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
const CModelEntity::Status & getStatus() const
void tearDown()
Definition: test000027.cpp:44
void setUp()
Definition: test000027.cpp:36
CCopasiObject * ObjectFromName(const std::vector< CCopasiContainer * > &listOfContainer, const CCopasiObjectName &CN) const
CCopasiContainer * getObjectParent() const