COPASI API  4.16.103
test000034.cpp
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1 // Begin CVS Header
2 // $Source: /Volumes/Home/Users/shoops/cvs/copasi_dev/copasi/sbml/unittests/test000034.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 "test000034.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* test000034::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 factor
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::ODE);
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  // check the kinetic laws
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  // check the kinetic law
99  const CFunction* pKineticFunction = pReaction1->getFunction();
100  CPPUNIT_ASSERT(pKineticFunction != NULL);
101  const CMassAction* pMassAction = dynamic_cast<const CMassAction*>(pKineticFunction);
102  //FTB: this no longer is recognized as mass action reaction because of the
103  // special case of a species with hOSU
104  CPPUNIT_ASSERT(pMassAction == NULL);
105  const CChemEq* pChemEq = &pReaction1->getChemEq();
106  CPPUNIT_ASSERT(pChemEq != NULL);
107  CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
108  CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
109  const CChemEqElement* pElement = pChemEq->getSubstrates()[0];
110  CPPUNIT_ASSERT(pElement != NULL);
111  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
112  CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
113  CPPUNIT_ASSERT(pChemEq->getProducts().size() == 0);
114  CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
115 
116  const CReaction* pReaction2 = pModel->getReactions()[1];
117  CPPUNIT_ASSERT(pReaction2 != NULL);
118  CPPUNIT_ASSERT(pReaction2->isReversible() == false);
119  // check the kinetic law
120  pKineticFunction = pReaction2->getFunction();
121  CPPUNIT_ASSERT(pKineticFunction != NULL);
122  CPPUNIT_ASSERT(pKineticFunction->getObjectName() == std::string("Henri-Michaelis-Menten (irreversible)"));
123  // check the function parameters one should be the reference to the substrate
124  pChemEq = &pReaction2->getChemEq();
125  CPPUNIT_ASSERT(pChemEq != NULL);
126  CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
127  CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
128  pElement = pChemEq->getSubstrates()[0];
129  CPPUNIT_ASSERT(pElement != NULL);
130  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
131  CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
132  CPPUNIT_ASSERT(pChemEq->getProducts().size() == 1);
133  pElement = pChemEq->getProducts()[0];
134  CPPUNIT_ASSERT(pElement != NULL);
135  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
136  CPPUNIT_ASSERT(pElement->getMetabolite() == pB);
137  CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
138  const std::vector<std::vector<std::string> > parameterMappings = pReaction2->getParameterMappings();
139  CPPUNIT_ASSERT(parameterMappings.size() == 3);
140  CPPUNIT_ASSERT(parameterMappings[0].size() == 1);
141  const std::string parameterKey = parameterMappings[0][0];
142  CPPUNIT_ASSERT(parameterKey == pA->getKey());
143 }
144 
145 const char* test000034::MODEL_STRING =
146  "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
147  "<sbml xmlns=\"http://www.sbml.org/sbml/level2/version3\" level=\"2\" version=\"3\">\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 ode rule 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 ode rule 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  " <model id=\"Model_1\" name=\"New Model\">\n"
155  " <listOfFunctionDefinitions>\n"
156  " <functionDefinition id=\"function_1\" name=\"Henri-Michaelis-Menten (irreversible)\">\n"
157  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
158  " <lambda>\n"
159  " <bvar>\n"
160  " <ci> substrate </ci>\n"
161  " </bvar>\n"
162  " <bvar>\n"
163  " <ci> Km </ci>\n"
164  " </bvar>\n"
165  " <bvar>\n"
166  " <ci> V </ci>\n"
167  " </bvar>\n"
168  " <apply>\n"
169  " <divide/>\n"
170  " <apply>\n"
171  " <times/>\n"
172  " <ci> V </ci>\n"
173  " <ci> substrate </ci>\n"
174  " </apply>\n"
175  " <apply>\n"
176  " <plus/>\n"
177  " <ci> Km </ci>\n"
178  " <ci> substrate </ci>\n"
179  " </apply>\n"
180  " </apply>\n"
181  " </lambda>\n"
182  " </math>\n"
183  " </functionDefinition>\n"
184  " </listOfFunctionDefinitions>\n"
185  " <listOfUnitDefinitions>\n"
186  " <unitDefinition id=\"volume\">\n"
187  " <listOfUnits>\n"
188  " <unit kind=\"litre\" scale=\"-3\"/>\n"
189  " </listOfUnits>\n"
190  " </unitDefinition>\n"
191  " <unitDefinition id=\"substance\">\n"
192  " <listOfUnits>\n"
193  " <unit kind=\"mole\" scale=\"-3\"/>\n"
194  " </listOfUnits>\n"
195  " </unitDefinition>\n"
196  " </listOfUnitDefinitions>\n"
197  " <listOfCompartments>\n"
198  " <compartment id=\"compartment_1\" name=\"compartment\" size=\"1\"/>\n"
199  " </listOfCompartments>\n"
200  " <listOfSpecies>\n"
201  " <species id=\"species_1\" name=\"A\" compartment=\"compartment_1\" initialAmount=\"1\" hasOnlySubstanceUnits=\"true\"/>\n"
202  " <species id=\"species_2\" name=\"B\" compartment=\"compartment_1\" initialAmount=\"1\" hasOnlySubstanceUnits=\"true\"/>\n"
203  " </listOfSpecies>\n"
204  " <listOfParameters>\n"
205  " <parameter id=\"parameter_1\" name=\"K\" value=\"0\" constant=\"false\"/>\n"
206  " <parameter id=\"parameter_2\" name=\"F\" value=\"6.0221415e20\" constant=\"true\"/>\n"
207  " </listOfParameters>\n"
208  " <listOfRules>\n"
209  " <rateRule variable=\"parameter_1\">\n"
210  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
211  " <apply>\n"
212  " <times/>\n"
213  " <ci> species_1 </ci>\n"
214  " <ci> parameter_2 </ci>\n"
215  " </apply>\n"
216  " </math>\n"
217  " </rateRule>\n"
218  " </listOfRules>\n"
219  " <listOfReactions>\n"
220  " <reaction id=\"reaction_1\" name=\"reaction_0\" reversible=\"false\">\n"
221  " <listOfReactants>\n"
222  " <speciesReference species=\"species_1\"/>\n"
223  " </listOfReactants>\n"
224  " <kineticLaw>\n"
225  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
226  " <apply>\n"
227  " <times/>\n"
228  " <ci> k1 </ci>\n"
229  " <ci> species_1 </ci>\n"
230  " </apply>\n"
231  " </math>\n"
232  " <listOfParameters>\n"
233  " <parameter id=\"k1\" value=\"0.1\"/>\n"
234  " </listOfParameters>\n"
235  " </kineticLaw>\n"
236  " </reaction>\n"
237  " <reaction id=\"reaction_2\" name=\"reaction_1\" reversible=\"false\">\n"
238  " <listOfReactants>\n"
239  " <speciesReference species=\"species_1\"/>\n"
240  " </listOfReactants>\n"
241  " <listOfProducts>\n"
242  " <speciesReference species=\"species_2\"/>\n"
243  " </listOfProducts>\n"
244  " <kineticLaw>\n"
245  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
246  " <apply>\n"
247  " <times/>\n"
248  " <ci> compartment_1 </ci>\n"
249  " <apply>\n"
250  " <ci> function_1 </ci>\n"
251  " <apply>\n"
252  " <divide/>\n"
253  " <ci> species_1 </ci>\n"
254  " <ci> compartment_1 </ci>\n"
255  " </apply> \n"
256  " <ci> Km </ci>\n"
257  " <ci> V </ci>\n"
258  " </apply>\n"
259  " </apply>\n"
260  " </math>\n"
261  " <listOfParameters>\n"
262  " <parameter id=\"Km\" value=\"0.1\"/>\n"
263  " <parameter id=\"V\" value=\"0.1\"/>\n"
264  " </listOfParameters>\n"
265  " </kineticLaw>\n"
266  " </reaction>\n"
267  " </listOfReactions>\n"
268  " </model>\n"
269  "</sbml>\n"
270  ;
const CExpression * getExpressionPtr() const
Header file of class CExpression.
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 setUp()
Definition: test000034.cpp:36
Definition: CMetab.h:178
const CCopasiVector< CChemEqElement > & getProducts() const
Definition: CChemEq.cpp:63
void tearDown()
Definition: test000034.cpp:44
bool isReference() const
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)
static CCopasiDataModel * pCOPASIDATAMODEL
Definition: test000034.h:32
The class for handling a chemical kinetic function.
Definition: CFunction.h:29
void test_hasOnlySubstanceUnits()
Definition: test000034.cpp:49
static void init(int argc, char *argv[], const bool &withGui=false)
static const char * MODEL_STRING
Definition: test000034.h:31
Definition: CModel.h:50
const CModelEntity::Status & getStatus() const
CCopasiObject * ObjectFromName(const std::vector< CCopasiContainer * > &listOfContainer, const CCopasiObjectName &CN) const
CCopasiContainer * getObjectParent() const