COPASI API  4.16.103
test000025.cpp
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1 // Begin CVS Header
2 // $Source: /Volumes/Home/Users/shoops/cvs/copasi_dev/copasi/sbml/unittests/test000025.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 "test000025.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* test000025::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() == 2);
70  // check second model value
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 CEvaluationNodeOperator* pOperatorNode = dynamic_cast<const CEvaluationNodeOperator*>(pNode);
83  CPPUNIT_ASSERT(pOperatorNode != NULL);
85  const CEvaluationNodeObject* pObjectNode = dynamic_cast<const CEvaluationNodeObject*>(pOperatorNode->getChild());
86  CPPUNIT_ASSERT(pObjectNode != NULL);
87  CCopasiObjectName objectCN = pObjectNode->getObjectCN();
88  CPPUNIT_ASSERT(!objectCN.empty());
89  std::vector<CCopasiContainer*> listOfContainers;
90  listOfContainers.push_back(pModel);
91  const CCopasiObject* pObject = pCOPASIDATAMODEL->ObjectFromName(listOfContainers, objectCN);
92  CPPUNIT_ASSERT(pObject != NULL);
93  CPPUNIT_ASSERT(pObject->isReference() == true);
94  CPPUNIT_ASSERT(pObject->getObjectName() == std::string("ParticleNumber"));
95  CPPUNIT_ASSERT(pObject->getObjectParent() == pA);
96  pObjectNode = dynamic_cast<const CEvaluationNodeObject*>(pOperatorNode->getChild()->getSibling());
97  CPPUNIT_ASSERT(pObjectNode != NULL);
98  objectCN = pObjectNode->getObjectCN();
99  CPPUNIT_ASSERT(!objectCN.empty());
100  pObject = pCOPASIDATAMODEL->ObjectFromName(listOfContainers, objectCN);
101  CPPUNIT_ASSERT(pObject != NULL);
102  CPPUNIT_ASSERT(pObject->isReference() == true);
103  CPPUNIT_ASSERT(pObject->getObjectName() == std::string("Value"));
104  CPPUNIT_ASSERT(pObject->getObjectParent() == pFactor);
105 
106  CPPUNIT_ASSERT(pModel->getReactions().size() == 2);
107  const CReaction* pReaction1 = pModel->getReactions()[0];
108  CPPUNIT_ASSERT(pReaction1 != NULL);
109  CPPUNIT_ASSERT(pReaction1->isReversible() == false);
110  // check the kinetic law
111  const CFunction* pKineticFunction = pReaction1->getFunction();
112  CPPUNIT_ASSERT(pKineticFunction != NULL);
113  const CMassAction* pMassAction = dynamic_cast<const CMassAction*>(pKineticFunction);
114  //FTB: this no longer is recognized as mass action reaction because of the
115  // special case of a species with hOSU
116  CPPUNIT_ASSERT(pMassAction == NULL);
117  const CChemEq* pChemEq = &pReaction1->getChemEq();
118  CPPUNIT_ASSERT(pChemEq != NULL);
119  CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
120  CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
121  const CChemEqElement* pElement = pChemEq->getSubstrates()[0];
122  CPPUNIT_ASSERT(pElement != NULL);
123  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
124  CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
125  CPPUNIT_ASSERT(pChemEq->getProducts().size() == 0);
126  CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
127 
128  const CReaction* pReaction2 = pModel->getReactions()[1];
129  CPPUNIT_ASSERT(pReaction2 != NULL);
130  CPPUNIT_ASSERT(pReaction2->isReversible() == false);
131  // check the kinetic law
132  pKineticFunction = pReaction2->getFunction();
133  CPPUNIT_ASSERT(pKineticFunction != NULL);
134  CPPUNIT_ASSERT(pKineticFunction->getObjectName() == std::string("Henri-Michaelis-Menten (irreversible)"));
135  // check the function parameters one should be the reference to the substrate
136  pChemEq = &pReaction2->getChemEq();
137  CPPUNIT_ASSERT(pChemEq != NULL);
138  CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
139  CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
140  pElement = pChemEq->getSubstrates()[0];
141  CPPUNIT_ASSERT(pElement != NULL);
142  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
143  CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
144  CPPUNIT_ASSERT(pChemEq->getProducts().size() == 1);
145  pElement = pChemEq->getProducts()[0];
146  CPPUNIT_ASSERT(pElement != NULL);
147  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
148  CPPUNIT_ASSERT(pElement->getMetabolite() == pB);
149  CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
150  const std::vector<std::vector<std::string> > parameterMappings = pReaction2->getParameterMappings();
151  CPPUNIT_ASSERT(parameterMappings.size() == 3);
152  CPPUNIT_ASSERT(parameterMappings[0].size() == 1);
153  const std::string parameterKey = parameterMappings[0][0];
154  CPPUNIT_ASSERT(parameterKey == pA->getKey());
155 }
156 
157 const char* test000025::MODEL_STRING =
158  "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
159  "<sbml xmlns=\"http://www.sbml.org/sbml/level2/version3\" level=\"2\" version=\"3\">\n"
160  " <model id=\"Model_1\" name=\"New Model\">\n"
161  " <notes>\n"
162  " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
163  " <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 assignment rule for the global parameter that contains a reference to species A.</p>\n"
164  " <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 (6.023e17). The species references in the reactions should be imported multiplied by the volume.</p>\n"
165  " </body>\n"
166  " </notes>\n"
167  " <listOfFunctionDefinitions>\n"
168  " <functionDefinition id=\"function_1\" name=\"Henri-Michaelis-Menten (irreversible)\">\n"
169  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
170  " <lambda>\n"
171  " <bvar>\n"
172  " <ci> substrate </ci>\n"
173  " </bvar>\n"
174  " <bvar>\n"
175  " <ci> Km </ci>\n"
176  " </bvar>\n"
177  " <bvar>\n"
178  " <ci> V </ci>\n"
179  " </bvar>\n"
180  " <apply>\n"
181  " <divide/>\n"
182  " <apply>\n"
183  " <times/>\n"
184  " <ci> V </ci>\n"
185  " <ci> substrate </ci>\n"
186  " </apply>\n"
187  " <apply>\n"
188  " <plus/>\n"
189  " <ci> Km </ci>\n"
190  " <ci> substrate </ci>\n"
191  " </apply>\n"
192  " </apply>\n"
193  " </lambda>\n"
194  " </math>\n"
195  " </functionDefinition>\n"
196  " </listOfFunctionDefinitions>\n"
197  " <listOfUnitDefinitions>\n"
198  " <unitDefinition id=\"volume\">\n"
199  " <listOfUnits>\n"
200  " <unit kind=\"litre\" scale=\"-3\"/>\n"
201  " </listOfUnits>\n"
202  " </unitDefinition>\n"
203  " <unitDefinition id=\"substance\">\n"
204  " <listOfUnits>\n"
205  " <unit kind=\"mole\" scale=\"-6\"/>\n"
206  " </listOfUnits>\n"
207  " </unitDefinition>\n"
208  " </listOfUnitDefinitions>\n"
209  " <listOfCompartments>\n"
210  " <compartment id=\"compartment_1\" name=\"compartment\" size=\"1\"/>\n"
211  " </listOfCompartments>\n"
212  " <listOfSpecies>\n"
213  " <species id=\"species_1\" name=\"A\" compartment=\"compartment_1\" initialAmount=\"1\" hasOnlySubstanceUnits=\"true\"/>\n"
214  " <species id=\"species_2\" name=\"B\" compartment=\"compartment_1\" initialAmount=\"1\" hasOnlySubstanceUnits=\"true\"/>\n"
215  " </listOfSpecies>\n"
216  " <listOfParameters>\n"
217  " <parameter id=\"parameter_1\" name=\"K\" value=\"0\" constant=\"false\"/>\n"
218  " </listOfParameters>\n"
219  " <listOfRules>\n"
220  " <assignmentRule variable=\"parameter_1\">\n"
221  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
222  " <ci> species_1 </ci>\n"
223  " </math>\n"
224  " </assignmentRule>\n"
225  " </listOfRules>\n"
226  " <listOfReactions>\n"
227  " <reaction id=\"reaction_1\" name=\"reaction_0\" reversible=\"false\">\n"
228  " <listOfReactants>\n"
229  " <speciesReference species=\"species_1\"/>\n"
230  " </listOfReactants>\n"
231  " <kineticLaw>\n"
232  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
233  " <apply>\n"
234  " <times/>\n"
235  " <ci> k1 </ci>\n"
236  " <ci> species_1 </ci>\n"
237  " </apply>\n"
238  " </math>\n"
239  " <listOfParameters>\n"
240  " <parameter id=\"k1\" value=\"0.1\"/>\n"
241  " </listOfParameters>\n"
242  " </kineticLaw>\n"
243  " </reaction>\n"
244  " <reaction id=\"reaction_2\" name=\"reaction_1\" reversible=\"false\">\n"
245  " <listOfReactants>\n"
246  " <speciesReference species=\"species_1\"/>\n"
247  " </listOfReactants>\n"
248  " <listOfProducts>\n"
249  " <speciesReference species=\"species_2\"/>\n"
250  " </listOfProducts>\n"
251  " <kineticLaw>\n"
252  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
253  " <apply>\n"
254  " <times/>\n"
255  " <ci> compartment_1 </ci>\n"
256  " <apply>\n"
257  " <ci> function_1 </ci>\n"
258  " <apply>\n"
259  " <divide/>\n"
260  " <ci> species_1 </ci>\n"
261  " <ci> compartment_1 </ci>\n"
262  " </apply> \n"
263  " <ci> Km </ci>\n"
264  " <ci> V </ci>\n"
265  " </apply>\n"
266  " </apply>\n"
267  " </math>\n"
268  " <listOfParameters>\n"
269  " <parameter id=\"Km\" value=\"0.1\"/>\n"
270  " <parameter id=\"V\" value=\"0.1\"/>\n"
271  " </listOfParameters>\n"
272  " </kineticLaw>\n"
273  " </reaction>\n"
274  " </listOfReactions>\n"
275  " </model>\n"
276  "</sbml>\n"
277  ;
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
static CCopasiDataModel * pCOPASIDATAMODEL
Definition: test000025.h:32
const Type & getType() const
void test_hasOnlySubstanceUnits()
Definition: test000025.cpp:49
Definition: CMetab.h:178
const CCopasiVector< CChemEqElement > & getProducts() const
Definition: CChemEq.cpp:63
void tearDown()
Definition: test000025.cpp:44
bool isReference() const
static const char * MODEL_STRING
Definition: test000025.h:31
const CCopasiVector< CChemEqElement > & getSubstrates() const
Definition: CChemEq.cpp:60
static CCopasiDataModel * addDatamodel()
static Type subType(const Type &type)
const CCopasiVector< CChemEqElement > & getModifiers() const
Definition: CChemEq.cpp:66
void setUp()
Definition: test000025.cpp:36
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
CCopasiNode< Data > * getChild()
Definition: CCopasiNode.h:210
CCopasiObject * ObjectFromName(const std::vector< CCopasiContainer * > &listOfContainer, const CCopasiObjectName &CN) const
CCopasiContainer * getObjectParent() const