COPASI API  4.16.103
test000026.cpp
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1 // Begin CVS Header
2 // $Source: /Volumes/Home/Users/shoops/cvs/copasi_dev/copasi/sbml/unittests/test000026.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 "test000026.h"
20 
21 #include <sstream>
22 #include "utilities.hpp"
23 #include "copasi/CopasiDataModel/CCopasiDataModel.h"
24 #include "copasi/model/CModel.h"
25 #include "copasi/model/CMetab.h"
26 #include "copasi/model/CCompartment.h"
27 #include "copasi/model/CModelValue.h"
28 #include "copasi/model/CReaction.h"
29 #include "copasi/function/CEvaluationNode.h"
30 #include "copasi/function/CExpression.h"
31 
32 #include "copasi/report/CCopasiRootContainer.h"
33 
34 CCopasiDataModel* test000026::pCOPASIDATAMODEL = NULL;
35 
36 void test000026::setUp()
37 {
38  // Create the root container.
39  CCopasiRootContainer::init(0, NULL, false);
40  // Create the global data model.
41  pCOPASIDATAMODEL = CCopasiRootContainer::addDatamodel();
42 }
43 
44 void test000026::tearDown()
45 {
46  CCopasiRootContainer::destroy();
47 }
48 
49 void test000026::test_hasOnlySubstanceUnits()
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  const CModelValue* pModelValue = pModel->getModelValues()[0];
71  CPPUNIT_ASSERT(pModelValue != NULL);
72  const CModelValue* pFactor = pModel->getModelValues()[1];
73  CPPUNIT_ASSERT(pFactor != NULL);
74  CPPUNIT_ASSERT(pFactor->getStatus() == CModelEntity::FIXED);
75  CPPUNIT_ASSERT(fabs((pFactor->getInitialValue() - pModel->getQuantity2NumberFactor()) / pModel->getQuantity2NumberFactor()) < 1e-3);
76  CPPUNIT_ASSERT(pModelValue->getStatus() == CModelEntity::ASSIGNMENT);
77  const CExpression* pExpr = pModelValue->getExpressionPtr();
78  // check the expression
79  const CEvaluationNode* pNode = pExpr->getRoot();
80  CPPUNIT_ASSERT(pNode != NULL);
81  const CEvaluationNodeOperator* pOperatorNode = dynamic_cast<const CEvaluationNodeOperator*>(pNode);
82  CPPUNIT_ASSERT(pOperatorNode != NULL);
83  CPPUNIT_ASSERT(((CEvaluationNodeOperator::SubType)CEvaluationNode::subType(pOperatorNode->getType())) == CEvaluationNodeOperator::MULTIPLY);
84  const CEvaluationNodeNumber* pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pNode->getChild()->getSibling());
85  CPPUNIT_ASSERT(pNumberNode != NULL);
86  CPPUNIT_ASSERT(((CEvaluationNodeNumber::SubType)CEvaluationNode::subType(pNumberNode->getType())) == CEvaluationNodeNumber::DOUBLE);
87  pOperatorNode = dynamic_cast<const CEvaluationNodeOperator*>(pOperatorNode->getChild());
88  CPPUNIT_ASSERT(pOperatorNode != NULL);
89  CPPUNIT_ASSERT(((CEvaluationNodeOperator::SubType)CEvaluationNode::subType(pOperatorNode->getType())) == CEvaluationNodeOperator::DIVIDE);
90  const CEvaluationNodeObject* pObjectNode = dynamic_cast<const CEvaluationNodeObject*>(pOperatorNode->getChild());
91  CPPUNIT_ASSERT(pObjectNode != NULL);
92  CCopasiObjectName objectCN = pObjectNode->getObjectCN();
93  CPPUNIT_ASSERT(!objectCN.empty());
94  std::vector<CCopasiContainer*> listOfContainers;
95  listOfContainers.push_back(pModel);
96  const CCopasiObject* pObject = pCOPASIDATAMODEL->ObjectFromName(listOfContainers, objectCN);
97  CPPUNIT_ASSERT(pObject != NULL);
98  CPPUNIT_ASSERT(pObject->isReference() == true);
99  CPPUNIT_ASSERT(pObject->getObjectName() == std::string("ParticleNumber"));
100  CPPUNIT_ASSERT(pObject->getObjectParent() == pA);
101  pObjectNode = dynamic_cast<const CEvaluationNodeObject*>(pOperatorNode->getChild()->getSibling());
102  CPPUNIT_ASSERT(pObjectNode != NULL);
103  objectCN = pObjectNode->getObjectCN();
104  CPPUNIT_ASSERT(!objectCN.empty());
105  pObject = pCOPASIDATAMODEL->ObjectFromName(listOfContainers, objectCN);
106  CPPUNIT_ASSERT(pObject != NULL);
107  CPPUNIT_ASSERT(pObject->isReference() == true);
108  CPPUNIT_ASSERT(pObject->getObjectName() == std::string("Value"));
109  CPPUNIT_ASSERT(pObject->getObjectParent() == pFactor);
110 
111  CPPUNIT_ASSERT(pModel->getReactions().size() == 2);
112  const CReaction* pReaction1 = pModel->getReactions()[0];
113  CPPUNIT_ASSERT(pReaction1 != NULL);
114  CPPUNIT_ASSERT(pReaction1->isReversible() == false);
115  // check the kinetic law
116  const CFunction* pKineticFunction = pReaction1->getFunction();
117  CPPUNIT_ASSERT(pKineticFunction != NULL);
118  const CMassAction* pMassAction = dynamic_cast<const CMassAction*>(pKineticFunction);
119  //FTB: this no longer is recognized as mass action reaction because of the
120  // special case of a species with hOSU
121  CPPUNIT_ASSERT(pMassAction == NULL);
122  const CChemEq* pChemEq = &pReaction1->getChemEq();
123  CPPUNIT_ASSERT(pChemEq != NULL);
124  CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
125  CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
126  const CChemEqElement* pElement = pChemEq->getSubstrates()[0];
127  CPPUNIT_ASSERT(pElement != NULL);
128  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
129  CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
130  CPPUNIT_ASSERT(pChemEq->getProducts().size() == 0);
131  CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
132 
133  const CReaction* pReaction2 = pModel->getReactions()[1];
134  CPPUNIT_ASSERT(pReaction2 != NULL);
135  CPPUNIT_ASSERT(pReaction2->isReversible() == false);
136  // check the kinetic law
137  pKineticFunction = pReaction2->getFunction();
138  CPPUNIT_ASSERT(pKineticFunction != NULL);
139  CPPUNIT_ASSERT(pKineticFunction->getObjectName() == std::string("Henri-Michaelis-Menten (irreversible)"));
140  // check the function parameters one should be the reference to the substrate
141  pChemEq = &pReaction2->getChemEq();
142  CPPUNIT_ASSERT(pChemEq != NULL);
143  CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
144  CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
145  pElement = pChemEq->getSubstrates()[0];
146  CPPUNIT_ASSERT(pElement != NULL);
147  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
148  CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
149  CPPUNIT_ASSERT(pChemEq->getProducts().size() == 1);
150  pElement = pChemEq->getProducts()[0];
151  CPPUNIT_ASSERT(pElement != NULL);
152  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
153  CPPUNIT_ASSERT(pElement->getMetabolite() == pB);
154  CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
155  const std::vector<std::vector<std::string> > parameterMappings = pReaction2->getParameterMappings();
156  CPPUNIT_ASSERT(parameterMappings.size() == 3);
157  CPPUNIT_ASSERT(parameterMappings[0].size() == 1);
158  const std::string parameterKey = parameterMappings[0][0];
159  CPPUNIT_ASSERT(parameterKey == pA->getKey());
160 }
161 
162 const char* test000026::MODEL_STRING =
163  "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
164  "<sbml xmlns=\"http://www.sbml.org/sbml/level2/version3\" level=\"2\" version=\"3\">\n"
165  " <model id=\"Model_1\" name=\"New Model\">\n"
166  " <notes>\n"
167  " <body xmlns=\"http://www.w3.org/1999/xhtml\">\n"
168  " <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 rule for the global parameter that contains a reference to species A multiplied by a constant that is not the quantity2number factor.</p>\n"
169  " <p>The imported model should contain an assignment for the global parameter that consists of the reference to the particle number of species A multiplied by the factor and divided by the quantity2unit factor. The species references in the reactions should be imported multiplied by the volume.</p>\n"
170  " </body>\n"
171  " </notes>\n"
172  " <listOfFunctionDefinitions>\n"
173  " <functionDefinition id=\"function_1\" name=\"Henri-Michaelis-Menten (irreversible)\">\n"
174  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
175  " <lambda>\n"
176  " <bvar>\n"
177  " <ci> substrate </ci>\n"
178  " </bvar>\n"
179  " <bvar>\n"
180  " <ci> Km </ci>\n"
181  " </bvar>\n"
182  " <bvar>\n"
183  " <ci> V </ci>\n"
184  " </bvar>\n"
185  " <apply>\n"
186  " <divide/>\n"
187  " <apply>\n"
188  " <times/>\n"
189  " <ci> V </ci>\n"
190  " <ci> substrate </ci>\n"
191  " </apply>\n"
192  " <apply>\n"
193  " <plus/>\n"
194  " <ci> Km </ci>\n"
195  " <ci> substrate </ci>\n"
196  " </apply>\n"
197  " </apply>\n"
198  " </lambda>\n"
199  " </math>\n"
200  " </functionDefinition>\n"
201  " </listOfFunctionDefinitions>\n"
202  " <listOfUnitDefinitions>\n"
203  " <unitDefinition id=\"volume\">\n"
204  " <listOfUnits>\n"
205  " <unit kind=\"litre\" scale=\"-3\"/>\n"
206  " </listOfUnits>\n"
207  " </unitDefinition>\n"
208  " <unitDefinition id=\"substance\">\n"
209  " <listOfUnits>\n"
210  " <unit kind=\"mole\" scale=\"-3\"/>\n"
211  " </listOfUnits>\n"
212  " </unitDefinition>\n"
213  " </listOfUnitDefinitions>\n"
214  " <listOfCompartments>\n"
215  " <compartment id=\"compartment_1\" name=\"compartment\" size=\"1\"/>\n"
216  " </listOfCompartments>\n"
217  " <listOfSpecies>\n"
218  " <species id=\"species_1\" name=\"A\" compartment=\"compartment_1\" initialAmount=\"1\" hasOnlySubstanceUnits=\"true\"/>\n"
219  " <species id=\"species_2\" name=\"B\" compartment=\"compartment_1\" initialAmount=\"1\" hasOnlySubstanceUnits=\"true\"/>\n"
220  " </listOfSpecies>\n"
221  " <listOfParameters>\n"
222  " <parameter id=\"parameter_1\" name=\"K\" value=\"0\" constant=\"false\"/>\n"
223  " </listOfParameters>\n"
224  " <listOfRules>\n"
225  " <assignmentRule variable=\"parameter_1\">\n"
226  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
227  " <apply>\n"
228  " <times/>\n"
229  " <ci> species_1 </ci>\n"
230  " <cn> 3.0221415e20 </cn>\n"
231  " </apply>\n"
232  " </math>\n"
233  " </assignmentRule>\n"
234  " </listOfRules>\n"
235  " <listOfReactions>\n"
236  " <reaction id=\"reaction_1\" name=\"reaction_0\" reversible=\"false\">\n"
237  " <listOfReactants>\n"
238  " <speciesReference species=\"species_1\"/>\n"
239  " </listOfReactants>\n"
240  " <kineticLaw>\n"
241  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
242  " <apply>\n"
243  " <times/>\n"
244  " <ci> k1 </ci>\n"
245  " <ci> species_1 </ci>\n"
246  " </apply>\n"
247  " </math>\n"
248  " <listOfParameters>\n"
249  " <parameter id=\"k1\" value=\"0.1\"/>\n"
250  " </listOfParameters>\n"
251  " </kineticLaw>\n"
252  " </reaction>\n"
253  " <reaction id=\"reaction_2\" name=\"reaction_1\" reversible=\"false\">\n"
254  " <listOfReactants>\n"
255  " <speciesReference species=\"species_1\"/>\n"
256  " </listOfReactants>\n"
257  " <listOfProducts>\n"
258  " <speciesReference species=\"species_2\"/>\n"
259  " </listOfProducts>\n"
260  " <kineticLaw>\n"
261  " <math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
262  " <apply>\n"
263  " <times/>\n"
264  " <ci> compartment_1 </ci>\n"
265  " <apply>\n"
266  " <ci> function_1 </ci>\n"
267  " <apply>\n"
268  " <divide/>\n"
269  " <ci> species_1 </ci>\n"
270  " <ci> compartment_1 </ci>\n"
271  " </apply> \n"
272  " <ci> Km </ci>\n"
273  " <ci> V </ci>\n"
274  " </apply>\n"
275  " </apply>\n"
276  " </math>\n"
277  " <listOfParameters>\n"
278  " <parameter id=\"Km\" value=\"0.1\"/>\n"
279  " <parameter id=\"V\" value=\"0.1\"/>\n"
280  " </listOfParameters>\n"
281  " </kineticLaw>\n"
282  " </reaction>\n"
283  " </listOfReactions>\n"
284  " </model>\n"
285  "</sbml>\n"
286  ;
CExpression.h
Header file of class CExpression.
CChemEq::getCompartmentNumber
size_t getCompartmentNumber() const
Definition: CChemEq.cpp:110
CModelValue.h
Header file of class CModelEntity and CModelValue.
CCopasiObject::getObjectName
const std::string & getObjectName() const
Definition: CCopasiObject.cpp:258
CCopasiVector::size
virtual size_t size() const
Definition: CCopasiVector.h:386
test000026::setUp
void setUp()
Definition: test000026.cpp:36
CEvaluationNode::getType
const Type & getType() const
Definition: CEvaluationNode.cpp:357
CMetab
Definition: CMetab.h:178
test000026::tearDown
void tearDown()
Definition: test000026.cpp:44
test000026::test_hasOnlySubstanceUnits
void test_hasOnlySubstanceUnits()
Definition: test000026.cpp:49
CModelEntity::getInitialValue
const C_FLOAT64 & getInitialValue() const
Definition: CModelValue.cpp:138
CChemEq::getProducts
const CCopasiVector< CChemEqElement > & getProducts() const
Definition: CChemEq.cpp:63
CCopasiObject::isReference
bool isReference() const
Definition: CCopasiObject.cpp:572
test000026::MODEL_STRING
static const char * MODEL_STRING
Definition: test000026.h:31
CChemEq::getSubstrates
const CCopasiVector< CChemEqElement > & getSubstrates() const
Definition: CChemEq.cpp:60
CCopasiRootContainer::addDatamodel
static CCopasiDataModel * addDatamodel()
Definition: CCopasiRootContainer.cpp:149
CEvaluationNode::subType
static Type subType(const Type &type)
Definition: CEvaluationNode.cpp:120
test000026::pCOPASIDATAMODEL
static CCopasiDataModel * pCOPASIDATAMODEL
Definition: test000026.h:32
CChemEq::getModifiers
const CCopasiVector< CChemEqElement > & getModifiers() const
Definition: CChemEq.cpp:66
CCopasiDataModel::importSBMLFromString
bool importSBMLFromString(const std::string &sbmlDocumentText, CProcessReport *pImportHandler=NULL, const bool &deleteOldData=true)
Definition: CCopasiDataModel.cpp:526
CFunction
The class for handling a chemical kinetic function.
Definition: CFunction.h:29
CCopasiRootContainer::init
static void init(int argc, char *argv[], const bool &withGui=false)
Definition: CCopasiRootContainer.cpp:78
CModel
Definition: CModel.h:50
CModelEntity::getStatus
const CModelEntity::Status & getStatus() const
Definition: CModelValue.cpp:141
CCopasiNode::getChild
CCopasiNode< Data > * getChild()
Definition: CCopasiNode.h:210
CCopasiDataModel::ObjectFromName
CCopasiObject * ObjectFromName(const std::vector< CCopasiContainer * > &listOfContainer, const CCopasiObjectName &CN) const
Definition: CCopasiDataModel.cpp:1940
CCopasiObject::getObjectParent
CCopasiContainer * getObjectParent() const
Definition: CCopasiObject.cpp:276
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