COPASI API  4.16.103
test000017.cpp
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1 // Begin CVS Header
2 // $Source: /Volumes/Home/Users/shoops/cvs/copasi_dev/copasi/sbml/unittests/test000017.cpp,v $
3 // $Revision: 1.8 $
4 // $Name: $
5 // $Author: gauges $
6 // $Date: 2010/03/11 11:52:00 $
7 // End CVS Header
8 
9 // Copyright (C) 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 "test000017.hpp"
20 
21 #include <sstream>
22 #include "utilities.hpp"
23 #include "copasi/CopasiDataModel/CCopasiDataModel.h"
24 
25 #include "sbml/SBMLDocument.h"
26 #include "sbml/Model.h"
27 #include "sbml/Rule.h"
28 #include "sbml/Species.h"
29 #include "sbml/Parameter.h"
30 #include "sbml/math/ASTNode.h"
31 
32 #include "copasi/report/CCopasiRootContainer.h"
33 
34 CCopasiDataModel* test000017::pCOPASIDATAMODEL = NULL;
35 
36 void test000017::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 test000017::tearDown()
45 {
46  CCopasiRootContainer::destroy();
47 }
48 
49 void test000017::test_references_to_species()
50 {
51  // load the CPS file
52  // export to SBML
53  // check the resulting SBML model
54  CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
55  std::istringstream iss(test000017::MODEL_STRING);
56  CPPUNIT_ASSERT(load_cps_model_from_stream(iss, *pDataModel) == true);
57  CPPUNIT_ASSERT(pDataModel->getModel() != NULL);
58  CPPUNIT_ASSERT(pDataModel->exportSBMLToString(NULL, 2, 3).empty() == false);
59  SBMLDocument* pDocument = pDataModel->getCurrentSBMLDocument();
60  CPPUNIT_ASSERT(pDocument != NULL);
61  Model* pModel = pDocument->getModel();
62  CPPUNIT_ASSERT(pModel != NULL);
63  // assert that there is only one compartment and
64  // assert the compartment is constant
65  CPPUNIT_ASSERT(pModel->getNumCompartments() == 1);
66  Compartment* pCompartment = pModel->getCompartment(0);
67  CPPUNIT_ASSERT(pCompartment->getConstant() == false);
68  CPPUNIT_ASSERT(pModel->getNumSpecies() == 2);
69  Species* pSpecies = pModel->getSpecies(1);
70  CPPUNIT_ASSERT(pSpecies->getHasOnlySubstanceUnits() == true);
71  pSpecies = pModel->getSpecies(0);
72  std::string idSpeciesA = pSpecies->getId();
73  CPPUNIT_ASSERT(pSpecies->getHasOnlySubstanceUnits() == true);
74  CPPUNIT_ASSERT(pModel->getNumRules() == 2);
75  // there are two rules, one is for the compartment
76  AssignmentRule* pRule = dynamic_cast<AssignmentRule*>(pModel->getRule(0));
77  CPPUNIT_ASSERT(pRule != NULL);
78  CPPUNIT_ASSERT(pModel->getNumParameters() == 1);
79  Parameter* pParameter = pModel->getParameter(0);
80  CPPUNIT_ASSERT(pParameter != NULL);
81 
82  if (pRule->getVariable() != pParameter->getId())
83  {
84  pRule = dynamic_cast<AssignmentRule*>(pModel->getRule(1));
85  }
86 
87  CPPUNIT_ASSERT(pRule->getVariable() == pParameter->getId());
88  const ASTNode* pMath = pRule->getMath();
89  CPPUNIT_ASSERT(pMath != NULL);
90  // the expression should be the species divided by the volume
91  CPPUNIT_ASSERT(pMath->getType() == AST_DIVIDE);
92  CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
93  CPPUNIT_ASSERT(pMath->getChild(0) != NULL);
94  CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
95  CPPUNIT_ASSERT(pMath->getChild(0)->getName() == idSpeciesA);
96  CPPUNIT_ASSERT(pMath->getChild(1) != NULL);
97  CPPUNIT_ASSERT(pMath->getChild(1)->getType() == AST_NAME);
98  CPPUNIT_ASSERT(pMath->getChild(1)->getName() == pCompartment->getId());
99  CPPUNIT_ASSERT(pModel->getNumReactions() == 2);
100  Reaction* pReaction = pModel->getReaction(0);
101  // make sure this is reaction A ->
102  CPPUNIT_ASSERT(pReaction != NULL);
103  CPPUNIT_ASSERT(pReaction->getNumReactants() == 1);
104  CPPUNIT_ASSERT(pReaction->getNumProducts() == 0);
105  // check if all references in the kinetic law are unmodified
106  // math element must be a multiplication of the mass action term by
107  // the compartment volume
108  // the mass action term is a multiplication of the parameter node by
109  // the species node
110  CPPUNIT_ASSERT(pReaction->isSetKineticLaw() == true);
111  KineticLaw* pLaw = pReaction->getKineticLaw();
112  CPPUNIT_ASSERT(pLaw != NULL);
113  CPPUNIT_ASSERT(pLaw->isSetMath() == true);
114  pMath = pLaw->getMath();
115  CPPUNIT_ASSERT(pMath->getType() == AST_TIMES);
116  CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
117  CPPUNIT_ASSERT(pMath->getChild(0) != NULL);
118  CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
119  CPPUNIT_ASSERT(pMath->getChild(0)->getName() == std::string("k1"));
120  CPPUNIT_ASSERT(pMath->getChild(1) != NULL);
121  CPPUNIT_ASSERT(pMath->getChild(1)->getType() == AST_NAME);
122  CPPUNIT_ASSERT(pMath->getChild(1)->getName() == idSpeciesA);
123 
124  pReaction = pModel->getReaction(1);
125  // make sure this is reaction A -> S
126  CPPUNIT_ASSERT(pReaction != NULL);
127  CPPUNIT_ASSERT(pReaction->getNumReactants() == 1);
128  CPPUNIT_ASSERT(pReaction->getNumProducts() == 1);
129  // check if all references in the kinetic law are unmodified
130  // math element must be a multiplication of the compartments volume with
131  // a function call with three arguments
132  // the first argument is the reference to the species
133  CPPUNIT_ASSERT(pReaction->isSetKineticLaw() == true);
134  pLaw = pReaction->getKineticLaw();
135  CPPUNIT_ASSERT(pLaw != NULL);
136  CPPUNIT_ASSERT(pLaw->isSetMath() == true);
137  pMath = pLaw->getMath();
138  CPPUNIT_ASSERT(pMath->getType() == AST_TIMES);
139  CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
140  CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
141  CPPUNIT_ASSERT(pMath->getChild(0)->getName() == pCompartment->getId());
142  pMath = pMath->getChild(1);
143  CPPUNIT_ASSERT(pMath != NULL);
144  CPPUNIT_ASSERT(pMath->getType() == AST_FUNCTION);
145  CPPUNIT_ASSERT(pMath->getNumChildren() == 3);
146  pMath = pMath->getChild(0);
147  CPPUNIT_ASSERT(pMath != NULL);
148  CPPUNIT_ASSERT(pMath->getType() == AST_DIVIDE);
149  CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
150  CPPUNIT_ASSERT(pMath->getChild(0) != NULL);
151  CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
152  CPPUNIT_ASSERT(pMath->getChild(0)->getName() == idSpeciesA);
153  CPPUNIT_ASSERT(pMath->getChild(1) != NULL);
154  CPPUNIT_ASSERT(pMath->getChild(1)->getType() == AST_NAME);
155  CPPUNIT_ASSERT(pMath->getChild(1)->getName() == pCompartment->getId());
156 }
157 
158 const char* test000017::MODEL_STRING =
159  "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
160  "<!-- generated with COPASI 4.3.25 (Debug) (http://www.copasi.org) at 2008-02-15 09:43:49 UTC -->\n"
161  "<COPASI xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:noNamespaceSchemaLocation=\"http://www.copasi.org/static/schema.xsd\" versionMajor=\"1\" versionMinor=\"0\" versionDevel=\"25\">\n"
162  " <ListOfFunctions>\n"
163  " <Function key=\"Function_8\" name=\"Henri-Michaelis-Menten (irreversible)\" type=\"PreDefined\" reversible=\"false\">\n"
164  " <Expression>\n"
165  " V*substrate/(Km+substrate)\n"
166  " </Expression>\n"
167  " <ListOfParameterDescriptions>\n"
168  " <ParameterDescription key=\"FunctionParameter_41\" name=\"substrate\" order=\"0\" role=\"substrate\"/>\n"
169  " <ParameterDescription key=\"FunctionParameter_30\" name=\"Km\" order=\"1\" role=\"constant\"/>\n"
170  " <ParameterDescription key=\"FunctionParameter_45\" name=\"V\" order=\"2\" role=\"constant\"/>\n"
171  " </ListOfParameterDescriptions>\n"
172  " </Function>\n"
173  " <Function key=\"Function_13\" name=\"Mass action (irreversible)\" type=\"MassAction\" reversible=\"false\">\n"
174  " <Expression>\n"
175  " k1*PRODUCT&lt;substrate_i&gt;\n"
176  " </Expression>\n"
177  " <ListOfParameterDescriptions>\n"
178  " <ParameterDescription key=\"FunctionParameter_81\" name=\"k1\" order=\"0\" role=\"constant\"/>\n"
179  " <ParameterDescription key=\"FunctionParameter_79\" name=\"substrate\" order=\"1\" role=\"substrate\"/>\n"
180  " </ListOfParameterDescriptions>\n"
181  " </Function>\n"
182  " </ListOfFunctions>\n"
183  " <Model key=\"Model_1\" name=\"New Model\" timeUnit=\"s\" volumeUnit=\"ml\" quantityUnit=\"µmol\" type=\"deterministic\">\n"
184  " <Comment>\n"
185  " <html xmlns=\"http://www.w3.org/1999/xhtml\"><head><meta name=\"qrichtext\" content=\"1\" /></head><body style=\"font-size:13pt;font-family:Lucida Grande\">\n"
186  "<p>Model with variable volume compartment, micromol quantity units and a reference to the species transient concentration.</p>\n"
187  "<p>On export this should create an SBML file with the hasOnlySubstanceUnits flag on the species set.</p>\n"
188  "<p>The reference in the rule for the parameter should be divided by the volume. The references in the reactions should be divided by the volume.</p>\n"
189  "</body></html>\n"
190  " </Comment>\n"
191  " <ListOfCompartments>\n"
192  " <Compartment key=\"Compartment_0\" name=\"compartment\" simulationType=\"assignment\">\n"
193  " <Expression>\n"
194  " 3+4\n"
195  " </Expression>\n"
196  " </Compartment>\n"
197  " </ListOfCompartments>\n"
198  " <ListOfMetabolites>\n"
199  " <Metabolite key=\"Metabolite_0\" name=\"A\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
200  " </Metabolite>\n"
201  " <Metabolite key=\"Metabolite_1\" name=\"S\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
202  " </Metabolite>\n"
203  " </ListOfMetabolites>\n"
204  " <ListOfModelValues>\n"
205  " <ModelValue key=\"ModelValue_0\" name=\"K\" simulationType=\"assignment\">\n"
206  " <Expression>\n"
207  " &lt;CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[A],Reference=Concentration&gt;\n"
208  " </Expression>\n"
209  " </ModelValue>\n"
210  " </ListOfModelValues>\n"
211  " <ListOfReactions>\n"
212  " <Reaction key=\"Reaction_0\" name=\"reaction\" reversible=\"false\">\n"
213  " <ListOfSubstrates>\n"
214  " <Substrate metabolite=\"Metabolite_0\" stoichiometry=\"1\"/>\n"
215  " </ListOfSubstrates>\n"
216  " <ListOfConstants>\n"
217  " <Constant key=\"Parameter_93\" name=\"k1\" value=\"0.1\"/>\n"
218  " </ListOfConstants>\n"
219  " <KineticLaw function=\"Function_13\">\n"
220  " <ListOfCallParameters>\n"
221  " <CallParameter functionParameter=\"FunctionParameter_81\">\n"
222  " <SourceParameter reference=\"Parameter_93\"/>\n"
223  " </CallParameter>\n"
224  " <CallParameter functionParameter=\"FunctionParameter_79\">\n"
225  " <SourceParameter reference=\"Metabolite_0\"/>\n"
226  " </CallParameter>\n"
227  " </ListOfCallParameters>\n"
228  " </KineticLaw>\n"
229  " </Reaction>\n"
230  " <Reaction key=\"Reaction_1\" name=\"reaction_1\" reversible=\"false\">\n"
231  " <ListOfSubstrates>\n"
232  " <Substrate metabolite=\"Metabolite_0\" stoichiometry=\"1\"/>\n"
233  " </ListOfSubstrates>\n"
234  " <ListOfProducts>\n"
235  " <Product metabolite=\"Metabolite_1\" stoichiometry=\"1\"/>\n"
236  " </ListOfProducts>\n"
237  " <ListOfConstants>\n"
238  " <Constant key=\"Parameter_92\" name=\"Km\" value=\"0.1\"/>\n"
239  " <Constant key=\"Parameter_91\" name=\"V\" value=\"0.1\"/>\n"
240  " </ListOfConstants>\n"
241  " <KineticLaw function=\"Function_8\">\n"
242  " <ListOfCallParameters>\n"
243  " <CallParameter functionParameter=\"FunctionParameter_41\">\n"
244  " <SourceParameter reference=\"Metabolite_0\"/>\n"
245  " </CallParameter>\n"
246  " <CallParameter functionParameter=\"FunctionParameter_30\">\n"
247  " <SourceParameter reference=\"Parameter_92\"/>\n"
248  " </CallParameter>\n"
249  " <CallParameter functionParameter=\"FunctionParameter_45\">\n"
250  " <SourceParameter reference=\"Parameter_91\"/>\n"
251  " </CallParameter>\n"
252  " </ListOfCallParameters>\n"
253  " </KineticLaw>\n"
254  " </Reaction>\n"
255  " </ListOfReactions>\n"
256  " <StateTemplate>\n"
257  " <StateTemplateVariable objectReference=\"Model_1\"/>\n"
258  " <StateTemplateVariable objectReference=\"Metabolite_0\"/>\n"
259  " <StateTemplateVariable objectReference=\"Metabolite_1\"/>\n"
260  " <StateTemplateVariable objectReference=\"Compartment_0\"/>\n"
261  " <StateTemplateVariable objectReference=\"ModelValue_0\"/>\n"
262  " </StateTemplate>\n"
263  " <InitialState type=\"initialState\">\n"
264  " 0 4.21549905e+18 4.215499050000001e+17 7 1\n"
265  " </InitialState>\n"
266  " </Model>\n"
267  "</COPASI>\n"
268  ;
CCopasiDataModel::getCurrentSBMLDocument
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Definition: utilities.cpp:21
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Definition: CCopasiRootContainer.cpp:149
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