19 #include "test000015.hpp"
22 #include "utilities.hpp"
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"
36 void test000015::setUp()
44 void test000015::tearDown()
49 void test000015::test_references_to_species()
55 std::istringstream iss(test000015::MODEL_STRING);
57 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
60 CPPUNIT_ASSERT(pDocument != NULL);
61 Model* pModel = pDocument->getModel();
62 CPPUNIT_ASSERT(pModel != NULL);
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() == 1);
75 CPPUNIT_ASSERT(pModel->getNumInitialAssignments() == 1);
76 InitialAssignment* pAssignment = pModel->getInitialAssignment(0);
77 CPPUNIT_ASSERT(pAssignment != NULL);
78 CPPUNIT_ASSERT(pModel->getNumParameters() == 2);
79 Parameter* pParameter = pModel->getParameter(0);
80 CPPUNIT_ASSERT(pParameter != NULL);
81 Parameter* pFactor = pModel->getParameter(1);
82 CPPUNIT_ASSERT(pFactor != NULL);
83 CPPUNIT_ASSERT(fabs((pFactor->getValue() - (
AVOGADRO / 1000.0)) / (
AVOGADRO / 1000.0)) < 1e-3);
84 CPPUNIT_ASSERT(pAssignment->getSymbol() == pParameter->getId());
85 const ASTNode* pMath = pAssignment->getMath();
86 CPPUNIT_ASSERT(pMath != NULL);
88 CPPUNIT_ASSERT(pMath->getType() == AST_TIMES);
89 CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
90 CPPUNIT_ASSERT(pMath->getChild(0) != NULL);
91 CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
92 CPPUNIT_ASSERT(pMath->getChild(0)->getName() == idSpeciesA);
93 CPPUNIT_ASSERT(pMath->getChild(1) != NULL);
94 CPPUNIT_ASSERT(pMath->getChild(1)->getType() == AST_NAME);
95 CPPUNIT_ASSERT(pMath->getChild(1)->getName() == pFactor->getId());
96 CPPUNIT_ASSERT(pModel->getNumReactions() == 2);
97 Reaction* pReaction = pModel->getReaction(0);
99 CPPUNIT_ASSERT(pReaction != NULL);
100 CPPUNIT_ASSERT(pReaction->getNumReactants() == 1);
101 CPPUNIT_ASSERT(pReaction->getNumProducts() == 0);
107 CPPUNIT_ASSERT(pReaction->isSetKineticLaw() ==
true);
108 KineticLaw* pLaw = pReaction->getKineticLaw();
109 CPPUNIT_ASSERT(pLaw != NULL);
110 CPPUNIT_ASSERT(pLaw->isSetMath() ==
true);
111 pMath = pLaw->getMath();
112 CPPUNIT_ASSERT(pMath->getType() == AST_TIMES);
113 CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
114 CPPUNIT_ASSERT(pMath->getChild(0) != NULL);
115 CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
116 CPPUNIT_ASSERT(pMath->getChild(0)->getName() == std::string(
"k1"));
117 CPPUNIT_ASSERT(pMath->getChild(1) != NULL);
118 CPPUNIT_ASSERT(pMath->getChild(1)->getType() == AST_NAME);
119 CPPUNIT_ASSERT(pMath->getChild(1)->getName() == idSpeciesA);
121 pReaction = pModel->getReaction(1);
123 CPPUNIT_ASSERT(pReaction != NULL);
124 CPPUNIT_ASSERT(pReaction->getNumReactants() == 1);
125 CPPUNIT_ASSERT(pReaction->getNumProducts() == 1);
130 CPPUNIT_ASSERT(pReaction->isSetKineticLaw() ==
true);
131 pLaw = pReaction->getKineticLaw();
132 CPPUNIT_ASSERT(pLaw != NULL);
133 CPPUNIT_ASSERT(pLaw->isSetMath() ==
true);
134 pMath = pLaw->getMath();
135 CPPUNIT_ASSERT(pMath->getType() == AST_TIMES);
136 CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
137 CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
138 CPPUNIT_ASSERT(pMath->getChild(0)->getName() == pCompartment->getId());
139 pMath = pMath->getChild(1);
140 CPPUNIT_ASSERT(pMath != NULL);
141 CPPUNIT_ASSERT(pMath->getType() == AST_FUNCTION);
142 CPPUNIT_ASSERT(pMath->getNumChildren() == 3);
143 pMath = pMath->getChild(0);
144 CPPUNIT_ASSERT(pMath != NULL);
145 CPPUNIT_ASSERT(pMath->getType() == AST_DIVIDE);
146 CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
147 CPPUNIT_ASSERT(pMath->getChild(0) != NULL);
148 CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
149 CPPUNIT_ASSERT(pMath->getChild(0)->getName() == idSpeciesA);
150 CPPUNIT_ASSERT(pMath->getChild(1) != NULL);
151 CPPUNIT_ASSERT(pMath->getChild(1)->getType() == AST_NAME);
152 CPPUNIT_ASSERT(pMath->getChild(1)->getName() == pCompartment->getId());
155 const char* test000015::MODEL_STRING =
156 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
157 "<!-- generated with COPASI 4.3.25 (Debug) (http://www.copasi.org) at 2008-02-15 09:41:38 UTC -->\n"
158 "<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"
159 " <ListOfFunctions>\n"
160 " <Function key=\"Function_8\" name=\"Henri-Michaelis-Menten (irreversible)\" type=\"PreDefined\" reversible=\"false\">\n"
162 " V*substrate/(Km+substrate)\n"
164 " <ListOfParameterDescriptions>\n"
165 " <ParameterDescription key=\"FunctionParameter_41\" name=\"substrate\" order=\"0\" role=\"substrate\"/>\n"
166 " <ParameterDescription key=\"FunctionParameter_30\" name=\"Km\" order=\"1\" role=\"constant\"/>\n"
167 " <ParameterDescription key=\"FunctionParameter_45\" name=\"V\" order=\"2\" role=\"constant\"/>\n"
168 " </ListOfParameterDescriptions>\n"
170 " <Function key=\"Function_13\" name=\"Mass action (irreversible)\" type=\"MassAction\" reversible=\"false\">\n"
172 " k1*PRODUCT<substrate_i>\n"
174 " <ListOfParameterDescriptions>\n"
175 " <ParameterDescription key=\"FunctionParameter_81\" name=\"k1\" order=\"0\" role=\"constant\"/>\n"
176 " <ParameterDescription key=\"FunctionParameter_79\" name=\"substrate\" order=\"1\" role=\"substrate\"/>\n"
177 " </ListOfParameterDescriptions>\n"
179 " </ListOfFunctions>\n"
180 " <Model key=\"Model_1\" name=\"New Model\" timeUnit=\"s\" volumeUnit=\"ml\" quantityUnit=\"mmol\" type=\"deterministic\">\n"
182 " <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"
183 "<p>Model with variable volume compartment,mmol quantity units and a reference to the species initial amount.</p>\n"
184 "<p>On export this should create an SBML file with the hasOnlySubstanceUnits flag on the species set.</p>\n"
185 "<p>The reference in the initial assignment should be multiplied by a factor (6.023e20), the references in the reactions should be divided by the volume.</p>\n"
188 " <ListOfCompartments>\n"
189 " <Compartment key=\"Compartment_0\" name=\"compartment\" simulationType=\"assignment\">\n"
194 " </ListOfCompartments>\n"
195 " <ListOfMetabolites>\n"
196 " <Metabolite key=\"Metabolite_0\" name=\"A\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
198 " <Metabolite key=\"Metabolite_1\" name=\"S\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
200 " </ListOfMetabolites>\n"
201 " <ListOfModelValues>\n"
202 " <ModelValue key=\"ModelValue_0\" name=\"K\" simulationType=\"fixed\">\n"
203 " <InitialExpression>\n"
204 " <CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[A],Reference=InitialParticleNumber>\n"
205 " </InitialExpression>\n"
207 " </ListOfModelValues>\n"
208 " <ListOfReactions>\n"
209 " <Reaction key=\"Reaction_0\" name=\"reaction\" reversible=\"false\">\n"
210 " <ListOfSubstrates>\n"
211 " <Substrate metabolite=\"Metabolite_0\" stoichiometry=\"1\"/>\n"
212 " </ListOfSubstrates>\n"
213 " <ListOfConstants>\n"
214 " <Constant key=\"Parameter_93\" name=\"k1\" value=\"0.1\"/>\n"
215 " </ListOfConstants>\n"
216 " <KineticLaw function=\"Function_13\">\n"
217 " <ListOfCallParameters>\n"
218 " <CallParameter functionParameter=\"FunctionParameter_81\">\n"
219 " <SourceParameter reference=\"Parameter_93\"/>\n"
220 " </CallParameter>\n"
221 " <CallParameter functionParameter=\"FunctionParameter_79\">\n"
222 " <SourceParameter reference=\"Metabolite_0\"/>\n"
223 " </CallParameter>\n"
224 " </ListOfCallParameters>\n"
227 " <Reaction key=\"Reaction_1\" name=\"reaction_1\" reversible=\"false\">\n"
228 " <ListOfSubstrates>\n"
229 " <Substrate metabolite=\"Metabolite_0\" stoichiometry=\"1\"/>\n"
230 " </ListOfSubstrates>\n"
231 " <ListOfProducts>\n"
232 " <Product metabolite=\"Metabolite_1\" stoichiometry=\"1\"/>\n"
233 " </ListOfProducts>\n"
234 " <ListOfConstants>\n"
235 " <Constant key=\"Parameter_92\" name=\"Km\" value=\"0.1\"/>\n"
236 " <Constant key=\"Parameter_91\" name=\"V\" value=\"0.1\"/>\n"
237 " </ListOfConstants>\n"
238 " <KineticLaw function=\"Function_8\">\n"
239 " <ListOfCallParameters>\n"
240 " <CallParameter functionParameter=\"FunctionParameter_41\">\n"
241 " <SourceParameter reference=\"Metabolite_0\"/>\n"
242 " </CallParameter>\n"
243 " <CallParameter functionParameter=\"FunctionParameter_30\">\n"
244 " <SourceParameter reference=\"Parameter_92\"/>\n"
245 " </CallParameter>\n"
246 " <CallParameter functionParameter=\"FunctionParameter_45\">\n"
247 " <SourceParameter reference=\"Parameter_91\"/>\n"
248 " </CallParameter>\n"
249 " </ListOfCallParameters>\n"
252 " </ListOfReactions>\n"
254 " <StateTemplateVariable objectReference=\"Model_1\"/>\n"
255 " <StateTemplateVariable objectReference=\"Metabolite_0\"/>\n"
256 " <StateTemplateVariable objectReference=\"Metabolite_1\"/>\n"
257 " <StateTemplateVariable objectReference=\"Compartment_0\"/>\n"
258 " <StateTemplateVariable objectReference=\"ModelValue_0\"/>\n"
259 " </StateTemplate>\n"
260 " <InitialState type=\"initialState\">\n"
261 " 0 4.215499050000001e+21 4.215499050000002e+20 7 4.215499050000001e+21\n"
SBMLDocument * getCurrentSBMLDocument()
std::string exportSBMLToString(CProcessReport *pExportHandler, int sbmlLevel, int sbmlVersion)
bool load_cps_model_from_stream(std::istream &is, CCopasiDataModel &dataModel)
static CCopasiDataModel * addDatamodel()
static void init(int argc, char *argv[], const bool &withGui=false)