def test_Model_getReactionById(self): r1 = libsbml.Reaction(2, 4) r2 = libsbml.Reaction(2, 4) r1.setId("reaction_1") r2.setId("reaction_2") self.M.addReaction(r1) self.M.addReaction(r2) self.assert_(self.M.getNumReactions() == 2) self.assert_(self.M.getReaction("reaction_1") != r1) self.assert_(self.M.getReaction("reaction_2") != r2) self.assert_(self.M.getReaction("reaction_3") == None) pass
def test_Model_getReaction(self): r1 = libsbml.Reaction(2, 4) r2 = libsbml.Reaction(2, 4) r1.setId("reaction_1") r2.setId("reaction_2") self.M.addReaction(r1) self.M.addReaction(r2) self.assert_(self.M.getNumReactions() == 2) r1 = self.M.getReaction(0) r2 = self.M.getReaction(1) self.assert_(("reaction_1" == r1.getId())) self.assert_(("reaction_2" == r2.getId())) pass
def test_KineticLaw_getParameterById(self): k1 = libsbml.Parameter(2, 4) k2 = libsbml.Parameter(2, 4) k1.setId("k1") k2.setId("k2") k1.setValue(3.14) k2.setValue(2.72) self.M.addParameter(k1) self.M.addParameter(k2) r1 = libsbml.Reaction(2, 4) r1.setId("reaction_1") kl = libsbml.KineticLaw(2, 4) kl.setFormula("k1 * X0") k3 = libsbml.Parameter(2, 4) k4 = libsbml.Parameter(2, 4) k3.setId("k1") k4.setId("k2") k3.setValue(2.72) k4.setValue(3.14) kl.addParameter(k3) kl.addParameter(k4) r1.setKineticLaw(kl) self.M.addReaction(r1) kl1 = self.M.getReaction(0).getKineticLaw() self.assert_(kl1.getParameter("k1") != k3) self.assert_(kl1.getParameter("k1") != k1) self.assert_(kl1.getParameter("k2") != k4) self.assert_(kl1.getParameter("k3") == None) pass
def test_Reaction_setFast2(self): R1 = libsbml.Reaction(2, 4) i = R1.unsetFast() self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS) self.assert_(R1.getFast() == False) self.assertEqual(False, R1.isSetFast()) pass
def test_Reaction_addProduct1(self): m = libsbml.Reaction(2, 2) p = libsbml.SpeciesReference(2, 2) p1 = libsbml.SpeciesReference(2, 2) p1.setSpecies("k") p1.setId("k1") i = m.addProduct(p) self.assert_(i == libsbml.LIBSBML_INVALID_OBJECT) p.setSpecies("k") p.setId("k1") i = m.addProduct(p) self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS) self.assert_(m.getNumProducts() == 1) i = m.addProduct(p1) self.assert_(i == libsbml.LIBSBML_DUPLICATE_OBJECT_ID) self.assert_(m.getNumProducts() == 1) _dummyList = [p] _dummyList[:] = [] del _dummyList _dummyList = [p1] _dummyList[:] = [] del _dummyList _dummyList = [m] _dummyList[:] = [] del _dummyList pass
def test_L3_Reaction_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add("http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(3, 1) sbmlns.addNamespaces(xmlns) r = libsbml.Reaction(sbmlns) self.assert_(r.getTypeCode() == libsbml.SBML_REACTION) self.assert_(r.getMetaId() == "") self.assert_(r.getNotes() == None) self.assert_(r.getAnnotation() == None) self.assert_(r.getLevel() == 3) self.assert_(r.getVersion() == 1) self.assert_(r.getNamespaces() != None) self.assert_(r.getNamespaces().getLength() == 2) self.assert_(r.getId() == "") self.assert_(r.getName() == "") self.assert_(r.getCompartment() == "") self.assert_(r.getFast() == False) self.assert_(r.getReversible() == True) self.assertEqual(False, r.isSetId()) self.assertEqual(False, r.isSetName()) self.assertEqual(False, r.isSetCompartment()) self.assertEqual(False, r.isSetFast()) self.assertEqual(False, r.isSetReversible()) _dummyList = [r] _dummyList[:] = [] del _dummyList pass
def test_Reaction(self): r = libsbml.Reaction(2, 4) self.assertEqual(False, (r.hasRequiredAttributes())) r.setId("r") self.assertEqual(True, r.hasRequiredAttributes()) r = None pass
def test_KineticLaw_parent_add(self): kl = libsbml.KineticLaw(2, 4) kl.setMath(libsbml.parseFormula("1")) r = libsbml.Reaction(2, 4) r.setKineticLaw(kl) self.assert_(r == r.getKineticLaw().getParentSBMLObject()) r = None pass
def test_SpeciesReference_Modifier_parent_create(self): r = libsbml.Reaction(2, 4) sr = r.createModifier() lo = r.getListOfModifiers() self.assert_(lo == sr.getParentSBMLObject()) self.assert_(lo == r.getModifier(0).getParentSBMLObject()) self.assert_(r == lo.getParentSBMLObject()) pass
def test_SpeciesReference_Reactant_parent_create(self): r = libsbml.Reaction(2, 4) sr = r.createReactant() lo = r.getListOfReactants() self.assert_(lo == r.getReactant(0).getParentSBMLObject()) self.assert_(lo == sr.getParentSBMLObject()) self.assert_(r == lo.getParentSBMLObject()) pass
def test_Reaction_copyConstructor(self): o1 = libsbml.Reaction(2,4) o1.setId("c") self.assert_( o1.getId() == "c" ) kl = libsbml.KineticLaw(2,4) kl.setMath(libsbml.parseFormula("1")) o1.setKineticLaw(kl) kl = None self.assert_( o1.isSetKineticLaw() == True ) self.assert_( o1.getKineticLaw() != None ) o2 = libsbml.Reaction(o1) self.assert_( o2.getId() == "c" ) self.assert_( o2.isSetKineticLaw() == True ) self.assert_( o2.getKineticLaw() != None ) self.assert_( o2.getParentSBMLObject() == o1.getParentSBMLObject() ) o2 = None o1 = None pass
def test_Reaction_setName3(self): p = libsbml.Reaction(2, 2) i = p.setName("") self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS) self.assertEqual(False, p.isSetName()) _dummyList = [p] _dummyList[:] = [] del _dummyList pass
def test_Model_getSpeciesReferenceById(self): r1 = libsbml.Reaction(2, 4) r1.setId("r1") sr = r1.createReactant() sr.setId("s1") self.M.addReaction(r1) self.assert_(self.M.getNumReactions() == 1) self.assert_(self.M.getSpeciesReference("s1") != sr) pass
def test_Reaction_parent_add(self): ia = libsbml.Reaction(2, 4) m = libsbml.Model(2, 4) ia.setId("k") m.addReaction(ia) ia = None lo = m.getListOfReactions() self.assert_(lo == m.getReaction(0).getParentSBMLObject()) self.assert_(m == lo.getParentSBMLObject()) pass
def test_SpeciesReference_Modifier_parent_add(self): sr = libsbml.ModifierSpeciesReference(2, 4) sr.setSpecies("s") r = libsbml.Reaction(2, 4) r.addModifier(sr) sr = None lo = r.getListOfModifiers() self.assert_(lo == r.getModifier(0).getParentSBMLObject()) self.assert_(r == lo.getParentSBMLObject()) pass
def test_Reaction_createReactant(self): m = libsbml.Reaction(2, 2) p = m.createReactant() self.assert_(m.getNumReactants() == 1) self.assert_((p).getLevel() == 2) self.assert_((p).getVersion() == 2) _dummyList = [m] _dummyList[:] = [] del _dummyList pass
def test_Reaction_addReactant4(self): m = libsbml.Reaction(2, 2) p = None i = m.addReactant(p) self.assert_(i == libsbml.LIBSBML_OPERATION_FAILED) self.assert_(m.getNumReactants() == 0) _dummyList = [m] _dummyList[:] = [] del _dummyList pass
def test_Reaction_createKineticLaw(self): r = libsbml.Reaction(2, 2) kl = r.createKineticLaw() self.assert_(r.isSetKineticLaw() == True) self.assert_((kl).getLevel() == 2) self.assert_((kl).getVersion() == 2) _dummyList = [r] _dummyList[:] = [] del _dummyList pass
def test_SpeciesReference_Reactant_parent_add(self): sr = libsbml.SpeciesReference(2, 4) r = libsbml.Reaction(2, 4) sr.setSpecies("s") r.addReactant(sr) sr = None lo = r.getListOfReactants() self.assert_(lo == r.getReactant(0).getParentSBMLObject()) self.assert_(r == lo.getParentSBMLObject()) pass
def test_L3_Reaction_hasRequiredAttributes(self): r = libsbml.Reaction(3,1) self.assertEqual( False, r.hasRequiredAttributes() ) r.setId( "id") self.assertEqual( False, r.hasRequiredAttributes() ) r.setFast(False) self.assertEqual( False, r.hasRequiredAttributes() ) r.setReversible(False) self.assertEqual( True, r.hasRequiredAttributes() ) _dummyList = [ r ]; _dummyList[:] = []; del _dummyList pass
def test_KineticLaw_ancestor_add(self): kl = libsbml.KineticLaw(2,4) kl.setMath(libsbml.parseFormula("1")) r = libsbml.Reaction(2,4) r.setKineticLaw(kl) obj = r.getKineticLaw() self.assert_( obj.getAncestorOfType(libsbml.SBML_REACTION) == r ) self.assert_( obj.getAncestorOfType(libsbml.SBML_MODEL) == None ) self.assert_( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == None ) r = None pass
def test_internal_consistency_check_99911_react(self): d = libsbml.SBMLDocument(2,4) m = d.createModel() r = libsbml.Reaction(2,4) d.setLevelAndVersion(2,1,False) r.setId("r") r.setSBOTerm(2) m.addReaction(r) errors = d.checkInternalConsistency() self.assert_( errors == 0 ) d = None pass
def test_Reaction_ancestor_add(self): ia = libsbml.Reaction(2,4) m = libsbml.Model(2,4) ia.setId("k") m.addReaction(ia) ia = None lo = m.getListOfReactions() obj = m.getReaction(0) self.assert_( obj.getAncestorOfType(libsbml.SBML_MODEL) == m ) self.assert_( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo ) self.assert_( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == None ) self.assert_( obj.getAncestorOfType(libsbml.SBML_EVENT) == None ) pass
def test_SpeciesReference_Reactant_ancestor_add(self): sr = libsbml.SpeciesReference(2,4) r = libsbml.Reaction(2,4) sr.setSpecies("s") r.addReactant(sr) sr = None lo = r.getListOfReactants() obj = r.getReactant(0) self.assert_( obj.getAncestorOfType(libsbml.SBML_REACTION) == r ) self.assert_( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo ) self.assert_( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == None ) self.assert_( obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == None ) pass
def test_Model_addReaction5(self): m = libsbml.Model(2, 2) r = libsbml.Reaction(2, 2) r.setId("r") r1 = libsbml.Reaction(2, 2) r1.setId("r") i = m.addReaction(r) self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS) self.assert_(m.getNumReactions() == 1) i = m.addReaction(r1) self.assert_(i == libsbml.LIBSBML_DUPLICATE_OBJECT_ID) self.assert_(m.getNumReactions() == 1) _dummyList = [r] _dummyList[:] = [] del _dummyList _dummyList = [r1] _dummyList[:] = [] del _dummyList _dummyList = [m] _dummyList[:] = [] del _dummyList pass
def test_internal_consistency_check_99904_react(self): d = libsbml.SBMLDocument(2,4) r = libsbml.Reaction(2,4) d.setLevelAndVersion(1,2,False) m = d.createModel() c = m.createCompartment() c.setId("cc") r.setId("r") r.setMetaId("mmm") m.addReaction(r) errors = d.checkInternalConsistency() self.assert_( errors == 0 ) d = None pass
def test_Reaction_addProduct3(self): m = libsbml.Reaction(2, 2) p = libsbml.SpeciesReference(1, 2) p.setSpecies("k") i = m.addProduct(p) self.assert_(i == libsbml.LIBSBML_LEVEL_MISMATCH) self.assert_(m.getNumProducts() == 0) _dummyList = [p] _dummyList[:] = [] del _dummyList _dummyList = [m] _dummyList[:] = [] del _dummyList pass
def test_Reaction_addReactant2(self): m = libsbml.Reaction(2, 2) p = libsbml.SpeciesReference(2, 1) p.setSpecies("k") i = m.addReactant(p) self.assert_(i == libsbml.LIBSBML_VERSION_MISMATCH) self.assert_(m.getNumReactants() == 0) _dummyList = [p] _dummyList[:] = [] del _dummyList _dummyList = [m] _dummyList[:] = [] del _dummyList pass
def test_SpeciesReference_Reactant_ancestor_create(self): r = libsbml.Reaction(2,4) sr = r.createReactant() lo = r.getListOfReactants() self.assert_( sr.getAncestorOfType(libsbml.SBML_REACTION) == r ) self.assert_( sr.getAncestorOfType(libsbml.SBML_LIST_OF) == lo ) self.assert_( sr.getAncestorOfType(libsbml.SBML_DOCUMENT) == None ) self.assert_( sr.getAncestorOfType(libsbml.SBML_COMPARTMENT) == None ) obj = r.getReactant(0) self.assert_( obj.getAncestorOfType(libsbml.SBML_REACTION) == r ) self.assert_( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo ) self.assert_( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == None ) self.assert_( obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == None ) pass
def test_Model_addReaction3(self): m = libsbml.Model(2, 2) r = libsbml.Reaction(1, 2) r.setId("r") i = m.addReaction(r) self.assert_(i == libsbml.LIBSBML_LEVEL_MISMATCH) self.assert_(m.getNumReactions() == 0) _dummyList = [r] _dummyList[:] = [] del _dummyList _dummyList = [m] _dummyList[:] = [] del _dummyList pass