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
