def test_Model_getNumSpeciesWithBoundaryCondition(self): s1 = libsbml.Species(2, 4) s2 = libsbml.Species(2, 4) s3 = libsbml.Species(2, 4) s1.setId("s1") s2.setId("s2") s3.setId("s3") s1.setCompartment("c1") s2.setCompartment("c2") s3.setCompartment("c3") s1.setBoundaryCondition(True) s2.setBoundaryCondition(False) s3.setBoundaryCondition(True) self.assert_(self.M.getNumSpecies() == 0) self.assert_(self.M.getNumSpeciesWithBoundaryCondition() == 0) self.M.addSpecies(s1) self.assert_(self.M.getNumSpecies() == 1) self.assert_(self.M.getNumSpeciesWithBoundaryCondition() == 1) self.M.addSpecies(s2) self.assert_(self.M.getNumSpecies() == 2) self.assert_(self.M.getNumSpeciesWithBoundaryCondition() == 1) self.M.addSpecies(s3) self.assert_(self.M.getNumSpecies() == 3) self.assert_(self.M.getNumSpeciesWithBoundaryCondition() == 2) pass
def test_Species_copyConstructor(self): o1 = libsbml.Species(2,4) o1.setId("c") o1.setSpeciesType("c1") self.assert_( o1.getId() == "c" ) self.assert_( o1.getSpeciesType() == "c1" ) o2 = libsbml.Species(o1) self.assert_( o2.getId() == "c" ) self.assert_( o2.getSpeciesType() == "c1" ) self.assert_( o2.getParentSBMLObject() == o1.getParentSBMLObject() ) o2 = None o1 = None pass
def test_Species_assignmentOperator(self): o1 = libsbml.Species(2,4) o1.setId("c") o1.setSpeciesType("c1") self.assert_( o1.getId() == "c" ) self.assert_( o1.getSpeciesType() == "c1" ) o2 = libsbml.Species(2,4) o2 = o1 self.assert_( o2.getId() == "c" ) self.assert_( o2.getSpeciesType() == "c1" ) self.assert_( o2.getParentSBMLObject() == o1.getParentSBMLObject() ) o2 = None o1 = None pass
def test_Model_getSpeciesById(self): s1 = libsbml.Species(2, 4) s2 = libsbml.Species(2, 4) s1.setId("Glucose") s2.setId("Glucose_6_P") s1.setCompartment("c") s2.setCompartment("c") self.M.addSpecies(s1) self.M.addSpecies(s2) self.assert_(self.M.getNumSpecies() == 2) self.assert_(self.M.getSpecies("Glucose") != s1) self.assert_(self.M.getSpecies("Glucose_6_P") != s2) self.assert_(self.M.getSpecies("Glucose2") == None) pass
def test_Model_getSpecies(self): s1 = libsbml.Species(2, 4) s2 = libsbml.Species(2, 4) s1.setId("Glucose") s2.setId("Glucose_6_P") s1.setCompartment("c") s2.setCompartment("c") self.M.addSpecies(s1) self.M.addSpecies(s2) self.assert_(self.M.getNumSpecies() == 2) s1 = self.M.getSpecies(0) s2 = self.M.getSpecies(1) self.assert_(("Glucose" == s1.getId())) self.assert_(("Glucose_6_P" == s2.getId())) pass
def test_ListOf_remove(self): lo = libsbml.ListOf(2,4) sp = libsbml.Species(2,4) self.assert_( lo.size() == 0 ) lo.append(sp) lo.append(sp) lo.append(sp) lo.append(sp) lo.append(sp) self.assert_( lo.size() == 5 ) elem = lo.remove(0) _dummyList = [ elem ]; _dummyList[:] = []; del _dummyList elem = lo.remove(0) _dummyList = [ elem ]; _dummyList[:] = []; del _dummyList elem = lo.remove(0) _dummyList = [ elem ]; _dummyList[:] = []; del _dummyList elem = lo.remove(0) _dummyList = [ elem ]; _dummyList[:] = []; del _dummyList elem = lo.remove(0) _dummyList = [ elem ]; _dummyList[:] = []; del _dummyList self.assert_( lo.size() == 0 ) lo.append(sp) lo.append(sp) lo.append(sp) lo.append(sp) lo.appendAndOwn(sp) self.assert_( lo.size() == 5 ) _dummyList = [ lo ]; _dummyList[:] = []; del _dummyList pass
def test_Species_setSpatialSizeUnits4(self): c = libsbml.Species(2,2) i = c.setSpatialSizeUnits("") self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assertEqual( False, c.isSetSpatialSizeUnits() ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_Species_setCharge2(self): c = libsbml.Species(2,2) i = c.setCharge(4) self.assert_( i == libsbml.LIBSBML_UNEXPECTED_ATTRIBUTE ) self.assertEqual( False, c.isSetCharge() ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_Species_setCharge3(self): c = libsbml.Species(2,1) i = c.unsetCharge() self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assertEqual( False, c.isSetCharge() ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_Species_setConstant2(self): c = libsbml.Species(2,2) i = c.setConstant(True) self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assert_( c.getConstant() == True ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_Model_addSpecies(self): s = libsbml.Species(2, 4) s.setId("s") s.setCompartment("c") self.M.addSpecies(s) self.assert_(self.M.getNumSpecies() == 1) pass
def test_ListOf_clear(self): lo = libsbml.ListOf(2,4) sp = libsbml.Species(2,4) lo.append(sp) lo.append(sp) lo.append(sp) lo.append(sp) lo.append(sp) self.assert_( lo.size() == 5 ) lo.clear(True) self.assert_( lo.size() == 0 ) lo.append(sp) lo.append(sp) lo.append(sp) lo.append(sp) lo.appendAndOwn(sp) self.assert_( lo.size() == 5 ) elem = lo.get(0) _dummyList = [ elem ]; _dummyList[:] = []; del _dummyList elem = lo.get(1) _dummyList = [ elem ]; _dummyList[:] = []; del _dummyList elem = lo.get(2) _dummyList = [ elem ]; _dummyList[:] = []; del _dummyList elem = lo.get(3) _dummyList = [ elem ]; _dummyList[:] = []; del _dummyList elem = lo.get(4) _dummyList = [ elem ]; _dummyList[:] = []; del _dummyList lo.clear(False) self.assert_( lo.size() == 0 ) _dummyList = [ lo ]; _dummyList[:] = []; del _dummyList pass
def test_Species_setSubstanceUnits2(self): c = libsbml.Species(2,2) i = c.setSubstanceUnits( "1cell") self.assert_( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE ) self.assertEqual( False, c.isSetSubstanceUnits() ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_Species_setSubstanceUnits3(self): c = libsbml.Species(2,2) i = c.setSubstanceUnits( "mole") self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assert_(( "mole" == c.getSubstanceUnits() )) self.assertEqual( True, c.isSetSubstanceUnits() ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_Species_setId3(self): c = libsbml.Species(2,2) i = c.setId( "cell") self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assertEqual( True, c.isSetId() ) self.assert_(( "cell" == c.getId() )) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def __init__(self, model, met=None): if met is None: self._sbml = libsbml.Species(3, 1) model.getListOfSpecies().append(self._sbml) else: self._sbml = met if not self.meta_id: self.meta_id = self.id
def test_Species(self): s = libsbml.Species(2, 4) self.assertEqual(False, (s.hasRequiredAttributes())) s.setId("s") self.assertEqual(False, (s.hasRequiredAttributes())) s.setCompartment("c") self.assertEqual(True, s.hasRequiredAttributes()) s = None pass
def test_Species_setHasOnlySubstanceUnits2(self): c = libsbml.Species(2,2) i = c.setHasOnlySubstanceUnits(False) self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assert_( c.getHasOnlySubstanceUnits() == False ) i = c.setHasOnlySubstanceUnits(True) self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assert_( c.getHasOnlySubstanceUnits() == True ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_Species_setSpeciesType2(self): c = libsbml.Species(2,2) i = c.setSpeciesType( "1cell") self.assert_( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE ) self.assertEqual( False, c.isSetSpeciesType() ) i = c.unsetSpeciesType() self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assertEqual( False, c.isSetSpeciesType() ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_Species_setName2(self): c = libsbml.Species(2,2) i = c.setName( "1cell") self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assertEqual( True, c.isSetName() ) i = c.unsetName() self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assertEqual( False, c.isSetName() ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_Species_parent_add(self): ia = libsbml.Species(2, 4) ia.setId("s") ia.setCompartment("c") m = libsbml.Model(2, 4) m.addSpecies(ia) ia = None lo = m.getListOfSpecies() self.assert_(lo == m.getSpecies(0).getParentSBMLObject()) self.assert_(m == lo.getParentSBMLObject()) pass
def test_Species_setInitialConcentration2(self): c = libsbml.Species(2,2) i = c.setInitialConcentration(4) self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assert_( c.getInitialConcentration() == 4 ) self.assertEqual( True, c.isSetInitialConcentration() ) i = c.unsetInitialConcentration() self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assertEqual( False, c.isSetInitialConcentration() ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_Species_setInitialAmount2(self): c = libsbml.Species(2, 2) i = c.setInitialAmount(4) self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS) self.assert_(c.getInitialAmount() == 4.0) self.assertEqual(True, c.isSetInitialAmount()) i = c.unsetInitialAmount() self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS) self.assertEqual(False, c.isSetInitialAmount()) _dummyList = [c] _dummyList[:] = [] del _dummyList pass
def test_Species_setSpeciesType4(self): c = libsbml.Species(2, 2) i = c.setSpeciesType("cell") self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS) self.assertEqual(True, c.isSetSpeciesType()) self.assert_(("cell" == c.getSpeciesType())) i = c.setSpeciesType("") self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS) self.assertEqual(False, c.isSetSpeciesType()) _dummyList = [c] _dummyList[:] = [] del _dummyList pass
def test_ListOf_copyConstructor(self): o1 = libsbml.ListOf(2,1) s = libsbml.Species(2,1) s.setId("species_1") o1.append(s) s = None o2 = libsbml.ListOf(o1) self.assert_( o2.size() == 1 ) self.assert_( o2.get(0).getId() == "species_1" ) self.assert_( o2.getParentSBMLObject() == o1.getParentSBMLObject() ) o2 = None o1 = None pass
def test_Species_ancestor_add(self): ia = libsbml.Species(2,4) m = libsbml.Model(2,4) ia.setId("s") ia.setCompartment("c") m.addSpecies(ia) ia = None lo = m.getListOfSpecies() obj = m.getSpecies(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_internal_consistency_check_99904_species(self): d = libsbml.SBMLDocument(2,4) s = libsbml.Species(2,4) d.setLevelAndVersion(1,2,False) m = d.createModel() c = m.createCompartment() c.setId("c") s.setCompartment("c") s.setId("s") s.setMetaId("mmm") m.addSpecies(s) errors = d.checkInternalConsistency() self.assert_( errors == 0 ) d = None pass
def test_Model_addSpecies5(self): m = libsbml.Model(2, 2) s = libsbml.Species(2, 2) s.setId("s") s.setCompartment("c") s1 = libsbml.Species(2, 2) s1.setId("s") s1.setCompartment("c") i = m.addSpecies(s) self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS) self.assert_(m.getNumSpecies() == 1) i = m.addSpecies(s1) self.assert_(i == libsbml.LIBSBML_DUPLICATE_OBJECT_ID) self.assert_(m.getNumSpecies() == 1) _dummyList = [s] _dummyList[:] = [] del _dummyList _dummyList = [s1] _dummyList[:] = [] del _dummyList _dummyList = [m] _dummyList[:] = [] del _dummyList pass
def test_Model_addSpecies2(self): m = libsbml.Model(2, 2) s = libsbml.Species(2, 1) s.setId("s") s.setCompartment("c") i = m.addSpecies(s) self.assert_(i == libsbml.LIBSBML_VERSION_MISMATCH) self.assert_(m.getNumSpecies() == 0) _dummyList = [s] _dummyList[:] = [] del _dummyList _dummyList = [m] _dummyList[:] = [] del _dummyList pass
def test_SBMLConvert_convertToL1_Species_Amount(self): d = libsbml.SBMLDocument(2,1) m = d.createModel() sid = "C"; c = libsbml.Compartment(2,4) s = libsbml.Species(2,4) c.setId(sid) m.addCompartment(c) s.setCompartment(sid) s.setInitialAmount(2.34) m.addSpecies(s) self.assert_( d.setLevelAndVersion(1,2,True) == True ) self.assert_( s.getInitialAmount() == 2.34 ) _dummyList = [ d ]; _dummyList[:] = []; del _dummyList pass