def rxn_add_stoich(srxn, rid, stoich, is_product=True):
try:
stoich = float(stoich)
if stoich < 0:
sr = srxn.createReactant()
sr.setStoichiometry(-stoich)
elif stoich > 0:
sr = srxn.createProduct()
sr.setStoichiometry(stoich)
elif stoich == 0:
sr = srxn.createModifier()
sr.setSpecies(rid)
except ValueError:
formula = stoich.replace('**', '^')
math_ast = libsbml.parseFormula(formula)
#try:
# smath = libsbml.StoichiometryMath(math_ast)
#except:
# normally this is in an except block but the try above doesn't throw erro
# I am expecting in libSBML 4.0
try:
smath = libsbml.StoichiometryMath(math_ast)
except NotImplementedError:
smath = libsbml.StoichiometryMath(sbml_level, sbml_version)
smath.setMath(math_ast)
if is_product == True:
sr = srxn.createProduct()
else:
sr = srxn.createReactant()
sr.setSpecies(rid)
sr.setStoichiometryMath(smath)
def test_StoichiometryMath(self):
sm = libsbml.StoichiometryMath(2,4)
self.assertEqual( False, (sm.hasRequiredElements()) )
sm.setMath(libsbml.parseFormula("ar"))
self.assertEqual( True, sm.hasRequiredElements() )
sm = None
pass
def test_SpeciesReference_setStoichiometryMath6(self):
sm = libsbml.StoichiometryMath(2,1)
sm.setMath(libsbml.parseFormula("1 + 1"))
i = self.sr.setStoichiometryMath(sm)
self.assert_( i == libsbml.LIBSBML_VERSION_MISMATCH )
self.assertEqual( False, self.sr.isSetStoichiometryMath() )
_dummyList = [ sm ]; _dummyList[:] = []; del _dummyList
pass
def test_StoichiometryMath_parent_add(self):
m = libsbml.StoichiometryMath(2, 4)
m.setMath(libsbml.parseFormula("1"))
sr = libsbml.SpeciesReference(2, 4)
sr.setStoichiometryMath(m)
m = None
self.assert_(sr == sr.getStoichiometryMath().getParentSBMLObject())
sr = None
pass
def test_SpeciesReference_setStoichiometryMath2(self): sm = libsbml.StoichiometryMath(2,4) math = libsbml.ASTNode(libsbml.AST_TIMES) a = libsbml.ASTNode() a.setName( "a") math.addChild(a) sm.setMath(math) i = self.sr.setStoichiometryMath(sm) self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assertEqual( True, self.sr.isSetStoichiometryMath() ) _dummyList = [ sm ]; _dummyList[:] = []; del _dummyList pass
def test_SpeciesReference_setStoichiometryMath(self):
math = libsbml.parseFormula("k3 / k2")
stoich = libsbml.StoichiometryMath(2, 4)
stoich.setMath(math)
self.SR.setStoichiometryMath(stoich)
math1 = self.SR.getStoichiometryMath()
self.assert_(math1 != None)
formula = libsbml.formulaToString(math1.getMath())
self.assert_(formula != None)
self.assert_(("k3 / k2" == formula))
self.assertEqual(True, self.SR.isSetStoichiometryMath())
pass
def test_StoichiometryMath_ancestor_add(self):
m = libsbml.StoichiometryMath(2,4)
m.setMath(libsbml.parseFormula("1"))
sr = libsbml.SpeciesReference(2,4)
sr.setStoichiometryMath(m)
m = None
obj = sr.getStoichiometryMath()
self.assert_( obj.getAncestorOfType(libsbml.SBML_SPECIES_REFERENCE) == sr )
self.assert_( obj.getAncestorOfType(libsbml.SBML_MODEL) == None )
self.assert_( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == None )
sr = None
pass
def test_SpeciesReference_setStoichiometryMath4(self): sm = libsbml.StoichiometryMath(2,4) math = None sm.setMath(math) i = self.sr.setStoichiometryMath(sm) self.assert_( i == libsbml.LIBSBML_INVALID_OBJECT ) self.assertEqual( False, self.sr.isSetStoichiometryMath() ) self.assert_( self.sr.getStoichiometry() == 1 ) i = self.sr.unsetStoichiometryMath() self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assertEqual( False, self.sr.isSetStoichiometryMath() ) _dummyList = [ sm ]; _dummyList[:] = []; del _dummyList pass
def test_StoichiometryMath_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add( "http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(2,1) sbmlns.addNamespaces(xmlns) object = libsbml.StoichiometryMath(sbmlns) self.assert_( object.getTypeCode() == libsbml.SBML_STOICHIOMETRY_MATH ) self.assert_( object.getMetaId() == "" ) self.assert_( object.getNotes() == None ) self.assert_( object.getAnnotation() == None ) self.assert_( object.getLevel() == 2 ) self.assert_( object.getVersion() == 1 ) self.assert_( object.getNamespaces() != None ) self.assert_( object.getNamespaces().getLength() == 2 ) _dummyList = [ object ]; _dummyList[:] = []; del _dummyList pass
def test_SpeciesReference_setStoichiometryMath5(self): sr1 = libsbml.SpeciesReference(1,2) sm = libsbml.StoichiometryMath(2,4) math = libsbml.ASTNode(libsbml.AST_TIMES) a = libsbml.ASTNode() b = libsbml.ASTNode() a.setName( "a") b.setName( "b") math.addChild(a) math.addChild(b) sm.setMath(math) i = sr1.setStoichiometryMath(sm) self.assert_( i == libsbml.LIBSBML_UNEXPECTED_ATTRIBUTE ) self.assertEqual( False, sr1.isSetStoichiometryMath() ) _dummyList = [ sm ]; _dummyList[:] = []; del _dummyList _dummyList = [ sr1 ]; _dummyList[:] = []; del _dummyList pass
def test_internal_consistency_check_99923(self):
d = libsbml.SBMLDocument(2,4)
sm = libsbml.StoichiometryMath(2,4)
m = d.createModel()
d.setLevelAndVersion(1,2,False)
s = m.createSpecies()
s.setId("s")
c = m.createCompartment()
c.setId("c")
s.setCompartment("c")
r = m.createReaction()
r.setId("r")
sr = r.createProduct()
sr.setSpecies("s")
sr.setStoichiometryMath(sm)
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
def test_StoichiometryMath(self):
sm = libsbml.StoichiometryMath(2, 4)
self.assertEqual(True, sm.hasRequiredAttributes())
sm = None
pass
def setUp(self):
self.D = libsbml.StoichiometryMath(2,4)
if (self.D == None):
pass
pass
def test_StoichiometryMath_constructor(self):
s = None
try:
s = libsbml.StoichiometryMath(2, 1)
s = libsbml.StoichiometryMath(2, 2)
s = libsbml.StoichiometryMath(2, 3)
s = libsbml.StoichiometryMath(2, 4)
s = libsbml.StoichiometryMath(self.SN21)
s = libsbml.StoichiometryMath(self.SN22)
s = libsbml.StoichiometryMath(self.SN23)
s = libsbml.StoichiometryMath(self.SN24)
except ValueError:
inst = sys.exc_info()[1]
s = None
pass
self.assert_(s != None)
msg = ""
try:
s = libsbml.StoichiometryMath(1, 1)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
msg = ""
try:
s = libsbml.StoichiometryMath(1, 2)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
msg = ""
try:
s = libsbml.StoichiometryMath(9, 9)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
msg = ""
try:
s = libsbml.StoichiometryMath(self.SN11)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
msg = ""
try:
s = libsbml.StoichiometryMath(self.SN12)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
try:
s = libsbml.StoichiometryMath(self.SN99)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
