def setModifiers(self, modifierIdString):
if self.Type != TYPE.REACTION: # can only do this for Reactions
return False
modifierIds = modifierIdString.replace(" ", "").split(",")
if modifierIds is None or len(modifierIds) == 0:
return False
modifierRefs = self.Item.getListOfModifiers()
IdsToRemove = []
for modifierRef in modifierRefs:
orgId = modifierRef.getSpecies()
IdsToRemove.append(orgId)
for Id in IdsToRemove:
logging.info("Removing Modifier: %s" % Id)
self.Item.removeModifier(Id)
for Id in modifierIds:
if self.speciesIDExists(Id):
speciesRef = libsbml.ModifierSpeciesReference(self.Item.getLevel(), self.Item.getVersion())
speciesRef.setSpecies(Id)
self.Item.addModifier(speciesRef)
return True
def test_ModifierSpeciesReference(self):
msr = libsbml.ModifierSpeciesReference(2, 4)
self.assertEqual(False, (msr.hasRequiredAttributes()))
msr.setSpecies("msr")
self.assertEqual(True, msr.hasRequiredAttributes())
msr = None
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_SpeciesReference_Modifier_ancestor_add(self):
sr = libsbml.ModifierSpeciesReference(2,4)
sr.setSpecies("s")
r = libsbml.Reaction(2,4)
r.addModifier(sr)
sr = None
lo = r.getListOfModifiers()
obj = r.getModifier(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_ModifierSpeciesReference_createWithNS(self):
xmlns = libsbml.XMLNamespaces()
xmlns.add("http://www.sbml.org", "testsbml")
sbmlns = libsbml.SBMLNamespaces(2, 1)
sbmlns.addNamespaces(xmlns)
object = libsbml.ModifierSpeciesReference(sbmlns)
self.assert_(
object.getTypeCode() == libsbml.SBML_MODIFIER_SPECIES_REFERENCE)
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)
n = object.getNamespaces()
self.assert_(n.getLength() == 2)
_dummyList = [object]
_dummyList[:] = []
del _dummyList
pass
def writeSBML( self, aSBMLDocument ):
aModel = aSBMLDocument.getModel()
aReaction = aModel.getReaction( self.id )
if not aReaction:
aReaction = aModel.createReaction()
aReaction.setId( self.id )
if not aReaction.isSetKineticLaw():
aKineticLaw = libsbml.KineticLaw()
else:
aKineticLaw = aReaction.getKineticLaw()
fullID = ecell.ecssupport.createFullID( self.fullID )
if self.isSetId():
setSBaseAnnotation( aReaction, 'ID', fullID[ 2 ], aSBMLDocument.getNamespaces() )
compartment = ecell.ecssupport.createFullIDFromSystemPath( fullID[ 1 ] )
compartment = ecell.ecssupport.createFullIDString( compartment )
( compartment, sbmlType ) \
= self.theSBMLExporter.searchIdFromFullID( compartment )
setSBaseAnnotation( aReaction, 'compartment', compartment, aSBMLDocument.getNamespaces() )
anExpression = self.theSBMLExporter.theEml.getEntityProperty( '%s:Expression' % ( self.fullID ) )[ 0 ]
namespaceDict = self.createNamespaceFromVariableReferenceList()
anExpressionParser = ExpressionParser( namespaceDict, compartment )
anASTNode = anExpressionParser.convertExpressionToASTNode( anExpression )
aKineticLaw.setFormula( libsbml.formulaToString( anASTNode ) )
parameterList = []
for i in range( aKineticLaw.getNumParameters() ):
aParameter = aKineticLaw.getParameter( i )
if not aParameter.isSetId():
continue
parameterList.append( aParameter.getId() )
reactantList = []
for i in range( aReaction.getNumReactants() ):
aReactant = aReaction.getReactant( i )
if not aReactant.isSetSpecies():
continue
reactantList.append( aReactant.getSpecies() )
productList = []
for i in range( aReaction.getNumProducts() ):
aProduct = aReaction.getProduct( i )
if not aProduct.isSetSpecies():
continue
productList.append( aProduct.getSpecies() )
modifierList = []
for i in range( aReaction.getNumModifiers() ):
aModifier = aReaction.getModifier( i )
if not aModifier.isSetSpecies():
continue
modifierList.append( aModifier.getSpecies() )
for ( id, coeff ) in namespaceDict.values():
if coeff > 0 and type( id ) == tuple:
if productList.count( id[ 0 ] ) == 0:
aReaction.addProduct( libsbml.SpeciesReference( id[ 0 ], coeff ) )
else:
i = productList.index( id[ 0 ] )
aProduct = aReaction.getProduct( i )
aProduct.setStoichiometry( coeff )
elif coeff < 0 and type( id ) == tuple:
if reactantList.count( id[ 0 ] ) == 0:
aReaction.addReactant( libsbml.SpeciesReference( id[ 0 ], -coeff ) )
else:
i = reactantList.index( id[ 0 ] )
aReactant = aReaction.getReactant( i )
aReactant.setStoichiometry( -coeff )
for id in anExpressionParser.modifierList:
if modifierList.count( id ) == 0:
aReaction.addModifier( libsbml.ModifierSpeciesReference( id ) )
propertyList = self.theSBMLExporter.theEml.getEntityPropertyList( self.fullID )
for pn in propertyList:
if pn == 'Name':
name = self.theSBMLExporter.theEml.getEntityProperty( '%s:Name' % ( self.fullID ) )
if len( name ) != 1:
raise SBMLConvertError, \
'The format of property [%s:Name] is invalid' \
% ( self.fullID )
name = name[ 0 ]
aReaction.setName( name )
elif pn == 'VariableReferenceList' \
or pn == 'Expression' \
or pn == 'StepperID':
pass
elif pn == 'Priority':
value = self.theSBMLExporter.theEml.getEntityProperty( '%s:Priority' % ( self.fullID ) )
if len( value ) != 1:
raise SBMLConvertError, \
'The type of Parameter [%s:Priority] is invalid' \
% ( self.fullID )
value = int( value[ 0 ] )
if value != 0:
raise SBMLConvertError, 'The Parameter [%s:Priority] is not equal to 0. It cannnot be converted' % ( self.fullID )
else:
value = self.theSBMLExporter.theEml.getEntityProperty( '%s:%s' % ( self.fullID, pn ) )
if len( value ) != 1:
raise SBMLConvertError, \
'The type of Parameter [%s] is invalid' % ( pn )
value = float( value[ 0 ] )
if parameterList.count( pn ) == 0:
aParameter = libsbml.Parameter( pn, value )
aKineticLaw.addParameter( aParameter )
else:
i = parameterList.index( pn )
aParameter = aKineticLaw.getParameter( i )
aParameter.setValue( value )
aReaction.setKineticLaw( aKineticLaw )
def test_ModifierSpeciesReference(self): msr = libsbml.ModifierSpeciesReference(2,4) self.assertEqual( True, msr.hasRequiredElements() ) msr = None pass
def setUp(self):
self.MSR = libsbml.ModifierSpeciesReference(2, 4)
if (self.MSR == None):
pass
pass
def test_ModifierSpeciesReference_constructor(self):
s = None
try:
s = libsbml.ModifierSpeciesReference(2, 1)
s = libsbml.ModifierSpeciesReference(2, 2)
s = libsbml.ModifierSpeciesReference(2, 3)
s = libsbml.ModifierSpeciesReference(2, 4)
s = libsbml.ModifierSpeciesReference(3, 1)
s = libsbml.ModifierSpeciesReference(self.SN21)
s = libsbml.ModifierSpeciesReference(self.SN22)
s = libsbml.ModifierSpeciesReference(self.SN23)
s = libsbml.ModifierSpeciesReference(self.SN24)
s = libsbml.ModifierSpeciesReference(self.SN31)
except ValueError:
inst = sys.exc_info()[1]
s = None
pass
self.assert_(s != None)
msg = ""
try:
s = libsbml.ModifierSpeciesReference(1, 1)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
msg = ""
try:
s = libsbml.ModifierSpeciesReference(1, 2)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
msg = ""
try:
s = libsbml.ModifierSpeciesReference(9, 9)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
msg = ""
try:
s = libsbml.ModifierSpeciesReference(self.SN11)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
msg = ""
try:
s = libsbml.ModifierSpeciesReference(self.SN12)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
try:
s = libsbml.ModifierSpeciesReference(self.SN99)
except ValueError:
inst = sys.exc_info()[1]
msg = inst.args[0]
pass
self.assertEqual(msg, self.ERR_MSG)
