def parseComponent(component):
'''
parses a bngxml molecule types section
'''
comp = st.Component(component.get('id'),component.get('id'))
states = component.find('.//{http://www.sbml.org/sbml/level3}ListOfAllowedStates')
if states != None:
for state in states.getchildren():
comp.addState(state.get('id'))
return comp
def createMolecule(molecule, bonds):
nameDict = {}
mol = st.Molecule(molecule.get('name'),molecule.get('id'))
if molecule.get('compartment') not in ['',None]:
mol.setCompartment(molecule.get('compartment'))
nameDict[molecule.get('id')] = molecule.get('name')
listOfComponents = molecule.find('.//{http://www.sbml.org/sbml/level3}ListOfComponents')
if listOfComponents != None:
for element in listOfComponents:
component = st.Component(element.get('name'),element.get('id'))
nameDict[element.get('id')] = element.get('name')
if element.get('numberOfBonds') in ['+','?']:
component.addBond(element.get('numberOfBonds'))
elif element.get('numberOfBonds') != '0':
component.addBond(findBond(bonds, element.get('id')))
state = element.get('state') if element.get('state') != None else ''
component.states.append(state)
component.activeState = state
mol.addComponent(component)
return mol, nameDict