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 create_molecule_from_pattern(molecule_pattern, idx):
tmp_molecule = st.Molecule(molecule_pattern['moleculeName'], idx)
if 'moleculeCompartment' in molecule_pattern:
tmp_molecule.compartment = molecule_pattern['moleculeCompartment'][1]
if 'components' in molecule_pattern.keys():
for idx2, component in enumerate(molecule_pattern['components']):
tmp_component = st.Component(component['componentName'],
'{0}_{1}'.format(idx, idx2))
if 'state' in component:
for state in component['state']:
if state != '':
tmp_component.addState(state)
if 'bond' in component.keys():
for bond in component['bond']:
tmp_component.addBond(bond)
tmp_molecule.addComponent(tmp_component)
return tmp_molecule
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 is not 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