def parseMolecules(molecules):
'''
Parses an XML molecule section
Returns: a molecule structure
'''
mol = st.Molecule(molecules.get('id'), molecules.get('id'))
components = \
molecules.find('.//{http://www.sbml.org/sbml/level3}ListOfComponentTypes')
if components != None:
for component in components.getchildren():
comp = parseComponent(component)
mol.addComponent(comp)
return mol
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
def parseRule(rule, parameterDict):
'''
Parses a rule XML section
Returns: a list of the reactants and products used, followed by the mapping
between the two and the list of operations that were performed
'''
rp = rule.find(
'.//{http://www.sbml.org/sbml/level3}ListOfReactantPatterns')
pp = rule.find('.//{http://www.sbml.org/sbml/level3}ListOfProductPatterns')
mp = rule.find('.//{http://www.sbml.org/sbml/level3}Map')
op = rule.find('.//{http://www.sbml.org/sbml/level3}ListOfOperations')
rt = rule.find('.//{http://www.sbml.org/sbml/level3}RateLaw')
nameDict = {}
reactants = []
products = []
actions = []
mappings = []
if len(rp) == 0:
sp = st.Species()
ml = st.Molecule('0', '')
sp.addMolecule(ml)
reactants.append(sp)
if len(pp) == 0:
sp = st.Species()
ml = st.Molecule('0', '')
sp.addMolecule(ml)
products.append(sp)
for pattern in rp:
elm, tmpDict = createSpecies(pattern)
reactants.append(elm)
nameDict.update(tmpDict)
for pattern in pp:
elm, tmpDict = createSpecies(pattern)
products.append(elm)
nameDict.update(tmpDict)
for operation in op:
action = st.Action()
tag = operation.tag
tag = tag.replace('{http://www.sbml.org/sbml/level3}', '')
if operation.get('site1') != None:
action.setAction(tag, operation.get('site1'),
operation.get('site2'))
else:
action.setAction(tag, operation.get('site'), None)
actions.append(action)
for mapping in mp:
tmpMap = (mapping.get('sourceID'), mapping.get('targetID'))
mappings.append(tmpMap)
rateConstants = rt.find(
'.//{http://www.sbml.org/sbml/level3}ListOfRateConstants')
if rateConstants == None:
rateConstants = rt.get('name')
else:
for constant in rateConstants:
tmp = constant.get('value')
rateConstants = tmp
rateConstantsValue = parameterDict[
rateConstants] if rateConstants in parameterDict else rateConstants
#rule = st.Rule()
label = rule.get('name')
label = label.replace('(', '_').replace(')', '_')
rule = st.Rule(label)
rule.addReactantList(reactants)
rule.addProductList(products)
rule.addActionList(actions)
rule.addMappingList(mappings)
rule.addRate(rateConstants)
# return reactants, products, actions, mappings, nameDict,rateConstantsValue,rateConstants
return rule, nameDict, rateConstantsValue, rateConstants