def create_species_from_pattern(speciesPattern):
tmp_species = st.Species()
if 'speciesCompartment' in speciesPattern.keys():
tmp_species.compartment = speciesPattern['speciesCompartment'][1]
for idx, element in enumerate(speciesPattern['speciesPattern']):
tmp_species.addMolecule(create_molecule_from_pattern(element, idx))
return tmp_species
def createSpecies(pattern):
tmpDict = {}
species = st.Species()
species.idx = pattern.get('id')
species.trueName = pattern.get('name')
compartment = pattern.get('compartment')
if compartment != None:
species.compartment = compartment
mol = pattern.find('.//{http://www.sbml.org/sbml/level3}ListOfMolecules')
bonds = pattern.find('.//{http://www.sbml.org/sbml/level3}ListOfBonds')
for molecule in mol.getchildren():
molecule, nameDict = createMolecule(molecule, bonds)
tmpDict.update(nameDict)
species.addMolecule(molecule)
if bonds != None:
species.bonds = [(bond.get('site1'), bond.get('site2'))
for bond in bonds]
tmpDict.update(nameDict)
return species, tmpDict
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