def postAnalyzeFile(outputFile, bngLocation, database):
"""
Performs a postcreation file analysis based on context information
"""
#print('Transforming generated BNG file to BNG-XML representation for analysis')
postAnalysisHelper(outputFile, bngLocation, database)
# recreate file using information from the post analysis
returnArray = analyzeHelper(database.document, database.reactionDefinitions, database.useID,
outputFile, database.speciesEquivalence, database.atomize, database.translator, database)
with open(outputFile, 'w') as f:
f.write(returnArray.finalString)
# recompute bng-xml file
consoleCommands.bngl2xml(outputFile)
bngxmlFile = '.'.join(outputFile.split('.')[:-1]) + '.xml'
# recompute context information
contextAnalysis = postAnalysis.ModelLearning(bngxmlFile)
# get those species patterns that follow uncommon motifs
motifSpecies, motifDefinitions = contextAnalysis.processContextMotifInformation(database.assumptions['lexicalVsstoch'], database)
#motifSpecies, motifDefinitions = contextAnalysis.processAllContextInformation()
if len(motifDefinitions) > 0:
logMess('INFO:CTX003', 'Species with suspect context information were found. Information is being dumped to {0}_context.log'.format(outputFile))
with open('{0}_context.log'.format(outputFile), 'w') as f:
pprint.pprint(dict(motifSpecies), stream=f)
pprint.pprint(motifDefinitions, stream=f)
def changeToBNGL(functionList,rule,function):
oldrule = ''
#if the rule contains any mathematical function we need to reformat
while any([re.search(r'(\W|^)({0})(\W|$)'.format(x),rule) != None for x in functionList]) and (oldrule != rule):
oldrule = rule
for x in functionList:
rule = re.sub('({0})\(([^,]+),([^)]+)\)'.format(x),function,rule)
if rule == oldrule:
logMess('ERROR:Translation','Malformed pow or root function %s' % rule)
print 'meep'
return rule
def sanityCheck(database):
'''
checks for critical atomization errors like isomorphism
'''
stringrep = {x: str(database.translator[x]) for x in database.translator}
repeats = set()
for key in range(0, len(database.translator.keys()) - 1):
for key2 in range(key + 1, len(database.translator.keys())):
if stringrep[database.translator.keys()[key]] == stringrep[database.translator.keys()[key2]]:
repeats.add((database.translator.keys()[key], database.translator.keys()[key2]))
for repeat in repeats:
temp = sorted(repeat)
logMess('ERROR:SCT241', '{0}:{1}:produce the same translation:{2}:{1}:was empied'.format(temp[0], temp[1], database.prunnedDependencyGraph[temp[0]][0]))
if temp[1] in database.translator:
database.translator.pop(repeat[1])
def changeToBNGL(functionList, rule, function):
oldrule = ''
#if the rule contains any mathematical function we need to reformat
while any([
re.search(r'(\W|^)({0})(\W|$)'.format(x), rule) != None
for x in functionList
]) and (oldrule != rule):
oldrule = rule
for x in functionList:
rule = re.sub('({0})\(([^,]+),([^)]+)\)'.format(x), function,
rule)
if rule == oldrule:
logMess('ERROR', 'Malformed pow or root function %s' % rule)
print 'meep'
return rule
def propagateChanges(translator, dependencyGraph):
flag = True
while flag:
flag = False
for dependency in dependencyGraph:
if dependencyGraph[dependency] == []:
continue
for molecule in dependencyGraph[dependency][0]:
try:
if updateSpecies(translator[dependency],
translator[getTrueTag(dependencyGraph,
molecule)].molecules[0]):
flag = True
except:
logMess('CRITICAL:Program',
'Species is not being properly propagated')
flag = False
def postAnalyzeFile(outputFile, bngLocation, database):
"""
Performs a postcreation file analysis based on context information
"""
#print('Transforming generated BNG file to BNG-XML representation for analysis')
consoleCommands.setBngExecutable(bngLocation)
outputDir = os.sep.join(outputFile.split(os.sep)[:-1])
if outputDir != '':
retval = os.getcwd()
os.chdir(outputDir)
consoleCommands.bngl2xml(outputFile.split(os.sep)[-1])
if outputDir != '':
os.chdir(retval)
bngxmlFile = '.'.join(outputFile.split('.')[:-1]) + '.xml'
#print('Sending BNG-XML file to context analysis engine')
contextAnalysis = postAnalysis.ModelLearning(bngxmlFile)
# analysis of redundant bonds
deleteBonds = contextAnalysis.analyzeRedundantBonds(database.assumptions['redundantBonds'])
modificationFlag = True
for molecule in database.assumptions['redundantBondsMolecules']:
if molecule[0] in deleteBonds:
for bond in deleteBonds[molecule[0]]:
database.translator[molecule[1]].deleteBond(bond)
logMess('INFO:Atomization', 'Used context information to determine that the bond {0} in species {1} is not likely'.format(bond,molecule[1]))
returnArray = analyzeHelper(database.document, database.reactionDefinitions, database.useID,
outputFile, database.speciesEquivalence, database.atomize, database.translator)
with open(outputFile, 'w') as f:
f.write(returnArray.finalString)
# recompute bng-xml file
consoleCommands.bngl2xml(outputFile)
bngxmlFile = '.'.join(outputFile.split('.')[:-1]) + '.xml'
# recompute context information
contextAnalysis = postAnalysis.ModelLearning(bngxmlFile)
# get those species patterns that follow uncommon motifs
motifSpecies, motifDefinitions = contextAnalysis.processContextMotifInformation(database.assumptions['lexicalVsstoch'], database)
#motifSpecies, motifDefinitions = contextAnalysis.processAllContextInformation()
if len(motifDefinitions) > 0:
logMess('WARNING:ContextAnalysis', 'Species with suspect context information were found. Information is being dumped to {0}_context.log'.format(outputFile))
with open('{0}_context.log'.format(outputFile), 'w') as f:
pprint.pprint(dict(motifSpecies), stream=f)
pprint.pprint(motifDefinitions, stream=f)
def postAnalysisHelper(outputFile, bngLocation, database):
consoleCommands.setBngExecutable(bngLocation)
outputDir = os.sep.join(outputFile.split(os.sep)[:-1])
if outputDir != '':
retval = os.getcwd()
os.chdir(outputDir)
consoleCommands.bngl2xml(outputFile.split(os.sep)[-1])
if outputDir != '':
os.chdir(retval)
bngxmlFile = '.'.join(outputFile.split('.')[:-1]) + '.xml'
#print('Sending BNG-XML file to context analysis engine')
contextAnalysis = postAnalysis.ModelLearning(bngxmlFile)
# analysis of redundant bonds
deleteBonds = contextAnalysis.analyzeRedundantBonds(database.assumptions['redundantBonds'])
for molecule in database.assumptions['redundantBondsMolecules']:
if molecule[0] in deleteBonds:
for bond in deleteBonds[molecule[0]]:
database.translator[molecule[1]].deleteBond(bond)
logMess('INFO:CTX002', 'Used context information to determine that the bond {0} in species {1} is not likely'.format(bond,molecule[1]))
def printTranslate(chemical,tags,translator={}):
tmp = []
if chemical[0] not in translator:
app = chemical[0] + '()' + tags
else:
translator[chemical[0]].addCompartment(tags)
app = str(translator[chemical[0]])
if float(int(chemical[1])) == chemical[1]:
for item in range(0,int(chemical[1])):
tmp.append(app)
else:
idx = logMess("ERROR:Simulation","Cannot deal with non integer stoicheometries: {0}* {1}".format(chemical[1],chemical[0]))
tmp.append(app)
return ' + '.join(tmp)
def printTranslate(chemical, tags, translator={}):
tmp = []
if chemical[0] not in translator:
app = chemical[0] + '()' + tags
else:
translator[chemical[0]].addCompartment(tags)
app = str(translator[chemical[0]])
if float(int(chemical[1])) == chemical[1]:
for item in range(0, int(chemical[1])):
tmp.append(app)
else:
idx = logMess(
"ERROR:Simulation",
"Cannot deal with non integer stoicheometries: {0}* {1}".format(
chemical[1], chemical[0]))
tmp.append(app)
return ' + '.join(tmp)
def atomize(dependencyGraph, weights, translator, reactionProperties,
equivalenceDictionary, bioGridFlag, sbmlAnalyzer, database, parser):
'''
The atomizer's main methods. Receives a dependency graph
'''
redrawflag = True
loops = 0
while redrawflag and loops < 10:
loops +=1
bindingCounter = Counter()
bindingFailureDict = {}
for idx, element in enumerate(weights):
# 0 molecule
if element[0] == '0':
continue
# user defined molecules to be the zero molecule
if dependencyGraph[element[0]] == [['0']]:
zeroSpecies = st.Species()
zeroMolecule = st.Molecule('0')
zeroSpecies.addMolecule(zeroMolecule)
translator[element[0]] = zeroSpecies
continue
# undivisible molecules
elif dependencyGraph[element[0]] == []:
if element[0] not in translator:
translator[element[0]] = createEmptySpecies(element[0])
else:
if len(dependencyGraph[element[0]][0]) == 1:
# catalysis
createCatalysisRBM(dependencyGraph, element, translator, reactionProperties,
equivalenceDictionary, sbmlAnalyzer, database)
else:
try:
createBindingRBM(element, translator, dependencyGraph,
bioGridFlag, database.pathwaycommons, parser, database)
except BindingException as e:
for c in e.combinations:
bindingCounter[c] += 1
bindingFailureDict[element[0]] = e.combinations
logMess('DEBUG:ATO003', "We don't know how {0} binds together in complex {1}. Not atomizing".format(
e.value, element[0]))
# there awas an issue during binding, don't atomize
translator[element[0]] = createEmptySpecies(element[0])
# evaluate species that weren't bound properly and see if we can get information from all over the model to find the right binding partner
bindingTroubleLog = defaultdict(list)
modifiedPairs = set()
redrawflag = False
for molecule in bindingFailureDict:
bindingWinner = defaultdict(list)
for candidateTuple in bindingFailureDict[molecule]:
bindingWinner[bindingCounter[candidateTuple]].append(candidateTuple)
bestBindingCandidates = bindingWinner[max(bindingWinner.keys())]
if len(bestBindingCandidates) > 1:
bindingTroubleLog[tuple(sorted(bestBindingCandidates))].append(molecule)
else:
bindingPair = bestBindingCandidates[0]
if bindingPair not in modifiedPairs:
modifiedPairs.add(bindingPair)
else:
continue
c1 = st.Component(bindingPair[1].lower())
c2 = st.Component(bindingPair[0].lower())
molecule1 = translator[translator[bindingPair[0]].molecules[0].name].molecules[0]
molecule2 = translator[translator[bindingPair[1]].molecules[0].name].molecules[0]
molecule1.addComponent(c1)
molecule2.addComponent(c2)
redrawflag = True
logMess('INFO:ATO031','Determining that {0} binds together based on frequency of the bond in the reaction network.'.format(bindingPair))
for trouble in bindingTroubleLog:
logMess('ERROR:ATO202','{0}:{1}:We need information to resolve the bond structure of these complexes . \
Please choose among the possible binding candidates that had the most observed frequency in the reaction network or provide a new one'.format(bindingTroubleLog[trouble],trouble))
def createCatalysisRBM(dependencyGraph, element, translator, reactionProperties,
equivalenceDictionary, sbmlAnalyzer, database):
'''
if it's a catalysis reaction create a new component/state
'''
if dependencyGraph[element[0]][0][0] == element[0]:
if element[0] not in translator:
translator[element[0]] = createEmptySpecies(element[0])
else:
componentStateArray = []
tmp = element[0]
existingComponents = []
memory = []
forceActivationSwitch = False
while dependencyGraph[tmp] != []:
# what kind of catalysis are we dealing with
# classification = identifyReaction(
# equivalenceDictionary,
# dependencyGraph[tmp][0][0],tmp)
classifications = None
if not classifications:
classifications = identifyReaction(
equivalenceDictionary,
dependencyGraph[tmp][0][0], tmp)
classifications = classifications if classifications in reactionProperties else None
if classifications is not None:
classifications = [classifications]
if not classifications:
classifications = sbmlAnalyzer.findMatchingModification(
tmp, dependencyGraph[tmp][0][0])
if not classifications:
classifications = sbmlAnalyzer.findMatchingModification(
element[0], dependencyGraph[tmp][0][0])
# if we know what classification it is then add the corresponding
# components and states
if classifications is not None:
for classification in classifications:
componentStateArray.append(
reactionProperties[classification])
# classificationArray.append([classification,
# tmp,dependencyGraph[tmp]
# [0][0]])
existingComponents.append(
reactionProperties[classification][0])
# if we don't know we can create a force 1:1 modification
elif database.forceModificationFlag and classifications is None and not forceActivationSwitch:
forceActivationSwitch = True
baseName = getTrueTag(dependencyGraph,
dependencyGraph[element[0]][0][0])
species = createEmptySpecies(baseName)
componentStateArray.append(['{0}'.format(tmp), tmp])
if not (element[0] in database.userLabelDictionary and database.userLabelDictionary[element[0]][0][0] == baseName):
logMess('WARNING:LAE002', 'adding forced transformation: {0}:{1}:{2}'.format(
baseName, dependencyGraph[element[0]][0][0], element[0]))
# return
# bail out if we couldn't figure out what modification it is
elif classifications is None:
logMess('DEBUG:MSC001', 'unregistered modification: {0}:{1}'.format(
element[0], dependencyGraph[element[0]]))
memory.append(tmp)
tmp = dependencyGraph[tmp][0][0]
if tmp in memory:
raise atoAux.CycleError(memory)
baseName = getTrueTag(
dependencyGraph, dependencyGraph[element[0]][0][0])
species = createEmptySpecies(baseName)
# use the already existing structure if its in the
# translator,otherwise empty
if baseName in translator:
species = translator[baseName]
#modifiedSpecies = deepcopy(translator[dependencyGraph[element[0]][0][0]])
# modified species needs to start from the base speceis sine componentStateArray should contain the full set of modifications
# check that this works correctly for double modifications
modifiedSpecies = deepcopy(translator[baseName])
# this counter is here for multi level modification events (e.g. double
# phosporylation)
modificationCounter = {
componentState[0]: 2 for componentState in componentStateArray}
for componentState in componentStateArray:
addComponentToMolecule(species, baseName, componentState[0])
addComponentToMolecule(
modifiedSpecies, baseName, componentState[0])
tmp = addStateToComponent(species, baseName,
componentState[0], componentState[1])
if tmp == componentState[1]:
addStateToComponent(species, baseName, componentState[0],
componentState[1] + componentState[1])
# this modification was already activated so create a second
# modification component
if addStateToComponent(modifiedSpecies, baseName,
componentState[0], componentState[1]) == componentState[1]:
componentName = '{0}{1}'.format(
componentState[0], modificationCounter[componentState[0]])
modificationCounter[componentState[0]] += 1
addComponentToMolecule(
modifiedSpecies, baseName, componentName)
addStateToComponent(modifiedSpecies, baseName, componentName,
componentState[1])
addStateToComponent(species, baseName, componentState[0], '0')
# update the base species
if len(componentStateArray) > 0:
translator[baseName] = deepcopy(species)
translator[element[0]] = modifiedSpecies
def getComplexationComponents2(moleculeName, species, bioGridFlag, pathwaycommonsFlag=False,
parser=None, bondSeeding=[], bondExclusion=[], database=None):
'''
method used during the atomization process. It determines how molecules
in a species bind together
'''
def sortMolecules(array, reverse):
return sorted(array, key=lambda molecule: (len(molecule.components),
len([
x for x in molecule.components if x.activeState not in [0, '0']]),
len(str(molecule)), str(molecule)),
reverse=reverse)
def getBiggestMolecule(array):
sortedMolecule = sortMolecules(array, reverse=False)
#sortedMolecule = sorted(sortedMolecule, key=lambda rule: len(rule.components))
return sortedMolecule[-1]
def getNamedMolecule(array, name):
for molecule in sortMolecules(array, True):
if molecule.name == name:
return molecule
speciesDict = {}
# this array will contain all molecules that bind together
pairedMolecules = []
for x in sortMolecules(species.molecules, reverse=True):
for y in x.components:
if y.name not in speciesDict:
speciesDict[y.name] = []
speciesDict[y.name].append(x)
# this array wil contain all molecules that dont bind to anything
orphanedMolecules = [x for x in species.molecules]
# seed the list of pairs from the seeds
pairedMolecules = copy(bondSeeding)
if bondSeeding:
orphanedMolecules = [
x for x in orphanedMolecules for y in bondSeeding if x not in y]
# determine how molecules bind together
redundantBonds = []
for x in sortMolecules(species.molecules, reverse=True):
for component in [y for y in x.components if y.name.lower()
in speciesDict.keys()]:
if x.name.lower() in speciesDict:
if(x in speciesDict[component.name.lower()]) and component.name in [y.name.lower() for y
in speciesDict[x.name.lower()]]:
for mol in speciesDict[x.name.lower()]:
if mol.name.lower() == component.name and x != mol and x in \
speciesDict[component.name]:
speciesDict[x.name.lower()].remove(mol)
speciesDict[component.name].remove(x)
if x not in orphanedMolecules and mol not in orphanedMolecules:
# FIXME: is it necessary to remove double bonds
# in complexes?
lhs = set([])
rhs = set([])
repeatedFlag = False
for pair in pairedMolecules:
if x in pair:
lhs.add(pair[0])
lhs.add(pair[1])
elif mol in pair:
rhs.add(pair[0])
rhs.add(pair[1])
# is this particular pair of molecules bound together?
if x in pair and mol in pair:
repeatedFlag = True
break
# this pair already exists
if repeatedFlag:
continue
redundantBonds.append([x, mol])
intersection = lhs.intersection(rhs)
redundantBonds[-1].extend(list(intersection))
if len(redundantBonds[-1]) < 3:
redundantBonds.pop()
# continue
if [x, mol] not in bondSeeding and [mol, x] not in bondSeeding and [x, mol] not in bondExclusion and [mol, x] not in bondExclusion:
pairedMolecules.append([x, mol])
if x in orphanedMolecules:
orphanedMolecules.remove(x)
if mol in orphanedMolecules:
orphanedMolecules.remove(mol)
if len(redundantBonds) > 0:
for x in redundantBonds:
if database:
atoAux.addAssumptions(
'redundantBonds', tuple(sorted([y.name for y in x])), database.assumptions)
atoAux.addAssumptions(
'redundantBondsMolecules', (tuple(sorted([y.name for y in x])), moleculeName), database.assumptions)
logMess('WARNING:CTX001', 'Redundant bonds detected between molecules {0} in species {1}'.format(
[y.name for y in x], moleculeName))
totalComplex = [set(x) for x in pairedMolecules]
isContinuousFlag = True
# iterate over orphaned and find unidirectional interactions
# e.g. if a molecule has a previous known interaction with the
# same kind of molecule, even if it has no available components
# e.g. k-mers`
for element in speciesDict:
for individualMolecule in speciesDict[element]:
if individualMolecule in orphanedMolecules:
candidatePartner = [x for x in species.molecules if x.name.lower(
) == element and x != individualMolecule]
if len(candidatePartner) == 1:
pairedMolecules.append(
[candidatePartner[0], individualMolecule])
orphanedMolecules.remove(individualMolecule)
# determine which pairs form a continuous chain
while isContinuousFlag:
isContinuousFlag = False
for idx in range(0, len(totalComplex) - 1):
for idx2 in range(idx + 1, len(totalComplex)):
if len([x for x in totalComplex[idx] if x in totalComplex[idx2]]) > 0:
totalComplex[idx] = totalComplex[
idx].union(totalComplex[idx2])
totalComplex.pop(idx2)
isContinuousFlag = True
break
if isContinuousFlag:
break
# now we process those molecules where we need to create a new component
for element in orphanedMolecules:
for mol1 in species.molecules:
# when adding orphaned molecules make sure it's not already in
# the list
if mol1 == element and mol1 not in set().union(*totalComplex):
totalComplex.append(set([mol1]))
# now we process for those molecules we are not sure how do they bind
while len(totalComplex) > 1:
if len(totalComplex[0]) == 1 and len(totalComplex[1]) == 1:
mol1 = list(totalComplex[0])[0]
mol2 = list(totalComplex[1])[0]
else:
mol1, mol2 = solveComplexBinding(totalComplex, pathwaycommonsFlag, parser, database.prunnedDependencyGraph[moleculeName][0])
pairedMolecules.append([mol1, mol2])
totalComplex[0] = totalComplex[0].union(totalComplex[1])
totalComplex.pop(1)
# totalComplex.extend(orphanedMolecules)
return pairedMolecules
def solveComplexBinding(totalComplex, pathwaycommonsFlag, parser, compositionEntry):
'''
given two binding complexes it will attempt to find the ways in which they bind using different criteria
'''
def sortMolecules(array, reverse):
return sorted(array, key=lambda molecule: (len(molecule.components),
len([
x for x in molecule.components if x.activeState not in [0, '0']]),
len(str(molecule)), str(molecule)), reverse=reverse)
def getBiggestMolecule(array):
sortedMolecule = sortMolecules(array, reverse=False)
#sortedMolecule = sorted(sortedMolecule, key=lambda rule: len(rule.components))
return sortedMolecule[-1]
def getNamedMolecule(array, name):
for molecule in sortMolecules(array, True):
if molecule.name == name:
return molecule
elif molecule.trueName == name:
return molecule
names1 = [str(x.trueName) for x in totalComplex[0] ]
names2 = [str(x.trueName) for x in totalComplex[1] ]
bioGridDict = {}
# find all pairs of molecules
comb = set([tuple(sorted([x, y])) for x in names1 for y in names2])
comb2 = set([tuple(sorted([x,y])) for x in compositionEntry for y in compositionEntry])
dbPair = set([])
combTemp = set()
# search pathway commons for binding candidates
if pathwaycommonsFlag:
dbPair = isInComplexWith(comb, parser)
else:
for element in comb:
if element[0].upper() in bioGridDict and element[1] in bioGridDict[element[0].upper()] or \
element[1].upper() in bioGridDict and element[0] in bioGridDict[element[1].upper()]:
#logMess('INFO:ATO001', 'Biogrid info: {0}:{1}'.format(element[0], element[1]))
dbPair.add((element[0], element[1]))
# elif pathwaycommonsFlag:
# if pwcm.isInComplexWith(element[0], element[1]):
# dbPair.add((element[0], element[1]))
dbPair = list(dbPair)
if dbPair != []:
mol1 = mol2 = None
# select the best candidate if there's many ways to bind (in general
# one that doesn't overlap with an already exising pair)
finalDBpair = []
if len(dbPair) > 1:
for element in dbPair:
mset1 = Counter(element)
mset2 = Counter(names1)
mset3 = Counter(names2)
intersection1 = mset1 & mset2
intersection2 = mset1 & mset3
intersection1 = list(intersection1.elements())
intersection2 = list(intersection2.elements())
if len(intersection1) < 2 and len(intersection2) < 2:
finalDBpair.append(element)
if len(finalDBpair) > 0:
dbPair = finalDBpair
if len(dbPair) > 1:
# @FIXME: getNamedMolecule should never receive parameters that cause it to return null, but somehow that's what is happening
# when you receive a malformed user definition file. The error
# should be caught way before we reach this point
tmpComplexSubset1 = [getNamedMolecule(totalComplex[0], element[0])
for element in dbPair if getNamedMolecule(totalComplex[0], element[0]) is not None]
if not tmpComplexSubset1:
tmpComplexSubset1 = [getNamedMolecule(totalComplex[0], element[
1]) for element in dbPair if getNamedMolecule(totalComplex[0], element[1]) is not None]
tmpComplexSubset2 = [getNamedMolecule(totalComplex[1], element[
0]) for element in dbPair if getNamedMolecule(totalComplex[1], element[0]) is not None]
else:
tmpComplexSubset2 = [getNamedMolecule(totalComplex[1], element[
1]) for element in dbPair if getNamedMolecule(totalComplex[1], element[1]) is not None]
mol1 = getBiggestMolecule(tmpComplexSubset1)
mol2 = getBiggestMolecule(tmpComplexSubset2)
#was ATO002
logMess('WARNING:ATO111', "{0}-{1}:The two pairs can bind in these ways according to BioGrid/Pathwaycommons:{2}:Defaulting to:('{3}', '{4}')".format(names1, names2, dbPair,
mol1.name, mol2.name))
else:
mol1 = getNamedMolecule(totalComplex[0], dbPair[0][0])
if not mol1:
mol1 = getNamedMolecule(totalComplex[1], dbPair[0][0])
mol2 = getNamedMolecule(totalComplex[0], dbPair[0][1])
else:
mol2 = getNamedMolecule(totalComplex[1], dbPair[0][1])
if not mol2:
mol1 = getNamedMolecule(totalComplex[1], dbPair[0][0])
mol2 = getNamedMolecule(totalComplex[0], dbPair[0][1])
logMess('INFO:ATO001', 'Binding information found in BioGrid/Pathwaycommons for for {0}-{1}'.format(mol1.name, mol2.name))
else:
#mol1 = getBiggestMolecule(totalComplex[0])
#mol2 = getBiggestMolecule(totalComplex[1])
'''
if pathwaycommonsFlag:
logMess('ERROR:ATO201', "We don't know how {0} and {1} bind together and there's no relevant BioGrid/Pathway commons information. Not atomizing".format(
[x.name for x in totalComplex[0]], [x.name for x in totalComplex[1]]))
# addAssumptions('unknownBond',(mol1.name,mol2.name))
else:
logMess('ERROR:ATO202', "We don't know how {0} and {1} bind together. Not atomizing".format(
[x.name for x in totalComplex[0]], [x.name for x in totalComplex[1]]))
# addAssumptions('unknownBond',(mol1.name,mol2.name))
'''
raise BindingException(
'{0}-{1}'.format(sorted([x.name for x in totalComplex[0]]), sorted([x.name for x in totalComplex[1]])), comb)
return mol1, mol2
def analyzeHelper(document, reactionDefinitions, useID, outputFile, speciesEquivalence, atomize, translator, database, bioGrid=False):
'''
taking the atomized dictionary and a series of data structure, this method
does the actual string output.
'''
useArtificialRules = False
parser = SBML2BNGL(document.getModel(), useID)
parser.setConversion(database.isConversion)
#database = structures.Databases()
#database.assumptions = defaultdict(set)
#translator,log,rdf = m2c.transformMolecules(parser,database,reactionDefinitions,speciesEquivalence)
#try:
#bioGridDict = {}
#if biogrid:
# bioGridDict = biogrid()
#if atomize:
# translator = mc.transformMolecules(parser,database,reactionDefinitions,speciesEquivalence,bioGridDict)
#else:
# translator={}
#except:
# print 'failure'
# return None,None,None,None
#translator = {}
param,zparam = parser.getParameters()
rawSpecies = {}
for species in parser.model.getListOfSpecies():
rawtemp = parser.getRawSpecies(species,[x.split(' ')[0] for x in param])
rawSpecies[rawtemp['identifier']] = rawtemp
parser.reset()
molecules, initialConditions, observables, speciesDict,\
observablesDict, annotationInfo = parser.getSpecies(translator, [x.split(' ')[0] for x in param])
# finally, adjust parameters and initial concentrations according to whatever initialassignments say
param, zparam, initialConditions = parser.getInitialAssignments(translator, param, zparam, molecules, initialConditions)
# FIXME: this method is a mess, improve handling of assignmentrules since we can actually handle those
aParameters, aRules, nonzparam, artificialRules, removeParams, artificialObservables = parser.getAssignmentRules(zparam, param, rawSpecies,
observablesDict, translator)
compartments = parser.getCompartments()
functions = []
assigmentRuleDefinedParameters = []
reactionParameters, rules, rateFunctions = parser.getReactions(translator, len(compartments) > 1,
atomize=atomize, parameterFunctions=artificialObservables, database=database)
functions.extend(rateFunctions)
for element in nonzparam:
param.append('{0} 0'.format(element))
param = [x for x in param if x not in removeParams]
tags = '@{0}'.format(compartments[0].split(' ')[0]) if len(compartments) == 1 else '@cell'
molecules.extend([x.split(' ')[0] for x in removeParams])
if len(molecules) == 0:
compartments = []
observables.extend('Species {0} {0}'.format(x.split(' ')[0]) for x in removeParams)
for x in removeParams:
initialConditions.append(x.split(' ')[0] + tags + ' ' + ' '.join(x.split(' ')[1:]))
## Comment out those parameters that are defined with assignment rules
## TODO: I think this is correct, but it may need to be checked
tmpParams = []
for idx, parameter in enumerate(param):
for key in artificialObservables:
if re.search('^{0}\s'.format(key),parameter)!= None:
assigmentRuleDefinedParameters.append(idx)
tmpParams.extend(artificialObservables)
tmpParams.extend(removeParams)
tmpParams = set(tmpParams)
correctRulesWithParenthesis(rules,tmpParams)
for element in assigmentRuleDefinedParameters:
param[element] = '#' + param[element]
deleteMolecules = []
deleteMoleculesFlag = True
for key in artificialObservables:
flag = -1
for idx,observable in enumerate(observables):
if 'Species {0} {0}()'.format(key) in observable:
flag = idx
if flag != -1:
observables.pop(flag)
functions.append(artificialObservables[key])
flag = -1
if '{0}()'.format(key) in molecules:
flag = molecules.index('{0}()'.format(key))
if flag != -1:
if deleteMoleculesFlag:
deleteMolecules.append(flag)
else:
deleteMolecules.append(key)
#result =validateReactionUsage(molecules[flag],rules)
#if result != None:
# logMess('ERROR','Pseudo observable {0} in reaction {1}'.format(molecules[flag],result))
#molecules.pop(flag)
flag = -1
for idx,specie in enumerate(initialConditions):
if ':{0}('.format(key) in specie:
flag = idx
if flag != -1:
initialConditions[flag] = '#' + initialConditions[flag]
for flag in sorted(deleteMolecules,reverse=True):
if deleteMoleculesFlag:
logMess('WARNING:SIM101','{0} reported as function, but usage is ambiguous'.format(molecules[flag]) )
result = validateReactionUsage(molecules[flag], rules)
if result is not None:
logMess('ERROR:Simulation','Pseudo observable {0} in reaction {1}'.format(molecules[flag],result))
#since we are considering it an observable delete it from the molecule and
#initial conditions list
#s = molecules.pop(flag)
#initialConditions = [x for x in initialConditions if '$' + s not in x]
else:
logMess('WARNING:SIM101','{0} reported as species, but usage is ambiguous.'.format(flag) )
artificialObservables.pop(flag)
sbmlfunctions = parser.getSBMLFunctions()
functions.extend(aRules)
#print functions
processFunctions(functions,sbmlfunctions,artificialObservables,rateFunctions)
for interation in range(0,3):
for sbml2 in sbmlfunctions:
for sbml in sbmlfunctions:
if sbml == sbml2:
continue
if sbml in sbmlfunctions[sbml2]:
sbmlfunctions[sbml2] = writer.extendFunction(sbmlfunctions[sbml2],sbml,sbmlfunctions[sbml])
functions = reorderFunctions(functions)
functions = changeNames(functions, aParameters)
# change reference for observables with compartment name
functions = changeNames(functions, observablesDict)
# print [x for x in functions if 'functionRate60' in x]
functions = unrollFunctions(functions)
rules = changeRates(rules, aParameters)
if len(compartments) > 1 and 'cell 3 1.0' not in compartments:
compartments.append('cell 3 1.0')
#sbml always has the 'cell' default compartment, even when it
#doesn't declare it
elif len(compartments) == 0 and len(molecules) != 0:
compartments.append('cell 3 1.0')
if len(artificialRules) + len(rules) == 0:
logMess('ERROR:SIM203','The file contains no reactions')
if useArtificialRules or len(rules) == 0:
rules =['#{0}'.format(x) for x in rules]
evaluate = evaluation(len(observables),translator)
artificialRules.extend(rules)
rules = artificialRules
else:
artificialRules =['#{0}'.format(x) for x in artificialRules]
evaluate = evaluation(len(observables),translator)
rules.extend(artificialRules)
commentDictionary = {}
if atomize:
commentDictionary['notes'] = "'This is an atomized translation of an SBML model created on {0}.".format(time.strftime("%d/%m/%Y"))
else:
commentDictionary['notes'] = "'This is a plain translation of an SBML model created on {0}.".format(time.strftime("%d/%m/%Y"))
commentDictionary['notes'] += " The original model has {0} molecules and {1} reactions. The translated model has {2} molecules and {3} rules'".format(parser.model.getNumSpecies(),parser.model.getNumReactions(),len(molecules),len(set(rules)))
meta = parser.getMetaInformation(commentDictionary)
finalString = writer.finalText(meta, param + reactionParameters, molecules, initialConditions,
list(OrderedDict.fromkeys(observables)), list(OrderedDict.fromkeys(rules)), functions, compartments,
annotationInfo, outputFile)
logMess('INFO:SUM001','File contains {0} molecules out of {1} original SBML species'.format(len(molecules), len(observables)))
# rate of each classified rule
evaluate2 = 0 if len(observables) == 0 else len(molecules)*1.0/len(observables)
# add unit information to annotations
annotationInfo['units'] = parser.getUnitDefinitions()
return AnalysisResults(len(rules), len(observables), evaluate, evaluate2, len(compartments),
parser.getSpeciesAnnotation(), finalString, speciesDict, None, annotationInfo)
'''
def bnglFunction(rule,
functionTitle,
reactants,
compartments=[],
parameterDict={},
reactionDict={}):
def powParse(match):
if match.group(1) == 'root':
exponent = '(1/%s)' % match.group(3)
else:
exponent = match.group(3)
if match.group(1) in ['root', 'pow']:
operator = '^'
return '({0}){1}({2})'.format(match.group(2), operator, exponent)
def compParse(match):
translator = {
'gt': '>',
'lt': '<',
'and': '&&',
'or': '||',
'geq': '>=',
'leq': '<=',
'eq': '=='
}
exponent = match.group(3)
operator = translator[match.group(1)]
return '{0} {1} {2}'.format(match.group(2), operator, exponent)
def ceilfloorParse(math):
flag = False
if math.group(1) == 'ceil':
flag = True
if flag:
return 'min(rint({0}+0.5),rint({0} + 1))'.format(math.group(2))
else:
return 'min(rint({0}-0.5),rint({0}+0.5))'.format(math.group(2))
def parameterRewrite(match):
return match.group(1) + 'param_' + match.group(2) + match.group(3)
def constructFromList(argList, optionList):
parsedString = ''
idx = 0
translator = {
'gt': '>',
'lt': '<',
'and': '&&',
'or': '||',
'geq': '>=',
'leq': '<=',
'eq': '=='
}
while idx < len(argList):
if type(argList[idx]) is list:
parsedString += '(' + constructFromList(
argList[idx], optionList) + ')'
elif argList[idx] in optionList:
if argList[idx] == 'ceil':
parsedString += 'min(rint(({0}) + 0.5),rint(({0}) + 1))'.format(
constructFromList(argList[idx + 1], optionList))
idx += 1
elif argList[idx] == 'floor':
parsedString += 'min(rint(({0}) -0.5),rint(({0}) + 0.5))'.format(
constructFromList(argList[idx + 1], optionList))
idx += 1
elif argList[idx] in ['pow']:
index = rindex(argList[idx + 1], ',')
parsedString += '((' + constructFromList(
argList[idx + 1][0:index], optionList) + ')'
parsedString += ' ^ ' + '(' + constructFromList(
argList[idx + 1][index + 1:], optionList) + '))'
idx += 1
elif argList[idx] in ['sqr', 'sqrt']:
tag = '1/' if argList[idx] == 'sqrt' else ''
parsedString += '((' + constructFromList(
argList[idx + 1],
optionList) + ') ^ ({0}2))'.format(tag)
idx += 1
elif argList[idx] == 'root':
index = rindex(argList[idx + 1], ',')
tmp = '1/(' + constructFromList(argList[idx + 1][0:index],
optionList) + '))'
parsedString += '((' + constructFromList(
argList[idx + 1][index + 1:],
optionList) + ') ^ ' + tmp
idx += 1
elif argList[idx] == 'piecewise':
index1 = argList[idx + 1].index(',')
try:
index2 = argList[idx + 1][index1 +
1:].index(',') + index1 + 1
try:
index3 = argList[idx +
1][index2 +
1:].index(',') + index2 + 1
except ValueError:
index3 = -1
except ValueError:
parsedString += constructFromList(
[argList[idx + 1][index1 + 1:]], optionList)
index2 = -1
if index2 != -1:
condition = constructFromList(
[argList[idx + 1][index1 + 1:index2]], optionList)
result = constructFromList([argList[idx + 1][:index1]],
optionList)
if index3 == -1:
result2 = constructFromList(
[argList[idx + 1][index2 + 1:]], optionList)
else:
result2 = constructFromList(
['piecewise', argList[idx + 1][index2 + 1:]],
optionList)
parsedString += 'if({0},{1},{2})'.format(
condition, result, result2)
idx += 1
elif argList[idx] in ['and', 'or']:
symbolDict = {'and': ' && ', 'or': ' || '}
indexArray = [-1]
elementArray = []
for idx2, element in enumerate(argList[idx + 1]):
if element == ',':
indexArray.append(idx2)
indexArray.append(len(argList[idx + 1]))
tmpStr = argList[idx + 1]
for idx2, _ in enumerate(indexArray[0:-1]):
elementArray.append(
constructFromList(
tmpStr[indexArray[idx2] +
1:indexArray[idx2 + 1]], optionList))
parsedString += symbolDict[argList[idx]].join(elementArray)
idx += 1
elif argList[idx] == 'lambda':
tmp = '('
upperLimit = rindex(argList[idx + 1], ',')
parsedParams = []
for x in argList[idx + 1][0:upperLimit]:
if x == ',':
tmp += ', '
else:
tmp += 'param_' + x
parsedParams.append(x)
#tmp = ''.join([x for x in constructFromList(argList[idx+1][0:upperLimit])])
tmp2 = ') = ' + constructFromList(
argList[idx + 1][rindex(argList[idx + 1], ',') + 1:],
optionList)
for x in parsedParams:
while re.search(r'(\W|^)({0})(\W|$)'.format(x),
tmp2) != None:
tmp2 = re.sub(r'(\W|^)({0})(\W|$)'.format(x),
r'\1param_\2 \3', tmp2)
idx += 1
parsedString += tmp + tmp2
else:
parsedString += argList[idx]
idx += 1
return parsedString
def changeToBNGL(functionList, rule, function):
oldrule = ''
#if the rule contains any mathematical function we need to reformat
while any([
re.search(r'(\W|^)({0})(\W|$)'.format(x), rule) != None
for x in functionList
]) and (oldrule != rule):
oldrule = rule
for x in functionList:
rule = re.sub('({0})\(([^,]+),([^)]+)\)'.format(x), function,
rule)
if rule == oldrule:
logMess('ERROR', 'Malformed pow or root function %s' % rule)
print 'meep'
return rule
#rule = changeToBNGL(['pow','root'],rule,powParse)
rule = changeToBNGL(['gt', 'lt', 'leq', 'geq', 'eq'], rule, compParse)
#rule = changeToBNGL(['and','or'],rule,compParse)
flag = True
contentRule = pyparsing.Word(
pyparsing.alphanums + '_'
) | ',' | '.' | '+' | '-' | '*' | '/' | '^' | '&' | '>' | '<' | '=' | '|'
parens = pyparsing.nestedExpr('(', ')', content=contentRule)
finalString = ''
#remove ceil,floor
if any([
re.search(r'(\W|^)({0})(\W|$)'.format(x), rule) != None for x in
['ceil', 'floor', 'pow', 'sqrt', 'sqr', 'root', 'and', 'or']
]):
argList = parens.parseString('(' + rule + ')').asList()
rule = constructFromList(
argList[0],
['floor', 'ceil', 'pow', 'sqrt', 'sqr', 'root', 'and', 'or'])
while 'piecewise' in rule:
argList = parens.parseString('(' + rule + ')').asList()
rule = constructFromList(argList[0], ['piecewise'])
#remove references to lambda functions
if 'lambda(' in rule:
lambdaList = parens.parseString('(' + rule + ')')
functionBody = constructFromList(lambdaList[0].asList(), ['lambda'])
flag = False
rule = '{0}{1}'.format(functionTitle, functionBody)
tmp = rule
#delete the compartment from the rate function since cBNGL already does it
for compartment in compartments:
tmp = re.sub('^{0}\s*[*]'.format(compartment[0]), '', tmp)
tmp = re.sub('([*]\s*{0})$'.format(compartment[0]), '', tmp)
if compartment[0] in tmp:
tmp = re.sub(r'(\W|^)({0})(\W|$)'.format(compartment[0]),
r'\1 {0} \3'.format(str(compartment[1])), tmp)
#tmp = re.sub(r'(\W)({0})(\W)'.format(compartment[0]),r'\1%s\3' % str(compartment[1]),tmp)
logMess(
'INFO',
'Exchanging reference to compartment %s for its dimensions' %
compartment[0])
#change references to time for time()
#tmp =re.sub(r'(\W|^)(time)(\W|$)',r'\1time()\3',tmp)
#tmp =re.sub(r'(\W|^)(Time)(\W|$)',r'\1time()\3',tmp)
while re.search(r'(\W|^)inf(\W|$)', tmp) != None:
tmp = re.sub(r'(\W|^)(inf)(\W|$)', r'\1 1e20 \3', tmp)
#BNGL has ^ for power.
if flag:
finalString = '%s = %s' % (functionTitle, tmp)
else:
finalString = tmp
#change references to local parameters
for parameter in parameterDict:
finalString = re.sub(r'(\W|^)({0})(\W|$)'.format(parameter),
r'\g<1>{0}\g<3>'.format(parameterDict[parameter]),
finalString)
#change references to reaction Id's to their netflux equivalent
for reaction in reactionDict:
if reaction in finalString:
finalString = re.sub(
r'(\W|^)({0})(\W|$)'.format(reaction),
r'\g<1>{0}\g<3>'.format(reactionDict[reaction]), finalString)
#combinations '+ -' break ibonetgen
finalString = re.sub(r'(\W|^)([-])(\s)+', r'\1-', finalString)
#changing reference of 't' to time()
#finalString = re.sub(r'(\W|^)(t)(\W|$)',r'\1time()\3',finalString)
#pi
finalString = re.sub(r'(\W|^)(pi)(\W|$)', r'\g<1>3.1415926535\g<3>',
finalString)
#print reactants,finalString
#log for log 10
finalString = re.sub(r'(\W|^)log\(', r'\1 ln(', finalString)
#reserved keyword: e
finalString = re.sub(r'(\W|^)(e)(\W|$)', r'\g<1>are\g<3>', finalString)
#changing ceil
#avoiding variables whose name starts with a number
#removing mass-action elements
tmp = finalString
#print finalString,reactants
#for reactant in reactants:
# finalString = re.sub(r'(\W|^)({0}\s+\*)'.format(reactant[0]),r'\1',finalString)
# finalString = re.sub(r'(\W|^)(\*\s+{0}(\s|$))'.format(reactant[0]),r'\1',finalString)
#print finalString
#if finalString != tmp:
# logMess('WARNING','Removed mass action elements from )
return finalString
def bnglFunction(rule,functionTitle,reactants,compartments=[],parameterDict={},reactionDict={}):
def powParse(match):
if match.group(1) == 'root':
exponent = '(1/%s)' % match.group(3)
else:
exponent = match.group(3)
if match.group(1) in ['root','pow']:
operator = '^'
return '({0}){1}({2})'.format(match.group(2),operator,exponent)
def compParse(match):
translator = {'gt':'>','lt':'<','and':'&&','or':'||','geq':'>=','leq':'<=','eq':'=='}
exponent = match.group(3)
operator = translator[match.group(1)]
return '{0} {1} {2}'.format(match.group(2),operator,exponent)
def ceilfloorParse(math):
flag = False
if math.group(1) == 'ceil':
flag = True
if flag:
return 'min(rint({0}+0.5),rint({0} + 1))'.format(math.group(2))
else:
return 'min(rint({0}-0.5),rint({0}+0.5))'.format(math.group(2))
def parameterRewrite(match):
return match.group(1) + 'param_' + match.group(2) + match.group(3)
def constructFromList(argList,optionList):
parsedString = ''
idx = 0
translator = {'gt':'>','lt':'<','and':'&&','or':'||','geq':'>=','leq':'<=','eq':'=='}
while idx < len(argList):
if type(argList[idx]) is list:
parsedString += '(' + constructFromList(argList[idx],optionList) + ')'
elif argList[idx] in optionList:
if argList[idx] == 'ceil':
parsedString += 'min(rint(({0}) + 0.5),rint(({0}) + 1))'.format(constructFromList(argList[idx+1],optionList))
idx += 1
elif argList[idx] == 'floor':
parsedString += 'min(rint(({0}) -0.5),rint(({0}) + 0.5))'.format(constructFromList(argList[idx+1],optionList))
idx += 1
elif argList[idx] in ['pow']:
index = rindex(argList[idx+1],',')
parsedString += '(('+ constructFromList(argList[idx+1][0:index],optionList) + ')'
parsedString += ' ^ ' + '(' + constructFromList(argList[idx+1][index+1:] ,optionList) + '))'
idx += 1
elif argList[idx] in ['sqr','sqrt']:
tag = '1/' if argList[idx] == 'sqrt' else ''
parsedString += '((' + constructFromList(argList[idx+1],optionList) + ') ^ ({0}2))'.format(tag)
idx += 1
elif argList[idx] == 'root':
index = rindex(argList[idx+1],',')
tmp = '1/('+ constructFromList(argList[idx+1][0:index],optionList) + '))'
parsedString += '((' + constructFromList(argList[idx+1][index+1:] ,optionList) + ') ^ ' + tmp
idx += 1
elif argList[idx] == 'piecewise':
index1 = argList[idx+1].index(',')
try:
index2 = argList[idx+1][index1+1:].index(',') + index1+1
try:
index3 = argList[idx+1][index2+1:].index(',') + index2+1
except ValueError:
index3 = -1
except ValueError:
parsedString += constructFromList([argList[idx+1][index1+1:]],optionList)
index2 = -1
if index2 != -1:
condition = constructFromList([argList[idx+1][index1+1:index2]],optionList)
result = constructFromList([argList[idx+1][:index1]],optionList)
if index3 == -1:
result2 = constructFromList([argList[idx+1][index2+1:]],optionList)
else:
result2 = constructFromList(['piecewise', argList[idx+1][index2+1:]],optionList)
parsedString += 'if({0},{1},{2})'.format(condition,result,result2)
idx+=1
elif argList[idx] in ['and', 'or']:
symbolDict = {'and':' && ','or':' || '}
indexArray = [-1]
elementArray = []
for idx2,element in enumerate(argList[idx+1]):
if element ==',':
indexArray.append(idx2)
indexArray.append(len(argList[idx+1]))
tmpStr = argList[idx+1]
for idx2,_ in enumerate(indexArray[0:-1]):
elementArray.append(constructFromList(tmpStr[indexArray[idx2]+1:indexArray[idx2+1]],optionList))
parsedString += symbolDict[argList[idx]].join(elementArray)
idx+=1
elif argList[idx] == 'lambda':
tmp = '('
upperLimit = rindex(argList[idx+1],',')
parsedParams = []
for x in argList[idx+1][0:upperLimit]:
if x == ',':
tmp += ', '
else:
tmp += 'param_' + x
parsedParams.append(x)
#tmp = ''.join([x for x in constructFromList(argList[idx+1][0:upperLimit])])
tmp2 = ') = ' + constructFromList(argList[idx+1][rindex(argList[idx+1],',')+1:],optionList)
for x in parsedParams:
while re.search(r'(\W|^)({0})(\W|$)'.format(x),tmp2) != None:
tmp2 = re.sub(r'(\W|^)({0})(\W|$)'.format(x),r'\1param_\2 \3',tmp2)
idx+= 1
parsedString += tmp + tmp2
else:
parsedString += argList[idx]
idx += 1
return parsedString
def changeToBNGL(functionList,rule,function):
oldrule = ''
#if the rule contains any mathematical function we need to reformat
while any([re.search(r'(\W|^)({0})(\W|$)'.format(x),rule) != None for x in functionList]) and (oldrule != rule):
oldrule = rule
for x in functionList:
rule = re.sub('({0})\(([^,]+),([^)]+)\)'.format(x),function,rule)
if rule == oldrule:
logMess('ERROR','Malformed pow or root function %s' % rule)
print 'meep'
return rule
#rule = changeToBNGL(['pow','root'],rule,powParse)
rule = changeToBNGL(['gt','lt','leq','geq','eq'],rule,compParse)
#rule = changeToBNGL(['and','or'],rule,compParse)
flag = True
contentRule = pyparsing.Word(pyparsing.alphanums + '_') | ',' | '.' | '+' | '-' | '*' | '/' | '^' | '&' | '>' | '<' | '=' | '|'
parens = pyparsing.nestedExpr( '(', ')', content=contentRule)
finalString = ''
#remove ceil,floor
if any([re.search(r'(\W|^)({0})(\W|$)'.format(x),rule) != None for x in ['ceil','floor','pow','sqrt','sqr','root','and','or']]):
argList = parens.parseString('('+ rule + ')').asList()
rule = constructFromList(argList[0],['floor','ceil','pow','sqrt','sqr','root','and','or'])
while 'piecewise' in rule:
argList = parens.parseString('('+ rule + ')').asList()
rule = constructFromList(argList[0],['piecewise'])
#remove references to lambda functions
if 'lambda(' in rule:
lambdaList = parens.parseString('(' + rule + ')')
functionBody = constructFromList(lambdaList[0].asList(),['lambda'])
flag = False
rule = '{0}{1}'.format(functionTitle,functionBody)
tmp = rule
#delete the compartment from the rate function since cBNGL already does it
for compartment in compartments:
tmp = re.sub('^{0}\s*[*]'.format(compartment[0]),'',tmp)
tmp = re.sub('([*]\s*{0})$'.format(compartment[0]),'',tmp)
if compartment[0] in tmp:
tmp =re.sub(r'(\W|^)({0})(\W|$)'.format(compartment[0]),r'\1 {0} \3'.format(str(compartment[1])),tmp)
#tmp = re.sub(r'(\W)({0})(\W)'.format(compartment[0]),r'\1%s\3' % str(compartment[1]),tmp)
logMess('INFO','Exchanging reference to compartment %s for its dimensions' % compartment[0])
#change references to time for time()
#tmp =re.sub(r'(\W|^)(time)(\W|$)',r'\1time()\3',tmp)
#tmp =re.sub(r'(\W|^)(Time)(\W|$)',r'\1time()\3',tmp)
while re.search(r'(\W|^)inf(\W|$)',tmp) != None:
tmp =re.sub(r'(\W|^)(inf)(\W|$)',r'\1 1e20 \3',tmp)
#BNGL has ^ for power.
if flag:
finalString = '%s = %s' % (functionTitle,tmp)
else:
finalString = tmp
#change references to local parameters
for parameter in parameterDict:
finalString = re.sub(r'(\W|^)({0})(\W|$)'.format(parameter),r'\g<1>{0}\g<3>'.format(parameterDict[parameter]),finalString)
#change references to reaction Id's to their netflux equivalent
for reaction in reactionDict:
if reaction in finalString:
finalString = re.sub(r'(\W|^)({0})(\W|$)'.format(reaction),r'\g<1>{0}\g<3>'.format(reactionDict[reaction]),finalString)
#combinations '+ -' break ibonetgen
finalString = re.sub(r'(\W|^)([-])(\s)+',r'\1-',finalString)
#changing reference of 't' to time()
#finalString = re.sub(r'(\W|^)(t)(\W|$)',r'\1time()\3',finalString)
#pi
finalString = re.sub(r'(\W|^)(pi)(\W|$)',r'\g<1>3.1415926535\g<3>',finalString)
#print reactants,finalString
#log for log 10
finalString = re.sub(r'(\W|^)log\(',r'\1 ln(',finalString)
#reserved keyword: e
finalString = re.sub(r'(\W|^)(e)(\W|$)',r'\g<1>are\g<3>',finalString)
#changing ceil
#avoiding variables whose name starts with a number
#removing mass-action elements
tmp = finalString
#print finalString,reactants
#for reactant in reactants:
# finalString = re.sub(r'(\W|^)({0}\s+\*)'.format(reactant[0]),r'\1',finalString)
# finalString = re.sub(r'(\W|^)(\*\s+{0}(\s|$))'.format(reactant[0]),r'\1',finalString)
#print finalString
#if finalString != tmp:
# logMess('WARNING','Removed mass action elements from )
return finalString