def updateSpecies(species, referenceMolecule):
flag = False
#print '--',str(species),str(referenceMolecule)
for moleculeStructure in species.molecules:
if moleculeStructure.name == referenceMolecule.name:
for component in referenceMolecule.components:
count = [x.name for x in referenceMolecule.components
].count(component.name)
count -= [x.name for x in moleculeStructure.components
].count(component.name)
newComponent = st.Component(component.name)
if len(component.states) > 0:
newComponent.addState('0')
if count > 0:
for _ in range(0, count):
moleculeStructure.addComponent(deepcopy(newComponent))
elif count < 0:
for _ in range(0, -count):
referenceMolecule.addComponent(deepcopy(newComponent))
flag = True
elif count == 0:
localComponents = [
x for x in moleculeStructure.components
if x.name == component.name
]
referenceComponents = [
x for x in referenceMolecule.components
if x.name == component.name
]
if [x.states for x in localComponents
] != [x.states for x in referenceComponents]:
for lc in localComponents:
for rc in referenceComponents:
for ls in lc.states:
if ls not in rc.states:
rc.addState(ls, update=False)
for rs in rc.states:
if rs not in lc.states:
lc.addState(rs, update=False)
for component in moleculeStructure.components:
count = [x.name for x in referenceMolecule.components
].count(component.name)
count -= [x.name for x in moleculeStructure.components
].count(component.name)
newComponent = st.Component(component.name)
if len(component.states) > 0:
newComponent.addState(component.states[0])
newComponent.addState('0')
if count > 0:
for idx in range(0, count):
moleculeStructure.addComponent(deepcopy(newComponent))
elif count < 0:
for idx in range(0, -count):
referenceMolecule.addComponent(deepcopy(newComponent))
flag = True
return flag
def makeUnboundPattern(mol,comp): '''Make unbound pattern from Molecule Component ''' c = st.Component(comp.name,comp.idx,[],[]) m = st.Molecule(mol.name,mol.idx) m.addComponent(c) sp = st.Species() sp.addMolecule(m) return sp
def makeBondPattern(mc1,mc2):
'''Make bond pattern from [Molecule Component], [Molecule Component]
'''
[m1,c1] = mc1
[m2,c2] = mc2
c_1 = st.Component(c1.name,c1.idx,[],[])
c_1.addBond('1')
m_1 = st.Molecule(m1.name, m1.idx)
m_1.addComponent(c_1)
c_2 = st.Component(c2.name,c2.idx,[],[])
c_2.addBond('1')
m_2 = st.Molecule(m2.name, m2.idx)
m_2.addComponent(c_2)
sp = st.Species()
sp.addMolecule(m_1)
sp.addMolecule(m_2)
return sp
def makeStatePattern(mol,comp,state): '''Make state pattern from Molecule Component State ''' c = st.Component(comp.name,comp.idx,[],[]) c.addState(state) c.setActiveState(state) m = st.Molecule(mol.name,mol.idx) m.addComponent(c) sp = st.Species() sp.addMolecule(m) return sp
def parseMolecules(molecules):
'''
Parses an XML molecule section
Returns: a molecule structure
'''
mol = st.Molecule(molecules.get('name'), molecules.get('id'))
components = \
molecules.find('.//{http://www.sbml.org/sbml/level3}ListOfComponentTypes')
if components != None:
for component in components.getchildren():
comp = st.Component(component.get('name'), component.get('id'))
mol.addComponent(comp)
return mol
def merge(reactant1, reactant2, r1, r2, translator, outputFlag=False):
'''
Receives two species reactant1 and reactant1, and their intersection points
r1 and r2 and creates a new complex that is the union
'''
species = st.Species()
if reactant1 in translator:
species.append(translator[reactant1])
if reactant2 in translator:
species.append(translator[reactant2])
if outputFlag:
print '-----------', species, reactant1, reactant2, reactant2 in translator
rnd = max(species.getBondNumbers()) + 1
molecule1 = st.Molecule(binding1)
molecule2 = st.Molecule(binding2)
component1 = st.Component(r1)
component2 = st.Component(r2)
component1.addBond(str(rnd))
component2.addBond(str(rnd))
molecule1.addComponent(component1)
molecule2.addComponent(component2)
species.addMolecule(molecule1, True, 1)
counter = 2 if binding1 == binding2 else 1
species.addMolecule(molecule2, True, counter)
####TODO: update the rawDAtabase with the m1m2 information
if molecule1.name in translator:
sp = st.Species()
sp.addMolecule(deepcopy(molecule1))
translator[molecule1.name].extend(sp)
translator[molecule1.name].reset()
if molecule2.name in translator:
sp = st.Species()
sp.addMolecule(deepcopy(molecule2))
translator[molecule2.name].extend(sp)
translator[molecule2.name].reset()
def createMolecule(molecule, bonds):
nameDict = {}
mol = st.Molecule(molecule.get('name'), molecule.get('id'))
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
def addBondToComponent(species, moleculeName, componentName, bond, priority=1):
order = 1
for molecule in species.molecules:
if moleculeName == molecule.name:
if priority == order or len([
x for x in species.molecules if x.name == moleculeName
]) == order:
for component in molecule.components:
if componentName == component.name:
# if we are adding a second bond to the same component
#it actually means that we have two components with the
#same name
if len(component.bonds) == 0:
component.addBond(bond)
return
else:
newComponent = st.Component(componentName)
newComponent.addBond(bond)
molecule.addComponent(newComponent)
return
else:
order += 1
def catalysis(original, dictionary, rawDatabase, catalysisDatabase, translator,
namingConvention, classification, reactionProperties):
"""
This method is for reactions of the form A+ B -> A' + B
"""
#if 'EGF_EGFRim2_GAP_Grb2_Sos_Ras_GDP' in original[0] or 'EGF_EGFRim2_GAP_Grb2_Sos_Ras_GDP' in original[1]:
# print original,'EGF_EGFRim2_GAP_Grb2_Sos_Ras_GDP' in translator
result = catalyze(namingConvention[0], namingConvention[1], classification,
rawDatabase, translator, reactionProperties)
k = [min(namingConvention, key=len) in x for x in original[0]]
k2 = [max(namingConvention, key=len) in x for x in original[1]]
k = k and k2
sortedResult = [result[0], result[1]] if any(k) else [result[1], result[0]]
sortedConvention = [
namingConvention[0], namingConvention[1]
] if any(k) else [namingConvention[1], namingConvention[0]]
flag = False
if 'EGF_EGFRm2' in original[1]:
print 'hello'
for reactantGroup, res, conv in zip(original, sortedResult,
sortedConvention):
for reactant in reactantGroup:
flag = False
species = st.Species()
#if original[0][0] in translator:
# species = deepcopy(translator[original[0][0]])
#make a copy of the original element we are going to modify
if reactant in translator:
species = deepcopy(translator[reactant])
elif sortedConvention[0] in translator:
species = deepcopy(translator[sortedConvention[0]])
tmp = dictionary[reactant]
for element in tmp:
molecule = st.Molecule(element)
#here it would be much more precise to have the molecule
#that is going to be modified instead of just modifying the
#first thing you find
if element in conv:
#chunk = result[1] if reactant == max(namingConvention,key=len) else result[0]
component = st.Component(res[0])
component.addState(res[1])
molecule.addComponent(component, 1)
flag = True
finalMolecule = molecule
'''
else:
if conv in reactant:
component = st.Component(res[0])
component.addState(res[1])
molecule.addComponent(component,1)
print conv,molecule,element
flag = True
#continue
'''
#FIXME: the comparison should be done a lil more carefully
#to avoid overlap
species.addMolecule(molecule, True)
if str(species) == '':
species.addMolecule(molecule)
break
if flag:
if reactant not in translator:
translator[reactant] = species
else:
translator[reactant].extend(species, False)
if finalMolecule.name in translator:
if len(translator[finalMolecule.name].molecules) == 1:
sp = st.Species()
sp.addMolecule(deepcopy(finalMolecule))
translator[finalMolecule.name].extend(sp, False)
translator[finalMolecule.name].reset()
else:
sp = st.Species()
sp.addMolecule(molecule)
translator[molecule.name] = deepcopy(sp)
if len(original[0]) < len(original[1]):
rebalance(original, sortedConvention, translator)
def getIntersection(reactants,
product,
dictionary,
rawDatabase,
translator,
synthesisDatabase,
originalProductName,
outputFlag=False):
'''
this method goes through two complexes and tries to check how they
get together to create a product (e.g. how their components link)
either by using previous knowledge or by creating a new complex
'''
#global log
extended1 = (copy(dictionary[reactants[0]]))
extended2 = (copy(dictionary[reactants[1]]))
if isinstance(extended1, str):
extended1 = [extended1]
if isinstance(extended2, str):
extended2 = [extended2]
#if we can find an element in the database that is a subset of
#union(extended1,extended2) we take it
intersection = findIntersection(extended1, extended2, synthesisDatabase)
#otherwise we create it from scratch
if not intersection:
r1 = getFreeRadical(extended1, extended2[0], rawDatabase, translator,
product, dictionary)
r2 = getFreeRadical(extended2, extended1[0], rawDatabase, translator,
product, dictionary)
binding1, binding2 = getBindingPoints(extended1, extended2, reactants,
originalProductName[0])
if not r1 or not r2:
#prin t 'Cannot infer how',extended1,'binds to',extended2
#log['reactions'].append((reactants,product))
#return None,None,None
#TODO this section should be activated by a flag instead
#of being accessed by default
#print extended1,extended2
createIntersection((binding1, binding2), rawDatabase, translator,
dictionary)
r1 = getFreeRadical((binding1, ), binding2, rawDatabase,
translator, product, dictionary)
r2 = getFreeRadical((binding2, ), binding1, rawDatabase,
translator, product, dictionary)
#print 'rrrrrrrrrrr',r1,r2
if not r1 or not r2:
return (None, None, None, None)
##todo: modify code to allow for carry over free radicals
#FIXME: we can remove synthesisDatabase easily
species = st.Species()
if reactants[0] in translator:
species.append(translator[reactants[0]])
if reactants[1] in translator:
species.append(translator[reactants[1]])
if outputFlag:
print '-----------', species, reactants[0], reactants[
1], reactants[1] in translator
print '+++', binding1, binding2, r1, r2
bondName = max(species.getBondNumbers()) + 1
molecule1 = st.Molecule(binding1)
molecule2 = st.Molecule(binding2)
component1 = st.Component(r1)
component2 = st.Component(r2)
component1.addBond(str(bondName))
component2.addBond(str(bondName))
molecule1.addComponent(component1)
molecule2.addComponent(component2)
if outputFlag:
print '////////', molecule1, molecule2
species.addMolecule(molecule1, True, 1)
counter = 2 if binding1 == binding2 else 1
species.addMolecule(molecule2, True, counter)
if outputFlag:
print '\\\\\\', species
####TODO: update the rawDAtabase with the m1m2 information
sp = st.Species()
sp.addMolecule(deepcopy(molecule1))
if molecule1.name in translator:
translator[molecule1.name].extend(sp)
else:
translator[molecule1.name] = sp
translator[molecule1.name].reset()
sp = st.Species()
sp.addMolecule(deepcopy(molecule2))
if molecule2.name in translator:
translator[molecule2.name].extend(sp)
else:
translator[molecule2.name] = sp
translator[molecule2.name].reset()
if outputFlag:
print '||||||||||||||||||||||', translator[molecule2.name]
#print reactants,product,str(species)
#print name1,name2,extended1,extended2
#print {x:str(translator[x]) for x in translator}, translator
if len(species.molecules) == 0:
return (None, None, None, None)
return species, [], [], []
return extended1, extended2, intersection, []
def createBindingRBM(element, translator, dependencyGraph, bioGridFlag):
species = st.Species()
#go over the sct and reuse existing stuff
for molecule in dependencyGraph[element[0]][0]:
if molecule in translator:
tmpSpecies = translator[molecule]
if molecule != getTrueTag(dependencyGraph, molecule):
original = translator[getTrueTag(dependencyGraph, molecule)]
updateSpecies(tmpSpecies, original.molecules[0])
species.addMolecule(deepcopy(tmpSpecies.molecules[0]))
else:
mol = st.Molecule(molecule)
dependencyGraph[molecule] = deepcopy(mol)
species.addMolecule(mol)
#how do things bind together?
moleculePairsList = getComplexationComponents2(species, bioGridFlag)
#TODO: update basic molecules with new components
#translator[molecule[0].name].molecules[0].components.append(deepcopy(newComponent1))
#translator[molecule[1].name].molecules[0].components.append(deepcopy(newComponent2))
for idx, molecule in enumerate(moleculePairsList):
flag = False
#add bonds where binding components already exist
for component in molecule[0].components:
if component.name == molecule[1].name.lower() and \
len(component.bonds) == 0:
component.bonds.append(idx)
flag = True
break
if not flag:
#create components if they dont exist already.
#Add a bond afterwards
newComponent1 = st.Component(molecule[1].name.lower())
molecule[0].components.append(newComponent1)
if newComponent1.name not in [x.name for x in translator[molecule[0].name].molecules[0]. \
components]:
translator[molecule[0].name].molecules[0]. \
components.append(deepcopy(newComponent1))
molecule[0].components[-1].bonds.append(idx)
flag = False
#same thing for the other member of the bond
for component in molecule[1].components:
if component.name == molecule[0].name.lower() and len(
component.bonds) == 0:
component.bonds.append(idx)
flag = True
break
if not flag:
newComponent2 = st.Component(molecule[0].name.lower())
molecule[1].components.append(newComponent2)
if molecule[0].name != molecule[1].name:
if newComponent2.name not in [x.name for x in translator[molecule[0].name].molecules[0]. \
components]:
translator[
molecule[1].name].molecules[0].components.append(
deepcopy(newComponent2))
molecule[1].components[-1].bonds.append(idx)
#update the translator
translator[element[0]] = species
def addComponentToMolecule(species, moleculeName, componentName):
for molecule in species.molecules:
if moleculeName == molecule.name:
if componentName not in [x.name for x in molecule.components]:
component = st.Component(componentName)
molecule.addComponent(component)