def addSmallMolToXml( self, parsedSmallMol, xmlElement ):
smallMolElt = XmlObject("small-mol")
smallMolElt.addAttribute( "name", parsedSmallMol.getName() )
smallMolElt.attachToParent( xmlElement)
return smallMolElt
def writeParsedLineAsXmlMol(self, parsedLine, xmlobject):
parsedComplex = parsedLine.getParsedComponents()[0]
assert (len(parsedComplex.getMols()) == 1)
parsedMol = parsedComplex.getMols()[0]
newMolElement = 0
if parsedMol.isSmallMol():
newMolElement = self.addSmallMolToXml(parsedMol, xmlobject)
else:
newMolElement = self.addModMolToXml(parsedMol, xmlobject)
# Now add the mass element to the thing.
mass = 0.0
if (parsedLine.hasAssignment("mass")):
mass = parsedLine.getAssignment("mass")
elif self.getTranslationLevel == self.STRICT:
raise Exception()
weightElmt = XmlObject("weight")
weightElmt.addAttribute("daltons", mass)
newMolElement.addSubElement(weightElmt)
def writeParsedLineAsXmlMol(self, parsedLine, xmlobject):
parsedComplex = parsedLine.getParsedComponents()[0]
assert( len( parsedComplex.getMols() ) == 1)
parsedMol = parsedComplex.getMols()[0]
newMolElement = 0
if parsedMol.isSmallMol():
newMolElement = self.addSmallMolToXml( parsedMol, xmlobject )
else:
newMolElement = self.addModMolToXml( parsedMol, xmlobject)
# Now add the mass element to the thing.
mass = 0.0
if ( parsedLine.hasAssignment("mass") ):
mass = parsedLine.getAssignment("mass")
elif self.getTranslationLevel == self.STRICT:
raise Exception()
weightElmt = XmlObject("weight")
weightElmt.addAttribute("daltons", mass)
newMolElement.addSubElement( weightElmt )
def writeOmniGenLineToParent(self, line, parElmt):
omniGenElment = XmlObject("omni-gen", parElmt)
reaction = line.getParsedComponents()[0]
enablingOmniplex = reaction.getReactants()[0]
additionalReactant = 0
if len(reaction.getReactants()) > 1:
additionalReactant = reaction.getReactants()[1]
product = reaction.getProducts()[0]
additionalProduct = 0
if len(reaction.getProducts()) > 1:
additionalProduct = reaction.getProducts()[1]
self.__writeEnablingOmniPlexElementToXml(enablingOmniplex,
omniGenElment)
self.__writeModificationExchanges(reaction, omniGenElment)
self.__writeSmallMolExchange(reaction, omniGenElment)
rateElmt = XmlObject("rate", omniGenElment)
rateElmt.addAttribute("value", line.getAssignment("k"))
return
def __writeSmallMolExchange(self, reaction, parElmt):
smallMolExchangesElmt = XmlObject("small-mol-exchanges", parElmt)
reactant_omniplex = reaction.getReactants()[0]
product_omniplex = reaction.getProducts()[0]
assert (len(reactant_omniplex.getMols()) == len(
product_omniplex.getMols()))
for ndx in range(len(reactant_omniplex.getMols())):
if reactant_omniplex.getMols()[ndx].getName(
) != product_omniplex.getMols()[ndx].getName():
assert (reactant_omniplex.getMols()[ndx].isSmallMol())
smallMolExchangeElmt = XmlObject("small-mol-exchage",
smallMolExchangesElmt)
smallMolInstRef = XmlObject("small-mol-instance-ref",
smallMolExchangeElmt)
smallMolRef = XmlObject("small-mol-ref", smallMolExchangeElmt)
smallMolInstRef.addAttribute(
"name",
self.getMolName(reactant_omniplex.getMols()[ndx].getName(),
ndx))
smallMolRef.addAttribute(
"name",
product_omniplex.getMols()[ndx].getName())
return
def writeSpeciesStreamLineToParent( self, line, parentElmt):
omniSpeciesStreamElmt = XmlObject("omni-species-stream", parentElmt)
omniSpeciesStreamElmt.addAttribute("name", line.getAssignment("name"))
self.writeParsedComplexAsPlex( line.getParsedComponents()[0], omniSpeciesStreamElmt)
return
def writeExplicitSpeciesLineToXml( self, parsedLine, parentObject):
parsedComplex = parsedLine.getParsedComponents()[0]
name = parsedLine.getAssignment("name")
plexSpeciesElmt = XmlObject( "plex-species", parentObject)
plexSpeciesElmt.addAttribute( "name", name)
self.writeParsedComplexAsPlex( parsedComplex, plexSpeciesElmt, writeComplexInstanceStates = True)
def writeSpeciesStreamLineToParent(self, line, parentElmt):
omniSpeciesStreamElmt = XmlObject("omni-species-stream", parentElmt)
omniSpeciesStreamElmt.addAttribute("name", line.getAssignment("name"))
self.writeParsedComplexAsPlex(line.getParsedComponents()[0],
omniSpeciesStreamElmt)
return
def writeExplicitSpeciesLineToXml(self, parsedLine, parentObject):
parsedComplex = parsedLine.getParsedComponents()[0]
name = parsedLine.getAssignment("name")
plexSpeciesElmt = XmlObject("plex-species", parentObject)
plexSpeciesElmt.addAttribute("name", name)
self.writeParsedComplexAsPlex(parsedComplex, plexSpeciesElmt)
def writeAllostericSitesElementToElement( self, parsedComplex, parentElement):
allostericSitesElmt = XmlObject("allosteric-sites", parentElement)
for ndx in range(len(parsedComplex.getMols())):
mol = parsedComplex.getMols()[ndx]
if mol.isSmallMol():
continue
# [x for x in mol.getBindingSites() \
# if x.hasBindingSiteSpecification() and \
# x.getBindingSiteSpecification().hasShapeSpecification() and \
# x.getBindingSiteSpecification().getShapeSpecification().isTransformation() ]:
for bndSiteWithTrans in [x for x in mol.getBindingSites() \
if x.hasBindingSiteSpecification() and \
x.getBindingSiteSpecification().hasShapeSpecification() and \
x.getBindingSiteSpecification().getShapeSpecification().isTransformation() ]:
transformation = \
bndSiteWithTrans.getBindingSiteSpecification().getShapeSpecification().getTransformation()
molElmt = XmlObject("mol-instance-ref", allostericSitesElmt)
molElmt.addAttribute("name", self.getMolName( mol.getName(), ndx) )
bindingRefElmt = XmlObject( "binding-site-ref", molElmt)
bindingRefElmt.addAttribute( "name", bndSiteWithTrans.getName() )
siteShapeRefElmt = XmlObject( "site-shape-ref", bindingRefElmt )
siteShapeRefElmt.addAttribute( "name", transformation )
def addModifications(self, parentElmt):
for modification in self.getUniversalModificationList():
modificationTypeElmt = XmlObject("modification")
modificationTypeElmt.addAttribute("name", modification)
modificationTypeElmt.attachToParent(parentElmt)
weightElmt = XmlObject("weight-delta")
weightElmt.attachToParent(modificationTypeElmt)
if self.representsNullModification(modification):
weightDelta = 0.0
else:
weightDelta = 1.0
weightElmt.addAttribute("daltons", weightDelta)
def __writeModMolInstanceToInstanceStates(self, parsedMol, molNdx, parentElmt):
modMolInstanceRefElmt = XmlObject("mod-mol-instance-ref", parentElmt)
modMolInstanceRefElmt.addAttribute("name", self.getMolName( parsedMol.getName(), molNdx))
modMapElmt = XmlObject("mod-map", modMolInstanceRefElmt)
for modSite in parsedMol.getModificationSites():
modSiteRefElmt = XmlObject("mod-site-ref", modMapElmt)
modSiteRefElmt.addAttribute("name", modSite.getName())
modRefElmt = XmlObject("mod-ref", modSiteRefElmt)
modRefElmt.addAttribute("name", modSite.getModificationSiteSpecification().getList()[0])
def __addSpeciesStreams(self, parentObject):
speciesStreamsElement = XmlObject("species-streams", parentObject)
if self.speciesStreamSection:
self.speciesStreamSection.writeSpeciesStreamSection(
speciesStreamsElement)
def __addReactionGens(self, parentObject):
reactionGenElmt = XmlObject("reaction-gens", parentObject)
if self.reactionGensSection:
self.reactionGensSection.writeReactionGensSection(reactionGenElmt)
return
def __addMols(self, parentObject):
molsSection = XmlObject("mols", parentObject)
if self.molsSection:
self.molsSection.writeMolsSection(molsSection)
return
def writeModificationToXml(self, modLine, modsElmt):
modElmt = XmlObject("modification", modsElmt)
modElmt.addAttribute("name", modLine.getAssignment("name"))
weightDeltaElmt = XmlObject("weight-delta", modElmt)
weightDeltaElmt.addAttribute("daltons", modLine.getAssignment("mass"))
return
def __addAllostericOmnis(self, parentObject):
allostericOmnis = XmlObject("allosteric-omnis", parentObject)
if self.allostericOmnisSection:
self.allostericOmnisSection.writeAllostericOmnisSection(
allostericOmnis)
return
def __addAllostericPlexes(self, parentObject):
allostericPlexes = XmlObject("allosteric-plexes", parentObject)
if self.allostericPlexesSection:
self.allostericPlexesSection.writeAllostericPlexesSection(
allostericPlexes)
return
def __addModifications(self, parentObject):
# Write me!!!
modificationsSection = XmlObject("modifications", parentObject)
if self.modificationsSection:
self.modificationsSection.writeModificationsSections(
modificationsSection)
return
def __addExplicitSpecies(self, parentObject):
explicitSpeciesElmt = XmlObject("explicit-species", parentObject)
if self.explicitSpeciesSection:
self.explicitSpeciesSection.writeExplicitSpeciesSection(
explicitSpeciesElmt)
return
def writeAllostericPlexLineToXml(self, lineToWrite, xmlobject):
alloPlexElmt = XmlObject("allosteric-plex", xmlobject)
self.writeParsedComplexAsPlex(lineToWrite.getParsedComponents()[0],
alloPlexElmt)
self.writeAllostericSitesElementToElement(
lineToWrite.getParsedComponents()[0], alloPlexElmt)
return
def __writeEnablingOmniPlexElementToXml(self, omniplex, omniGenElment):
enablingOmniplex = XmlObject("enabling-omniplex", omniGenElment)
self.writeParsedComplexAsPlex(omniplex, enablingOmniplex)
# We shouldn't always parse this, is this ok?
self.__writeInstanceStateToXml(omniplex, enablingOmniplex)
return enablingOmniplex
def __constructXMLRepresentation(self):
rootNode = XmlObject("moleculizer-input")
modelElmt = XmlObject("model")
modelElmt.attachToParent(rootNode)
streamsElmt = XmlObject("streams", rootNode)
self.__addModifications( modelElmt )
self.__addMols( modelElmt )
self.__addAllostericPlexes( modelElmt )
self.__addAllostericOmnis( modelElmt )
self.__addReactionGens( modelElmt )
self.__addExplicitSpecies( modelElmt )
self.__addExplicitReactions( modelElmt )
self.__addSpeciesStreams( streamsElmt )
return rootNode
def addSmallMolToXml(self, parsedSmallMol, xmlElement):
smallMolElt = XmlObject("small-mol")
smallMolElt.addAttribute("name", parsedSmallMol.getName())
smallMolElt.attachToParent(xmlElement)
return smallMolElt
def writeOmniGenLineToParent(self, line, parElmt):
omniGenElment = XmlObject("omni-gen", parElmt)
reaction = line.getParsedComponents()[0]
enablingOmniplex = reaction.getReactants()[0]
additionalReactant = 0
if len(reaction.getReactants()) > 1:
additionalReactant = reaction.getReactants()[1]
product = reaction.getProducts()[0]
additionalProduct = 0
if len(reaction.getProducts()) > 1:
additionalProduct = reaction.getProducts()[1]
self.__writeEnablingOmniPlexElementToXml(enablingOmniplex, omniGenElment)
self.__writeModificationExchanges( reaction, omniGenElment)
self.__writeSmallMolExchange( reaction, omniGenElment)
rateElmt = XmlObject("rate", omniGenElment)
rateElmt.addAttribute("value", line.getAssignment("k"))
return
def writeParsedComplexInstanceStates(self, complex, xmlobject):
# This is quite inelegant, but I can't obviously think of a
# better way to do it.
for mol_ndx, parsed_mol in enumerate(complex.getMols()):
if not parsed_mol.isModMol():
continue
if not parsed_mol.getModificationSiteList():
continue
break
else:
# If we get
return
instanceStatesElmt = XmlObject("instance-states", xmlobject)
# For each mol in complex which is a mod map that has modifications specified
for mol_ndx, parsed_mol in enumerate(complex.getMols()):
if not parsed_mol.isModMol():
continue
if not parsed_mol.getModificationSiteList():
continue
modMolInstanceRef = XmlObject("mod-mol-instance-ref", instanceStatesElmt)
modMolInstanceRef.addAttribute( "name", self.getMolName( parsed_mol.getName(), mol_ndx ))
modMapElmt = XmlObject("mod-map", modMolInstanceRef)
for modification in parsed_mol.getModificationSites():
modSiteRefNameElmt = XmlObject("mod-site-ref", modMapElmt)
modSiteRefNameElmt.addAttribute("name", modification.getName())
modRefElmt = XmlObject("mod-ref", modSiteRefNameElmt)
modState = modification.getModificationSiteSpecification().getList()[0]
modRefElmt.addAttribute("name", modState)
return
def __constructXMLRepresentation(self):
rootNode = XmlObject("moleculizer-input")
modelElmt = XmlObject("model")
modelElmt.attachToParent(rootNode)
self.__addModifications(modelElmt)
self.__addMols(modelElmt)
self.__addAllostericPlexes(modelElmt)
self.__addAllostericOmnis(modelElmt)
self.__addReactionGens(modelElmt)
self.__addExplicitSpecies(modelElmt)
self.__addExplicitReactions(modelElmt)
self.__addVolume(modelElmt)
# This adds the streams and events elements.
if self.streamsAndEventsFile:
rootNode.addSubFile(self.streamsAndEventsFile)
return rootNode
def __writeModificationExchanges( self, reaction, parElmt):
modExchanges = XmlObject("modification-exchanges", parElmt)
omniplex = reaction.getProducts()[0]
for ndx in range(len(omniplex.getMols())):
mol = omniplex.getMols()[ndx]
if mol.isSmallMol():
continue
for mod_site in mol.getModificationSites():
modExchange = XmlObject("modification-exchange", modExchanges)
modMolInstance = XmlObject("mod-mol-instance-ref", modExchange)
modMolInstance.addAttribute("name", self.getMolName( mol.getName(), ndx))
modSiteRefElmt = XmlObject("mod-site-ref", modMolInstance)
modSiteRefElmt.addAttribute("name", mod_site.getName())
installedModRefElmt = XmlObject("installed-mod-ref", modExchange)
installedModRefElmt.addAttribute("name", mod_site.getModificationSiteSpecification().getList()[0])
return
def __writeInstanceStateToXml(self, omniplex, enablingOmniplexElmt):
written_instance_states = False
instStatesElmt = 0
for ndx in range(len(omniplex.getMols())):
mol = omniplex.getMols()[ndx]
if mol.isSmallMol():
continue
for modSite in mol.getModificationSites():
if modSite.hasModificationSiteSpecification(
) and modSite.getModificationSiteSpecification().isList():
if not written_instance_states:
instStatesElmt = XmlObject("instance-states",
enablingOmniplexElmt)
written_instance_states = True
self.__writeModMolInstanceToInstanceStates(
mol, ndx, instStatesElmt)
def writeUnboundStates(self, complex, patternMatchingSitesSpec, xmlobject):
unboundPatterns = [x for x in patternMatchingSitesSpec if x[2] == "-"]
unboundSectionElmt = XmlObject("unbound-sites", xmlobject)
for pattern in unboundPatterns:
mol_ndx, site_ndx = pattern[0], pattern[1]
instanceRef = XmlObject("instance-ref", unboundSectionElmt)
instanceRef.addAttribute("name", \
self.getMolName(complex.getMols()[mol_ndx].getName(), \
mol_ndx))
siteRef = XmlObject("site-ref", instanceRef)
siteRef.addAttribute("name", pattern[1])
return
def __constructXMLRepresentation(self):
rootNode = XmlObject("moleculizer-input")
modelElmt = XmlObject("model")
modelElmt.attachToParent(rootNode)
self.__addModifications( modelElmt )
self.__addMols( modelElmt )
self.__addAllostericPlexes( modelElmt )
self.__addAllostericOmnis( modelElmt )
self.__addReactionGens( modelElmt )
self.__addExplicitSpecies( modelElmt )
self.__addExplicitReactions( modelElmt )
self.__addVolume( modelElmt )
# This adds the streams and events elements.
if self.streamsAndEventsFile:
rootNode.addSubFile(self.streamsAndEventsFile)
return rootNode
def __writeSmallMolExchange(self, reaction, parElmt):
smallMolExchangesElmt = XmlObject("small-mol-exchanges", parElmt)
reactant_omniplex = reaction.getReactants()[0]
product_omniplex = reaction.getProducts()[0]
assert(len(reactant_omniplex.getMols()) == len(product_omniplex.getMols()))
for ndx in range(len(reactant_omniplex.getMols())):
if reactant_omniplex.getMols()[ndx].getName() != product_omniplex.getMols()[ndx].getName():
assert( reactant_omniplex.getMols()[ndx].isSmallMol() )
smallMolExchangeElmt = XmlObject("small-mol-exchage", smallMolExchangesElmt)
smallMolInstRef = XmlObject("small-mol-instance-ref", smallMolExchangeElmt)
smallMolRef = XmlObject("small-mol-ref", smallMolExchangeElmt)
smallMolInstRef.addAttribute("name", self.getMolName(reactant_omniplex.getMols()[ndx].getName(), ndx))
smallMolRef.addAttribute("name", product_omniplex.getMols()[ndx].getName() )
return
def __constructXMLRepresentation(self):
rootNode = XmlObject("moleculizer-input")
modelElmt = XmlObject("model")
modelElmt.attachToParent(rootNode)
streamsElmt = XmlObject("streams", rootNode)
self.__addModifications(modelElmt)
self.__addMols(modelElmt)
self.__addAllostericPlexes(modelElmt)
self.__addAllostericOmnis(modelElmt)
self.__addReactionGens(modelElmt)
self.__addExplicitSpecies(modelElmt)
self.__addExplicitReactions(modelElmt)
self.__addSpeciesStreams(streamsElmt)
return rootNode
def __writeModificationExchanges(self, reaction, parElmt):
modExchanges = XmlObject("modification-exchanges", parElmt)
omniplex = reaction.getProducts()[0]
for ndx in range(len(omniplex.getMols())):
mol = omniplex.getMols()[ndx]
if mol.isSmallMol():
continue
for mod_site in mol.getModificationSites():
modExchange = XmlObject("modification-exchange", modExchanges)
modMolInstance = XmlObject("mod-mol-instance-ref", modExchange)
modMolInstance.addAttribute(
"name", self.getMolName(mol.getName(), ndx))
modSiteRefElmt = XmlObject("mod-site-ref", modMolInstance)
modSiteRefElmt.addAttribute("name", mod_site.getName())
installedModRefElmt = XmlObject("installed-mod-ref",
modExchange)
installedModRefElmt.addAttribute(
"name",
mod_site.getModificationSiteSpecification().getList()[0])
return
def addAllostericOmnis(self, allostericOmnisElement):
# pdb.set_trace()
for bindingWithAllostery in self.allosteryMapping.keys():
owningMolName, allostericBindingSiteName = bindingWithAllostery
complexAllosteryPairs = [
(key, self.allosteryMapping[bindingWithAllostery][key])
for key in self.allosteryMapping[bindingWithAllostery].keys()
]
for complex_allostery_pair in complexAllosteryPairs:
complex, allostericName = complex_allostery_pair
if allostericName == "default":
continue
allostericOmniElmt = XmlObject("allosteric-omni")
allostericOmnisElement.addSubElement(allostericOmniElmt)
# Now prepare the four sub-elements
plexElmt = XmlObject("plex")
instanceStatesElmt = XmlObject("instance-states")
unboundSitesElmt = XmlObject("unbound-sites")
boundSitesElmt = XmlObject("bound-sites")
allostericStatesElmt = XmlObject("allosteric-sites")
# First we construct the molRefToInstanceDict
molRefToInstanceDict = {}
tmpMolInstanceInt = {}
molArray = complex.split(".")
for molNdx in xrange(len(molArray)):
mol = molArray[molNdx]
parenNdx = mol.find("(")
molType = mol[:parenNdx]
if molType not in tmpMolInstanceInt:
tmpMolInstanceInt[molType] = 1
molInstance = "the-" + molType
else:
molInstance = molType + "-" + str(tmpMolInstanceInt[molType])
tmpMolInstanceInt[molType] = tmpMolInstanceInt[molType] + 1
molRefToInstanceDict[molInstance] = molType
molArray[molNdx] = molInstance + mol[parenNdx:]
# So now we calculate -- the plex.
bindingDict = {}
genericBoundSitesArray = []
unboundSitesArray = []
modificationSitesArray = []
for molSpec in molArray:
# Process the molNames
molInstance = util.getMolNameFromFullMolSpec(molSpec)
molInstanceElmt = XmlObject("mol-instance")
molInstanceElmt.addAttribute("name", molInstance)
molRefElmt = XmlObject("mol-ref")
molRefElmt.addAttribute("name", molRefToInstanceDict[molInstance])
molRefElmt.attachToParent(molInstanceElmt).attachToParent(plexElmt)
# Collect the bindings
bindingSites = util.getBindingSites(molSpec)
explicitlyBoundBindingSites = [
x.split("!") for x in bindingSites if ("!" in x and x[-1] != "!" and x[-1] != "+")
]
boundBindingSites = [
x.split("!") for x in bindingSites if ("!" in x and x[-1] != "!" and x[-1] == "+")
]
unboundBindingSites = [x for x in bindingSites if "!" not in x]
modificationSites = [x.split("~") for x in util.getModificationList(molSpec)]
for halfBinding in explicitlyBoundBindingSites:
bindingSite, bindingNdx = halfBinding[0], int(halfBinding[1])
if not bindingNdx in bindingDict:
bindingDict[bindingNdx] = []
bindingDict[bindingNdx].append((molInstance, bindingSite))
# Collect the unbound binding sites.
for unboundBindingSite in unboundBindingSites:
unboundSitesArray.append((molInstance, unboundBindingSite))
for boundSite in boundBindingSites:
genericBoundSitesArray.append((molInstance, boundSite[0]))
for modificationSite in modificationSites:
modificationSitesArray.append((molInstance, modificationSite[0], modificationSite[1]))
# Do the bindings
listOfBindings = [bindingDict[key] for key in bindingDict.keys()]
for binding in listOfBindings:
try:
assert len(binding) == 2
except:
pdb.set_trace()
a = 1
for binding in listOfBindings:
bindingElmt = XmlObject("binding")
bindingElmt.attachToParent(plexElmt)
for halfBinding in binding:
molInstance, bindingRef = halfBinding
molInstanceRefElmt = XmlObject("mol-instance-ref")
molInstanceRefElmt.addAttribute("name", molInstance)
bindingSiteRefElmt = XmlObject("binding-site-ref")
bindingSiteRefElmt.addAttribute("name", bindingRef)
bindingSiteRefElmt.attachToParent(molInstanceRefElmt).attachToParent(bindingElmt)
# Now we add in the modificationSitesArray
for modMolName in set([x[0] for x in modificationSitesArray]):
modMolModifications = [x for x in modificationSitesArray if x[0] == modMolName]
modMolInstanceRefElmt = XmlObject("mod-mol-instance-ref")
modMolInstanceRefElmt.attachToParent(instanceStatesElmt)
modMolInstanceRefElmt.addAttribute("name", modMolName)
modMapElmt = XmlObject("mod-map")
modMapElmt.attachToParent(modMolInstanceRefElmt)
for modification in modMolModifications:
modSiteRefElmt = XmlObject("mod-site-ref")
modSiteRefElmt.addAttribute("name", modification[1])
modRefElmt = XmlObject("mod-ref")
modRefElmt.addAttribute("name", modification[2])
modRefElmt.attachToParent(modSiteRefElmt).attachToParent(modMapElmt)
# Now we add in the unboundSitesArray
for molWithUnboundBindings in set([x[0] for x in unboundSitesArray]):
unboundSites = [x for x in unboundSitesArray if x[0] == molWithUnboundBindings]
for site in unboundSites:
instanceRefElmt = XmlObject("instance-ref")
instanceRefElmt.addAttribute("name", molWithUnboundBindings)
siteRefElmt = XmlObject("site-ref")
siteRefElmt.addAttribute("name", site[1])
siteRefElmt.attachToParent(instanceRefElmt).attachToParent(unboundSitesElmt)
# Now we add in the boundSitesArray
for molWithGenericBoundBindings in set([x[0] for x in genericBoundSitesArray]):
genericBoundSites = [x for x in genericBoundSitesArray if x[0] == molWithGenericBoundBindings]
for site in genericBoundSites:
instanceRefElmt = XmlObject("instance-ref")
instanceRefElmt.addAttribute("name", molWithGenericBoundBindings)
siteRefElmt = XmlObject("site-ref")
siteRefElmt.addAttribute("name", site[1])
siteRefElmt.attachToParent(instanceRefElmt).attachToParent(boundSitesElmt)
molInstanceRefElmt = XmlObject("mol-instance-ref")
molInstanceRefElmt.addAttribute("name", "the-" + owningMolName)
bindingSiteRefElmt = XmlObject("binding-site-ref")
bindingSiteRefElmt.addAttribute("name", allostericBindingSiteName)
siteShapeRefElmt = XmlObject("site-shape-ref")
siteShapeRefElmt.addAttribute("name", allostericName)
siteShapeRefElmt.attachToParent(bindingSiteRefElmt).attachToParent(molInstanceRefElmt).attachToParent(
allostericStatesElmt
)
## End of function
plexElmt.attachToParent(allostericOmniElmt)
if instanceStatesElmt.getNumberOfChildren() > 0:
instanceStatesElmt.attachToParent(allostericOmniElmt)
if unboundSitesElmt.getNumberOfChildren() > 0:
unboundSitesElmt.attachToParent(allostericOmniElmt)
if boundSitesElmt.getNumberOfChildren():
boundSitesElmt.attachToParent(allostericOmniElmt)
allostericStatesElmt.attachToParent(allostericOmniElmt)
def __addAllostericPlexes(self, parentObject):
allostericPlexesElmt = XmlObject("allosteric-plexes")
allostericPlexesElmt.attachToParent(parentObject)
def addBindingSiteElmtToModMolElmt(self, bindingName, moleculizerMol, xmlObject):
newBindingElmt = XmlObject("binding-site")
newBindingElmt.addAttribute("name", bindingName)
defaultShape = XmlObject("default-shape-ref")
defaultShape.addAttribute("name", "default")
defaultShape.attachToParent(newBindingElmt)
for shapeName in moleculizerMol.bindingSites[bindingName]:
siteShapeElmt = XmlObject("site-shape")
siteShapeElmt.addAttribute("name", shapeName)
siteShapeElmt.attachToParent(newBindingElmt)
xmlObject.addSubElement(newBindingElmt)
return
def writeExplicitSpecies(self, parentElmt):
for ss in self.seedSpeciesInModel:
plexSpeciesElmt = XmlObject("plex-species")
plexSpeciesElmt.attachToParent(parentElmt)
speciesDefinition, number = ss
# Inputs to the species numbers are given in micromolar...
# The inputs we have been given are in the form: Dig1_tot_conc=Dig1_num*1e6/(Cell_volume*Avogadros_number)
# So to get num we multiply by (Cell_v * Avog) / 1e6.
number = number * (6.0221415e23 * 40e-15) / 1e6
plexSpeciesElmt.addAttribute("name", speciesDefinition.constructEntireComplexInstanceName())
plexElmt = XmlObject("plex")
plexElmt.attachToParent(plexSpeciesElmt)
populationElmt = XmlObject("population")
populationElmt.attachToParent(plexSpeciesElmt)
populationElmt.addAttribute("count", int(number))
# Make this a method of class bndSpeciesDefinition.
for molNdx in speciesDefinition.moleculeRefsInComplex:
molReferenceName = speciesDefinition.moleculeRefsInComplex[molNdx]
molInstanceName = speciesDefinition.moleculeInstancesInComplex[molNdx]
molInstanceElmt = XmlObject("mol-instance")
molInstanceElmt.addAttribute("name", molInstanceName)
molReferenceElmt = XmlObject("mol-ref")
molReferenceElmt.addAttribute("name", molReferenceName)
molReferenceElmt.attachToParent(molInstanceElmt).attachToParent(plexElmt)
for bindingNdx in speciesDefinition.bindings:
bindingElmt = XmlObject("binding")
bindingElmt.attachToParent(plexElmt)
for hb in speciesDefinition.bindings[bindingNdx]:
molInstanceRefElmt = XmlObject("mol-instance-ref")
molInstanceRefElmt.addAttribute("name", speciesDefinition.moleculeInstancesInComplex[hb[0]])
bindingSiteRefElmt = XmlObject("binding-site-ref")
bindingSiteRefElmt.addAttribute("name", hb[1])
bindingSiteRefElmt.attachToParent(molInstanceRefElmt).attachToParent(bindingElmt)
def __addVolume(self, parentObject):
## So far, there is a parameter "Cell_volume" that does this.
volumeElement = XmlObject("volume")
volumeElement.addAttribute("liters", self.parameterEE.getVariableValue("Cell_volume"))
parentObject.addSubElement(volumeElement)
def addModifications(self, parentElmt):
for modification in self.getUniversalModificationList():
modificationTypeElmt = XmlObject("modification")
modificationTypeElmt.addAttribute("name", modification)
modificationTypeElmt.attachToParent(parentElmt)
weightElmt = XmlObject("weight-delta")
weightElmt.attachToParent(modificationTypeElmt)
if self.representsNullModification(modification):
weightDelta = 0.0
else:
weightDelta = 1.0
weightElmt.addAttribute("daltons", weightDelta)
def __addReactionGens(self, parentObject):
rxnGenElmt = XmlObject("reaction-gens")
rxnGenElmt.attachToParent(parentObject)
self.reactionRules.writeReactionGensElement(rxnGenElmt)
def __addAllostericOmnis(self, parentObject):
allostericOmnisElmt = XmlObject("allosteric-omnis")
allostericOmnisElmt.attachToParent(parentObject)
self.reactionRules.addAllostericOmnis(allostericOmnisElmt)
def writeAllostericSitesElementToElement(self, parsedComplex,
parentElement):
allostericSitesElmt = XmlObject("allosteric-sites", parentElement)
for ndx in range(len(parsedComplex.getMols())):
mol = parsedComplex.getMols()[ndx]
if mol.isSmallMol():
continue
# [x for x in mol.getBindingSites() \
# if x.hasBindingSiteSpecification() and \
# x.getBindingSiteSpecification().hasShapeSpecification() and \
# x.getBindingSiteSpecification().getShapeSpecification().isTransformation() ]:
for bndSiteWithTrans in [x for x in mol.getBindingSites() \
if x.hasBindingSiteSpecification() and \
x.getBindingSiteSpecification().hasShapeSpecification() and \
x.getBindingSiteSpecification().getShapeSpecification().isTransformation() ]:
try:
transformation = bndSiteWithTrans.getBindingSiteSpecification(
).getShapeSpecification().getTransformation()
except:
pdb.set_trace()
a = 10
raise e
molElmt = XmlObject("mol-instance-ref", allostericSitesElmt)
molElmt.addAttribute("name",
self.getMolName(mol.getName(), ndx))
bindingRefElmt = XmlObject("binding-site-ref", molElmt)
bindingRefElmt.addAttribute("name", bndSiteWithTrans.getName())
siteShapeRefElmt = XmlObject("site-shape-ref", bindingRefElmt)
siteShapeRefElmt.addAttribute("name", transformation)
def writeParsedComplexAsPlex( self, complex, xmlobject):
plexElmt = XmlObject( "plex", xmlobject)
for ndx in range(len(complex.getMols())):
parsedMol = complex.getMols()[ndx]
molInst = XmlObject("mol-instance", plexElmt)
molInst.addAttribute( "name", self.getMolName( parsedMol.getName(), ndx ))
molTypeElmt = XmlObject("mol-ref", molInst)
molTypeElmt.addAttribute( "name", parsedMol.getName() )
for bindingID in complex.getBindings().keys():
# Find the two bindings with that
newBindingElmt = XmlObject("binding", plexElmt)
try:
molNdx1, molNdx2 = complex.getBindings()[bindingID]
except ValueError:
pdb.set_trace()
raise Exception("Error unpacking bindings '%s' associated with complex '%s' -- Binding ID only has one value." % (repr(complex.getBindings()[bindingID]), complex.getOriginalLine(), bindingID))
parsedMol1 = complex.getMols()[molNdx1]
parsedMol2 = complex.getMols()[molNdx2]
bindingSite1 = ""
bindingSite2 = ""
if parsedMol1.isModMol():
for bindingSite in parsedMol1.getBindingSiteList():
parsedBindingSite = parsedMol1.getBindingSiteWithName( bindingSite )
if parsedBindingSite.hasBindingToken(bindingID):
bindingSite1 = parsedBindingSite.getName()
break
else:
print "Error, binding site 1 not found"
raise Exception()
else:
bindingSite1 = parsedMol1.getName()
if parsedMol2.isModMol():
for bindingSite in parsedMol2.getBindingSiteList():
bindingSite = parsedMol2.getBindingSiteWithName( bindingSite )
if bindingSite.hasBindingToken( bindingID ):
bindingSite2 = bindingSite.getName()
break
else:
print "Error, binding site 2 not found"
raise Exception()
else:
bindingSite2 = parsedMol2.getName()
molInstance1 = XmlObject("mol-instance-ref", newBindingElmt)
molInstance1.addAttribute( "name", self.getMolName(parsedMol1.getName(), molNdx1))
bindingSiteRef1 = XmlObject("binding-site-ref", molInstance1)
bindingSiteRef1.addAttribute("name", bindingSite1)
molInstance2 = XmlObject("mol-instance-ref", newBindingElmt)
molInstance2.addAttribute( "name", self.getMolName(parsedMol2.getName(), molNdx2))
bindingSiteRef2 = XmlObject("binding-site-ref", molInstance2)
bindingSiteRef2.addAttribute("name", bindingSite2)
return plexElmt
def writeDimerGenLineToParent(self, line, reactionGens):
dimerGen = XmlObject("dimerization-gen", reactionGens)
parsedRxn = line.getParsedComponents()[0]
theReactants = parsedRxn.getReactants()
theProducts = parsedRxn.getProducts()
reactant1 = theReactants[0].getMols()[0]
reactant2 = theReactants[1].getMols()[0]
molSpec1 = XmlObject("mol-ref", dimerGen)
molSpec2 = XmlObject("mol-ref", dimerGen)
molSpec1.addAttribute("name", reactant1.getName())
molSpec2.addAttribute("name", reactant2.getName())
siteRef1 = XmlObject("site-ref", molSpec1)
siteRef2 = XmlObject("site-ref", molSpec2)
self.__addSiteNameToElement(reactant1, siteRef1)
self.__addSiteNameToElement(reactant2, siteRef2)
defaultOnElmt = XmlObject("default-on-rate", dimerGen)
defaultOffElmt = XmlObject("default-off-rate", dimerGen)
defaultOnElmt.addAttribute("value", line.getAssignment("kon"))
defaultOffElmt.addAttribute("value", line.getAssignment("koff"))
if len(line.getParsedComponents()) == 3:
return
# Now add the allosteric on- and off- rates.
allosteryComponents = line.getParsedComponents()[3:]
allostery_index = 3
while (len(allosteryComponents) > 0):
# This is used in a hacky way to find the correct parameter
alloRatesElmt = XmlObject("allo-rates", dimerGen)
alloReactants = allosteryComponents[0].getReactants()
siteShapeRef1 = XmlObject("site-shape-ref", alloRatesElmt)
siteShapeRef2 = XmlObject("site-shape-ref", alloRatesElmt)
onRate = XmlObject("on-rate", alloRatesElmt)
offRate = XmlObject("off-rate", alloRatesElmt)
if alloReactants[0].getMols()[0].isModMol():
if alloReactants[0].getMols()[0].getBindingSites(
)[0].hasBindingSiteSpecification():
siteShapeRef1.addAttribute(
"name", alloReactants[0].getMols()
[0].getBindingSites()[0].getBindingSiteSpecification(
).getShapeSpecification().getShapeList()[0])
else:
siteShapeRef1.addAttribute("name", "default")
else:
siteShapeRef1.addAttribute("name", "default")
if alloReactants[1].getMols()[0].isModMol():
if alloReactants[1].getMols()[0].getBindingSites(
)[0].hasBindingSiteSpecification():
siteShapeRef2.addAttribute(
"name", alloReactants[1].getMols()
[0].getBindingSites()[0].getBindingSiteSpecification(
).getShapeSpecification().getShapeList()[0])
else:
siteShapeRef2.addAttribute("name", "default")
else:
siteShapeRef2.addAttribute("name", "default")
onRate.addAttribute("value",
line.getAssignment("kon", allostery_index))
offRate.addAttribute("value",
line.getAssignment("koff", allostery_index))
allosteryComponents = allosteryComponents[3:]
allostery_index += 3
return
def __addExplicitSpecies(self, parentObject):
explicitSpeciesElmt = XmlObject("explicit-species")
explicitSpeciesElmt.attachToParent(parentObject)
self.seedSpecies.writeExplicitSpecies(explicitSpeciesElmt)
def writeParsedComplexAsPlex( self, complex, xmlobject, writeComplexInstanceStates = False, writeBoundUnboundStates = False):
#
if writeBoundUnboundStates:
# This should be a list of things like (2, 1, +) = the
# first binding on the second mol must be bound.
patternMatchingSitesSpec = complex.externalizePatternMatchingSites()
plexElmt = XmlObject( "plex", xmlobject)
for ndx in range(len(complex.getMols())):
parsedMol = complex.getMols()[ndx]
molInst = XmlObject("mol-instance", plexElmt)
molInst.addAttribute( "name", self.getMolName( parsedMol.getName(), ndx ))
molTypeElmt = XmlObject("mol-ref", molInst)
molTypeElmt.addAttribute( "name", parsedMol.getName() )
for bindingID in complex.getBindings().keys():
# Find the two bindings with that
newBindingElmt = XmlObject("binding", plexElmt)
try:
molNdx1, molNdx2 = complex.getBindings()[bindingID]
except ValueError:
raise Exception("Error unpacking bindings '%s' associated with complex '%s' -- Binding ID only has one value." % (repr(complex.getBindings()[bindingID]), complex.getOriginalLine(), bindingID))
parsedMol1 = complex.getMols()[molNdx1]
parsedMol2 = complex.getMols()[molNdx2]
bindingSite1 = ""
bindingSite2 = ""
if parsedMol1.isModMol():
for bindingSite in parsedMol1.getBindingSiteList():
parsedBindingSite = parsedMol1.getBindingSiteWithName( bindingSite )
if parsedBindingSite.hasBindingToken(bindingID):
bindingSite1 = parsedBindingSite.getName()
break
else:
print "Error, binding site 1 not found"
raise Exception()
else:
bindingSite1 = parsedMol1.getName()
if parsedMol2.isModMol():
for bindingSite in parsedMol2.getBindingSiteList():
bindingSite = parsedMol2.getBindingSiteWithName( bindingSite )
if bindingSite.hasBindingToken( bindingID ):
bindingSite2 = bindingSite.getName()
break
else:
print "Error, binding site 2 not found"
raise Exception()
else:
bindingSite2 = parsedMol2.getName()
molInstance1 = XmlObject("mol-instance-ref", newBindingElmt)
molInstance1.addAttribute( "name", self.getMolName(parsedMol1.getName(), molNdx1))
bindingSiteRef1 = XmlObject("binding-site-ref", molInstance1)
bindingSiteRef1.addAttribute("name", bindingSite1)
molInstance2 = XmlObject("mol-instance-ref", newBindingElmt)
molInstance2.addAttribute( "name", self.getMolName(parsedMol2.getName(), molNdx2))
bindingSiteRef2 = XmlObject("binding-site-ref", molInstance2)
bindingSiteRef2.addAttribute("name", bindingSite2)
#pdb.set_trace()
if writeComplexInstanceStates:
self.writeParsedComplexInstanceStates(complex, xmlobject)
if writeBoundUnboundStates:
self.writeBoundUnboundStates(complex, patternMatchingSitesSpec, xmlobject)
return plexElmt
def __addMols(self, parentObject):
molsElmt = XmlObject("mols")
molsElmt.attachToParent(parentObject)
self.moleculeDictionary.addMols(molsElmt)
def addModMolToXml( self, parsedMol, xmlObject):
modMolElmt = XmlObject( "mod-mol")
modMolElmt.attachToParent(xmlObject)
modMolElmt.addAttribute( "name", parsedMol.getName() )
for bindingSiteName in parsedMol.getBindingSiteList():
bindingSiteElmt = XmlObject("binding-site")
bindingSiteElmt.attachToParent( modMolElmt)
bindingSiteElmt.addAttribute("name", bindingSiteName)
parsedBindingSite = parsedMol.getBindingSiteWithName( bindingSiteName )
if( parsedBindingSite.hasBindingSiteSpecification() and parsedBindingSite.getBindingSiteSpecification().hasShapeSpecification()):
bindingShapeNames = parsedBindingSite.getBindingSiteSpecification().getShapeSpecification().getShapeList()
assert( len(bindingShapeNames) > 0 )
defaultShapeElmt = XmlObject("default-shape-ref")
defaultShapeElmt.addAttribute("name", bindingShapeNames[0] )
defaultShapeElmt.attachToParent( bindingSiteElmt )
for shape_name in bindingShapeNames:
newShapeElmt = XmlObject("site-shape")
newShapeElmt.addAttribute("name", shape_name)
newShapeElmt.attachToParent( bindingSiteElmt )
else:
defaultShapeElmt = XmlObject( "default-shape-ref" )
defaultShapeElmt.addAttribute( "name", "default")
defaultShapeElmt.attachToParent( bindingSiteElmt )
shapeElmt = XmlObject("site-shape")
shapeElmt.addAttribute("name", "default")
shapeElmt.attachToParent( bindingSiteElmt )
for modSiteName in parsedMol.getModificationSiteList():
modSiteElmt = XmlObject("mod-site", modMolElmt)
modSiteElmt.addAttribute("name", modSiteName)
parsedModificationSite = parsedMol.getModificationSiteWithName( modSiteName )
if not parsedModificationSite.hasModificationSiteSpecification():
defaultModElmt = XmlObject("default-mod-ref", modSiteElmt)
defaultModElmt.addAttribute("name", "none")
else:
modValueArray = parsedModificationSite.getModificationSiteSpecification().getList()
try:
assert( len(modValueArray) > 1)
except:
print "Error, in sectionmols::addModMolToXml for mol with line '%s'. Mod Value Array '%s' should have more than one component..." % ( parsedMol.getOriginalLine(), str(modValueArray) )
defaultModification = modValueArray[0]
defaultModElmt = XmlObject("default-mod-ref", modSiteElmt)
defaultModElmt.addAttribute("name", defaultModification )
return modMolElmt
def addModMolToXml(self, parsedMol, xmlObject):
modMolElmt = XmlObject("mod-mol")
modMolElmt.attachToParent(xmlObject)
modMolElmt.addAttribute("name", parsedMol.getName())
for bindingSiteName in parsedMol.getBindingSiteList():
bindingSiteElmt = XmlObject("binding-site")
bindingSiteElmt.attachToParent(modMolElmt)
bindingSiteElmt.addAttribute("name", bindingSiteName)
parsedBindingSite = parsedMol.getBindingSiteWithName(
bindingSiteName)
if (parsedBindingSite.hasBindingSiteSpecification()
and parsedBindingSite.getBindingSiteSpecification(
).hasShapeSpecification()):
bindingShapeNames = parsedBindingSite.getBindingSiteSpecification(
).getShapeSpecification().getShapeList()
assert (len(bindingShapeNames) > 0)
defaultShapeElmt = XmlObject("default-shape-ref")
defaultShapeElmt.addAttribute("name", bindingShapeNames[0])
defaultShapeElmt.attachToParent(bindingSiteElmt)
for shape_name in bindingShapeNames:
newShapeElmt = XmlObject("site-shape")
newShapeElmt.addAttribute("name", shape_name)
newShapeElmt.attachToParent(bindingSiteElmt)
else:
defaultShapeElmt = XmlObject("default-shape-ref")
defaultShapeElmt.addAttribute("name", "default")
defaultShapeElmt.attachToParent(bindingSiteElmt)
shapeElmt = XmlObject("site-shape")
shapeElmt.addAttribute("name", "default")
shapeElmt.attachToParent(bindingSiteElmt)
for modSiteName in parsedMol.getModificationSiteList():
modSiteElmt = XmlObject("mod-site", modMolElmt)
modSiteElmt.addAttribute("name", modSiteName)
parsedModificationSite = parsedMol.getModificationSiteWithName(
modSiteName)
if not parsedModificationSite.hasModificationSiteSpecification():
defaultModElmt = XmlObject("default-mod-ref", modSiteElmt)
defaultModElmt.addAttribute("name", "none")
else:
modValueArray = parsedModificationSite.getModificationSiteSpecification(
).getList()
try:
assert (len(modValueArray) > 1)
except:
print "Error, in sectionmols::addModMolToXml for mol with line '%s'. Mod Value Array '%s' should have more than one component..." % (
parsedMol.getOriginalLine(), str(modValueArray))
defaultModification = modValueArray[0]
defaultModElmt = XmlObject("default-mod-ref", modSiteElmt)
defaultModElmt.addAttribute("name", defaultModification)
return modMolElmt
def addModMolElmtToMolsElmt(self, xmlObject, moleculizerMolObject):
assert(isinstance(xmlObject, XmlObject))
assert(isinstance(moleculizerMolObject, MoleculizerMol))
newModMol = XmlObject("mod-mol")
newModMol.addAttribute("name", moleculizerMolObject.getName())
weightElement = XmlObject("weight")
# Obviously this is one of the big deficiencies of this thing. What shall
# we set the (mandatory) weights to? For now, let's just put in something
# arbitratry. But this is a big issue that ought to be fixed as soon as all
# the basic facilities of the code have been built in.
if moleculizerMolObject.getName() == "Pheromone":
weightElement.addAttribute("daltons", 10.0)
else:
weightElement.addAttribute("daltons", 100.0)
newModMol.addSubElement(weightElement)
for binding in moleculizerMolObject.bindingSites:
self.addBindingSiteElmtToModMolElmt(binding, moleculizerMolObject, newModMol)
for modification in moleculizerMolObject.modificationSites:
modSite, defaultModState = modification
modSiteElmt = XmlObject("mod-site")
modSiteElmt.addAttribute("name", modSite)
defModRefElmt = XmlObject("default-mod-ref")
defModRefElmt.addAttribute("name", defaultModState)
defModRefElmt.attachToParent(modSiteElmt).attachToParent(newModMol)
xmlObject.addSubElement(newModMol)
return
def __writeModMolInstanceToInstanceStates(self, parsedMol, molNdx,
parentElmt):
modMolInstanceRefElmt = XmlObject("mod-mol-instance-ref", parentElmt)
modMolInstanceRefElmt.addAttribute(
"name", self.getMolName(parsedMol.getName(), molNdx))
modMapElmt = XmlObject("mod-map", modMolInstanceRefElmt)
for modSite in parsedMol.getModificationSites():
modSiteRefElmt = XmlObject("mod-site-ref", modMapElmt)
modSiteRefElmt.addAttribute("name", modSite.getName())
modRefElmt = XmlObject("mod-ref", modSiteRefElmt)
modRefElmt.addAttribute(
"name",
modSite.getModificationSiteSpecification().getList()[0])
def addModMolElmtToMolsElmt(self, xmlObject, moleculizerMolObject):
assert (isinstance(xmlObject, XmlObject))
assert (isinstance(moleculizerMolObject, MoleculizerMol))
newModMol = XmlObject("mod-mol")
newModMol.addAttribute("name", moleculizerMolObject.getName())
weightElement = XmlObject("weight")
# Obviously this is one of the big deficiencies of this thing. What shall
# we set the (mandatory) weights to? For now, let's just put in something
# arbitratry. But this is a big issue that ought to be fixed as soon as all
# the basic facilities of the code have been built in.
if moleculizerMolObject.getName() == "Pheromone":
weightElement.addAttribute("daltons", 10.0)
else:
weightElement.addAttribute("daltons", 100.0)
newModMol.addSubElement(weightElement)
for binding in moleculizerMolObject.bindingSites:
self.addBindingSiteElmtToModMolElmt(binding, moleculizerMolObject,
newModMol)
for modification in moleculizerMolObject.modificationSites:
modSite, defaultModState = modification
modSiteElmt = XmlObject("mod-site")
modSiteElmt.addAttribute("name", modSite)
defModRefElmt = XmlObject("default-mod-ref")
defModRefElmt.addAttribute("name", defaultModState)
defModRefElmt.attachToParent(modSiteElmt).attachToParent(newModMol)
xmlObject.addSubElement(newModMol)
return
def __addModifications(self, parentObject):
modificationListElmt = XmlObject("modifications")
modificationListElmt.attachToParent(parentObject)
self.moleculeDictionary.addModifications(modificationListElmt)
def writeDimerGenLineToParent( self, line, reactionGens):
dimerGen = XmlObject("dimerization-gen", reactionGens)
parsedRxn = line.getParsedComponents()[0]
theReactants = parsedRxn.getReactants()
theProducts = parsedRxn.getProducts()
reactant1 = theReactants[0].getMols()[0]
reactant2 = theReactants[1].getMols()[0]
molSpec1 = XmlObject("mol-ref", dimerGen)
molSpec2 = XmlObject("mol-ref", dimerGen)
molSpec1.addAttribute("name", reactant1.getName() )
molSpec2.addAttribute("name", reactant2.getName() )
siteRef1 = XmlObject("site-ref", molSpec1)
siteRef2 = XmlObject("site-ref", molSpec2)
self.__addSiteNameToElement( reactant1, siteRef1)
self.__addSiteNameToElement( reactant2, siteRef2)
defaultOnElmt = XmlObject("default-on-rate", dimerGen)
defaultOffElmt = XmlObject("default-off-rate", dimerGen)
defaultOnElmt.addAttribute("value", line.getAssignment("kon"))
defaultOffElmt.addAttribute("value", line.getAssignment("koff"))
if len( line.getParsedComponents()) == 3:
return
# Now add the allosteric on- and off- rates.
allosteryComponents = line.getParsedComponents()[3:]
allostery_index = 3
while (len(allosteryComponents) > 0):
# This is used in a hacky way to find the correct parameter
alloRatesElmt = XmlObject("allo-rates", dimerGen)
alloReactants = allosteryComponents[0].getReactants()
siteShapeRef1 = XmlObject("site-shape-ref", alloRatesElmt)
siteShapeRef2 = XmlObject("site-shape-ref", alloRatesElmt)
onRate = XmlObject("on-rate", alloRatesElmt)
offRate = XmlObject("off-rate", alloRatesElmt)
if alloReactants[0].getMols()[0].isModMol():
if alloReactants[0].getMols()[0].getBindingSites()[0].hasBindingSiteSpecification():
siteShapeRef1.addAttribute("name", alloReactants[0].getMols()[0].getBindingSites()[0].getBindingSiteSpecification().getShapeSpecification().getShapeList()[0])
else:
siteShapeRef1.addAttribute("name", "default")
else:
siteShapeRef1.addAttribute("name", "default")
if alloReactants[1].getMols()[0].isModMol():
if alloReactants[1].getMols()[0].getBindingSites()[0].hasBindingSiteSpecification():
siteShapeRef2.addAttribute("name", alloReactants[1].getMols()[0].getBindingSites()[0].getBindingSiteSpecification().getShapeSpecification().getShapeList()[0])
else:
siteShapeRef2.addAttribute("name", "default")
else:
siteShapeRef2.addAttribute("name", "default")
onRate.addAttribute("value", line.getAssignment( "kon", allostery_index) )
offRate.addAttribute("value", line.getAssignment( "koff", allostery_index) )
allosteryComponents = allosteryComponents[3:]
allostery_index += 3
return
def addBindingSiteElmtToModMolElmt(self, bindingName, moleculizerMol,
xmlObject):
newBindingElmt = XmlObject("binding-site")
newBindingElmt.addAttribute("name", bindingName)
defaultShape = XmlObject("default-shape-ref")
defaultShape.addAttribute("name", "default")
defaultShape.attachToParent(newBindingElmt)
for shapeName in moleculizerMol.bindingSites[bindingName]:
siteShapeElmt = XmlObject("site-shape")
siteShapeElmt.addAttribute("name", shapeName)
siteShapeElmt.attachToParent(newBindingElmt)
xmlObject.addSubElement(newBindingElmt)
return
def __addExplicitReactions(self, modelElmt):
explicitReactionsElmt = XmlObject("explicit-reactions", modelElmt)
return
