def addSmallMolToXml( self, parsedSmallMol, xmlElement ):
smallMolElt = XmlObject("small-mol")
smallMolElt.addAttribute( "name", parsedSmallMol.getName() )
smallMolElt.attachToParent( xmlElement)
return smallMolElt
def addSmallMolToXml(self, parsedSmallMol, xmlElement):
smallMolElt = XmlObject("small-mol")
smallMolElt.addAttribute("name", parsedSmallMol.getName())
smallMolElt.attachToParent(xmlElement)
return smallMolElt
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, 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 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 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 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 __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 __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 __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 __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 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 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 __addAllostericPlexes(self, parentObject):
allostericPlexesElmt = XmlObject("allosteric-plexes")
allostericPlexesElmt.attachToParent(parentObject)
def __addAllostericOmnis(self, parentObject):
allostericOmnisElmt = XmlObject("allosteric-omnis")
allostericOmnisElmt.attachToParent(parentObject)
self.reactionRules.addAllostericOmnis(allostericOmnisElmt)
def __addReactionGens(self, parentObject):
rxnGenElmt = XmlObject("reaction-gens")
rxnGenElmt.attachToParent(parentObject)
self.reactionRules.writeReactionGensElement(rxnGenElmt)
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 __addMols(self, parentObject):
molsElmt = XmlObject("mols")
molsElmt.attachToParent(parentObject)
self.moleculeDictionary.addMols(molsElmt)
def __addModifications(self, parentObject):
modificationListElmt = XmlObject("modifications")
modificationListElmt.attachToParent(parentObject)
self.moleculeDictionary.addModifications(modificationListElmt)
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 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 __addAllostericOmnis(self, parentObject):
allostericOmnisElmt = XmlObject("allosteric-omnis")
allostericOmnisElmt.attachToParent(parentObject)
self.reactionRules.addAllostericOmnis(allostericOmnisElmt)
def __addAllostericPlexes(self, parentObject):
allostericPlexesElmt = XmlObject("allosteric-plexes")
allostericPlexesElmt.attachToParent(parentObject)
def __addMols(self, parentObject):
molsElmt = XmlObject("mols")
molsElmt.attachToParent(parentObject)
self.moleculeDictionary.addMols(molsElmt)
def __addExplicitSpecies(self, parentObject):
explicitSpeciesElmt = XmlObject("explicit-species")
explicitSpeciesElmt.attachToParent(parentObject)
self.seedSpecies.writeExplicitSpecies(explicitSpeciesElmt)
def __addReactionGens(self, parentObject):
rxnGenElmt = XmlObject("reaction-gens")
rxnGenElmt.attachToParent(parentObject)
self.reactionRules.writeReactionGensElement(rxnGenElmt)
def __addModifications(self, parentObject):
modificationListElmt = XmlObject("modifications")
modificationListElmt.attachToParent(parentObject)
self.moleculeDictionary.addModifications(modificationListElmt)
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 __addExplicitSpecies(self, parentObject):
explicitSpeciesElmt = XmlObject("explicit-species")
explicitSpeciesElmt.attachToParent(parentObject)
self.seedSpecies.writeExplicitSpecies(explicitSpeciesElmt)
