def checkComplexIsDefault(self, binding, complex):
try:
molName, bindingSiteName = binding
except:
pdb.set_trace()
a = 1
if "." in complex:
return False
if not complex.startswith(molName):
pdb.set_trace()
raise ValueError, "Bad complex"
if "!" in complex:
return False
theBindingSites = util.getBindingSites(complex)
if len(theBindingSites) != 1:
return False
for modSite in util.getModificationList(complex):
modSite = modSite.split("~")
if modSite[1] != "none":
return False
else:
return True
def checkComplexIsDefault(self, binding, complex):
try:
molName, bindingSiteName = binding
except:
pdb.set_trace()
a = 1
if "." in complex:
return False
if not complex.startswith(molName):
pdb.set_trace()
raise ValueError, "Bad complex"
if "!" in complex:
return False
theBindingSites = util.getBindingSites(complex)
if len(theBindingSites) != 1:
return False
for modSite in util.getModificationList(complex):
modSite = modSite.split("~")
if modSite[1] != "none":
return False
else:
return True
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 addModificationRxnToReactionGenElement(self, rxn, reactionGensElement,
modificationInfo):
# Create all the objects
omniGenElmt = XmlObject("omni-gen")
enablingOmniPlexElmt = XmlObject("enabling-omniplex")
smallMolExchangesElmt = XmlObject("small-mol-exchanges")
modificationExchangeElmt = XmlObject("modification-exchanges")
additionalReactantSpeciesElmt = XmlObject(
"additional-reactant-species")
additionalProductSpeciesElmt = XmlObject("additional-product-species")
rateElmt = XmlObject("rate")
# Now add them all to the xml structure
omniGenElmt.attachToParent(reactionGensElement)
enablingOmniPlexElmt.attachToParent(omniGenElmt)
smallMolExchangesElmt.attachToParent(omniGenElmt)
modificationExchangeElmt.attachToParent(omniGenElmt)
#additionalReactantSpeciesElmt.attachToParent(omniGenElmt)
#additionalProductSpeciesElmt.attachToParent(omniGenElmt)
# Add a plex element to the enablingOmniPlexElmt
plexElmt = XmlObject("plex")
plexElmt.attachToParent(enablingOmniPlexElmt)
assert (len(rxn.reactants) == 1 and len(rxn.products) == 1)
reactant = rxn.reactants[0]
reactantArray = reactant.split(".")
molNdxToInstanceName = {}
molNdxToRefName = {}
tmpNameGenerator = {}
bindingSites = {}
unboundSites = []
modificationSites = []
for ndx in range(len(reactantArray)):
molSpec = reactantArray[ndx]
parenNdx = molSpec.find("(")
molRefName = molSpec[:parenNdx]
if not molRefName in tmpNameGenerator.keys():
molInstanceName = "the-" + molRefName
tmpNameGenerator[molRefName] = 1
else:
molInstanceName = molRefName + "_" + str(
tmpNameGenerator[molRefName])
tmpNameGenerator[molRefName] += 1
molNdxToRefName[ndx] = molRefName
molNdxToInstanceName[ndx] = molInstanceName
# Create the mol-intance element
molInstanceElmt = XmlObject("mol-instance")
molInstanceElmt.addAttribute("name", molInstanceName)
molRefElmt = XmlObject("mol-ref")
molRefElmt.addAttribute("name", molRefName)
molRefElmt.attachToParent(molInstanceElmt).attachToParent(plexElmt)
# Now delve into the bindings of this muthafucka.
# Note bound components, unbound componends, and modifications...
bindingInformation = molSpec[parenNdx + 1:-1]
bindingInfoArray = bindingInformation.split(",")
bindings = [x for x in bindingInfoArray if "~" not in x]
modifications = [x for x in bindingInfoArray if "~" in x]
boundBindings = [x for x in bindings if "!" in x and x[-1] != "+"]
unboundBindings = [x for x in bindings if "!" not in x]
# Process modifications
for modification in modifications:
site, state = modification.split("~")
modificationSites.append((ndx, site, state))
# Process unbound binding sites
for unboundBinding in unboundBindings:
unboundSites.append((ndx, unboundBinding))
for boundHalfBinding in boundBindings:
site, bindingNdx = boundHalfBinding.split("!")
if not bindingNdx in bindingSites.keys():
bindingSites[bindingNdx] = []
bindingSites[bindingNdx].append((ndx, site))
# End initial pass, now we can put in all the bindingSites,
# unbound bindingSites, and modification states.
for ndx in bindingSites.keys():
bindingElmt = XmlObject("binding")
bindingElmt.attachToParent(plexElmt)
for halfBinding in bindingSites[ndx]:
molInstanceRefElmt = XmlObject("mol-instance-ref")
molInstanceRefElmt.addAttribute(
"name", molNdxToInstanceName[halfBinding[0]])
bindingSiteRefElmt = XmlObject("binding-site-ref")
bindingSiteRefElmt.addAttribute("name", halfBinding[1])
bindingSiteRefElmt.attachToParent(
molInstanceRefElmt).attachToParent(bindingElmt)
# I think I should try to filter out the modification(the relevant one)
if len(modificationSites) > 0:
instanceStatesElmt = XmlObject("instance-states")
instanceStatesElmt.attachToParent(plexElmt)
for modMolNdx in set([x[0] for x in modificationSites]):
modMap = [(x[1], x[2]) for x in modificationSites
if x[0] == modMolNdx]
modMolInstanceRefElmt = XmlObject("mod-mol-instance-ref")
modMolInstanceRefElmt.addAttribute("name",
molNdxToInstanceName[modMolNdx])
modMapElmt = XmlObject("mod-map")
modMapElmt.attachToParent(modMolInstanceRefElmt).attachToParent(
instanceStatesElmt)
for modification in modMap:
modSiteRefElmt = XmlObject("mod-site-ref")
modSiteRefElmt.addAttribute("name", modification[0])
modRefElmt = XmlObject("mod-ref")
modRefElmt.addAttribute("name", modification[1])
modRefElmt.attachToParent(modSiteRefElmt).attachToParent(
modMapElmt)
if len(unboundSites) > 0:
unboundSitesElmt = XmlObject("unbound-sites")
unboundSitesElmt.attachToParent(plexElmt)
for unboundSite in unboundSites:
instanceRefElmt = XmlObject("instance-ref")
instanceRefElmt.addAttribute("name",
molNdxToInstanceName[unboundSite[0]])
siteRefElmt = XmlObject("site-ref")
siteRefElmt.addAttribute("name", unboundSite[1])
siteRefElmt.attachToParent(instanceRefElmt).attachToParent(
unboundSitesElmt)
## Now create the modification exchange
molRef, modSite, modInitialState = modificationInfo
realNdx = -1
for ndx in range(len(reactantArray)):
if reactantArray[ndx].startswith(molRef) and (
modSite + "~" + modInitialState) in reactantArray[ndx]:
realNdx = ndx
break
else:
pdb.set_trace()
a = 1
raise ValueError
modMolInstanceRefElmt = XmlObject("mod-mol-instance-ref")
modMolInstanceRefElmt.addAttribute("name",
molNdxToInstanceName[realNdx])
modSiteRefElmt = XmlObject("mod-site-ref")
modSiteRefElmt.addAttribute("name", modSite)
modSiteRefElmt.attachToParent(modMolInstanceRefElmt).attachToParent(
modificationExchangeElmt)
installedModRefElmt = XmlObject("installed-mod-ref")
# To find the result, we must find out what state the modSite modification is in the realNdx-th plex on the product side
modifications = util.getModificationList(
rxn.products[0].split('.')[realNdx])
endState = ""
for x in modifications:
if x.startswith(modSite):
endState = x.split('~')[1]
break
else:
raise ValueError
installedModRefElmt.addAttribute("name", endState)
installedModRefElmt.attachToParent(modificationExchangeElmt)
rateElmt.addAttribute(
"value",
self.parameterDictionary.evaluateExpression(rxn.rateList[0]))
rateElmt.attachToParent(omniGenElmt)
def addModificationRxnToReactionGenElement(self, rxn, reactionGensElement, modificationInfo):
# Create all the objects
omniGenElmt = XmlObject("omni-gen")
enablingOmniPlexElmt = XmlObject("enabling-omniplex")
smallMolExchangesElmt = XmlObject("small-mol-exchanges")
modificationExchangeElmt = XmlObject("modification-exchanges")
additionalReactantSpeciesElmt = XmlObject("additional-reactant-species")
additionalProductSpeciesElmt = XmlObject("additional-product-species")
rateElmt = XmlObject("rate")
# Now add them all to the xml structure
omniGenElmt.attachToParent(reactionGensElement)
enablingOmniPlexElmt.attachToParent(omniGenElmt)
smallMolExchangesElmt.attachToParent(omniGenElmt)
modificationExchangeElmt.attachToParent(omniGenElmt)
#additionalReactantSpeciesElmt.attachToParent(omniGenElmt)
#additionalProductSpeciesElmt.attachToParent(omniGenElmt)
# Add a plex element to the enablingOmniPlexElmt
plexElmt = XmlObject("plex")
plexElmt.attachToParent(enablingOmniPlexElmt)
assert(len(rxn.reactants) == 1 and len(rxn.products) == 1)
reactant = rxn.reactants[0]
reactantArray = reactant.split(".")
molNdxToInstanceName = {}
molNdxToRefName = {}
tmpNameGenerator = {}
bindingSites = {}
unboundSites = []
modificationSites = []
for ndx in range(len(reactantArray)):
molSpec = reactantArray[ndx]
parenNdx = molSpec.find("(")
molRefName = molSpec[:parenNdx]
if not molRefName in tmpNameGenerator.keys():
molInstanceName = "the-" + molRefName
tmpNameGenerator[molRefName] = 1
else:
molInstanceName = molRefName + "_" + str(tmpNameGenerator[molRefName])
tmpNameGenerator[molRefName] += 1
molNdxToRefName[ndx] = molRefName
molNdxToInstanceName[ndx] = molInstanceName
# Create the mol-intance element
molInstanceElmt = XmlObject("mol-instance")
molInstanceElmt.addAttribute("name", molInstanceName)
molRefElmt = XmlObject("mol-ref")
molRefElmt.addAttribute("name", molRefName)
molRefElmt.attachToParent(molInstanceElmt).attachToParent(plexElmt)
# Now delve into the bindings of this muthafucka.
# Note bound components, unbound componends, and modifications...
bindingInformation = molSpec[parenNdx + 1: -1]
bindingInfoArray = bindingInformation.split(",")
bindings = [x for x in bindingInfoArray if "~" not in x]
modifications = [x for x in bindingInfoArray if "~" in x]
boundBindings = [x for x in bindings if "!" in x and x[-1] != "+"]
unboundBindings = [x for x in bindings if "!" not in x]
# Process modifications
for modification in modifications:
site, state = modification.split("~")
modificationSites.append( (ndx, site, state))
# Process unbound binding sites
for unboundBinding in unboundBindings:
unboundSites.append( (ndx, unboundBinding))
for boundHalfBinding in boundBindings:
site, bindingNdx = boundHalfBinding.split("!")
if not bindingNdx in bindingSites.keys():
bindingSites[bindingNdx] = []
bindingSites[bindingNdx].append( (ndx, site))
# End initial pass, now we can put in all the bindingSites,
# unbound bindingSites, and modification states.
for ndx in bindingSites.keys():
bindingElmt = XmlObject("binding")
bindingElmt.attachToParent(plexElmt)
for halfBinding in bindingSites[ndx]:
molInstanceRefElmt = XmlObject("mol-instance-ref")
molInstanceRefElmt.addAttribute("name", molNdxToInstanceName[halfBinding[0]])
bindingSiteRefElmt = XmlObject("binding-site-ref")
bindingSiteRefElmt.addAttribute("name", halfBinding[1])
bindingSiteRefElmt.attachToParent(molInstanceRefElmt).attachToParent(bindingElmt)
# I think I should try to filter out the modification(the relevant one)
if len(modificationSites) > 0:
instanceStatesElmt = XmlObject("instance-states")
instanceStatesElmt.attachToParent(plexElmt)
for modMolNdx in set([x[0] for x in modificationSites]):
modMap = [ (x[1], x[2]) for x in modificationSites if x[0] == modMolNdx]
modMolInstanceRefElmt = XmlObject("mod-mol-instance-ref")
modMolInstanceRefElmt.addAttribute("name", molNdxToInstanceName[modMolNdx])
modMapElmt = XmlObject("mod-map")
modMapElmt.attachToParent(modMolInstanceRefElmt).attachToParent(instanceStatesElmt)
for modification in modMap:
modSiteRefElmt = XmlObject("mod-site-ref")
modSiteRefElmt.addAttribute("name", modification[0])
modRefElmt = XmlObject("mod-ref")
modRefElmt.addAttribute("name", modification[1])
modRefElmt.attachToParent(modSiteRefElmt).attachToParent(modMapElmt)
if len(unboundSites) > 0:
unboundSitesElmt = XmlObject("unbound-sites")
unboundSitesElmt.attachToParent(plexElmt)
for unboundSite in unboundSites:
instanceRefElmt = XmlObject("instance-ref")
instanceRefElmt.addAttribute("name", molNdxToInstanceName[unboundSite[0]])
siteRefElmt = XmlObject("site-ref")
siteRefElmt.addAttribute("name", unboundSite[1])
siteRefElmt.attachToParent(instanceRefElmt).attachToParent(unboundSitesElmt)
## Now create the modification exchange
molRef, modSite, modInitialState = modificationInfo
realNdx = -1
for ndx in range(len(reactantArray)):
if reactantArray[ndx].startswith(molRef) and (modSite + "~" + modInitialState) in reactantArray[ndx]:
realNdx = ndx
break
else:
pdb.set_trace()
a = 1
raise ValueError
modMolInstanceRefElmt = XmlObject("mod-mol-instance-ref")
modMolInstanceRefElmt.addAttribute("name", molNdxToInstanceName[realNdx])
modSiteRefElmt = XmlObject("mod-site-ref")
modSiteRefElmt.addAttribute("name", modSite)
modSiteRefElmt.attachToParent(modMolInstanceRefElmt).attachToParent(modificationExchangeElmt)
installedModRefElmt = XmlObject("installed-mod-ref")
# To find the result, we must find out what state the modSite modification is in the realNdx-th plex on the product side
modifications = util.getModificationList(rxn.products[0].split('.')[realNdx])
endState = ""
for x in modifications:
if x.startswith(modSite):
endState = x.split('~')[1]
break
else:
raise ValueError
installedModRefElmt.addAttribute("name", endState)
installedModRefElmt.attachToParent(modificationExchangeElmt)
rateElmt.addAttribute("value", self.parameterDictionary.evaluateExpression(rxn.rateList[0]))
rateElmt.attachToParent(omniGenElmt)
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)
