def selectSubMatrix(self, model, rowFilter = None, columnFilter = None, union = False):
regexRow = None
regexColumn = None
if rowFilter != None:
regexRow = re.compile(rowFilter)
if columnFilter != None:
regexColumn = re.compile(columnFilter)
result = LinearModel()
for key in model.data.keys():
(rowName,columnName) = key
value = model.getData(rowName,columnName)
if regexRow: rowCheck = regexRow.match(rowName)
else: rowCheck = False
if regexColumn: columnCheck = regexColumn.match(columnName)
else: columnCheck = False
if union:
if rowCheck and columnCheck:
result.addData(rowName,columnName,value)
else:
if rowCheck or columnCheck:
result.addData(rowName,columnName,value)
return result
def _constructDualRegulation(self,model,names,prefix):
'''
Construct limit / freedom variable for dual
These are the dual analog control variables
S'lambda + ... - delta - c' = 0
'''
rName = self.dualRName + prefix
jmodel = LinearModel()
equation = "%s" % (self.cdName)
jmodel = self.parseEquations.applyRelation(jmodel,rName,equation,names,prefixPattern="%s"+prefix)
imodel = LinearModel()
for name in names:
rName = self.dualRName + prefix + name
sName = self.cdName + prefix + name
imodel.addData(rName,sName,1)
imodel.addColumnLimit(sName,(None,None))
if not imodel == jmodel:
print "---------------------------------apply equation faliure: Dual control-----------------------------------------"
model.addConstraints(imodel)
return model
def findBoundaryProduction(originalModel, bounds, combiLimits, objectiveName, productionName):
model = LinearModel()
model.extend(originalModel)
if combiLimits != None:
for (targetValues,limit) in combiLimits:
model = addCombinationLimit(model, targetValues,limit)
#objectiveMap = {objectiveName:-1.0}
objectiveMap = {productionName:1.0}
model.addColumnLimits(bounds)
lp = LPSolver()
fluxMap = lp.run(model,objectiveMap)
objectiveValue = fluxMap[objectiveName]
productionValue = fluxMap[productionName]
return (fluxMap,objectiveValue,productionValue)
def findMinMax(self, model, objectiveName, minValue, targets):
positive = {}
negative = {}
imodel = LinearModel()
imodel.extend(model)
if minValue < 0:
imodel.addColumnLimit(objectiveName,(None,minValue))
else:
imodel.addColumnLimit(objectiveName,(minValue,None))
lp = LinearOptimization()
lp.setModel(model)
for t in targets:
lp.clearObjective()
lp.setObjectiveMap({t: -1})
lp.runSimplex()
fluxes = lp.getPredictionMap()
lowValue = fluxes[t]
negative[t] = lowValue
lp.clearObjective()
lp.setObjectiveMap({t: 1})
lp.runSimplex()
fluxes = lp.getPredictionMap()
highValue = fluxes[t]
positive[t] = highValue
return (positive,negative)
def construct(self,model,controlNames,newObjective):
'''
Top Level Function
Build Complete Framework
'''
self.newObjective = newObjective
result = LinearModel()
result.addModel(model)
sObjective = self._scaleMap(model.getObjective(),self.objectiveCoeffecent)
sObjective[self.newObjective] = .01
result.setObjective(sObjective)
for (libName,libPrefix) in self.libdata:
result = self._constructRegulationObjecive(result, controlNames, libName, libPrefix, -1.0)
pass
result = self._primalDual(result, result.getObjective())
for (libName,libPrefix) in self.libdata:
result = self.constructControl(result,controlNames,libPrefix,libName)
if self.rGeneMap != None:
self.geneControl(result,libPrefix + "y__",controlNames,libName)
if self.simoLimit !=0:
result = self._controlValueLimit(result,controlNames,postfix="y__")
return result
def generateModel(self, modelName=None):
if modelName == None:
modelName = self.modelName
dir = self.basedir
model = None
fluxLimits = None
objective = None
if self.rxnfile != '':
rxnFile =dir + self.rxnfile
model = self.rxnParser.parse(rxnFile)
else:
model = LinearModel()
if self.fluxlimitfile != '':
fluxLimitFile = dir + self.fluxlimitfile
fluxLimits = self.limitParser.parse(fluxLimitFile)
else:
fluxLimits = {}
if self.objectivefile != '':
objectiveFile = dir + self.objectivefile
objective = self.objParser.parse(objectiveFile)
else:
objective = {}
if self.directionCheck:
#fluxLimits = self.checkDirectionality(network, fluxLimits)
pass
model.addColumnLimits(fluxLimits)
for (key,value) in objective.items():
model.addObjective(key, value)
for name in model.getRowNames():
model.addRowLimit(name, (0.0,0.0))
return model
def _parseNetwork(self,network,limits):
result = LinearModel()
result.data.rowCache.extend(network.speciesCache)
result.data.columnCache.extend(network.reactionCache)
result.addDataCache(network.dataCache)
rowNames = network.getOrderedSpeciesNames()
columnNames = network.getOrderedReactionNames()
for rowName in rowNames:
result.addRowLimit(rowName,(0.0,0.0))
for columnName in columnNames:
if columnName in limits.keys():
(lower,upper) = limits[columnName]
result.addColumnLimit(columnName,(lower,upper))
return result
def parse( self, file ):
model = LinearModel()
rxnParser = ReactionEquationParser()
self.startFile(file)
d = self.getTagedLine()
annotation = {}
while d != None:
if d != "":
(reaction,direction) = rxnParser.parseEquation(d["Equation"])
name = d["Name"]
model.addColumn(name, reaction)
model.addColumnLimit(name, direction)
annotation[name] = d.annotation
d = self.getTagedLine()
self.closeFile()
model.annotation = annotation
return model
def _constructControl(self,model,controlNames,binaryPrefix,controlValuePref,regPrefix,climits,zero):
'''
Create binary control variables
one = off:
if y = 0: low < v < high
if y = 1: v = 0
v + high*y <= high
v + low*y >= low
zero = off:
if y = 1: 0 < v < d
if y = 0: v = 0
v - high*y <= 0
v - low*y >= 0
==>
for v in reaction targets
pc: v - high*pc < 0
nc: v - low* < 0
'''
binaryLimitName = "control_"
posControlRow = regPrefix+"_pc_"
negControlRow = regPrefix+"_nc_"
jmodel = LinearModel()
if zero:
equation1 = "%s_pc_%s:%s + %s %s < 0" % (regPrefix,"%s",controlValuePref,-1.0*self.posControlBound,binaryPrefix)
equation2 = "%s_nc_%s:%s + %s %s > 0" % (regPrefix,"%s",controlValuePref,-1.0*self.negControlBound,binaryPrefix)
else:
equation1 = "%s_pc_%s:%s + %s %s < %s" % (regPrefix,"%s",controlValuePref,self.posControlBound,binaryPrefix,self.posControlBound)
equation2 = "%s_nc_%s:%s + %s %s > %s" % (regPrefix,"%s",controlValuePref,self.negControlBound,binaryPrefix,self.negControlBound)
jmodel = self.parseEquations.applyRelation(jmodel,posControlRow,equation1,controlNames,prefixPattern="%s")
jmodel = self.parseEquations.applyRelation(jmodel,negControlRow,equation2,controlNames,prefixPattern="%s")
result = LinearModel()
for columnName in controlNames:
iCName = binaryPrefix + columnName
iDName = controlValuePref + columnName
posControlName = regPrefix + "_pc_" + columnName
negControlName = regPrefix + "_nc_" + columnName
if columnName in climits and False: # this method is currently broken
(negBound,posBound) = climits[columnName]
if negBound == None:
negBound = self.negControlBound
if posBound == None:
posBound = self.posControlBound
else:
posBound = self.posControlBound
negBound = self.negControlBound
'''
y = 1: l < v < u
'''
if(zero):
result.addData(posControlName,iDName,1.0)
result.addData(negControlName,iDName,1.0)
result.addData(posControlName,iCName,-posBound)
result.addData(negControlName,iCName,-negBound)
result.addRowLimit(posControlName,(None,0.0))
result.addRowLimit(negControlName,(0.0,None))
else:
result.addData(posControlName, iDName, 1.0)
result.addData(negControlName, iDName, 1.0)
result.addData(posControlName, iCName, posBound)
result.addData(negControlName, iCName, negBound)
result.addRowLimit(posControlName,(None,posBound))
result.addRowLimit(negControlName,(negBound,None))
jmodel.columnLimits = {}
if not result == jmodel:
#print "---------------------------------apply equation failure: control-----------------------------------------"
#! currently apply version does not handleA a map/list of boundary values
pass
model.addConstraints(result)
'''
w is limit of controls
y is actual control state variable
w - y = 0 as starting state ie all controls default to 0
sum w > control min
sum w < control max
'''
self.parseEquations.defaultLimit = (0.0,1.0)
iCName = binaryPrefix
iDName = controlValuePref
rowName = "_rcr_" + binaryPrefix
equation = "_rcr_%s:_rc_%s + -1.0 %s = 0" % (binaryPrefix+"%s",iCName,iCName)
jmodel = LinearModel()
jmodel = self.parseEquations.applyRelation(jmodel,rowName,equation,controlNames,prefixPattern="%s")
jmodel.setMipColumnNames(controlNames,tag=iCName+"%s")
self.parseEquations.defaultLimit = (None,None)
result = LinearModel()
for columnName in controlNames:
iCName = binaryPrefix + columnName
iDName = controlValuePref + columnName
result.setMipColumnName(iCName)
result.addColumnLimit(iCName,(0.0,1.0))
result.addColumnLimit("_rc_" + iCName,(0.0,1.0))
result.addData("_rcr_" + iCName, "_rc_" + iCName, 1.0)
result.addData("_rcr_" + iCName, iCName, -1.0)
result.addRowLimit("_rcr_" + iCName, (0.0,0.0))
if not result == (jmodel):
print "---------------------------------apply equation failure: control-----------------------------------------"
for columnName in controlNames:
iCName = binaryPrefix + columnName
iDName = controlValuePref + columnName
result.addData(binaryLimitName,"_rc_"+ iCName,1.0)
#Limit on control variables
result.addRowLimit(binaryLimitName,(self.controlMin,self.controlMax))
model.addConstraints(result)
return model
def _constructRegulationObjecive(self,model,names,lib,prefix,dir):
'''
Hybrid Objective
Z += C'v + A'n
Control of adjustment objective in hybrid objective
if y = 1: n = v, d=0
if y = 0: n = 0, d=v
==>
n + d - v = 0
-G * (y(i)) <= n <= G * (y(i)) : objective coefficient
-G * (1-y(i))<= d <= G * (1-y(i)) : slack variable
==>
n + d - v = 0
0 <= n + G * y(i)
n - G * y(i) <= 0
0 <= d + (1- y(y(i)) * G
d - (1 - y(i)) * G <= 0
it is important to only create controls for coefficients that exist in the library
'''
#! This is a new addition and may change the way RD works. Added to fix target / lib comparison failure.
names = self._confirmControlTargets(lib, names)
limits = model.getColumnLimits()
rName = prefix + "reg__"
jmodel = LinearModel()
equation = "%s:n + d + %sI= 0" % (prefix+ "reg__%s",dir)
jmodel = self.parseEquations.applyRelation(jmodel,rName,equation,names,prefixPattern=prefix+"%s__")
imodel = LinearModel()
rName = prefix + "reg__"
for name in names:
if name in limits:
limit = limits[name]
else:
limit = (self.negfluxControlBound,self.posfluxControlBound)
vName = name
rName = prefix + "reg__" + name
cName = prefix + "n__" + name
dName = prefix + "d__" + name
imodel.addColumnLimit(cName,(None,None))
imodel.addColumnLimit(dName,(None,None))
#!imodel.addColumnLimit(cName,(limit[0],limit[1]))
#!imodel.addColumnLimit(dName,(limit[0],limit[1]))
imodel.addRowLimit(rName,(0.0,0.0))
imodel.addData(rName, vName, dir)
imodel.addData(rName, cName, 1.0)
imodel.addData(rName, dName, 1.0)
if not jmodel == imodel:
print "----------------------------apply equation failure-----------------------------"
model.addConstraints(imodel)
'''
Z^hybrid = C^nat*v + C^adj*n
'''
objective = {}
originalObjective = model.getObjective()
objective.update(originalObjective)
imodel = LinearModel()
#Set coefficients for controls
for name in names:
iname = prefix + "n__" + name
coeffecent = self._getRegulationCoeffecent(lib,name)
iCoeffecent = float(coeffecent) * float(self.regCoeffecent)
objective[iname] = -iCoeffecent
imodel.addData("adjValue",iname,-iCoeffecent)
#This constraint maybe cause of failure because of overloading of coefficients * fluxes in dual
#This constraint combined with the use of the control penalty causes infeasibility issues
#imodel.addRowLimit("adjValue",(None,None))
#model.addConstraints(imodel)
jmodel = LinearModel()
equation = "adjValue%s:objectiveVar + adjVar = 0"
jmodel = self.parseEquations.applyRelation(jmodel,relationName="adjValue",value=equation,targets=[''],prefixPattern="%s")
del jmodel.columnLimits["objectiveVar"]
jmodel.addColumnLimit("objectiveVar",(None,None))
imodel = LinearModel()
imodel.addData("adjValue","objectiveVar",1)
imodel.addData("adjValue","adjVar",1)
imodel.addRowLimit("adjValue",(0,0))
imodel.addColumnLimit("adjVar",(None,None))
imodel.addColumnLimit("objectiveVar",(None,None))
if not jmodel == imodel:
print "---------------------------------apply equation faliure: control objective-----------------------------------------"
#This constraint maybe cause of failure because of overloading of coefficients * fluxes in dual
#This constraint along with a control penalty causes infeasibility issues in the optimization
#model.addConstraints(imodel)#! consider removing to insure that adjValue is not messing up the system
model.setObjective(objective)
return model
def _primalDual(self,model,objective,prime=True,dual=True,equal=True):
'''
class PathwayTarget:
@type model: LinearModel
@rtype: LinearModel
Construct Core Linear Optimization Matrix with primal dual equality
row i and column j
Primal:
min Z = sum(j): [c(j)*v(j)]
ST.
sum(j) [S(ij)*v(j)] = 0 E i
l(j) < v(j) < u(j) E j
Hameltonian:
Max(lambda,mu,nu): Min(v): sum(j)c(j)*v(j) + sum(i)lambda(i)*S(ij)v(j) + mu(j)(l(j)-v(j)) + nu(j)(v(j)-u(j))
=> c'v + lambda*(Sv) + mu(l-v) + nu(v-u)
=> Max: mu*l - nu*u
ST
c + lambda*S + mu + nu = 0
Dual:
max Z_dual = l*mu - u*nu
ST.
S'*lambda - mu + nu = -c'
mu(j) > 0 E j
nu(j) > 0 E j
Equality condition:
Z = Z_dual
==> sum(j) [c(j)'*v(j)] = sum(j) [l(j)*mu(j) - u(j)*nu]
==> -c*v + mu*l - u*nu = 0
'''
pName = self.pName
dName = self.dName
result = LinearModel()
#Primal:
if prime:
#S*v
for (row, column, value) in model.getSparseMatrix():
result.addData(self.primeRName + row, pName + column, value)
#S*v <=> b
for row in model.getRowLimits().keys():
result.addRowLimit(self.primeRName + row, model.getRowLimit(row))
#u<=v<=l
for column in model.getColumnNames():
result.addColumnLimit(pName + column, model.getColumnLimit(column))
#Dual:
if dual:
#S'*lambda
for (row, column, value) in model.getSparseMatrix():
result.addData(self.dualRName + column, dName + row, value)
#lambda <=> +- inf
for row in model.getRowLimits().keys():
result.addColumnLimit(dName + row, (None,None))
#S'*lambda = -c'
for column in model.getColumnNames():
if column in objective.keys():
value = objective[column]
result.addRowLimit(self.dualRName + column, (-value, -value))
else:
result.addRowLimit(self.dualRName + column, (0.0, 0.0))
#S'*lambda - mu + nu = -c'
for column in model.getColumnLimits().keys():
(lower, upper) = model.getColumnLimit(column)
if lower != None:
result.addData(self.dualRName + column, '__mu__' + column, -1)
result.addColumnLimit('__mu__' + column, (0.0, None))
if upper != None:
result.addData(self.dualRName + column, '__nu__' + column, 1)
result.addColumnLimit('__nu__' + column, (0.0, None))
if equal:
#objective relation
#Z^prime = Z^dual
# cv = l*mu - u*nu = 0
# -cv + l*mu - u*nu = 0
for column in model.getColumnNames():
if column in objective.keys():
value = objective[column]
result.addData(self.equalityRName, pName + column, -value)
else:
result.addData(self.equalityRName, pName + column, 0)
for column in model.getColumnLimits().keys():
(lower, upper) = model.getColumnLimit(column)
if lower != None and lower != 0.0:
result.addData(self.equalityRName, '__mu__' + column, lower)
if upper != None and upper != 0.0:
result.addData(self.equalityRName, '__nu__' + column, -upper)
result.addRowLimit(self.equalityRName,(0,0))
objective = {}
objective[self.pName + self.newObjective] = -1
result.setObjective(objective)
return result
def LinearModelVariableBoundarys(originalModel, objectiveName, targets=None, pickleFileName=None, strict=False, minObjectivePercent=None,searchSize=1):
'''
Find min and max boundaries for the dependent variables of a linear model.
Uses limitMap as constraints on model.
Add cumulative boundary persistence as pickle file function.
@param linearModel: linear model to be analyzed
@type linearModel: LinearModel
@param limitMap: map of variable names and lower and upper limits
@type limitMap: {variableName, (float, float)
@param targets: list of variables to perform analysis on
@type targets: list
@return: dictionary of lower and upper limits for each variable
@rtype: {variableName: (lowerlimit, upperlimit)}
'''
linearModel = LinearModel()
linearModel.extend(originalModel)
if pickleFileName != None:
if os.path.isfile(pickleFileName):
print "loading saved flux boundaries"
pFile = open(pickleFileName)
result = pickle.load(pFile)
pFile.close()
return result
originalLimits = linearModel.getColumnLimits()
originalObjectiveLimit = originalLimits[objectiveName]
objectiveVector = {objectiveName:-1.0}
solver = LPSolver()
originalValues = solver.run(model=linearModel, objective=objectiveVector)
originalObjectiveValue = originalValues[objectiveName]
if minObjectivePercent != None:
minObjectiveValue = originalObjectiveValue * minObjectivePercent
linearModel.addColumnLimit(objectiveName,(minObjectiveValue,None))
if targets == None:
targets = linearModel.getColumnNames()
targets.add(objectiveName)
print "Searching flux boundaries for %s > %s" % (objectiveName, minObjectiveValue)
result = {}
targetValues = targetValueCombinations(targets, [-1.0,1.0])
controlSubSets = combinations(targetValues,searchSize)
xcontrolSubSets = set(controlSubSets)
for name in targets:
nameTag = name
# if name not in linearModel.getColumnNames():
# print "target %s not found in model"
# print "boundary discovery not possible"
# continue
#for iTargetValues in xcontrolSubSets:
# name = "testControlValue"
# nameTag = iTargetValues
# linearModel = combinationLimitBuilder(linearModel, iTargetValues, name)
result[name] = (None,None)
negObjective = {name:1.0}
posObjective = {name:-1.0}
solver.clearObjective()
negValues = solver.run(linearModel, objective=negObjective)
negValue = negValues[name]
solver.clearObjective()
posValues = solver.run(linearModel, objective=posObjective)
posValue = posValues[name]
delta = 1e-4
if posValue != 0 or negValue !=0:
pass
if False:
originalValue = originalValues[name]
originalLimit = originalLimits[name]
if not (negValue - delta <= originalValue <= posValue + delta):
print "original value not in boundary"
print "objective value [%s] (%s) %s <= %s <= %s (%s)" % (name, originalLimit[0], negValue, originalValue, posValue, originalLimit[1])
#print "value neg code %s pos code %s" % (nscode, pscode)
(negValue,posValue) = (originalLimit[0],originalLimit[1])
else:
#print "objective value [%s] (%s) %s <= %s <= %s (%s)" % (name, originalLimit[0], negValue, originalValue, posValue, originalLimit[1])
pass
if negValue == None or negValue == float("-inf"):
continue
if posValue == None or posValue == float("-inf"):
continue
result[nameTag] = (negValue,posValue)
print "%s < [%s] < %s " % (negValue,nameTag,posValue)
if pickleFileName != None:
pFile = open(pickleFileName,'w')
pickle.dump(result, pFile)
pFile.close()
solver.clear()
del solver
linearModel.addColumnLimit(objectiveName,originalObjectiveLimit)
#targets.remove(objectiveName)
return result