def calculates(self, cell):
if self.__isLocalSearch:
newcell = self.__LocalSearch.initLocalSearch(cell)
else:
newcell = Gene()
newcell.copyGene(cell) #copy.deepcopy(cell)
auxLigand = copy.deepcopy(self.__ligand)
if self.__isKB:
for i in range(len(auxLigand.branch)):
torAngle = auxLigand.rotateBranchKB(i, newcell.rotateBonds[i])
auxLigand.rotateAtomsBranch(i, torAngle)
else:
for i in range(len(auxLigand.branch)):
auxLigand.rotateAtomsBranch(i, newcell.rotateBonds[i])
auxLigand.translateToPoint([
self.__centerSpace[0] + newcell.x,
self.__centerSpace[1] + newcell.y,
self.__centerSpace[2] + newcell.z
])
sphVect = spherePoint(1, newcell.sph_theta, newcell.sph_phi)
auxLigand.rotateByVector(sphVect, newcell.theta)
auxLigand.writePDBQT(self.__temporalDir + "ligand.pdbqt")
newcell.score = calculateFreeEnergy()
self.__numberScoring += 1
return newcell #copy.deepcopy(newcell)
def getNeighbor(self, cell):
newCell = Gene()
newCell.copyGene(cell)
if self.__typeLS == 0:
newCell = self.mutationBlock(newCell)
elif self.__typeLS == 1:
alpha = self.__tempIterative
newCell = self.mutationReduce(newCell, alpha)
elif self.__typeLS == 2:
newCell = self.mutationRot(newCell)
newCell = self.calculates(newCell)
return newCell
def initLocalSearch(self, cell):
#print "Init Local Search..."
self.__tempIterative = 1.0
T = self.__temp
oldCell = Gene()
oldCell.copyGene(cell)
while T > self.__tempMin:
j = 1
while j <= self.__numIteration:
newCell = self.getNeighbor(oldCell)
criteria = self.accptance(oldCell, newCell, T)
if criteria > random.random():
oldCell.copyGene(newCell)
j += 1
T *= self.__tempAlpha
self.__tempIterative *= self.__alphaIt
return oldCell
def getNeighbor(self, cell): newCell = Gene() newCell.copyGene(cell) if self.__typeLS == 0: newCell = self.mutationBlock(newCell) elif self.__typeLS == 1: alpha = self.__tempIterative newCell = self.mutationReduce(newCell, alpha) elif self.__typeLS == 2: newCell = self.mutationRot(newCell) elif self.__typeLS == 3: localOpt = random.randint(1,3) if localOpt == 1: newCell = self.mutationBlock(newCell) self.__normalLSCount+=1 elif localOpt == 2: alpha = self.__tempIterative newCell = self.mutationReduce(newCell, alpha) self.__redLSCount+=1 elif localOpt == 3: newCell = self.mutationRot(newCell) self.__rotLSCount+=1 elif self.__typeLS == 4: localOpt = random.uniform(0,1) if localOpt <= 0.1: newCell == self.mutationBlock(newCell) self.__normalLSCount+=1 elif localOpt <= 0.35: alpha = self.__tempIterative newCell = self.mutationReduce(newCell, alpha) self.__redLSCount+=1 elif localOpt > 0.35: newCell == self.mutationRot(newCell) self.__rotLSCount+=1 newCell = self.calculates(newCell) return newCell
