def crossoverCenter(self, selectedCell1, selectedCell2):
newCell = Gene()
if random.randint(0, 1) == 1:
newCell.x = selectedCell1.x
else:
newCell.x = selectedCell2.x
if random.randint(0, 1) == 1:
newCell.y = selectedCell1.y
else:
newCell.y = selectedCell2.y
if random.randint(0, 1) == 1:
newCell.z = selectedCell1.z
else:
newCell.z = selectedCell2.z
if random.randint(0, 1) == 1:
newCell.sph_theta = selectedCell1.sph_theta
newCell.sph_phi = selectedCell1.sph_phi
newCell.theta = selectedCell1.theta
newCell.rotateBonds = selectedCell1.rotateBonds[:]
else:
newCell.sph_theta = selectedCell2.sph_theta
newCell.sph_phi = selectedCell2.sph_phi
newCell.theta = selectedCell2.theta
newCell.rotateBonds = selectedCell2.rotateBonds[:]
return newCell
def crossoverUniform(self, selectedCell1, selectedCell2):
newCell = Gene()
if random.randint(0, 1) == 1:
newCell.x = selectedCell1.x
else:
newCell.x = selectedCell2.x
if random.randint(0, 1) == 1:
newCell.y = selectedCell1.y
else:
newCell.y = selectedCell2.y
if random.randint(0, 1) == 1:
newCell.z = selectedCell1.z
else:
newCell.z = selectedCell2.z
if random.randint(0, 1) == 1:
newCell.sph_theta = selectedCell1.sph_theta
else:
newCell.sph_theta = selectedCell2.sph_theta
if random.randint(0, 1) == 1:
newCell.sph_phi = selectedCell1.sph_phi
else:
newCell.sph_phi = selectedCell2.sph_phi
if random.randint(0, 1) == 1:
newCell.theta = selectedCell1.theta
else:
newCell.theta = selectedCell2.theta
for i in range(len(selectedCell1.rotateBonds)):
if random.randint(0, 1) == 1:
newCell.rotateBonds.append(selectedCell1.rotateBonds[i])
else:
newCell.rotateBonds.append(selectedCell2.rotateBonds[i])
return newCell
def crossoverUniform(self, selectedCell1, selectedCell2): newCell = Gene() if random.randint(0,1) == 1: newCell.x = selectedCell1.x else: newCell.x = selectedCell2.x if random.randint(0,1) == 1: newCell.y = selectedCell1.y else: newCell.y = selectedCell2.y if random.randint(0,1) == 1: newCell.z = selectedCell1.z else: newCell.z = selectedCell2.z if random.randint(0,1) == 1: newCell.sph_theta = selectedCell1.sph_theta else: newCell.sph_theta = selectedCell2.sph_theta if random.randint(0,1) == 1: newCell.sph_phi = selectedCell1.sph_phi else: newCell.sph_phi = selectedCell2.sph_phi if random.randint(0,1) == 1: newCell.theta = selectedCell1.theta else: newCell.theta = selectedCell2.theta return newCell
def crossoverBlock(self, selectedCell1, selectedCell2): newCell = Gene() if random.randint(0,1) == 1: newCell.x = selectedCell1.x newCell.y = selectedCell1.y newCell.z = selectedCell1.z else: newCell.x = selectedCell2.x newCell.y = selectedCell2.y newCell.z = selectedCell2.z if random.randint(0,1) == 1: newCell.sph_theta = selectedCell1.sph_theta newCell.sph_phi = selectedCell1.sph_phi newCell.theta = selectedCell1.theta else: newCell.sph_theta = selectedCell2.sph_theta newCell.sph_phi = selectedCell2.sph_phi newCell.theta = selectedCell2.theta return newCell
def crossoverSPC(self, selectedCell1, selectedCell2):
pop1 = []
pop2 = []
pop1.append(selectedCell1.x)
pop1.append(selectedCell1.y)
pop1.append(selectedCell1.z)
pop1.append(selectedCell1.sph_theta)
pop1.append(selectedCell1.sph_phi)
pop1.append(selectedCell1.theta)
for angle in selectedCell1.rotateBonds:
pop1.append(angle)
pop2.append(selectedCell2.x)
pop2.append(selectedCell2.y)
pop2.append(selectedCell2.z)
pop2.append(selectedCell2.sph_theta)
pop2.append(selectedCell2.sph_phi)
pop2.append(selectedCell2.theta)
for angle in selectedCell2.rotateBonds:
pop2.append(angle)
genSize = len(pop1)
cutPoint = random.randint(0, genSize - 1)
length = random.randint(0, genSize - 1)
if length == 0:
return selectedCell1
elif length > (genSize - cutPoint):
newPop = pop1[cutPoint:]
turnTop = length - (genSize - cutPoint)
for i in range(0, turnTop):
newPop.insert(i, pop1[i])
for i in range(turnTop, cutPoint):
newPop.insert(i, pop2[i])
else:
newPop = pop1[cutPoint:cutPoint + length]
for i in range(0, cutPoint):
newPop.insert(i, pop2[i])
for i in range(cutPoint + length, genSize):
newPop.insert(i, pop2[i])
newCell = Gene()
newCell.x = newPop[0]
newCell.y = newPop[1]
newCell.z = newPop[2]
newCell.sph_theta = newPop[3]
newCell.sph_phi = newPop[4]
newCell.theta = newPop[5]
newCell.rotateBonds = newPop[6:]
return newCell
def randomCell(self):
gen = Gene()
gen.x = random.uniform(-self.__searchSpaceSize, self.__searchSpaceSize)
gen.y = random.uniform(-self.__searchSpaceSize, self.__searchSpaceSize)
gen.z = random.uniform(-self.__searchSpaceSize, self.__searchSpaceSize)
gen.sph_theta = math.pi * random.randint(0, 200) / 100.0
gen.sph_phi = math.pi * random.randint(0, 100) / 100.0
gen.theta = math.pi * random.randint(0, 200) / 100.0
for r in xrange(len(self.__rotateAtoms)):
gen.rotateAtoms.append(math.pi * random.randint(0, 200) / 100.0)
return copy.deepcopy(gen)
def randomCell(self):
gen = Gene()
gen.x = random.uniform(-self.__searchSpaceSize, self.__searchSpaceSize)
gen.y = random.uniform(-self.__searchSpaceSize, self.__searchSpaceSize)
gen.z = random.uniform(-self.__searchSpaceSize, self.__searchSpaceSize)
gen.sph_theta = math.pi * random.randint(0, 200) / 100.0
gen.sph_phi = math.pi * random.randint(0, 100) / 100.0
gen.theta = math.pi * random.randint(0, 200) / 100.0
for r in xrange(len(self.__rotateAtoms)):
gen.rotateAtoms.append(math.pi * random.randint(0, 200) / 100.0)
return copy.deepcopy(gen)
def crossover50(self, selectedCell1, selectedCell2): newCell = Gene() #switch center of ligand centrand = random.randint(0,5) if centrand == 0: newCell.x = selectedCell1.x newCell.y = selectedCell2.y newCell.z = selectedCell2.z elif centrand == 1: newCell.x = selectedCell1.x newCell.y = selectedCell1.y newCell.z = selectedCell2.z elif centrand == 2: newCell.x = selectedCell1.x newCell.y = selectedCell1.y newCell.z = selectedCell1.z elif centrand == 3: newCell.x = selectedCell2.x newCell.y = selectedCell2.y newCell.z = selectedCell2.z elif centrand == 4: newCell.x = selectedCell2.x newCell.y = selectedCell1.y newCell.z = selectedCell1.z else: newCell.x = selectedCell2.x newCell.y = selectedCell2.y newCell.z = selectedCell1.z #switch rotation of ligand rotrand = random.randint(0,5) if rotrand == 0: newCell.sph_theta = selectedCell1.sph_theta newCell.sph_phi = selectedCell2.sph_phi newCell.theta = selectedCell2.theta elif rotrand == 1: newCell.sph_theta = selectedCell1.sph_theta newCell.sph_phi = selectedCell1.sph_phi newCell.theta = selectedCell2.theta elif rotrand == 2: newCell.sph_theta = selectedCell1.sph_theta newCell.sph_phi = selectedCell1.sph_phi newCell.theta = selectedCell1.theta elif rotrand == 3: newCell.sph_theta = selectedCell2.sph_theta newCell.sph_phi = selectedCell2.sph_phi newCell.theta = selectedCell2.theta elif rotrand == 4: newCell.sph_theta = selectedCell2.sph_theta newCell.sph_phi = selectedCell1.sph_phi newCell.theta = selectedCell1.theta else: newCell.sph_theta = selectedCell2.sph_theta newCell.sph_phi = selectedCell2.sph_phi newCell.theta = selectedCell1.theta return newCell
def randomPopulation(self, sizePop):
population = []
for i in xrange(sizePop):
gen = Gene()
gen.id = i
gen.x = random.uniform(-self.__spaceLen, self.__spaceLen)
gen.y = random.uniform(-self.__spaceLen, self.__spaceLen)
gen.z = random.uniform(-self.__spaceLen, self.__spaceLen)
gen.sph_theta = math.pi * random.randint(0, 200) / 100.0
gen.sph_phi = math.pi * random.randint(0, 100) / 100.0
gen.theta = math.pi * random.randint(0, 200) / 100.0
for r in xrange(len(self.__rotateAtoms)):
gen.rotateAtoms.append(math.pi * random.randint(0, 200) / 100.0)
population.append(gen)
return population[:]
def randomPopulation(self, sizePop):
population = []
for i in xrange(sizePop):
gen = Gene()
gen.id = i
gen.x = random.uniform(-self.__spaceLen, self.__spaceLen)
gen.y = random.uniform(-self.__spaceLen, self.__spaceLen)
gen.z = random.uniform(-self.__spaceLen, self.__spaceLen)
gen.sph_theta = math.pi * random.randint(0, 200) / 100.0
gen.sph_phi = math.pi * random.randint(0, 100) / 100.0
gen.theta = math.pi * random.randint(0, 200) / 100.0
for r in xrange(len(self.__rotateAtoms)):
gen.rotateAtoms.append(math.pi * random.randint(0, 200) /
100.0)
population.append(gen)
return population[:]
def crossover50(self, selectedCell1, selectedCell2):
newCell = Gene()
#switch center of ligand
centrand = random.randint(0, 5)
if centrand == 0:
newCell.x = selectedCell1.x
newCell.y = selectedCell2.y
newCell.z = selectedCell2.z
elif centrand == 1:
newCell.x = selectedCell1.x
newCell.y = selectedCell1.y
newCell.z = selectedCell2.z
elif centrand == 2:
newCell.x = selectedCell1.x
newCell.y = selectedCell1.y
newCell.z = selectedCell1.z
elif centrand == 3:
newCell.x = selectedCell2.x
newCell.y = selectedCell2.y
newCell.z = selectedCell2.z
elif centrand == 4:
newCell.x = selectedCell2.x
newCell.y = selectedCell1.y
newCell.z = selectedCell1.z
else:
newCell.x = selectedCell2.x
newCell.y = selectedCell2.y
newCell.z = selectedCell1.z
#switch rotation of ligand
rotrand = random.randint(0, 5)
if rotrand == 0:
newCell.sph_theta = selectedCell1.sph_theta
newCell.sph_phi = selectedCell2.sph_phi
newCell.theta = selectedCell2.theta
elif rotrand == 1:
newCell.sph_theta = selectedCell1.sph_theta
newCell.sph_phi = selectedCell1.sph_phi
newCell.theta = selectedCell2.theta
elif rotrand == 2:
newCell.sph_theta = selectedCell1.sph_theta
newCell.sph_phi = selectedCell1.sph_phi
newCell.theta = selectedCell1.theta
elif rotrand == 3:
newCell.sph_theta = selectedCell2.sph_theta
newCell.sph_phi = selectedCell2.sph_phi
newCell.theta = selectedCell2.theta
elif rotrand == 4:
newCell.sph_theta = selectedCell2.sph_theta
newCell.sph_phi = selectedCell1.sph_phi
newCell.theta = selectedCell1.theta
else:
newCell.sph_theta = selectedCell2.sph_theta
newCell.sph_phi = selectedCell2.sph_phi
newCell.theta = selectedCell1.theta
#switch rotational bonds
bondrand = random.randint(0, (len(selectedCell1.rotateBonds) - 1))
if random.randint(0, 1) == 1:
newCell.rotateBonds = selectedCell1.rotateBonds[:
bondrand] + selectedCell2.rotateBonds[
bondrand:]
else:
newCell.rotateBonds = selectedCell2.rotateBonds[:
bondrand] + selectedCell1.rotateBonds[
bondrand:]
return newCell