def load_jmol_conf(self, file_name, number_of_chains=1):
"""
Load chain configuration from JMOL file
@string file_name: Name of jmol file
@dict map_dict: dict with Monomer class
@int number_of_chains: number of chains in jmol file
"""
f = open(file_name, "r+")
data = f.readlines()
header = int(data[0])
coordinate_data = map(lambda x: x.split(" "), data[2:])
chains = []
for chain_idx in range(number_of_chains):
chain_seq = []
slice_coordinate = coordinate_data[chain_idx * header:]
self.chain_list[chain_idx].positions_list = []
for c_idx in range(len(slice_coordinate)):
c = slice_coordinate[c_idx]
crr = tuple(map(lambda x: float(x)/settings.JMOL_SCALE, tuple(c[1:])))
print "Load", crr
self.chain_list[chain_idx].chain[c_idx]._open = crr
self.chain_list[chain_idx].chain[c_idx].position = Lattice.convert_to_periodic_coordinate(crr)
self.chain_list[chain_idx].positions_list.append(self.chain_list[chain_idx].chain[c_idx]._position)
self.chain_list[chain_idx] = self.rebuild_direction(self.chain_list[chain_idx])
def begin_rotate(self, monomer_idx = None):
"""
rotate with begin
"""
random_direction = randrange(0, Lattice.z)
#new_position = Lattice.get_coordinate(self.chain[1]._position, random_direction)
new_position = self.chain[1].neighbours_position[random_direction]
if self.box.is_occupied(new_position) or new_position in self.positions_list:
#logging.info("Reject rotate; position: (%d, %d, %d) is occupied" % (new_position))
return False
new_monomer = self.chain[0]
old_position = self.chain[0]._position
old_open_position = self.chain[0]._open
old_next_direction = self.chain[0].next_direction
old_energy = self.total_energy
self.chain[0].position = new_position
self.chain[0]._open = Lattice.get_open_coordinate(self.chain[1]._open, random_direction)
self.chain[0].next_direction = Lattice.TURN_DIRECTION[random_direction]
self.positions_list[0] = new_position
perform_move = True
new_energy = None
if self.box.athermal_state == False:
new_energy = self.box.calculate_chain_energy(self)
dE = new_energy - old_energy
if self.box.accept(dE, None):
perform_move = True
else:
perform_move = False
if perform_move:
if not new_energy:
new_energy = self.box.calculate_chain_energy(self)
self.total_energy = new_energy
else:
new_monomer.position = old_position
new_monomer._open = old_open_position
new_monomer.next_direction = old_next_direction
self.chain[0] = new_monomer
self.positions_list[0] = old_position
# restore old energy
self.total_energy = old_energy
return perform_move
def create_valid_lists(list):
point_monomer = {}
monomer_list = []
position_set = set()
for line in list:
type = line[0]
ll = np.array(line[1:]) * scale
position = tuple(ll)
m = DummyMonomer(position, type, Lattice.get_neighbours(tuple(position)))
point_monomer[position] = m
monomer_list.append(m)
position_set.add(position)
return point_monomer, monomer_list, position_set
def get_direction(self, monomer_b, monomer_a):
"""
Return direction between two monomers, use to avoid some moves
End point: b
Start point: a
"""
if not isinstance(monomer_a, Monomer):
monomer_a = self[monomer_a]
if not isinstance(monomer_b, Monomer):
monomer_b = self[monomer_b]
vector = np.array(monomer_b._open) - np.array(monomer_a._open)
try:
direction = Lattice.get_direction(tuple(vector))
except Exception, e:
#logging.debug("get_direction for (%d, %d, %d) - (%d, %d, %d): (%d, %d, %d)" % (monomer_b._open, monomer_a._open, vector))
raise e
def process(file, step=None, output_file=None):
if isinstance(file, str):
f = open(file)
else:
f = file
try:
line = f.readlines()
nr = int(line[0].replace("\n", ""))
except:
print line
sys.exit(1)
data = np.loadtxt(file, dtype=str, skiprows=1)
# data = f.readlines()[1:]
point_monomer = {}
monomer_list = []
position_set = set()
if parser.scale == -1 and "." in data[0]:
print "Atom position are float, please set -scale parameter to rescale them!"
sys.exit(1)
for line in data:
# tmp = line.replace("\n","").split(" ")
type = line[0]
ll = map(float, line[1:])
x = int(ll[0] * scale)
y = int(ll[1] * scale)
z = int(ll[2] * scale)
position = (x, y, z)
m = DummyMonomer(position, type, Lattice.get_neighbours(tuple(position)))
point_monomer[position] = m
monomer_list.append(m)
position_set.add(position)
return point_monomer, monomer_list, position_set
def pull_move(self, monomer_idx = None):
"""
Pull move, N. Lesh, M. Mitzemacher, S. Whitesides
"""
## flags
valid_configuration = False
if settings.DEBUG: self.valid_chain()
#if monomer_idx is None:
monomer_idx = randrange(0, self._total_length - 1)
## two special cases at the begin/end
case = 3
old_energy = self.total_energy
is_occupied = self.box.is_occupied
is_neighbour = self.box.lattice.is_neighbour
## trials with optimization
last_affected_idx = 0
# case
# 0 - left
# 1 - right
# 3 - inside
# 0 - right
# 1 - left
#mod_pos = 0
if monomer_idx == 0: ## left
dir_1 = randrange(0, Lattice.z)
dir_2 = randrange(0, Lattice.z)
pos_1 = self.chain[0].neighbours_position[dir_1]
pos_2 = self.box.lattice.get_coordinate(pos_1, dir_2)
if is_occupied(pos_1) or is_occupied(pos_2):
return False
#if not is_neighbour(pos_1, pos_2):
# return False
m1 = self.chain[0]
m2 = self.chain[1]
open_pos_1 = self.box.lattice.get_open_coordinate(m1._open, dir_1)
open_pos_2 = self.box.lattice.get_open_coordinate(open_pos_1, dir_2)
old_position_list = self.positions_list[:]
#old_monomer_position = [ m._position for m in self.chain ]
old_monomer_position = old_position_list
old_monomer_open_position = [ m._open for m in self.chain ]
old_monomer_next_direction = [ m.next_direction for m in self.chain ]
m1.position = pos_2
m1._open = open_pos_2
m2.position = pos_1
m2._open = open_pos_1
## old energy
#self[0] = m1
m1.chain = self
self.chain[0] = m1
self.positions_list[0] = m1._position
#self[1] = m2
m2.chain = self
self.chain[1] = m2
self.positions_list[1] = m2._position
#mod_pos = 2
for idx in xrange(2, self._total_length):
i_monomer = self.chain[idx]
p_monomer = self.chain[idx - 1]
diff = np.array(i_monomer._open) - np.array(p_monomer._open)
diff = diff.dot(diff)
if diff == 2:
p_monomer.next_direction = p_monomer.neighbours_position.index(i_monomer._position)
break
#mod_pos += 1
i_monomer.position = old_monomer_position[idx - 2]
i_monomer._open = old_monomer_open_position[idx - 2]
i_monomer.next_direction = old_monomer_next_direction[idx - 2]
#self[idx] = i_monomer
i_monomer.chain = self
self.chain[idx] = i_monomer
self.positions_list[idx] = i_monomer._position
last_affected_idx = idx
self.chain[0].next_direction = self.chain[0].neighbours_position.index(self.chain[1]._position)
self.chain[1].next_direction = self.chain[1].neighbours_position.index(self.chain[2]._position)
case = 0
if settings.DEBUG: self.valid_chain()
elif monomer_idx == self._total_length - 1: ## right
dir_1 = randrange(0, Lattice.z)
dir_2 = randrange(0, Lattice.z)
pos_1 = self.chain[-1].neighbours_position[dir_1]
pos_2 = self.box.lattice.get_coordinate(pos_1, dir_2)
if is_occupied(pos_1) or is_occupied(pos_2):
return False
open_pos_1 = self.box.lattice.get_open_coordinate(self.chain[-1]._open, dir_1)
open_pos_2 = self.box.lattice.get_open_coordinate(open_pos_1, dir_2)
old_position_list = self.positions_list[:]
#old_monomer_position = [ m._position for m in self.chain ]
old_monomer_position = old_position_list
old_monomer_open_position = [ m._open for m in self.chain ]
old_monomer_next_direction = [ m.next_direction for m in self.chain ]
m1 = self.chain[-1]
m2 = self.chain[-2]
m1.position = pos_2
m1._open = open_pos_2
m2.position = pos_1
m2._open = open_pos_1
#mod_pos = 2
for idx in xrange(self._total_length - 2, -1, -1):
i_monomer = self.chain[idx]
n_monomer = self.chain[idx+1]
diff = np.array(i_monomer._open) - np.array(n_monomer._open)
diff = diff.dot(diff)
if diff == 2:
i_monomer.next_direction = i_monomer.neighbours_position.index(n_monomer._position)
break
#mod_pos += 1
i_monomer.position = old_monomer_position[idx + 2]
i_monomer._open = old_monomer_open_position[idx + 2]
i_monomer.next_direction = old_monomer_next_direction[idx + 2]
#self[idx] = i_monomer
i_monomer.chain = self
self.chain[idx] = i_monomer
self.positions_list[idx] = i_monomer._position
last_affected_idx = idx
case = 1
self.chain[-2].next_direction = self.chain[-2].neighbours_position.index(self.chain[-1]._position)
self.chain[-1].next_direction = 0
if settings.DEBUG: self.valid_chain()
if case == 3:
prev_monomer = self.chain[monomer_idx - 1]
monomer = self.chain[monomer_idx]
next_monomer = self.chain[monomer_idx + 1]
random_neighbour_prev = randrange(0, Lattice.z)
#if self.box.is_occupied(prev_monomer.neighbours_position[random_neighbour_prev]):
# return False
#L can be adjenct to i-1 or i+1, randomly choose
sub_case = randrange(0, 2) ## 0 - right, 1 - left
if sub_case == 0:
L_position = next_monomer.neighbours_position[random_neighbour_prev]
L_open_position = Lattice.get_open_coordinate(next_monomer._open, random_neighbour_prev)
Lnext_direction = self.box.lattice.get_neighbours(L_position).index(next_monomer._position)
elif sub_case == 1:
L_position = prev_monomer.neighbours_position[random_neighbour_prev]
L_open_position = Lattice.get_open_coordinate(prev_monomer._open, random_neighbour_prev)
Lprev_direction = self.box.lattice.get_neighbours(L_position).index(prev_monomer._position)
C_position = monomer.neighbours_position[random_neighbour_prev]
C_open_position = Lattice.get_open_coordinate(monomer._open, random_neighbour_prev)
diff = np.array(L_position) - np.array(C_position)
diff = diff.dot(diff)
if diff != 2:
return False
if is_occupied(L_position):
return False
if is_occupied(C_position):
if (sub_case == 0 and C_position != prev_monomer._position) or (sub_case == 1 and C_position != next_monomer._position):
return False
# old_energy
#old_energy = self.box.calculate_chain_energy(self)
# direction L->C
C_nb = self.box.lattice.get_neighbours(C_position)
CL_direction = C_nb.index(L_position)
LC_direction = self.box.lattice.TURN_DIRECTION[CL_direction]
# save old position list
old_position_list = self.positions_list[:]
#old_monomer_position = [ m._position for m in self.chain ]
old_monomer_position = old_position_list
old_monomer_open_position = [ m._open for m in self.chain ]
old_monomer_next_direction = [ m.next_direction for m in self.chain ]
if (sub_case == 0 and prev_monomer._position == C_position) or \
(sub_case == 1 and next_monomer._position == C_position):
valid_configuration = True
monomer.position = L_position
monomer._open = L_open_position
if sub_case == 0:
monomer.next_direction = Lnext_direction
elif sub_case == 1:
monomer.next_direction = LC_direction
#self[monomer_idx] = monomer
monomer.chain = self
self.chain[monomer_idx] = monomer
self.positions_list[monomer_idx] = monomer._position
if sub_case == 0:
prev_monomer.position = C_position
prev_monomer._open = C_open_position
prev_monomer.next_direction = CL_direction
#self[monomer_idx - 1] = prev_monomer
prev_monomer.chain = self
self.chain[monomer_idx - 1] = prev_monomer
self.positions_list[monomer_idx - 1] = prev_monomer._position
elif sub_case == 1:
if not valid_configuration:
next_monomer.position = C_position
next_monomer._open = C_open_position
next_monomer.next_direction = self.box.lattice.TURN_DIRECTION[random_neighbour_prev]
#self[monomer_idx + 1] = next_monomer
next_monomer.chain = self
self.chain[monomer_idx + 1] = next_monomer
self.positions_list[monomer_idx + 1] = next_monomer._position
prev_monomer.next_direction = random_neighbour_prev
#self[monomer_idx - 1] = prev_monomer
prev_monomer.chain = self
self.chain[monomer_idx - 1] = prev_monomer
self.positions_list[monomer_idx - 1] = prev_monomer._position
#mod_pos = 2
if not valid_configuration:
if sub_case == 0: ## right
for j in xrange(monomer_idx - 2, -1, -1):
j_monomer = self.chain[j]
i_monomer = self.chain[j+1]
diff = np.array(j_monomer._open) - np.array(i_monomer._open)
diff = diff.dot(diff)
if diff == 2:
j_monomer.next_direction = j_monomer.neighbours_position.index(i_monomer._position)
break
#mod_pos += 1
j_monomer.position = old_monomer_position[j+2]
j_monomer._open = old_monomer_open_position[j+2]
j_monomer.next_direction = j_monomer.neighbours_position.index(i_monomer._position)
#self[j] = j_monomer
j_monomer.chain = self
self.chain[j] = j_monomer
self.positions_list[j] = j_monomer._position
elif sub_case == 1:
for j in xrange(monomer_idx + 2, self._total_length):
j_monomer = self.chain[j]
i_monomer = self.chain[j-1]
diff = np.array(j_monomer._open) - np.array(i_monomer._open)
diff = diff.dot(diff)
if diff == 2:
i_monomer.next_direction = i_monomer.neighbours_position.index(j_monomer._position)
break
#mod_pos += 1
j_monomer.position = old_monomer_position[j-2]
j_monomer._open = old_monomer_open_position[j-2]
i_monomer.next_direction = i_monomer.neighbours_position.index(j_monomer._position)
#self[j] = j_monomer
j_monomer.chain = self
self.chain[j] = j_monomer
self.positions_list[j] = j_monomer._position
if settings.DEBUG: self.valid_chain()
## end move procedure
# old_energy, emergency case
new_energy = self.box.calculate_chain_energy(self)
dE = new_energy - old_energy
accept_move = False
if dE <= 0.0 or self.box.athermal_state:
accept_move = True
else:
accept_move = self.box.accept(dE, None)
if accept_move is True:
self.total_energy = new_energy
#self.positions_list = [ m._position for m in self.chain ]
self.box.global_energy_update([self.idx])
#f = open("mod_pos_%d" % self._total_length, "w+")
#f.write("%d\n" % mod_pos)
#f.close()
#self.valid_chain()
else: ## revert
if case == 3:
if sub_case == 0:
monomer_list = xrange(0, monomer_idx+2)
elif sub_case == 1:
monomer_list = xrange(monomer_idx-1, self._total_length)
elif case == 0:
monomer_list = xrange(0, self._total_length)
elif case == 1: ##
monomer_list = xrange(0, self._total_length)
#monomer_list = changed_monomer_idx
for idx in monomer_list:
m = self.chain[idx]
old_pos = old_monomer_position[idx]
old_dir = old_monomer_next_direction[idx]
if m._position != old_pos or m.next_direction != old_dir:
m.position = old_monomer_position[idx]
m._open = old_monomer_open_position[idx]
m.next_direction = old_monomer_next_direction[idx]
#self[idx] = m
m.chain = self
self.chain[idx] = m
self.positions_list[idx] = m._position
#self.positions_list = old_position_list[:]
self.total_energy = old_energy
#self.valid_chain()
return accept_move
def _snake(self, move_type):
"""
Snake move
"""
#direction_to_choice = range(0, Lattice.z)
if settings.DEBUG: self.valid_chain()
if move_type == 0:
monomer = self.chain[0]
elif move_type == 1:
monomer = self.chain[-1]
#random new position
random_direction = randrange(0, Lattice.z)
new_position = monomer.neighbours_position[random_direction]
open_position = Lattice.get_open_coordinate(monomer._open, random_direction)
if self.box.is_occupied(new_position) or new_position in self.positions_list:
return False
# copy
old_position_list = self.positions_list[:]
old_open_position_list = [ x._open for x in self.chain ]
old_next_direction_list = [ x.next_direction for x in self.chain ]
old_energy = self.total_energy
self.positions_list = []
"""
Update position of monomers in chain (copy)
"""
if move_type == 0: # left
self.positions_list = [new_position]
for idx in range(1, self._total_length):
self.chain[idx].position = old_position_list[idx - 1]
self.chain[idx]._open = old_open_position_list[idx - 1]
self.chain[idx].next_direction = old_next_direction_list[idx - 1]
self.positions_list += old_position_list[0: self._total_length - 1]
self.chain[0].position = new_position
self.chain[0]._open = open_position
self.chain[0].next_direction = self.box.lattice.TURN_DIRECTION[random_direction]
elif move_type == 1: # right
for idx in range(0, self._total_length - 1):
self.chain[idx].position = old_position_list[idx + 1]
self.chain[idx]._open = old_open_position_list[idx + 1]
self.chain[idx].next_direction = old_next_direction_list[idx + 1]
self.chain[-1].position = new_position
self.chain[-1]._open = open_position
self.chain[-2].next_direction = random_direction
self.positions_list = old_position_list[1:] + [new_position]
new_energy = self.box.calculate_chain_energy(self)
dE = new_energy - old_energy
if dE <= 0.0 or self.box.athermal_state:
if settings.DEBUG: self.valid_chain()
self.total_energy = new_energy
return True
elif self.box.accept(dE, None):
if settings.DEBUG: self.valid_chain()
self.total_energy = new_energy
return True
else:
for idx in xrange(self._total_length):
self.chain[idx].position = old_position_list[idx]
self.chain[idx]._open = old_open_position_list[idx]
self.chain[idx].next_direction = old_next_direction_list[idx]
self.positions_list = old_position_list[:]
self.total_energy = old_energy
if settings.DEBUG: self.valid_chain()
return False
if number_of_positions == 0:
return False
new_position = list(common_neighbours_positions)[randrange(0, number_of_positions)]
if not new_position or len(new_position) != 3:
if __debug__: logging.debug("New_position %s:" % str(new_position))
return False
try:
direction = prev_monomer.neighbours_position.index(new_position)
except Exception, e:
if __debug__: logging.error("Reject segment, error in direction, (%d, %d, %d)" % (new_position))
return False
open_position = Lattice.get_open_coordinate(prev_monomer._open, direction)
if self.box.is_occupied(new_position):
#logging.debug("Reject segment; Position: (%d, %d, %d) is occupied" % (new_position))
return False
# make copy of old monomer
old_position = rotate_monomer._position
old_open_position = rotate_monomer._open
old_prev_next_direction = self.chain[monomer_idx - 1].next_direction
old_next_direction = rotate_monomer.next_direction
old_energy = self.total_energy
self.chain[monomer_idx].position = new_position
self.chain[monomer_idx]._open = open_position
def random_strategy(self, chain):
"""
Put chain in random mode
"""
random_point = tuple(map(lambda x: x/2, self.box_size))
while self.is_occupied(random_point) or not Lattice.is_valid_coordinate(random_point):
random_point = tuple([ random.randrange(0, self.box_size[x]) for x in range(3) ])
if __debug__: logging.info("Chain start point: %d, %d, %d" % random_point)
f_monomer = chain.chain[0]
f_monomer.position = random_point
f_monomer._open = random_point
chain[0] = f_monomer
for idx in range(1, chain._total_length):
prev_monomer = chain.chain[idx - 1]
monomer = chain.chain[idx]
not_found = True
direction_list = range(0, Lattice.z)
direction_list_idx = Lattice.z
while not_found:
try:
direction_idx = random.randrange(0, direction_list_idx)
except:
return False
direction = direction_list[direction_idx]
pos = Lattice.get_coordinate(prev_monomer._position, direction)
open_pos = Lattice.get_open_coordinate(prev_monomer._open, direction)
if pos in chain.positions_list or \
(self.number_of_chains > 1 and self.is_occupied(pos)):
not_found = True
direction_list.remove(direction)
direction_list_idx -= 1
else:
not_found = False
monomer.position = pos
monomer.open_position = open_pos
#monomer.next_direction = None
prev_monomer.next_monomer = monomer
prev_monomer.next_direction = direction
chain[idx] = monomer
chain.chain[idx-1] = prev_monomer
## rebuild directions
for idx in range(1, chain._total_length):
p = chain.chain[idx - 1]
m = chain.chain[idx]
d = p.neighbours_position.index(m._position)
p.next_direction = d
chain.chain[idx - 1].next_direction = d
chain.chain[-1].next_direction = 0
if __debug__: logging.info('Chain inside box, length=%d' % chain.length)
return chain
def greedy_strategy(self, chain):
"""
Put chain in the box based on a greedy strategy
"""
random_point = tuple(map(lambda x: x/2, self.box_size))
while self.is_occupied(random_point) or not Lattice.is_valid_coordinate(random_point):
random_point = tuple([ random.randrange(0, self.box_size[x]) for x in range(3) ])
f_monomer0 = chain.chain[0]
f_monomer0.position = random_point
f_monomer0._open = random_point
chain[0] = f_monomer0
next_direction = random.randrange(0, Lattice.z)
f_monomer1 = chain.chain[1]
f_monomer1.position = Lattice.get_coordinate(random_point, next_direction)
f_monomer1._open = Lattice.get_open_coordinate(random_point, next_direction)
chain[1] = f_monomer1
chain[0].next_direction = next_direction
pos_list = [f_monomer0._position, f_monomer1._position]
direction_list = range(0, Lattice.z)
for idx in range(2, chain._total_length):
prev_monomer = chain.chain[idx - 1]
monomer = chain.chain[idx]
min_energy = self.calculate_chain_energy(chain)
min_pos = None
min_open_pos = None
min_dir = 0
np.random.shuffle(direction_list)
last_valid_pos = None
last_valid_open_pos = None
for dir in direction_list:
pos = Lattice.get_coordinate(prev_monomer._position, dir)
open_pos = Lattice.get_open_coordinate(prev_monomer._open, dir)
if pos in chain.positions_list or \
(self.number_of_chains > 1 and self.is_occupied(pos)) or \
pos in pos_list:
pass
else:
last_valid_pos = pos
last_valid_open_pos = open_pos
monomer.position = pos
monomer._open = open_pos
chain[idx] = monomer
m_e = self.calculate_chain_energy(chain, slice=[0, idx+1])
if min_energy > m_e:
min_energy = m_e
min_pos = pos
min_open_pos = open_pos
min_dir = dir
monomer.position = min_pos if min_pos else last_valid_pos
monomer._open = min_open_pos if min_open_pos else last_valid_open_pos
chain[idx] = monomer
prev_monomer.next_direction = min_dir
chain[idx - 1] = prev_monomer
## rebuild directions
for idx in range(1, chain._total_length):
p = chain.chain[idx - 1]
m = chain.chain[idx]
d = p.neighbours_position.index(m._position)
p.next_direction = d
chain.chain[idx - 1].next_direction = d
if __debug__: logging.info("Greedy strategy, chain with min energy: %f" % \
self.calculate_chain_energy(chain))
return chain