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