def make_first_node(grid_object, index):
"""
Create first Node and set type as first protein character.
:param grid_object: grid object
:param index: index
:return: first node
"""
first_node = Node(0, 0, 0)
first_node.type = grid_object.protein[0]
# Put in Grid
grid_object.add_point(first_node, index)
return first_node
def random_chain(grid_object):
"""
Creates a protein chain starting at (0, 0, 0)
then filling in the grid with Nodes by doing a random move from last added
Node to the next one until it has length of whole protein string.
:param grid_object: grid object
:return: grid object
"""
# n'th Node
index = 0
# Clear grid if it exists
if not len(grid_object.grid) != 0:
grid_object.clear_grid()
grid_object.grid_chain = {}
first_node = make_first_node(grid_object, index)
# repeat until the whole protein has finished
while index < len(grid_object.protein) - 1:
# select last added Node
current_node_key = grid_object.grid_chain[index][0]
current_node = grid_object.grid[current_node_key].nodes[0]
new_x, new_y, new_z = make_new_coords(grid_object, current_node)
# if the move doesnt overlap own chain -> add to grid
if not grid_object.overlap(new_x, new_y, new_z):
index += 1
new_node = Node(new_x, new_y, new_z)
new_node.n = index
new_node.type = grid_object.protein[index]
grid_object.add_point(new_node, index)
# start over if chain is stuck
if grid_object.chain_stuck(new_x, new_y, new_z):
index = 0
grid_object.clear_grid()
grid_object.grid_chain = {}
grid_object.add_point(first_node, index)
grid_object.update_all_bonds()
return grid_object