def get_ranks(line):
##INPUT
filename = line.strip().split()[0]
chain_names = line.strip().split()[1].strip().split(':')
##GET INTERFACE
chain1, chain2 = first.get_residues(filename, chain_names)
interface_nodes_1, interface_nodes_2, edges = first.calc_interface(chain1, chain2)
##GET NODES CONNECTED TO INTERFACE
within1, within2 = first.calc_within(interface_nodes_1, interface_nodes_2, chain1, chain2)
##ADD NODES AND EDGES (with weights) TO GRAPH
G0 = first.make_graph(chain1, chain2, edges, within1, within2) #add nodes and edges to the graph
##FIND NODE RANKS
functions = [find_weights, find_changes, find_seq_changes,find_centrality]
for i in range(num):
if i>fixed:
j = fixed
else:
j = i
G0 = find_ranks(interface_nodes_1+interface_nodes_2, G0, functions[j], names[i])
maxrank = len(interface_nodes_1 + interface_nodes_2)
return G0, maxrank, interface_nodes_1+interface_nodes_2
def get_changes(line):
##INPUT
filename = line.strip().split()[0]
chain_names = line.strip().split()[1].strip().split(':')
'''
chain_choices = []
with open(filename+'.pdb') as f:
for line in f:
line = line.strip().split()
if line[0]=='COMPND' and line[2]=='CHAIN:':
chain_choices.append(line[3][0])
print "Choose 2 chains/sets of chains from the following: "
print chain_choices
chain_names = raw_input("Enter chain names separated by space: ")
chain_names = chain_names.strip().split()
'''
##GET INTERFACE
chain1, chain2 = first.get_residues(filename, chain_names)
interface_nodes_1, interface_nodes_2, edges = first.calc_interface(chain1, chain2)
##GET NODES CONNECTED TO INTERFACE
within1, within2 = first.calc_within(interface_nodes_1, interface_nodes_2, chain1, chain2)
##ADD NODES AND EDGES (with weights) TO GRAPH
G0 = first.make_graph(chain1, chain2, edges, within1, within2) #add nodes and edges to the graph
##FIND NODE RANKS
maxrank = len(interface_nodes_1)+len(interface_nodes_2)+1
for node in nx.nodes(G0):
G0.node[node]['rank']= maxrank #Initialise all ranks to worst. Non-interface residues retain this rank.
G0 = find_node_ranks(interface_nodes_1+interface_nodes_2, G0) #find node rank by sorting node weights
''' For changing edge width based on weight.
widths = np.array([edge[2]['weight'] for edge in edges])
widths = widths / float(max(widths)) * 2
'''
ranks = nx.get_node_attributes(G0,"rank")
ranks_keys = {y:x for x,y in ranks.iteritems()}
##FIND SUM OF SQUARE CHANGES WHEN NODE OF RANK 'rank' IS REMOVED
errors =[]
for rank in range(1,maxrank):
G1, interface_nodes_new = delete_node_by_rank(interface_nodes_1+interface_nodes_2, G0, rank)
G1 = find_node_ranks(interface_nodes_new, G1)
weights_original = nx.get_node_attributes(G0, "weight_sum")
weights_new = nx.get_node_attributes(G1, "weight_sum")
error =0.0
for node in weights_new:
error += np.square(weights_original[node] - weights_new[node])
errors.append((ranks_keys[rank], round(error,2)))
return errors
