def find_networks(M, VW, L, n_finish=1, n_start=0, delta=30, rcut=1.0, ndna=25):
#The total number of frames we are going to look at
x=np.arange(n_start,n_finish,delta)
print len(x)
#Find the number of connections at specific points x
import MD.canalysis.connections as con
import MD.analysis.connections as conn
import MD.analysis.graph as graph
try:
connections = util.pickle_load('con.pkl')
except:
try:
C = util.pickle_load('C.pkl')
G = util.pickle_load('G.pkl')
except:
G=M.cord_auto(['G'])
C=M.cord_auto(['C'])
util.pickle_dump(C,'C.pkl')
util.pickle_dump(G,'G.pkl')
connections = con.connections(C[x],G[x],L,rcut=rcut)
util.pickle_dump(connections,'con.pkl')
#plot total number of connections
num_connections=conn.num_connections(connections,VW.shape[1])
con_all = []
for i in range(len(connections)):
con_all.append(len(connections[i])/2.)
pyplot.plot(x,num_connections,xlabel='Time',
ylabel='hyrbid. density', save='connections')
pyplot.plot(x,con_all,xlabel='Time',
ylabel='hyrbid', save='connections_all')
plt.close()
#get the info
networks, num_networks, deg, neighbors, num_n, gr = graph.grapher(connections,VW.shape[1],ndna)
util.pickle_dump(networks,'net.pkl')
#plot the number of neighbors at each timesteps
pyplot_eps.plot(x,num_n,xlabel='Time',
ylabel='num neighbors', save='neighbors')
plt.close()
print 'making plot'
net = []
for i in networks:
net.append(len(i))
pyplot_eps.plot(x,net,xlabel='t',ylabel='networks',save='net')
label = ['networks','1','2','3','4','5','6','7','8','9']
pyplot_eps.plot(x,networks,xlabel='t',ylabel='Networks',save='net')
pyplot.plot_multi(x,deg,label,xlabel='time',ylabel='number',save='con_net')
return x, networks, connections
def find_networks(M, VW, L,x,ndna=25):
import MD.canalysis.connections as con
import MD.analysis.connections as conn
import MD.analysis.graph as graph
#plot total number of connections
connections = _connections(M)
num_connections=conn.num_connections(connections,VW.shape[1])
con_all = []
for i in range(len(connections)):
con_all.append(len(connections[i][0]))
print len(x),len(num_connections)
pyplot.plot(x,num_connections,xlabel='Time',
ylabel='hyrbid. density', save='connections')
pyplot.plot(x,con_all,xlabel='Time',
ylabel='hyrbid', save='connections_all')
plt.close()
#get the info
networks, num_networks, deg, neighbors, num_n, gr = graph.grapher(connections,VW.shape[1],ndna)
util.pickle_dump(networks,'net.pkl')
#plot the number of neighbors at each timesteps
pyplot.plot(x,num_n,xlabel='Time',
ylabel='num neighbors', save='neighbors')
plt.close()
print 'making plot'
net = []
for i in networks:
net.append(len(i))
pyplot.plot(x,net,xlabel='t',ylabel='networks',save='net')
label = ['networks','1','2','3','4','5','6','7','8','9']
x = [x for i in range(len(deg))]
#pyplot.plot(x,num_networks,xlabel='t',ylabel='Networks',save='net')
#pyplot.plot_multi(x[:4],deg[:4],label,xlabel='time',ylabel='number',save='con_net')
plt.close()
return networks, num_networks, deg, neighbors, num_n, gr
#pyplot.plot_multi(x[:4],deg[:4],label,xlabel='time',ylabel='number',save='con_net')
plt.close()
return networks, num_networks, deg, neighbors, num_n, gr