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added graph member function

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This commit is contained in:
Marat Valiev 2012-02-16 01:23:31 +00:00
parent acb81accf9
commit fc6f511e92
1 changed files with 38 additions and 4 deletions
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42
contrib/marat/nwchem-python/my_system.py
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@ -168,12 +168,44 @@ class MySystem(object):
plt.axis('off')
plt.savefig(name)
T=nx.dfs_tree(G)
print(sorted(T.edges(data=True)))
nx.write_dot(G,"shell.dot")
# T=nx.dfs_tree(G)
# print(sorted(T.edges(data=True)))
# nx.write_dot(G,"shell.dot")
# print "density=",nx.density(G)
# plt.show() # display
# return G
def graph(self):
'''
'''
import networkx as nx
G=nx.MultiGraph()
for i,r in enumerate(self.reslist):
G.add_node(i+1,name=r.name)
solvent = [n for n,d in G.nodes_iter(data=True) if d['name'] in ['WAT','HOH','WTR' ]]
solute = [n for n,d in G.nodes_iter(data=True) if d['name'] not in ['WAT','HOH','WTR' ]]
h = self.hbond_matrix1()
nr = numpy.size(h,0)
for i in range(nr):
for j in range(i+1,nr):
if h[i][j]==1:
G.add_edge(i+1,j+1,name="hbond")
if h[i][j]==2:
G.add_edge(i+1,j+1,name="hbond2")
G.add_edge(i+1,j+1,name="hbond2")
elif GenericResidue.spec_bonded(self.reslist[i], self.reslist[j]):
G.add_edge(i+1,j+1,name="special")
esolute = [(u,v) for u,v,d in G.edges_iter(data=True) if (u in solute or v in solute) and d['name']=='hbond' ]
esolute2 = [(u,v) for u,v,d in G.edges_iter(data=True) if (u in solute or v in solute) and d['name']=='hbond2' ]
esolvent= [(u,v) for u,v,d in G.edges_iter(data=True) if (u in solvent and v in solvent) and d['name']=='hbond']
especial= [(u,v) for u,v,d in G.edges_iter(data=True) if d['name']=='special' ]
return G
def create_simple_graph(self,name):
import networkx as nx
@ -311,7 +343,9 @@ if __name__ == '__main__':
sim1 = MySystem.fromPDBfile("w4-1.pdb")
print sim1.hbond_matrix1()
# sim1.toPDBfile("shell-1.pdb")
sim1.create_graph("shell.png")
# sim1.create_graph("shell.png")
G=sim1.graph()
print nx.density(G)
# dm=sim1.dist_matrix(2.8)
# chain0=[0]
# level=2