/
topology_utils.py
86 lines (75 loc) · 3.22 KB
/
topology_utils.py
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# coding=utf-8
# Copyright © 2018 Computational Molecular Biology Group,
# Freie Universität Berlin (GER)
#
# Redistribution and use in source and binary forms, with or
# without modification, are permitted provided that the
# following conditions are met:
# 1. Redistributions of source code must retain the above
# copyright notice, this list of conditions and the
# following disclaimer.
# 2. Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials
# provided with the distribution.
# 3. Neither the name of the copyright holder nor the names of
# its contributors may be used to endorse or promote products
# derived from this software without specific
# prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND
# CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
# INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
# STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
def plot_networkx_topology_graph(topology):
import matplotlib.pyplot as plt
import networkx as nx
G = nx.Graph()
top_graph = topology.get_graph()
labels = {}
types = {}
n_types = 0
colors = []
for v in top_graph.get_vertices():
G.add_node(v.particle_index)
labels[v.particle_index] = v.label
if not v.particle_type() in types:
types[v.particle_type()] = n_types
n_types += 1
colors.append(types[v.particle_type()])
for v in top_graph.get_vertices():
for vv in v:
G.add_edge(v.particle_index, vv.get().particle_index)
pos = nx.spring_layout(G) # positions for all nodes
nx.draw_networkx_nodes(G, pos, node_size=700, node_color=colors, cmap=plt.cm.summer)
nx.draw_networkx_edges(G, pos, width=3)
nx.draw_networkx_labels(G, pos, font_size=20, labels=labels, font_family='sans-serif')
plt.show()
def plot_networkx_graph(G):
import matplotlib.pyplot as plt
import networkx as nx
pos = nx.spring_layout(G) # positions for all nodes
labels = {}
for node in G.nodes():
labels[node] = G.node[node]["label"]
if not labels[node]:
labels[node] = node
nx.draw_networkx_nodes(G, pos, node_size=700, cmap=plt.cm.summer)
nx.draw_networkx_edges(G, pos, width=3)
nx.draw_networkx_labels(G, pos, font_size=20, labels=labels, font_family='sans-serif')
plt.show()
def plot_gexf_string(string):
import networkx as nx
from io import StringIO
strio = StringIO(u"%s" % string)
graph = nx.read_gexf(strio, relabel=False)
plot_networkx_graph(graph)