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IMP Reference Guide
2.8.0
The Integrative Modeling Platform
IMP Manual
Reference Guide
Modules
Classes
Examples
doc
examples
kernel
graph.py
1
## \example kernel/graph.py
2
# A simple example showing how to use the graph interface for in python.
3
4
from
__future__
import
print_function
5
import
IMP
6
import
sys
7
8
IMP.setup_from_argv
(sys.argv,
"Graph interface"
)
9
10
m =
IMP.Model
()
11
# An undirected graph with an IMP::Object for each node
12
g =
IMP.DependencyGraph
()
13
vs = []
14
ps = []
15
for
i
in
range(0, 10):
16
ps.append(
IMP.Particle
(m))
17
vs.append(g.add_vertex(ps[-1]))
18
g.add_edge(vs[0], vs[1])
19
g.add_edge(vs[1], vs[2])
20
21
# try to use the altgraph package to visualize
22
IMP.show_graphviz
(g)
23
try
:
24
IMP.show_graphviz
(g)
25
except
:
26
print(
"Oh well, no altgraph"
)
27
28
try
:
29
import
matplotlib
30
# the engine to be used must be selected before pyplot is imported
31
matplotlib.use(
"macosx"
)
32
import
matplotlib.pyplot
33
34
# the method below requires the altgraph python package
35
xg =
IMP.get_networkx_graph
(g)
36
37
# the networkx visualization tools suck, so skip them
38
#import networkx
39
# networkx.draw(xg)
40
# networkx.draw_shell(xg)
41
# matplotlib.pyplot.show()
42
except
:
43
print(
"networkx not fully installed"
)
44
45
g.remove_vertex(0)
46
47
# we can also try another show method
48
try
:
49
IMP.show_graphviz
(g)
50
except
:
51
print(
"oh well, something not working with graphviz"
)
52
53
# finally, we can
54
# in and out neighbors are the same
55
for
n
in
g.get_in_neighbors(8):
56
print(g.get_vertex_name(n).get_name())
IMP::setup_from_argv
Strings setup_from_argv(const Strings &argv, std::string description, std::string positional_description, int num_positional)
IMP::DependencyGraph
boost::graph DependencyGraph
A directed graph on the interactions between the various objects in the model.
Definition:
dependency_graph.h:37
IMP::Model
Class for storing model, its restraints, constraints, and particles.
Definition:
Model.h:72
IMP::Particle
Class to handle individual particles of a Model object.
Definition:
Particle.h:41
IMP::show_graphviz
std::string show_graphviz(Graph g)
IMP::get_networkx_graph
networkx::DiGraph get_networkx_graph(Graph g)