IMP  2.0.1
The Integrative Modeling Platform
domino/merge_tree.py

The example shows how to generate and inspect a merge tree for use in Domino.

1 ## \example domino/merge_tree.py
2 ## The example shows how to generate and inspect a merge tree for use in Domino.
3 
4 import IMP
5 import IMP.domino
6 import IMP.core
7 import IMP.container
8 import IMP.algebra
9 
10 IMP.base.set_log_level(IMP.base.TERSE)
11 m=IMP.Model()
12 # don't print messages about evaluation
13 m.set_log_level(IMP.base.SILENT)
14 
15 bb= IMP.algebra.BoundingBox3D((0,0,0), (10,10,10))
16 allc=[]
17 for i in range(0,7):
18  p= IMP.Particle(m)
19  d= IMP.core.XYZR.setup_particle(p, IMP.algebra.Sphere3D(IMP.algebra.get_random_vector_in(bb), 1))
20  allc.append(d.get_coordinates())
21 pst= IMP.domino.ParticleStatesTable()
22 ss= IMP.domino.XYZStates(allc)
23 for p in m.get_particles():
24  pst.set_particle_states(p, ss)
25 # generate a set of restraints based on the close pairs in this randomly chosen configuration
26 cp= IMP.core.GridClosePairsFinder()
27 cp.set_distance(1)
28 cps=cp.get_close_pairs(m.get_particles())
29 
30 if len(cps)>0:
31  # one cannot create a container from an empty list
32  acp= IMP.container.ListPairContainer(cps)
33 else:
34  acp= IMP.container.ListPairContainer(m)
35 ps= IMP.core.SoftSpherePairScore(1)
36 r= IMP.container.PairsRestraint(ps, acp)
37 r.set_model(m)
38 
39 # compute the interaction graph based on all the restraints
40 ig= IMP.domino.get_interaction_graph([r],
41  pst)
42 # generate a junction tree from the interaction graph
43 jt= IMP.domino.get_junction_tree(ig)
44 print dir(jt)
45 print type(jt)
46 # create a merge tree from the junction tree, this can be passed to IMP.domin.DominoSampler
47 mt= IMP.domino.get_merge_tree(jt)
48 s=pst.get_subset()
49 print s, type(s)