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2.0.0
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Examples
domino/merge_tree.py
The example shows how to generate and inspect a merge tree for use in Domino.
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## \example domino/merge_tree.py
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## The example shows how to generate and inspect a merge tree for use in Domino.
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import
IMP
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import
IMP.domino
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import
IMP.core
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import
IMP.container
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import
IMP.algebra
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IMP.base.set_log_level
(IMP.base.TERSE)
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m=
IMP.Model
()
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# don't print messages about evaluation
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m.set_log_level(IMP.base.SILENT)
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bb=
IMP.algebra.BoundingBox3D
((0,0,0), (10,10,10))
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allc=[]
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for
i
in
range(0,7):
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p=
IMP.Particle
(m)
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d=
IMP.core.XYZR.setup_particle
(p,
IMP.algebra.Sphere3D
(
IMP.algebra.get_random_vector_in
(bb), 1))
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allc.append(d.get_coordinates())
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pst=
IMP.domino.ParticleStatesTable
()
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ss=
IMP.domino.XYZStates
(allc)
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for
p
in
m.get_particles():
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pst.set_particle_states(p, ss)
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# generate a set of restraints based on the close pairs in this randomly chosen configuration
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cp=
IMP.core.GridClosePairsFinder
()
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cp.set_distance(1)
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cps=cp.get_close_pairs(m.get_particles())
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if
len(cps)>0:
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# one cannot create a container from an empty list
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acp=
IMP.container.ListPairContainer
(cps)
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else
:
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acp=
IMP.container.ListPairContainer
(m)
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ps=
IMP.core.SoftSpherePairScore
(1)
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r=
IMP.container.PairsRestraint
(ps, acp)
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r.set_model(m)
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# compute the interaction graph based on all the restraints
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ig=
IMP.domino.get_interaction_graph
([r],
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pst)
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# generate a junction tree from the interaction graph
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jt=
IMP.domino.get_junction_tree
(ig)
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print
dir(jt)
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print
type(jt)
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# create a merge tree from the junction tree, this can be passed to IMP.domin.DominoSampler
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mt=
IMP.domino.get_merge_tree
(jt)
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s=pst.get_subset()
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print
s, type(s)