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IMP Reference Guide
2.6.1
The Integrative Modeling Platform
IMP Manual
Reference Guide
Modules
Classes
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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4
import
IMP
5
import
IMP.domino
6
import
IMP.core
7
import
IMP.container
8
import
IMP.algebra
9
import
sys
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IMP.setup_from_argv
(sys.argv,
"merge tree"
)
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IMP.set_log_level
(IMP.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.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
(
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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_particle_indexes():
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pst.set_particle_states(m.get_particle(p), ss)
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# generate a set of restraints based on the close pairs in this randomly
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# 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, m.get_particle_indexes())
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if
len(cps) > 0:
36
# one cannot create a container from an empty list
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acp =
IMP.container.ListPairContainer
(m, 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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# 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
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# 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))