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IMP Reference Guide
2.20.0
The Integrative Modeling Platform
IMP Manual
Reference Guide
Tutorial Index
Modules
Classes
Examples
version 2.20.0
core/simple.py
Illustration of simple usage of the
IMP
library from Python.
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## \example core/simple.py
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# Illustration of simple usage of the IMP library from Python.
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#
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5
import
IMP
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import
IMP.algebra
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import
IMP.core
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import
sys
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IMP.setup_from_argv
(sys.argv,
"simple example"
)
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m =
IMP.Model
()
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# Create two "untyped" particles
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p1 = m.add_particle(
'p1'
)
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p2 = m.add_particle(
'p2'
)
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# "Decorate" the particles with x,y,z attributes (point-like particles)
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d1 =
IMP.core.XYZ.setup_particle
(m, p1)
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d2 =
IMP.core.XYZ.setup_particle
(m, p2)
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# Use some XYZ-specific functionality (set coordinates)
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d1.set_coordinates(
IMP.algebra.Vector3D
(10.0, 10.0, 10.0))
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d2.set_coordinates(
IMP.algebra.Vector3D
(-10.0, -10.0, -10.0))
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print(d1, d2)
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# Harmonically restrain p1 to be zero distance from the origin
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f =
IMP.core.Harmonic
(0.0, 1.0)
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s =
IMP.core.DistanceToSingletonScore
(f,
IMP.algebra.Vector3D
(0., 0., 0.))
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r1 =
IMP.core.SingletonRestraint
(m, s, p1)
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# Harmonically restrain p1 and p2 to be distance 5.0 apart
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f =
IMP.core.Harmonic
(5.0, 1.0)
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s =
IMP.core.DistancePairScore
(f)
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r2 =
IMP.core.PairRestraint
(m, s, (p1, p2))
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# Optimize the x,y,z coordinates of both particles with conjugate gradients
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sf =
IMP.core.RestraintsScoringFunction
([r1, r2],
"scoring function"
)
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d1.set_coordinates_are_optimized(
True
)
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d2.set_coordinates_are_optimized(
True
)
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o =
IMP.core.ConjugateGradients
(m)
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o.set_scoring_function(sf)
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o.optimize(50)
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print(d1, d2)