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IMP Reference Guide
2.20.2
The Integrative Modeling Platform
IMP Manual
Reference Guide
Tutorial Index
Modules
Classes
Examples
doc
examples
parallel
tasks.py
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## \example parallel/tasks.py
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# This module contains the setup and task functions used by local_distance.py.
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#
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import
IMP
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import
IMP.algebra
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import
IMP.core
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9
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def
setup():
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"""Create a Model containing two XYZ particles linked by a harmonic
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distance restraint, one fixed at the origin. Return the Model,
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the ScoringFunction, and the free XYZ particle."""
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m =
IMP.Model
()
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p1 =
IMP.Particle
(m)
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d1 =
IMP.core.XYZ.setup_particle
(p1)
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p2 =
IMP.Particle
(m)
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d2 =
IMP.core.XYZ.setup_particle
(p2)
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d1.set_coordinates(
IMP.algebra.Vector3D
(0, 0, 0))
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r =
IMP.core.DistanceRestraint
(m,
IMP.core.Harmonic
(0, 1), p1, p2)
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sf =
IMP.core.RestraintsScoringFunction
([r])
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return
m, sf, d2
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# Note that setup and tasks are Python callables, i.e. functions (like setup
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# above) or classes that implement the __call__ method (like Task below).
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# The latter allows for parameters (Python objects) to be passed from the
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# manager to the workers.
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class
Task(object):
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def
__init__
(self, dist):
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self.dist = dist
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def
__call__(self, m, sf, d):
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"""Place the free XYZ particle at the specified distance from the
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origin. Return the distance and the model's score. Note that the
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input parameters to this method (m, sf, and d) are those returned by
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the setup function above."""
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d.set_coordinates(
IMP.algebra.Vector3D
(0, 0, self.dist))
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return
(self.dist, sf.evaluate(
False
))
setup
Definition:
setup.py:1
IMP::core::RestraintsScoringFunction
Create a scoring function on a list of restraints.
Definition:
RestraintsScoringFunction.h:23
IMP::core::DistanceRestraint
Distance restraint between two particles.
Definition:
DistanceRestraint.h:35
IMP::core::XYZ::setup_particle
static XYZ setup_particle(Model *m, ParticleIndex pi)
Definition:
XYZ.h:51
IMP::Model
Class for storing model, its restraints, constraints, and particles.
Definition:
Model.h:86
IMP::isd.TALOSReader.TALOSReader.__init__
def __init__
start the TALOSReader sequence : a dictionary of sequence number keys and 3-letter code values...
Definition:
TALOSReader.py:22
IMP::core
Basic functionality that is expected to be used by a wide variety of IMP users.
IMP::algebra
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
IMP::algebra::Vector3D
VectorD< 3 > Vector3D
Definition:
VectorD.h:425
IMP::Particle
Class to handle individual particles of a Model object.
Definition:
Particle.h:43
IMP::core::Harmonic
Harmonic function (symmetric about the mean)
Definition:
core/Harmonic.h:27