IMP::container::TripletsRestraint Class Reference

Applies a TripletScore to each Triplet in a list. More...

#include <IMP/container/TripletsRestraint.h>

Inheritance diagram for IMP::container::TripletsRestraint:

Detailed Description

Applies a TripletScore to each Triplet in a list.

This restraint stores the used particles in a kernel::ParticleTripletsTemp. The container used can be set so that the list can be shared with other containers (or a nonbonded list can be used).

Examples using various multiplicity containers:

## \example core/restrain_in_sphere.py
# This fragment shows how to restrain a set of points stored in a
# SingletonContainer in a sphere of radius 'radius' centered around
# 'center'.

import IMP
import IMP.core
radius = 10
stiffness = 2
center = IMP.algebra.Vector3D(1, 2, 3)
m = IMP.kernel.Model()
p = m.add_particle("particle")
IMP.core.XYZR.setup_particle(
    m, p, IMP.algebra.Sphere3D(IMP.algebra.Vector3D(100, 0, 0), 1))

ub = IMP.core.HarmonicUpperBound(radius, stiffness)

# Restrain based on the distance to a single point (hence a ball
ss = IMP.core.DistanceToSingletonScore(ub, center)

r = IMP.core.SingletonRestraint(ss, m.get_particle(p))
r.evaluate(False)

## \example container/nonbonded_interactions.py
# This example shows how to set up an excluded volume restraint for a set
# of XYZRDecorator-style particles.

import IMP
import IMP.core
import IMP.atom
import IMP.container

# This example addes a restraint on nonbonded interactions
# after excluding a set of bonded interactions.

m = IMP.kernel.Model()
# The set of particles
ps = IMP.container.ListSingletonContainer(
    IMP.core.create_xyzr_particles(m, 20, 1.0))

# create a bond between two particles
bd0 = IMP.atom.Bonded.setup_particle(ps.get_particle(0))
bd1 = IMP.atom.Bonded.setup_particle(ps.get_particle(1))
IMP.atom.create_custom_bond(bd0, bd1, 2.0)

# Set up the nonbonded list for all pairs at are touching
# and let things move 3 before updating the list
nbl = IMP.container.ClosePairContainer(ps, 0.0, 3.0)
nbl.add_pair_filter(IMP.atom.BondedPairFilter())

# Set up excluded volume
sdps = IMP.core.SoftSpherePairScore(1)
evr = IMP.container.PairsRestraint(sdps, nbl)
m.add_restraint(evr)

# Set up optimizer
o = IMP.core.ConjugateGradients(m)

o.optimize(1000)

See Also

IMP::core::TripletRestraint

Definition at line 34 of file TripletsRestraint.h.

Public Member Functions
	TripletsRestraint (kernel::TripletScore *ss, kernel::TripletContainerAdaptor pc, std::string name="TripletsRestraint %1%")
	Create the restraint with a shared container. More...
IMP::kernel::ModelObjectsTemp	do_get_inputs () const
virtual std::string	get_type_name () const
virtual ::IMP::base::VersionInfo	get_version_info () const
	Get information about the module and version of the object. More...
double	unprotected_evaluate (IMP::kernel::DerivativeAccumulator *accum) const
Public Member Functions inherited from IMP::kernel::Restraint
	Restraint (kernel::Model *m, std::string name)
void	add_score_and_derivatives (ScoreAccumulator sa) const
	Perform the actual restraint scoring. More...
Restraint *	create_current_decomposition () const
	Decompose this restraint into constituent terms for the current conf. More...
Restraint *	create_decomposition () const
	Decompose this restraint into constituent terms. More...
virtual ScoringFunction *	create_scoring_function (double weight=1.0, double max=NO_MAX) const
	Create a scoring function with only this restraint. More...
virtual double	get_last_score () const
double	get_score () const
bool	get_was_good () const
void	set_weight (Float weight)
Float	get_weight () const
double	get_maximum_score () const
void	set_maximum_score (double s)
Public Member Functions inherited from IMP::kernel::ModelObject
	ModelObject (kernel::Model *m, std::string name)
bool	get_has_dependencies () const
	Return whether this object has dependencies computed. More...
bool	get_has_required_score_states () const
	Return whether score states are computed. More...
ModelObjectsTemp	get_inputs () const
ModelObjectsTemps	get_interactions () const
	Get the interacting sets induced by this ModelObject. More...
Model *	get_model () const
ModelObjectsTemp	get_outputs () const
const ScoreStatesTemp &	get_required_score_states () const
	Get the score states that are ancestors of this in the dependency graph. More...
void	set_has_dependencies (bool tf)
	Either invalidate the dependencies or ensure they are correct. More...
void	set_has_required_score_states (bool tf)
	Compute the required score states. More...
Public Member Functions inherited from IMP::base::Object
virtual void	clear_caches ()
CheckLevel	get_check_level () const
LogLevel	get_log_level () const
void	set_check_level (CheckLevel l)
void	set_log_level (LogLevel l)
	Set the logging level used in this object. More...
void	set_was_used (bool tf) const
void	show (std::ostream &out=std::cout) const
const std::string &	get_name () const
void	set_name (std::string name)

Additional Inherited Members
Protected Member Functions inherited from IMP::kernel::Restraint
virtual void	do_add_score_and_derivatives (ScoreAccumulator sa) const
virtual Restraints	do_create_current_decomposition () const
virtual Restraints	do_create_decomposition () const
ModelObjectsTemp	do_get_outputs () const
Protected Member Functions inherited from IMP::kernel::ModelObject
virtual ModelObjectsTemps	do_get_interactions () const
virtual void	handle_set_has_required_score_states (bool)
Protected Member Functions inherited from IMP::base::Object
	Object (std::string name)
	Construct an object with the given name. More...
virtual void	do_destroy ()

Constructor & Destructor Documentation

IMP::container::TripletsRestraint::TripletsRestraint	(	kernel::TripletScore *	ss,
		kernel::TripletContainerAdaptor	pc,
		std::string	name = "TripletsRestraint %1%"
	)

Create the restraint with a shared container.

Parameters

[in]	ss	The function to apply to each particle.
[in]	pc	The container containing the stored particles. This container is not copied.
[in]	name	The object name

Definition at line 52 of file TripletsRestraint.h.

Member Function Documentation

IMP::kernel::ModelObjectsTemp IMP::container::TripletsRestraint::do_get_inputs ( ) const

virtual

Get any Particle, Container or other ModelObjects read by this during evaluation. If you read everything in a container, you can just return that container.

Implements IMP::kernel::ModelObject.

virtual ::IMP::base::VersionInfo IMP::container::TripletsRestraint::get_version_info ( ) const

virtual

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Definition at line 60 of file TripletsRestraint.h.

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The documentation for this class was generated from the following file:

• TripletsRestraint.h