IMP::container::PairsRestraint Class Reference

Applies a PairScore to each Pair in a list. More...

#include <IMP/container/PairsRestraint.h>

Inheritance diagram for IMP::container::PairsRestraint:

Public Member Functions
	PairsRestraint (PairScore *ss, PairContainerAdaptor pc, std::string name="PairsRestraint %1%")
	Create the restraint with a shared container. More...
IMP::kernel::ModelObjectsTemp	do_get_inputs () const
double	unprotected_evaluate (IMP::DerivativeAccumulator *accum) const
Public Member Functions inherited from IMP::kernel::Restraint
	Restraint (kernel::Model *m, std::string name)
	Restraint (std::string name="Restraint %1%")
void	add_score_and_derivatives (ScoreAccumulator sa) const
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
ContainersTemp	get_input_containers () const
ParticlesTemp	get_input_particles () const
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)
	ModelObject (std::string name)
virtual void	do_set_model (kernel::Model *)
bool	get_has_dependencies () const
	Return whether this object has dependencies computed.
bool	get_has_required_score_states () const
ModelObjectsTemp	get_inputs () const
ModelObjectsTemps	get_interactions () const
bool	get_is_part_of_model () const
Model *	get_model () const
ModelObjectsTemp	get_outputs () const
const ScoreStatesTemp &	get_required_score_states () const
void	set_has_dependencies (bool tf)
void	set_has_required_score_states (bool tf)
virtual void	set_model (kernel::Model *m)
Public Member Functions inherited from IMP::base::Object
virtual void	clear_caches ()
virtual void	do_destroy ()
CheckLevel	get_check_level () const
LogLevel	get_log_level () const
virtual VersionInfo	get_version_info () const
	Get information about the module and version of the object.
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)
virtual std::string	get_type_name () const

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...
	Object ()

Detailed Description

This restraint stores the used particles in a ParticlePairsTemp. 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()
o.set_model(m)

o.optimize(1000)

See Also

IMP::core::PairRestraint

Definition at line 35 of file PairsRestraint.h.

Constructor & Destructor Documentation

IMP::container::PairsRestraint::PairsRestraint	(	PairScore *	ss,
		PairContainerAdaptor	pc,
		std::string	name = "PairsRestraint %1%"
	)

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 PairsRestraint.h.

Member Function Documentation

IMP::kernel::ModelObjectsTemp IMP::container::PairsRestraint::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.

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

• PairsRestraint.h