IMP::container::TripletsRestraint Class Reference

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Detailed Description

Applies a TripletScore to each Triplet in a list.

This restraint stores the used particles in a ParticleTripletsTemp. The container used can be set so that the list can be shared with other containers (or a nonbonded list can be used). By default a ListTripletContainer is used and the {add_, set_, clear_}particle_triplet{s} methodas can be used.

Examples using various multiplicity containers:

import IMP.example
radius=10
stiffness=2
center= IMP.algebra.Vector3D(1,2,3)
(m,c)=IMP.example.create_model_and_particles()
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.container.SingletonsRestraint(ss, c)
m.add_restraint(r)
m.evaluate(False)

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.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:

TripletRestraint

Inheritance diagram for IMP::container::TripletsRestraint:

List of all members.

Public Member Functions
	TripletsRestraint (TripletScore *ss, TripletContainerInput pc, std::string name="TripletsRestraint %1%")
	Create the restraint with a shared container.
ParticleTripletsTemp	get_arguments () const
	Get the container used to store Particles.
TripletContainer *	get_container () const
TripletScore *	get_score () const
Public Member Functions inherited from IMP::Restraint
	Restraint (Model *m, std::string name)
Restraint *	create_current_decomposition () const
	Decompose this restraint into constituent terms for the current conf.
Restraint *	create_decomposition () const
	Decompose this restraint into constituent terms.
double	evaluate (bool calc_derivs) const
	Return the score for this restraint for the current state of the model.
double	evaluate_if_below (bool calc_derivatives, double max) const
	See Model::evaluate_with_maximum()
double	evaluate_if_good (bool calc_derivatives) const
	See Model::evaluate_if_good()
double	get_last_score () const
bool	get_was_good () const
virtual double	unprotected_evaluate (DerivativeAccumulator *) const =0
virtual double	unprotected_evaluate_if_good (DerivativeAccumulator *da, double max) const
virtual double	unprotected_evaluate_if_below (DerivativeAccumulator *da, double max) const
virtual ContainersTemp	get_input_containers () const =0
virtual ParticlesTemp	get_input_particles () const =0
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::ModelObject
	ModelObject (Model *m, std::string name)
ModelObjectsTemp	get_inputs () const
Model *	get_model () const
ModelObjectsTemp	get_outputs () const
Public Member Functions inherited from IMP::base::Object
std::size_t	__hash__ () const
virtual std::string	get_type_name () const =0
	Return a string identifying the type of the object.
virtual IMP::base::VersionInfo	get_version_info () const =0
	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.
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)

Static Public Member Functions
static TripletsRestraint *	get_from (IMP::base::Object *o)

Additional Inherited Members
Protected Member Functions inherited from IMP::Restraint
virtual Restraints	do_create_current_decomposition () const
virtual Restraints	do_create_decomposition () const
Protected Member Functions inherited from IMP::ModelObject
virtual ModelObjectsTemp	do_get_inputs () const =0
virtual ModelObjectsTemp	do_get_outputs () const =0
virtual void	do_update_dependencies (const DependencyGraph &, const DependencyGraphVertexIndex &)
void	update_dependencies (const DependencyGraph &dg, const DependencyGraphVertexIndex &index)
Protected Member Functions inherited from IMP::base::Object
	Object (std::string name)

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Constructor & Destructor Documentation

IMP::container::TripletsRestraint::TripletsRestraint	(	TripletScore *	ss,
		TripletContainerInput	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

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Member Function Documentation

ParticleTripletsTemp IMP::container::TripletsRestraint::get_arguments

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const

Get the container used to store Particles.

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

• TripletsRestraint.h