Detailed Description

Applies a PairScore to each Pair in a list.

This restraint stores the used particle indexes in a ParticleIndexPairs. 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
 import sys
 
 IMP.setup_from_argv(sys.argv, "restrain in sphere")
 
 radius = 10
 stiffness = 2
 center = IMP.algebra.Vector3D(1, 2, 3)
 m = IMP.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(m, ss, 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
 import sys
 
 IMP.setup_from_argv(sys.argv, "nonbonded interactions")
 
 # This example adds a restraint on nonbonded interactions
 # after excluding a set of bonded interactions.
 
 m = IMP.Model()
 # The set of particles
 ps = IMP.container.ListSingletonContainer(
     m, IMP.core.create_xyzr_particles(m, 20, 1.0))
 
 # create a bond between two particles
 bd0 = IMP.atom.Bonded.setup_particle(m, ps.get_indexes()[0])
 bd1 = IMP.atom.Bonded.setup_particle(m, ps.get_indexes()[1])
 IMP.atom.create_custom_bond(bd0, bd1, 2.0)
 
 # Set up the nonbonded list for all pairs that 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)
 
 # Set up optimizer
 o = IMP.core.ConjugateGradients(m)
 o.set_scoring_function([evr])
 
 o.optimize(1000)

See Also: IMP::core::PairRestraint

Definition at line 36 of file PairsRestraint.h.

Public Member Functions
	PairsRestraint (PairScore *ss, PairContainerAdaptor pc, std::string name="PairsRestraint %1%")
	Create the restraint with a shared container. More...

IMP::ModelObjectsTemp	do_get_inputs () const

virtual std::string	get_type_name () const override

virtual ::IMP::VersionInfo	get_version_info () const override
	Get information about the module and version of the object. More...

double	unprotected_evaluate (IMP::DerivativeAccumulator *accum) const
	Return the unweighted score for the restraint. More...

Public Member Functions inherited from IMP::Restraint
	Restraint (Model *m, std::string name)
	Create a restraint and register it with the model. More...

	Restraint ()
	Default constructor. 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 RestraintInfo *	get_dynamic_info () const

bool	get_is_aggregate () const
	Return whether this restraint wraps a number of other restraints. More...

double	get_last_last_score () const
	Get the unweighted score from the last-but-one time it was evaluated. More...

virtual double	get_last_score () const

double	get_score () const

virtual RestraintInfo *	get_static_info () const

bool	get_was_good () const

double	evaluate (bool calc_derivs) const

double	evaluate_moved (bool calc_derivs, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const

double	evaluate_moved_if_below (bool calc_derivatives, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const

double	evaluate_moved_if_good (bool calc_derivatives, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const

double	evaluate_if_good (bool calc_derivatives) const

double	evaluate_if_below (bool calc_derivatives, double max) const

virtual double	unprotected_evaluate_moved (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
	Return the unweighted score, taking moving particles into account. More...

virtual double	unprotected_evaluate_if_good (DerivativeAccumulator *da, double max) const

virtual double	unprotected_evaluate_if_below (DerivativeAccumulator *da, double max) const
	The function calling this will treat any score >= max as bad. More...

virtual double	unprotected_evaluate_moved_if_below (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const

virtual double	unprotected_evaluate_moved_if_good (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) 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::ModelObject
	ModelObject (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::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::Restraint
virtual void	do_add_score_and_derivatives (ScoreAccumulator sa) const

virtual void	do_add_score_and_derivatives_moved (ScoreAccumulator sa, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const

virtual Restraints	do_create_current_decomposition () const

virtual Restraints	do_create_decomposition () const

ModelObjectsTemp	do_get_outputs () const override

Protected Member Functions inherited from IMP::ModelObject
virtual ModelObjectsTemps	do_get_interactions () const

virtual void	handle_set_has_required_score_states (bool)

Protected Member Functions inherited from IMP::Object
	Object (std::string name)
	Construct an object with the given name. More...

virtual void	do_destroy ()

Protected Attributes inherited from IMP::Restraint
bool	is_aggregate_

Constructor & Destructor Documentation

IMP::container::PairsRestraint::PairsRestraint	(	PairScore *	ss,
		PairContainerAdaptor	pc,
		std::string	name = `"PairsRestraint %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 60 of file PairsRestraint.h.

Member Function Documentation

IMP::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::ModelObject.

virtual ::IMP::VersionInfo IMP::container::PairsRestraint::get_version_info ( ) const

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 69 of file PairsRestraint.h.

double IMP::container::PairsRestraint::unprotected_evaluate ( IMP::DerivativeAccumulator * da ) const

virtual

Return the unweighted score for the restraint.

Reimplemented from IMP::Restraint.

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

PairsRestraint.h

Detailed Description

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation