Abstract score function. More...

#include <IMP/kernel/PairScore.h>

Inheritance diagram for IMP::kernel::PairScore:

Public Types
typedef ParticlePair	Argument

typedef ParticleIndexPair	IndexArgument

typedef PairModifier	Modifier

typedef const ParticlePair &	PassArgument

typedef const ParticleIndexPair &	PassIndexArgument

Public Member Functions
	PairScore (std::string name="PairScore %1%")

Restraints	create_current_decomposition (kernel::Model *m, const ParticleIndexPair &vt) const

virtual double	evaluate (const ParticlePair &vt, DerivativeAccumulator *da) const
	Compute the score and the derivative if needed. More...

virtual double	evaluate_if_good_index (kernel::Model m, const ParticleIndexPair &vt, DerivativeAccumulator da, double max) const
	Compute the score and the derivative if needed.

virtual double	evaluate_if_good_indexes (kernel::Model m, const ParticleIndexPairs &o, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound) const

virtual double	evaluate_index (kernel::Model m, const ParticleIndexPair &vt, DerivativeAccumulator da) const
	Compute the score and the derivative if needed.

virtual double	evaluate_indexes (kernel::Model m, const ParticleIndexPairs &o, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound) const

Public Member Functions inherited from IMP::kernel::ParticleInputs
virtual ContainersTemp	get_input_containers (Particle *p) const

virtual ParticlesTemp	get_input_particles (Particle *p) const

ModelObjectsTemp	get_inputs (kernel::Model *m, const ParticleIndexes &pis) const

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

Protected Member Functions
virtual Restraints	do_create_current_decomposition (kernel::Model *m, const ParticleIndexPair &vt) const

Protected Member Functions inherited from IMP::kernel::ParticleInputs
virtual ModelObjectsTemp	do_get_inputs (kernel::Model *m, const ParticleIndexes &pis) const

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

	Object ()

Detailed Description

PairScores will evaluate the score and derivatives for the passed particles. Use in conjunction with various restraints such as IMP::core::PairsRestraint or IMP::core::PairRestraint.

Implementers should check out IMP_PAIR_SCORE().

Definition at line 33 of file kernel/PairScore.h.

Member Function Documentation

Restraints IMP::kernel::PairScore::create_current_decomposition	(	kernel::Model *	m,
		const ParticleIndexPair &	vt
	)		const

Decompose this pair score acting on the pair into a set of restraints. The scoring function and derivatives should be equal to the current score. The defualt implementation just returns this object bound to the pair.

virtual Restraints IMP::kernel::PairScore::do_create_current_decomposition	(	kernel::Model *	m,
		const ParticleIndexPair &	vt
	)		const

protectedvirtual

Overide this to return your own decomposition.

virtual double IMP::kernel::PairScore::evaluate	(	const ParticlePair &	vt,
		DerivativeAccumulator *	da
	)		const

virtual

Deprecated:: As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use the index-based evaluate instead.

virtual double IMP::kernel::PairScore::evaluate_if_good_indexes	(	kernel::Model *	m,
		const ParticleIndexPairs &	o,
		DerivativeAccumulator *	da,
		double	max,
		unsigned int	lower_bound,
		unsigned int	upper_bound
	)		const

virtual

Implementations for these are provided by the IMP_PAIR_SCORE() macro.

Reimplemented in IMP::core::WeightedSphereDistancePairScore, IMP::core::NormalizedSphereDistancePairScore, IMP::core::ClosePairsPairScore, IMP::atom::LennardJonesPairScore, IMP::core::HarmonicUpperBoundSphereDiameterPairScore, IMP::core::TypedPairScore, IMP::core::KClosePairsPairScore, IMP::atom::CoulombPairScore, IMP::isd::RepulsiveDistancePairScore, IMP::core::TransformedDistancePairScore, IMP::score_functor::DistancePairScore< DistanceScoreT >, IMP::score_functor::DistancePairScore< score_functor::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE > >, IMP::score_functor::DistancePairScore< score_functor::Statistical< ProteinLigandType, BIPARTITE, INTERPOLATE, false > >, IMP::score_functor::DistancePairScore< score_functor::Dope >, IMP::core::RefinedPairsPairScore, IMP::misc::LowestRefinedPairScore, IMP::container::MinimumPairScore, IMP::example::ExamplePairScore, and IMP::misc::SoftCylinderPairScore.

virtual double IMP::kernel::PairScore::evaluate_indexes	(	kernel::Model *	m,
		const ParticleIndexPairs &	o,
		DerivativeAccumulator *	da,
		unsigned int	lower_bound,
		unsigned int	upper_bound
	)		const

virtual

Implementations for these are provided by the IMP_PAIR_SCORE() macro.

Reimplemented in IMP::core::WeightedSphereDistancePairScore, IMP::core::NormalizedSphereDistancePairScore, IMP::core::ClosePairsPairScore, IMP::atom::LennardJonesPairScore, IMP::core::HarmonicUpperBoundSphereDiameterPairScore, IMP::core::TypedPairScore, IMP::core::KClosePairsPairScore, IMP::atom::CoulombPairScore, IMP::isd::RepulsiveDistancePairScore, IMP::core::TransformedDistancePairScore, IMP::score_functor::DistancePairScore< DistanceScoreT >, IMP::score_functor::DistancePairScore< score_functor::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE > >, IMP::score_functor::DistancePairScore< score_functor::Statistical< ProteinLigandType, BIPARTITE, INTERPOLATE, false > >, IMP::score_functor::DistancePairScore< score_functor::Dope >, IMP::core::RefinedPairsPairScore, IMP::misc::LowestRefinedPairScore, IMP::container::MinimumPairScore, IMP::example::ExamplePairScore, and IMP::misc::SoftCylinderPairScore.

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

kernel/PairScore.h

Public Types

Public Member Functions

Protected Member Functions

Detailed Description

Member Function Documentation