Detailed Description

Abstract class for scoring object(s) of type ParticlePair.

PairScore will evaluate the score and derivatives for passed object(s) of type ParticlePair.

Use in conjunction with various restraints such as IMP::core::PairsRestraint or IMP::core::PairRestraint. The restraints couple the score functions with appropariate lists of object(s) of type ParticlePair.

Implementers should check out IMP_PAIR_SCORE().

See Also: PredicatePairRestraint

Definition at line 38 of file kernel/PairScore.h.

Public Types
typedef kernel::ParticlePair	Argument

typedef kernel::ParticleIndexPair	IndexArgument

typedef PairModifier	Modifier

typedef const kernel::ParticlePair &	PassArgument

typedef const kernel::ParticleIndexPair &	PassIndexArgument

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

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

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

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

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

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

virtual double	evaluate_indexes (kernel::Model m, const kernel::ParticleIndexPairs &o, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound) const
	Compute the score and the derivative if needed over a set. More...

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 ()

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. More...

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 kernel::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...

virtual void	do_destroy ()

Member Function Documentation

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

protectedvirtual

Overide this to return your own decomposition.

Reimplemented in IMP::container::MinimumPairScore.

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

virtual

Compute the score and the derivative if needed.

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_index	(	kernel::Model *	m,
		const kernel::ParticleIndexPair &	vt,
		DerivativeAccumulator *	da,
		double	max
	)		const

virtual

Compute the score and the derivative if needed.

Compute the score and the derivative if needed as in evaluate_index(). but may terminate the computation early if the score is higher than max.

Returns: the score if score<= max or some arbitrary value > max otherwise.

Reimplemented in IMP::core::ClosePairsPairScore, and IMP::core::KClosePairsPairScore.

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

virtual

Compute the score and the derivative if needed as in evaluate_index(). but may terminate the computation early if the total score is higher than max.

Returns: the score if score<= max or some arbitrary value > max otherwise.

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::score_functor::DistancePairScore< DistanceScoreT >, IMP::score_functor::DistancePairScore< score_functor::OrientedSoap >, 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::atom::CoulombPairScore, IMP::core::TransformedDistancePairScore, IMP::isd::RepulsiveDistancePairScore, IMP::core::RefinedPairsPairScore, IMP::misc::LowestRefinedPairScore, IMP::container::MinimumPairScore, IMP::example::ExamplePairScore, and IMP::misc::SoftCylinderPairScore.

virtual double IMP::kernel::PairScore::evaluate_index	(	kernel::Model *	m,
		const kernel::ParticleIndexPair &	vt,
		DerivativeAccumulator *	da
	)		const

virtual

Compute the score and the derivative if needed.

evaluate the score and the derivative if needed over vt

Parameters

m	the model of vt
vt	the index in m of an object of type ParticlePair
da	a derivative accumulator that reweighting computed derivatives. If nullptr, derivatives will not be computed

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

virtual

Compute the score and the derivative if needed over a set.

evaluate the score and the derivative if needed over a set of objects in o

Parameters

m	the model of o
o	objects of type ParticlePair, specified by index
da	a derivative accumulator that reweighting computed derivatives. If nullptr, derivatives will not be computed
lower_bound	index of first item in o to evaluate
upper_bound	index of last item in o to evaluate

Note: 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::score_functor::DistancePairScore< DistanceScoreT >, IMP::score_functor::DistancePairScore< score_functor::OrientedSoap >, 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::atom::CoulombPairScore, IMP::core::TransformedDistancePairScore, IMP::isd::RepulsiveDistancePairScore, 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

Detailed Description

Public Types

Public Member Functions

Protected Member Functions

Member Function Documentation