Detailed Description

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

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

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

It is possible to call the various evaluate* methods directly, but this is not recommended as they do not ensure that Model invariants (e.g. ScoreStates) are preserved. Use a Restraint or ScoringFunction to score the model instead.

Implementers should check out IMP_PAIR_SCORE().

See Also: PredicatePairRestraint

Definition at line 44 of file PairScore.h.

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 (Model *m, const ParticleIndexPair &vt) const

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

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

virtual double	evaluate_index (Model m, const ParticleIndexPair &vt, DerivativeAccumulator da) const =0
	Compute the score and the derivative if needed. More...

virtual double	evaluate_indexes (Model m, const 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...

virtual double	evaluate_indexes_delta (Model m, const ParticleIndexPairs &o, DerivativeAccumulator da, const std::vector< unsigned > &indexes, std::vector< double > &score) const
	Compute the change in score and the derivative if needed over a set. More...

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

Public Member Functions inherited from IMP::ParticleInputs
ModelObjectsTemp	get_inputs (Model *m, const ParticleIndexes &pis) const
	Get the ModelObjects read when the given list of particles is used. More...

Public Member Functions inherited from IMP::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 (Model *m, const ParticleIndexPair &vt) const
	Override this to return your own decomposition. More...

Protected Member Functions inherited from IMP::ParticleInputs
virtual ModelObjectsTemp	do_get_inputs (Model *m, const ParticleIndexes &pis) const =0
	Overload this method to specify the inputs. More...

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

virtual void	do_destroy ()

Member Function Documentation

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

Decompose this PairScore into a set of currently positive restraints over vt. The scoring function and derivatives should be equal to the current score. The default implementation returns a single restraint with this score bound to vt, or zero restraints if the score equals zero.

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

protectedvirtual

Override this to return your own decomposition.

Reimplemented in IMP::container::MinimumPairScore.

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

virtual

Compute the score and the derivative if needed, only if "good".

This functions similarly to 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::PairScore::evaluate_if_good_indexes	(	Model *	m,
		const ParticleIndexPairs &	o,
		DerivativeAccumulator *	da,
		double	max,
		unsigned int	lower_bound,
		unsigned int	upper_bound
	)		const

virtual

Compute the score and the derivative if needed over a set, only if "good". This functions similarly to evaluate_indexes(), 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.

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

Reimplemented in IMP::npctransport::LinearWellPairScore, IMP::core::WeightedSphereDistancePairScore, IMP::core::NormalizedSphereDistancePairScore, IMP::npctransport::SitesPairScore, IMP::core::ClosePairsPairScore, IMP::npctransport::LinearSoftSpherePairScore, IMP::npctransport::HarmonicWellPairScore, IMP::npctransport::SlabWithCylindricalPorePairScore, IMP::npctransport::AnchorToCylidnricalPorePairScore, IMP::atom::LennardJonesPairScore, IMP::core::HarmonicUpperBoundSphereDiameterPairScore, IMP::npctransport::SlabWithToroidalPorePairScore, IMP::core::TypedPairScore, IMP::score_functor::SurfaceDistancePairScore< DistanceScoreT >, IMP::score_functor::DistancePairScore< DistanceScoreT >, IMP::score_functor::DistancePairScore< LinearInteractionScore >, IMP::score_functor::DistancePairScore< LinearSoftSphereScore >, IMP::score_functor::DistancePairScore< score_functor::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE > >, IMP::score_functor::DistancePairScore< score_functor::LoopStatistical >, IMP::score_functor::DistancePairScore< score_functor::Statistical< ProteinLigandType, BIPARTITE, INTERPOLATE, false > >, IMP::score_functor::DistancePairScore< score_functor::Dope >, IMP::core::KClosePairsPairScore, IMP::npc::MinimumSphereDistancePairScore, IMP::atom::CoulombPairScore, IMP::core::TransformedDistancePairScore, IMP::isd::RepulsiveDistancePairScore, IMP::spb::AttributeDistancePairScore, IMP::core::RefinedPairsPairScore, IMP::example::ExamplePairScore, IMP::spb::RigidBodyPackingScore, IMP::container::MinimumPairScore, IMP::misc::LowestRefinedPairScore, IMP::spb::KinkPairScore, IMP::misc::SoftCylinderPairScore, and IMP::core::RigidBodyAnglePairScore.

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

pure virtual

Compute the score and the derivative if needed.

Parameters

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

virtual double IMP::PairScore::evaluate_indexes	(	Model *	m,
		const 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.

Parameters

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

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

virtual double IMP::PairScore::evaluate_indexes_delta	(	Model *	m,
		const ParticleIndexPairs &	o,
		DerivativeAccumulator *	da,
		const std::vector< unsigned > &	indexes,
		std::vector< double > &	score
	)		const

virtual

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

The score for each o[indexes[x]] is updated in score[indexes[x]] and the total difference between the old and new score values (over the set) is returned.

virtual double IMP::PairScore::evaluate_indexes_scores	(	Model *	m,
		const ParticleIndexPairs &	o,
		DerivativeAccumulator *	da,
		unsigned int	lower_bound,
		unsigned int	upper_bound,
		std::vector< double > &	score
	)		const

virtual

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

Like regular evaluate_indexes(), but the score for each o[x] is also returned as score[x].

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

PairScore.h

Detailed Description

Public Types

Public Member Functions

Protected Member Functions

Member Function Documentation