Apply a UnaryFunction to the minimum transformed sphere-sphere distance. More...

#include <IMP/npc/MinimumSphereDistancePairScore.h>

Inheritance diagram for IMP::npc::MinimumSphereDistancePairScore:

Detailed Description

Apply a UnaryFunction to the minimum transformed sphere-sphere distance.

This is like a SphereDistancePairScore in that it calculates the inter-surface distance between two XYZR Particles (spheres) and then scores it with a provided UnaryFunction. However, it also considers the distance between the two particles with the second particle transformed by each of the provided transformations. The transformation which results in the minimum interparticle distance (not necessarily the minimum score) is then used for scoring. This can be used for periodic boundaries or other symmetric systems.

Definition at line 29 of file MinimumSphereDistancePairScore.h.

Public Member Functions
	MinimumSphereDistancePairScore (UnaryFunction *f, algebra::Transformation3Ds transforms)

virtual ModelObjectsTemp	do_get_inputs (Model *m, const ParticleIndexes &pis) const override
	Overload this method to specify the inputs. More...

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

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

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

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

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

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...

Public Member Functions inherited from IMP::PairScore
	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...

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

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
Public Types inherited from IMP::PairScore
typedef ParticlePair	Argument

typedef ParticleIndexPair	IndexArgument

typedef PairModifier	Modifier

typedef const ParticlePair &	PassArgument

typedef const ParticleIndexPair &	PassIndexArgument

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

virtual void	do_destroy ()

Member Function Documentation

virtual ModelObjectsTemp IMP::npc::MinimumSphereDistancePairScore::do_get_inputs	(	Model *	m,
		const ParticleIndexes &	pis
	)		const

overridevirtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

Definition at line 40 of file MinimumSphereDistancePairScore.h.

Here is the call graph for this function:

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

overridevirtual

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 from IMP::PairScore.

Definition at line 44 of file MinimumSphereDistancePairScore.h.

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

overridevirtual

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.

Implements IMP::PairScore.

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

finaloverridevirtual

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.

Reimplemented from IMP::PairScore.

Definition at line 44 of file MinimumSphereDistancePairScore.h.

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

finaloverridevirtual

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.

Reimplemented from IMP::PairScore.

Definition at line 44 of file MinimumSphereDistancePairScore.h.

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

finaloverridevirtual

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].

Reimplemented from IMP::PairScore.

Definition at line 44 of file MinimumSphereDistancePairScore.h.

virtual ::IMP::VersionInfo IMP::npc::MinimumSphereDistancePairScore::get_version_info ( ) const

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 45 of file MinimumSphereDistancePairScore.h.

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

MinimumSphereDistancePairScore.h

Detailed Description

Public Member Functions

Additional Inherited Members

Member Function Documentation