IMP::core::ClosePairsPairScore Class Reference

Apply the score to all pairs whose spheres are within a distance threshold. More...

#include <IMP/core/ClosePairsPairScore.h>

Inheritance diagram for IMP::core::ClosePairsPairScore:

Detailed Description

Apply the score to all pairs whose spheres are within a distance threshold.

Rigid bodies are special cased for efficiency.

See Also

ClosePairsScoreState

Definition at line 71 of file ClosePairsPairScore.h.

Public Member Functions
	ClosePairsPairScore (PairScore *f, Refiner *r, Float max_distance)
	Constructor. More...
Restraints	create_current_decomposition (Model *m, const ParticleIndexPair &vt) const
virtual ModelObjectsTemp	do_get_inputs (Model *m, const ParticleIndexes &pis) 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...
double	evaluate_if_good_indexes (Model *m, const ParticleIndexPairs &p, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const
virtual double	evaluate_index (Model *m, const ParticleIndexPair &p, DerivativeAccumulator *da) const
	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
	Compute the score and the derivative if needed over a set. More...
ParticlePairsTemp	get_close_pairs (const ParticlePair &pp) const
virtual std::string	get_type_name () const
virtual ::IMP::VersionInfo	get_version_info () const
	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
	Decompose this pair score acting on the pair into a set of restraints. More...
Public Member Functions inherited from IMP::ParticleInputs
ModelObjectsTemp	get_inputs (Model *m, const ParticleIndexes &pis) const
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 ()

Constructor & Destructor Documentation

IMP::core::ClosePairsPairScore::ClosePairsPairScore	(	PairScore *	f,
		Refiner *	r,
		Float	max_distance
	)

Constructor.

Parameters

[in]	r	The Refiner to call on each particle
[in]	f	The pair score to apply to the generated pairs
[in]	max_distance	Only score pairs which are close than the max_distance

Member Function Documentation

virtual ModelObjectsTemp IMP::core::ClosePairsPairScore::do_get_inputs ( Model *  m, const ParticleIndexes &  pis  ) const

virtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

virtual double IMP::core::ClosePairsPairScore::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 from IMP::PairScore.

double IMP::core::ClosePairsPairScore::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 from IMP::PairScore.

Definition at line 106 of file ClosePairsPairScore.h.

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

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.

Implements IMP::PairScore.

double IMP::core::ClosePairsPairScore::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 of 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 106 of file ClosePairsPairScore.h.

virtual ::IMP::VersionInfo IMP::core::ClosePairsPairScore::get_version_info ( ) const

virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 107 of file ClosePairsPairScore.h.

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

• ClosePairsPairScore.h