#include <IMP/npctransport/linear_distance_pair_scores.h>

Inheritance diagram for IMP::npctransport::LinearWellPairScore:

Detailed Description

A soft linear attractive / repulsive score between two spheres for the backbone of a chain.

Definition at line 407 of file linear_distance_pair_scores.h.

Public Member Functions
	LinearWellPairScore (double rest_length_factor, double k, std::string name="LinearIDPairScore%1%")

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

double	evaluate_index (Model m, const ParticleIndexPair &p, 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...

double	get_k ()

double	get_rest_length_factor () const

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...

void	set_k (double k)

void	set_rest_length_factor (double rest_length_factor)

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 ()

Constructor & Destructor Documentation

IMP::npctransport::LinearWellPairScore::LinearWellPairScore	(	double	rest_length_factor,
		double	k,
		std::string	name = `"LinearIDPairScore%1%"`
	)

a linear well pair potential that keeps two particles around a resting distance relative to their radii

Parameters

rest_length_factor	the resting distance between particles relative to their sum of radii
k	the force constant (attractive if beyond or repulsive if below rest length) in units kcal/mol/A
name	the name of the score

Member Function Documentation

ModelObjectsTemp IMP::npctransport::LinearWellPairScore::do_get_inputs	(	Model *	m,
		const ParticleIndexes &	pis
	)		const

overridevirtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

double IMP::npctransport::LinearWellPairScore::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: An implementation for this is provided by the IMP_PAIR_SCORE_METHODS() macro.

Reimplemented from IMP::PairScore.

Definition at line 435 of file linear_distance_pair_scores.h.

double IMP::npctransport::LinearWellPairScore::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::npctransport::LinearWellPairScore::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: An implementation for this is provided by the IMP_PAIR_SCORE_METHODS() macro.

Reimplemented from IMP::PairScore.

Definition at line 435 of file linear_distance_pair_scores.h.

double IMP::npctransport::LinearWellPairScore::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.

Note: An implementation for this is provided by the IMP_PAIR_SCORE_METHODS() macro.

Reimplemented from IMP::PairScore.

Definition at line 435 of file linear_distance_pair_scores.h.

double IMP::npctransport::LinearWellPairScore::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].

Note: An implementation for this is provided by the IMP_PAIR_SCORE_METHODS() macro.

Reimplemented from IMP::PairScore.

Definition at line 435 of file linear_distance_pair_scores.h.

virtual ::IMP::VersionInfo IMP::npctransport::LinearWellPairScore::get_version_info ( ) const

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 436 of file linear_distance_pair_scores.h.

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

linear_distance_pair_scores.h

Detailed Description

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation