Apply a function to the distance between the cylinders defined by two bonds. More...

#include <IMP/misc/SoftCylinderPairScore.h>

Inheritance diagram for IMP::misc::SoftCylinderPairScore:

Detailed Description

Apply a function to the distance between the cylinders defined by two bonds.

The two endpoints of the bond must have the same radius and that is used for the radius of the cylinder connecting them.

Definition at line 23 of file SoftCylinderPairScore.h.

Public Member Functions
	SoftCylinderPairScore (double k)

virtual kernel::ModelObjectsTemp	do_get_inputs (kernel::Model *m, const kernel::ParticleIndexes &pis) const

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

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

double	evaluate_indexes (kernel::Model m, const kernel::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...

virtual std::string	get_type_name () const

virtual ::IMP::base::VersionInfo	get_version_info () const
	Get information about the module and version of the object. More...

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

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

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::kernel::PairScore
typedef kernel::ParticlePair	Argument

typedef kernel::ParticleIndexPair	IndexArgument

typedef PairModifier	Modifier

typedef const kernel::ParticlePair &	PassArgument

typedef const kernel::ParticleIndexPair &	PassIndexArgument

Protected Member Functions inherited from IMP::kernel::PairScore
virtual Restraints	do_create_current_decomposition (kernel::Model *m, const kernel::ParticleIndexPair &vt) 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

virtual kernel::ModelObjectsTemp IMP::misc::SoftCylinderPairScore::do_get_inputs	(	kernel::Model *	m,
		const kernel::ParticleIndexes &	pis
	)		const

virtual

Overload this method to specify the inputs.

Reimplemented from IMP::kernel::ParticleInputs.

double IMP::misc::SoftCylinderPairScore::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 from IMP::kernel::PairScore.

Definition at line 33 of file SoftCylinderPairScore.h.

virtual double IMP::misc::SoftCylinderPairScore::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

Reimplemented from IMP::kernel::PairScore.

double IMP::misc::SoftCylinderPairScore::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 from IMP::kernel::PairScore.

Definition at line 33 of file SoftCylinderPairScore.h.

virtual ::IMP::base::VersionInfo IMP::misc::SoftCylinderPairScore::get_version_info ( ) const

virtual

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Definition at line 34 of file SoftCylinderPairScore.h.

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

SoftCylinderPairScore.h

Detailed Description

Public Member Functions

Additional Inherited Members

Member Function Documentation