Apply a function to the distance to a fixed point. More...

#include <IMP/core/DistanceToSingletonScore.h>

Inheritance diagram for IMP::core::SphereDistanceToSingletonScore:

Detailed Description

Apply a function to the distance to a fixed point.

A particle is scored based on the distance between it and a constant point as passed to a UnaryFunction. This is useful for anchoring constraining particles within a sphere.

To restrain a set of particles stored in SingletonContainer pc in a sphere do the following:

 ## \example core/restrain_in_sphere.py
 # This fragment shows how to restrain a set of points stored in a
 # SingletonContainer in a sphere of radius 'radius' centered around
 # 'center'.
 
 import IMP
 import IMP.core
 import sys
 
 IMP.setup_from_argv(sys.argv, "restrain in sphere")
 
 radius = 10
 stiffness = 2
 center = IMP.algebra.Vector3D(1, 2, 3)
 m = IMP.Model()
 p = m.add_particle("particle")
 IMP.core.XYZR.setup_particle(
     m, p, IMP.algebra.Sphere3D(IMP.algebra.Vector3D(100, 0, 0), 1))
 
 ub = IMP.core.HarmonicUpperBound(radius, stiffness)
 
 # Restrain based on the distance to a single point (hence a ball
 ss = IMP.core.DistanceToSingletonScore(ub, center)
 
 r = IMP.core.SingletonRestraint(m, ss, p)
 r.evaluate(False)

Definition at line 103 of file DistanceToSingletonScore.h.

Public Member Functions
	SphereDistanceToSingletonScore (UnaryFunction *f, const algebra::Vector3D &pt)

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 ParticleIndexes &p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=false) const override

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

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

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

double	evaluate_indexes_scores (Model m, const ParticleIndexes &p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score, bool all_indexes_checked=false) 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::SingletonScore
	SingletonScore (std::string name="SingletonScore %1%")

virtual bool	check_indexes (Model *m, const ParticleIndexes &pis) const
	Check the given particle indexes for necessary attributes. More...

Restraints	create_current_decomposition (Model *m, ParticleIndex vt) const

virtual double	evaluate_if_good_index (Model m, ParticleIndex 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::SingletonScore
typedef Particle *	Argument

typedef ParticleIndex	IndexArgument

typedef SingletonModifier	Modifier

typedef Particle *	PassArgument

typedef ParticleIndex	PassIndexArgument

Protected Member Functions inherited from IMP::SingletonScore
virtual Restraints	do_create_current_decomposition (Model *m, ParticleIndex 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::core::SphereDistanceToSingletonScore::do_get_inputs	(	Model *	m,
		const ParticleIndexes &	pis
	)		const

overridevirtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

Definition at line 120 of file DistanceToSingletonScore.h.

Here is the call graph for this function:

double IMP::core::SphereDistanceToSingletonScore::evaluate_if_good_indexes	(	Model *	m,
		const ParticleIndexes &	o,
		DerivativeAccumulator *	da,
		double	max,
		unsigned int	lower_bound,
		unsigned int	upper_bound,
		bool	all_indexes_checked = `false`
	)		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_SINGLETON_SCORE_METHODS() macro.

Reimplemented from IMP::SingletonScore.

Definition at line 124 of file DistanceToSingletonScore.h.

virtual double IMP::core::SphereDistanceToSingletonScore::evaluate_index	(	Model *	m,
		ParticleIndex	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 Particle
da	a DerivativeAccumulator that weights computed derivatives. If nullptr, derivatives will not be computed.

Implements IMP::SingletonScore.

double IMP::core::SphereDistanceToSingletonScore::evaluate_indexes	(	Model *	m,
		const ParticleIndexes &	o,
		DerivativeAccumulator *	da,
		unsigned int	lower_bound,
		unsigned int	upper_bound,
		bool	all_indexes_checked = `false`
	)		const

finaloverridevirtual

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

Parameters

m	the model of o
o	objects of type Particle, 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
all_indexes_checked	if true, all of the passed indexes have already been checked by check_indexes() for needed particle attributes, so a faster implementation (that doesn't check them again) can be used if available.

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

Reimplemented from IMP::SingletonScore.

Definition at line 124 of file DistanceToSingletonScore.h.

double IMP::core::SphereDistanceToSingletonScore::evaluate_indexes_delta	(	Model *	m,
		const ParticleIndexes &	o,
		DerivativeAccumulator *	da,
		const std::vector< unsigned > &	indexes,
		std::vector< double > &	score,
		bool	all_indexes_checked = `false`
	)		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_SINGLETON_SCORE_METHODS() macro.

Reimplemented from IMP::SingletonScore.

Definition at line 124 of file DistanceToSingletonScore.h.

double IMP::core::SphereDistanceToSingletonScore::evaluate_indexes_scores	(	Model *	m,
		const ParticleIndexes &	o,
		DerivativeAccumulator *	da,
		unsigned int	lower_bound,
		unsigned int	upper_bound,
		std::vector< double > &	score,
		bool	all_indexes_checked = `false`
	)		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_SINGLETON_SCORE_METHODS() macro.

Reimplemented from IMP::SingletonScore.

Definition at line 124 of file DistanceToSingletonScore.h.

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

overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 125 of file DistanceToSingletonScore.h.

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

DistanceToSingletonScore.h

Detailed Description

Public Member Functions

Additional Inherited Members

Member Function Documentation