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 store 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
 radius = 10
 stiffness = 2
 center = IMP.algebra.Vector3D(1, 2, 3)
 m = IMP.kernel.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(ss, m.get_particle(p))
 r.evaluate(False)

Definition at line 93 of file DistanceToSingletonScore.h.

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

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

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

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

double	evaluate_indexes (kernel::Model m, const kernel::ParticleIndexes &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::SingletonScore
	SingletonScore (std::string name="SingletonScore %1%")

Restraints	create_current_decomposition (kernel::Model *m, kernel::ParticleIndex vt) const

virtual double	evaluate (kernel::Particle vt, DerivativeAccumulator da) const
	Compute the score and the derivative if needed. More...

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

typedef kernel::ParticleIndex	IndexArgument

typedef SingletonModifier	Modifier

typedef kernel::Particle *	PassArgument

typedef kernel::ParticleIndex	PassIndexArgument

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

virtual

Overload this method to specify the inputs.

Reimplemented from IMP::kernel::ParticleInputs.

Definition at line 110 of file DistanceToSingletonScore.h.

Here is the call graph for this function:

double IMP::core::SphereDistanceToSingletonScore::evaluate_if_good_indexes	(	kernel::Model *	m,
		const kernel::ParticleIndexes &	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_SINGLETON_SCORE() macro.

Reimplemented from IMP::kernel::SingletonScore.

Definition at line 114 of file DistanceToSingletonScore.h.

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

Reimplemented from IMP::kernel::SingletonScore.

double IMP::core::SphereDistanceToSingletonScore::evaluate_indexes	(	kernel::Model *	m,
		const kernel::ParticleIndexes &	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 Particle, 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_SINGLETON_SCORE() macro.

Reimplemented from IMP::kernel::SingletonScore.

Definition at line 114 of file DistanceToSingletonScore.h.

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

virtual

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Definition at line 115 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