Detailed Description

template<class UF>
class IMP::core::GenericBoundingBox3DSingletonScore< UF >

A generic C++ template for scoring particles based on how far outside a box they are using unary function UF. The bounding box score is evaluated by applying a function f of class UF to a particle based on the distance of its center from the bounding box walls. The radius of the particle is ignored. If the particle is within the bounding box, the score is always 0. Logically, it is exepcted that f(0) = 0 and f(x) > 0 if x>0.

In Python, use the templated BoundingBox3DSingletonScore class as in the following example. In the example, 10 particles of radius 1.0 are generated in a 10 A x 10 A x 10 A bounding box. The particles are restrained in the bounding box by applying an upper-bounded harmonic potential. It is upper bounded because it is active only outside the bounding box.

 k_bb = 10.0 # bounding box force coefficient in kcal/mol/A^2
 bb_side = 10.0 # in A
 radius = 1.0 # in A
 number
 m = IMP.Model()
 bb = IMP.algebra.BoundingBox3D(IMP.algebra.Vector3D(0, 0, 0),
                            IMP.algebra.Vector3D(bb_side, bb_side, bb_side))
 particles = []
 for i in range(0,10):
   p = IMP.Particle(m) 
   s = IMP.algebra.Sphere3D(
             IMP.algebra.get_random_vector_in(bb), radius)
   d = IMP.core.XYZR.setup_particle(p, s)
   d.set_coordinates_are_optimized(True)
   particles.append(p)
 hpb = IMP.core.HarmonicUpperBound(0, k)
 bbss = IMP.core.BoundingBox3DSingletonScore(hpb, bb) 
 bbr = IMP.container.SingletonsRestraint(bbss, particles)

See Also: BoundingBox3DSingletonScore; create_bounding_box_3d_singleton_score

Definition at line 64 of file BoundingBox3DSingletonScore.h.

Public Member Functions
	GenericBoundingBox3DSingletonScore (UF *f, const algebra::BoundingBoxD< 3 > &bb)

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) const override

virtual double	evaluate_index (Model m, ParticleIndex p, DerivativeAccumulator da) const override

double	evaluate_indexes (Model m, const ParticleIndexes &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 ParticleIndexes &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 ParticleIndexes &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...

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%")

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 ()

Constructor & Destructor Documentation

template<class UF >

IMP::core::GenericBoundingBox3DSingletonScore< UF >::GenericBoundingBox3DSingletonScore	(	UF *	f,
		const algebra::BoundingBoxD< 3 > &	bb
	)

Parameters

f	an unary function applied to particles that are outside the box. f is passed the distance of the particle center from the bounding box walls, ignoring the particle radius. Logically, it is exepcted to satisfy f(0) = 0 and f(x) > 0 if x>0.
bb	the bounding box to which f is applied

Member Function Documentation

template<class UF >

virtual ModelObjectsTemp IMP::core::GenericBoundingBox3DSingletonScore< UF >::do_get_inputs	(	Model *	m,
		const ParticleIndexes &	pis
	)		const

overridevirtual

Overload this method to specify the inputs.

Implements IMP::ParticleInputs.

Definition at line 87 of file BoundingBox3DSingletonScore.h.

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template<class UF >

double IMP::core::GenericBoundingBox3DSingletonScore< UF >::evaluate_if_good_indexes	(	Model *	m,
		const ParticleIndexes &	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: Implementations for these are provided by the IMP_SINGLETON_SCORE() macro.

Reimplemented from IMP::SingletonScore.

Definition at line 91 of file BoundingBox3DSingletonScore.h.

template<class UF >

virtual double IMP::core::GenericBoundingBox3DSingletonScore< UF >::evaluate_index	(	Model *	m,
		ParticleIndex	p,
		DerivativeAccumulator *	da
	)		const

overridevirtual

return 0 if the p is within the bounding box or f(d) if it is outside the bounding box, where f is the unary function provided during construction and d is the distance of the center of p from the bounding box walls. Update derivatives as needed, weighted using da.

Implements IMP::SingletonScore.

template<class UF >

double IMP::core::GenericBoundingBox3DSingletonScore< UF >::evaluate_indexes	(	Model *	m,
		const ParticleIndexes &	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 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

Note: Implementations for these are provided by the IMP_SINGLETON_SCORE() macro.

Reimplemented from IMP::SingletonScore.

Definition at line 91 of file BoundingBox3DSingletonScore.h.

template<class UF >

double IMP::core::GenericBoundingBox3DSingletonScore< UF >::evaluate_indexes_delta	(	Model *	m,
		const ParticleIndexes &	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.

Reimplemented from IMP::SingletonScore.

Definition at line 91 of file BoundingBox3DSingletonScore.h.

template<class UF >

double IMP::core::GenericBoundingBox3DSingletonScore< UF >::evaluate_indexes_scores	(	Model *	m,
		const ParticleIndexes &	o,
		DerivativeAccumulator *	da,
		unsigned int	lower_bound,
		unsigned int	upper_bound,
		std::vector< double > &	score
	)		const