A container which keeps a set of pairs that connect a set of spheres. More...

#include <IMP/container/ConnectingPairContainer.h>

Inheritance diagram for IMP::container::ConnectingPairContainer:

Public Member Functions
	ConnectingPairContainer (SingletonContainer *sc, double error)

void	do_apply (const PairModifier *sm) const

void	do_before_evaluate ()

kernel::ModelObjectsTemp	do_get_inputs () const

kernel::ParticleIndexes	get_all_possible_indexes () const
	Get contained particles. More...

kernel::ParticleIndexPairs	get_indexes () const

kernel::ParticleIndexPairs	get_range_indexes () const

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.

Public Member Functions inherited from IMP::kernel::PairContainer
void	apply (const PairModifier *sm) const
	Apply a SingletonModifier to the contents.

void	apply_generic (const PairModifier *m) const
	Just use apply() in the base class.

bool	get_contains_particle_pair (ParticlePair v) const
	This function is very slow and you should think hard about using it. More...

unsigned int	get_number_of_particle_pairs () const

ParticlePair	get_particle_pair (unsigned int i) const

ParticlePairsTemp	get_particle_pairs () const

Public Member Functions inherited from IMP::kernel::Container
virtual void	do_after_evaluate (DerivativeAccumulator *accpt)
	Reset changed status.

ModelObjectsTemp	do_get_outputs () const
	containers don't have outputs

ParticlesTemp	get_all_possible_particles () const

int	get_contents_version () const

bool	get_is_changed () const

virtual bool	get_is_decomposable () const

Public Member Functions inherited from IMP::kernel::ScoreState
	ScoreState (kernel::Model *m, std::string name)

	ScoreState (kernel::Model *m)

	ScoreState (std::string name="ScoreState %1%")

void	after_evaluate (DerivativeAccumulator *accpt)
	Do post evaluation work if needed.

void	before_evaluate ()
	Force update of the structure.

ContainersTemp	get_input_containers () const

ParticlesTemp	get_input_particles () const

ContainersTemp	get_output_containers () const

ParticlesTemp	get_output_particles () const

Public Member Functions inherited from IMP::kernel::ModelObject
	ModelObject (kernel::Model *m, std::string name)

	ModelObject (std::string name)

virtual void	do_set_model (kernel::Model *)

bool	get_has_dependencies () const
	Return whether this object has dependencies computed.

bool	get_has_required_score_states () const

ModelObjectsTemp	get_inputs () const

ModelObjectsTemps	get_interactions () const

bool	get_is_part_of_model () const

Model *	get_model () const

ModelObjectsTemp	get_outputs () const

const ScoreStatesTemp &	get_required_score_states () const

void	set_has_dependencies (bool tf)

void	set_has_required_score_states (bool tf)

virtual void	set_model (kernel::Model *m)

Public Member Functions inherited from IMP::base::Object
virtual void	clear_caches ()

virtual void	do_destroy ()

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::PairContainer
typedef ParticleIndexPair	ContainedIndexType

typedef ParticleIndexPairs	ContainedIndexTypes

typedef ParticlePair	ContainedType

typedef ParticlePairsTemp	ContainedTypes

Protected Member Functions inherited from IMP::kernel::PairContainer
	PairContainer (kernel::Model *m, std::string name="PairContainer %1%")

virtual bool	do_get_provides_access () const

Protected Member Functions inherited from IMP::kernel::Container
	Container (kernel::Model *m, std::string name="Container %1%")

void	set_is_changed (bool tf)
	Call this with true when the contents of the container change. More...

Protected Member Functions inherited from IMP::kernel::ModelObject
virtual ModelObjectsTemps	do_get_interactions () const

virtual void	handle_set_has_required_score_states (bool)

Protected Member Functions inherited from IMP::base::Object
	Object (std::string name)
	Construct an object with the given name. More...

	Object ()

Detailed Description

This container is for implementing connectivity when

there is no ambiguity about the set of particles being connected
the distance score used in the restraint is a monotonic function of the distance between the two particles.

The contents of this container are a set of pairs defining a tree over the spheres in the supplied SingletonContainer. This set of edges has the property that

for particles whose balls do not intersect, if there is a path connecting those balls entirely contained in the union of the set of all balls, then there is no edge connecting those two particles.

It is significantly more efficient than the ConnectivityRestraint but less flexible.

See Also: {core::ConnectivityRestraint}

Definition at line 40 of file ConnectingPairContainer.h.

Constructor & Destructor Documentation

IMP::container::ConnectingPairContainer::ConnectingPairContainer	(	SingletonContainer *	sc,
		double	error
	)

For efficiency, the set of edges is only updated occasionally. The error parameter determines how far particles need to move before the set of edges is updated.

Member Function Documentation

kernel::ModelObjectsTemp IMP::container::ConnectingPairContainer::do_get_inputs ( ) const

virtual

Get any Particle, Container or other ModelObjects read by this during evaluation. If you read everything in a container, you can just return that container.

Implements IMP::kernel::ModelObject.

kernel::ParticleIndexes IMP::container::ConnectingPairContainer::get_all_possible_indexes ( ) const

virtual

Get a list of all particles contained in this one, given that the input containers are up to date.

Implements IMP::kernel::Container.

kernel::ParticleIndexPairs IMP::container::ConnectingPairContainer::get_indexes ( ) const

virtual

Get all the indexes contained in the container.

Implements IMP::kernel::PairContainer.

kernel::ParticleIndexPairs IMP::container::ConnectingPairContainer::get_range_indexes ( ) const

virtual

Get all the indexes that might possibly be contained in the container, useful with dynamic containers. For example, with a container::ClosePairContainer, this is the list of all pairs taken from input list (those that are far apart in addition to those that are close).

Implements IMP::kernel::PairContainer.

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

ConnectingPairContainer.h

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation