IMP  2.1.1
The Integrative Modeling Platform
IMP::container::ConnectingPairContainer Class Reference

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
 
Modelget_model () const
 
ModelObjectsTemp get_outputs () const
 
const ScoreStatesTempget_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: