IMP  2.0.1
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)
 
 IMP_IMPLEMENT_PAIR_CONTAINER (ConnectingPairContainer)
 
- 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...
 
virtual ParticleIndexPairs get_indexes () const =0
 
unsigned int get_number_of_particle_pairs () const
 
ParticlePair get_particle_pair (unsigned int i) const
 
ParticlePairsTemp get_particle_pairs () const
 
virtual ParticleIndexPairs get_range_indexes () const =0
 
- 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
 
virtual ParticleIndexes get_all_possible_indexes () const =0
 Get contained particles. More...
 
ParticlesTemp get_all_possible_particles () const
 
bool get_is_changed () const
 
virtual bool get_is_decomposable () const
 
- Public Member Functions inherited from IMP::kernel::ScoreState
 ScoreState (Model *m, 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 (Model *m, std::string name)
 
ModelObjectsTemp get_inputs () const
 
ModelObjectsTemps get_interactions () const
 
Modelget_model () const
 
ModelObjectsTemp get_outputs () const
 
- Public Member Functions inherited from IMP::base::Object
virtual void clear_caches ()
 
virtual IMP::base::VersionInfo get_version_info () const =0
 Get information about the module and version of the object.
 
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)
 

Related Functions

(Note that these are not member functions.)

typedef IMP::base::Vector
< IMP::base::WeakPointer
< ConnectingPairContainer > > 
ConnectingPairContainersTemp
 

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 (Model *m, std::string name="PairContainer %1%")
 
virtual void do_apply (const PairModifier *sm) const =0
 
virtual bool do_get_provides_access () const
 

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.

Friends And Related Function Documentation

Pass a set of objects.

Definition at line 67 of file ConnectingPairContainer.h.


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