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IMP Reference Guide  develop.63e71f5352,2022/07/06
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:

Detailed Description

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

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.

Public Member Functions

 ConnectingPairContainer (SingletonContainer *sc, double error)
 
void do_apply (const PairModifier *sm) const
 
ModelObjectsTemp do_get_inputs () const
 
ParticleIndexes get_all_possible_indexes () const
 Get contained particles. More...
 
ParticleIndexPairs get_indexes () const
 
ParticleIndexPairs get_range_indexes () const
 
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::PairContainer
void apply (const PairModifier *sm) const
 Apply a PairModifier to the contents. More...
 
void apply_generic (const PairModifier *m) const
 Just use apply() in the base class. More...
 
void apply_generic_moved (const PairModifier *m, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
 Just use apply_moved() in the base class. More...
 
void apply_moved (const PairModifier *sm, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
 Apply a PairModifier to the contents. More...
 
const ParticleIndexPairsget_contents () const
 
- Public Member Functions inherited from IMP::Container
ModelObjectsTemp do_get_outputs () const override
 containers don't have outputs More...
 
std::size_t get_contents_hash () const
 
virtual bool get_is_decomposable () const
 
- Public Member Functions inherited from IMP::ModelObject
 ModelObject (Model *m, std::string name)
 
bool get_has_dependencies () const
 Return whether this object has dependencies computed. More...
 
bool get_has_required_score_states () const
 Return whether score states are computed. More...
 
ModelObjectsTemp get_inputs () const
 
ModelObjectsTemps get_interactions () const
 Get the interacting sets induced by this ModelObject. More...
 
Modelget_model () const
 
ModelObjectsTemp get_outputs () const
 
const ScoreStatesTempget_required_score_states () const
 Get the score states that are ancestors of this in the dependency graph. More...
 
void set_has_dependencies (bool tf)
 Either invalidate the dependencies or ensure they are correct. More...
 
void set_has_required_score_states (bool tf)
 Compute the required score states. 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::PairContainer
typedef ParticleIndexPair ContainedIndexType
 
typedef ParticleIndexPairs ContainedIndexTypes
 
typedef ParticlePair ContainedType
 
typedef ParticlePairsTemp ContainedTypes
 
typedef PairModifier Modifier
 
typedef const ParticleIndexPairPassContainedIndexType
 
- Protected Member Functions inherited from IMP::PairContainer
 PairContainer (Model *m, std::string name="PairContainer %1%")
 
virtual void do_apply_moved (const PairModifier *sm, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const
 
virtual bool do_get_provides_access () const
 
- Protected Member Functions inherited from IMP::Container
 Container (Model *m, std::string name="Container %1%")
 
- Protected Member Functions inherited from IMP::ModelObject
virtual ModelObjectsTemps do_get_interactions () const
 
virtual void handle_set_has_required_score_states (bool)
 
- 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

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

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::ModelObject.

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

Get contained particles.

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

Implements IMP::Container.

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

Get all the indexes contained in the container.

This should be protected but isn't for compatibility reasons.

External callers should use get_contents().

Implements IMP::PairContainer.

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 the input list (those that are far apart in addition to those that are close).

Implements IMP::PairContainer.

virtual ::IMP::VersionInfo IMP::container::ConnectingPairContainer::get_version_info ( ) const
overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 67 of file ConnectingPairContainer.h.


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