IMP  2.4.0
The Integrative Modeling Platform
Public Member Functions | List of all members
IMP::core::ClosePairsFinder Class Referenceabstract

A base class for algorithms to find spatial proximities. More...

#include <IMP/core/ClosePairsFinder.h>

+ Inheritance diagram for IMP::core::ClosePairsFinder:

Detailed Description

A base class for algorithms to find spatial proximities.

In general, the algorithm should make sure it returns all pairs of appropriate objects which are within the distance of one another (including their radius). They are free to return more if it is convenient, but this is not recommended as the list can easily become very large.

See Also
ClosePairContainer
CloseBipartitePairContainer

Definition at line 35 of file ClosePairsFinder.h.

Public Member Functions

 ClosePairsFinder (std::string name)
 
kernel::ParticlePairsTemp get_close_pairs (const kernel::ParticlesTemp &pc) const
 
kernel::ParticlePairsTemp get_close_pairs (const kernel::ParticlesTemp &pca, const kernel::ParticlesTemp &pcb) const
 
virtual kernel::ParticleIndexPairs get_close_pairs (kernel::Model *m, const kernel::ParticleIndexes &pc) const =0
 
virtual kernel::ParticleIndexPairs get_close_pairs (kernel::Model *m, const kernel::ParticleIndexes &pca, const kernel::ParticleIndexes &pcb) const =0
 
virtual IntPairs get_close_pairs (const algebra::BoundingBox3Ds &bbs) const =0
 
virtual IntPairs get_close_pairs (const algebra::BoundingBox3Ds &bas, const algebra::BoundingBox3Ds &bbs) const =0
 
- Public Member Functions inherited from IMP::kernel::ParticleInputs
virtual ContainersTemp get_input_containers (Particle *p) const
 
virtual ParticlesTemp get_input_particles (Particle *p) const
 
ModelObjectsTemp get_inputs (kernel::Model *m, const ParticleIndexes &pis) const
 
- Public Member Functions inherited from IMP::base::Object
virtual void clear_caches ()
 
CheckLevel get_check_level () const
 
LogLevel get_log_level () const
 
virtual VersionInfo get_version_info () const
 Get information about the module and version of the object. More...
 
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)
 
virtual std::string get_type_name () const
 

The distance threshold

All pairs within this distance threshold are added to the output list.

virtual void set_distance (double d)
 
double get_distance () const
 

Methods to control the set of filters

PairPredicates objects can be used as filters to prevent the addition of pairs to the containeroutput list. Pairs for which the predicate evaluates to a non-zero value are excluded.

void remove_pair_filter (PairPredicate *d)
 
void remove_pair_filters (const PairPredicates &d)
 
void set_pair_filters (const PairPredicates &ps)
 
void set_pair_filters_order (const PairPredicates &objs)
 
unsigned int add_pair_filter (PairPredicate *obj)
 
void add_pair_filters (const PairPredicates &objs)
 
void clear_pair_filters ()
 
unsigned int get_number_of_pair_filters () const
 
bool get_has_pair_filters ()
 
PairPredicateget_pair_filter (unsigned int i) const
 
PairPredicates get_pair_filters () const
 
void reserve_pair_filters (unsigned int sz)
 

Additional Inherited Members

- Protected Member Functions inherited from IMP::kernel::ParticleInputs
virtual ModelObjectsTemp do_get_inputs (kernel::Model *m, const ParticleIndexes &pis) const
 
- Protected Member Functions inherited from IMP::base::Object
 Object (std::string name)
 Construct an object with the given name. More...
 
virtual void do_destroy ()
 

Member Function Documentation

kernel::ParticlePairsTemp IMP::core::ClosePairsFinder::get_close_pairs ( const kernel::ParticlesTemp pc) const
Deprecated:
As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. use the index-based one instead.
kernel::ParticlePairsTemp IMP::core::ClosePairsFinder::get_close_pairs ( const kernel::ParticlesTemp pca,
const kernel::ParticlesTemp pcb 
) const
Deprecated:
As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. use the index-based one instead.

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