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IMP Reference Guide  develop.ba5ef9f91e,2024/02/26
The Integrative Modeling Platform
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 37 of file ClosePairsFinder.h.

Public Member Functions

 ClosePairsFinder (std::string name)
 
virtual ParticleIndexPairs get_close_pairs (Model *m, const ParticleIndexes &pc) const =0
 return all close pairs among pc in model m More...
 
virtual ParticleIndexPairs get_close_pairs (Model *m, const ParticleIndexes &pca, const ParticleIndexes &pcb) const =0
 return all close pairs among pc in model m More...
 
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::ParticleInputs
ModelObjectsTemp get_inputs (Model *m, const ParticleIndexes &pis) const
 Get the ModelObjects read when the given list of particles is used. More...
 
- Public Member Functions inherited from IMP::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 container output list. Pairs for which the predicate evaluates to a non-zero value are excluded.

list pair_filters
 A Python list of PairFilters More...
 
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 erase_pair_filter (unsigned int i)
 
void reserve_pair_filters (unsigned int sz)
 

Additional Inherited Members

- Protected Member Functions inherited from IMP::ParticleInputs
virtual ModelObjectsTemp do_get_inputs (Model *m, const ParticleIndexes &pis) const =0
 Overload this method to specify the inputs. More...
 
- Protected Member Functions inherited from IMP::Object
 Object (std::string name)
 Construct an object with the given name. More...
 
virtual void do_destroy ()
 

Member Function Documentation

virtual ParticleIndexPairs IMP::core::ClosePairsFinder::get_close_pairs ( Model m,
const ParticleIndexes pca,
const ParticleIndexes pcb 
) const
pure virtual

Member Data Documentation

list IMP::core::ClosePairsFinder::pair_filters

A Python list of PairFilters

Note
This class member is only available in Python.

Definition at line 84 of file ClosePairsFinder.h.


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