IMP  2.0.0
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:

Public Member Functions

 ClosePairsFinder (std::string name)
 
ContainersTemp get_input_containers (const ParticlesTemp &ps) const
 
ContainersTemp get_input_containers (Particle *p) const
 
ParticlesTemp get_input_particles (const ParticlesTemp &ps) const
 
ParticlesTemp get_input_particles (Particle *p) const
 
ModelObjectsTemp get_inputs (Model *m, const ParticleIndexes &pis) 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)
 

Protected Member Functions

virtual ModelObjectsTemp do_get_inputs (Model *m, const ParticleIndexes &pis) const =0
 
- Protected Member Functions inherited from IMP::base::Object
 Object (std::string name)
 Construct an object with the given name. More...
 

Methods to find close pairs

The methods add appropriately close pairs of particles from the input list (or lists, for the bipartite version) to the out list. The ones that take bounding boxes return pairs of ints indexing the input list(s).

virtual ParticlePairsTemp get_close_pairs (const ParticlesTemp &pc) const =0
 
virtual ParticlePairsTemp get_close_pairs (const ParticlesTemp &pca, const ParticlesTemp &pcb) const =0
 
virtual ParticleIndexPairs get_close_pairs (Model *m, const ParticleIndexes &pc) const
 
virtual ParticleIndexPairs get_close_pairs (Model *m, const ParticleIndexes &pca, const ParticleIndexes &pcb) const
 
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
 

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

Detailed Description

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 36 of file ClosePairsFinder.h.

Member Function Documentation

virtual ModelObjectsTemp IMP::core::ClosePairsFinder::do_get_inputs ( Model m,
const ParticleIndexes pis 
) const
protectedpure virtual

Override if this reads other objects during evaluate.

ContainersTemp IMP::core::ClosePairsFinder::get_input_containers ( Particle p) const

Get the set of input containers when this modifier is applied to the arguments.

Deprecated:
use get_outputs() instead.
ParticlesTemp IMP::core::ClosePairsFinder::get_input_particles ( Particle p) const

Get the set of particles read when applied to the arguments.

Deprecated:
use get_inputs() instead.
ModelObjectsTemp IMP::core::ClosePairsFinder::get_inputs ( Model m,
const ParticleIndexes pis 
) const

Get all the ModelObject objects that are read when the referenced particles are passed in.


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