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IMP Reference Guide
2.11.1
The Integrative Modeling Platform
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A base class for algorithms to find spatial proximities. More...
#include <IMP/core/ClosePairsFinder.h>
Inheritance diagram for IMP::core::ClosePairsFinder: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.
Definition at line 35 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 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 () |
| PairPredicate * | get_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::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 () |
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pure virtual |
return all close pairs among pc in model m
Implemented in IMP::misc::MetricClosePairsFinder< LowerBound, UpperBound >, IMP::core::RigidClosePairsFinder, IMP::core::QuadraticClosePairsFinder, IMP::core::BoxSweepClosePairsFinder, IMP::core::GridClosePairsFinder, and IMP::core::NearestNeighborsClosePairsFinder.
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pure virtual |
return all close pairs among pc in model m
Implemented in IMP::misc::MetricClosePairsFinder< LowerBound, UpperBound >, IMP::core::RigidClosePairsFinder, IMP::core::QuadraticClosePairsFinder, IMP::core::BoxSweepClosePairsFinder, IMP::core::GridClosePairsFinder, and IMP::core::NearestNeighborsClosePairsFinder.