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 () |
| PairPredicate * | get_pair_filter (unsigned int i) const |
| PairPredicates | get_pair_filters () const |
| void | reserve_pair_filters (unsigned int sz) |
Additional Inherited Members | |
| Related Functions inherited from IMP::base::Object | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < Object > > | ObjectsTemp |
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
|
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: