IMP Reference Guide
2.14.0
The Integrative Modeling Platform
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Perform more efficient close pair finding when rigid bodies are involved. More...
#include <IMP/core/RigidClosePairsFinder.h>
Perform more efficient close pair finding when rigid bodies are involved.
The class finds all close pairs consisting of particles taken from the passed list(s) (if they are not rigid bodies) or members of rigid bodies passed as input. That is, given an input list l
, for each pair of particles p
, q
taken from the list that are closer than the distance threshold, it returns
p
,q
) if neither p
or q
are RigidBody particles
(r
,s
) where r
is a member of p
, s
is a member of q
, and r
and s
are closer than the distance threshold if both p
and q
are RigidBody particles
(p
,s
) or
(r
,q
) as appropriate if only one of p
or q
is a rigid body.Consequently, the user must ensure that each RigidBody is assigned a radius that encloses all of its RigidMember particles.
It uses another ClosePairsFinder to find which pairs of particles in the input list or lists are close. Your choice of this can be passed to the constructor.
The class RigidClosePairsFinder uses CGAL in order to improve its functionality. It will fall back on less good code without it.
Definition at line 59 of file RigidClosePairsFinder.h.
Public Member Functions | |
RigidClosePairsFinder (ClosePairsFinder *cpf=nullptr) | |
virtual ModelObjectsTemp | do_get_inputs (Model *m, const ParticleIndexes &pis) const |
Overload this method to specify the inputs. More... | |
ParticleIndexPairs | get_close_pairs (Model *m, ParticleIndex a, ParticleIndex b, const ParticleIndexes &pa, const ParticleIndexes &pb) const |
virtual IntPairs | get_close_pairs (const algebra::BoundingBox3Ds &bbs) const |
virtual IntPairs | get_close_pairs (const algebra::BoundingBox3Ds &bas, const algebra::BoundingBox3Ds &bbs) const |
virtual ParticleIndexPairs | get_close_pairs (Model *m, const ParticleIndexes &pc) const |
return all close pairs among pc in model m More... | |
virtual ParticleIndexPairs | get_close_pairs (Model *m, const ParticleIndexes &pca, const ParticleIndexes &pcb) const |
return all close pairs among pc in model m More... | |
virtual std::string | get_type_name () const |
virtual ::IMP::VersionInfo | get_version_info () const |
Get information about the module and version of the object. More... | |
void | set_distance (double d) |
Public Member Functions inherited from IMP::core::ClosePairsFinder | |
ClosePairsFinder (std::string name) | |
double | get_distance () const |
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) |
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 |
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) |
Additional Inherited Members | |
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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virtual |
Overload this method to specify the inputs.
Implements IMP::ParticleInputs.
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virtual |
return all close pairs among pc in model m
Implements IMP::core::ClosePairsFinder.
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virtual |
return all close pairs among pc in model m
Implements IMP::core::ClosePairsFinder.
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virtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 93 of file RigidClosePairsFinder.h.