IMP Reference Guide
develop.714915d50b,2024/12/07
The Integrative Modeling Platform
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Return all spatially-proximal pairs of particles (a,b) from the two SingletonContainers A and B, where a is in A and b is in B. More...
#include <IMP/container/CloseBipartitePairContainer.h>
Return all spatially-proximal pairs of particles (a,b) from the two SingletonContainers A and B, where a is in A and b is in B.
Definition at line 35 of file CloseBipartitePairContainer.h.
Public Member Functions | |
CloseBipartitePairContainer (SingletonContainerAdaptor a, SingletonContainerAdaptor b, double distance, double slack=1, std::string name="CloseBipartitePairContainer%1%") | |
Get the individual particles from the passed SingletonContainer. More... | |
void | do_apply (const PairModifier *sm) const |
ModelObjectsTemp | do_get_inputs () const |
ParticleIndexes | get_all_possible_indexes () const |
Get contained particles. More... | |
ParticleIndexPairs | get_indexes () const |
ParticleIndexPairs | get_range_indexes () const |
virtual std::string | get_type_name () const override |
virtual ::IMP::VersionInfo | get_version_info () const override |
Get information about the module and version of the object. More... | |
Public Member Functions inherited from IMP::PairContainer | |
void | apply (const PairModifier *sm) const |
Apply a PairModifier to the contents. More... | |
void | apply_generic (const PairModifier *m) const |
Just use apply() in the base class. More... | |
void | apply_generic_moved (const PairModifier *m, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const |
Just use apply_moved() in the base class. More... | |
void | apply_moved (const PairModifier *sm, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const |
Apply a PairModifier to the contents. More... | |
const ParticleIndexPairs & | get_contents () const |
Public Member Functions inherited from IMP::Container | |
ModelObjectsTemp | do_get_outputs () const override |
containers don't have outputs More... | |
std::size_t | get_contents_hash () const |
virtual bool | get_is_decomposable () const |
Public Member Functions inherited from IMP::ModelObject | |
ModelObject (Model *m, std::string name) | |
bool | get_has_dependencies () const |
Return whether this object has dependencies computed. More... | |
bool | get_has_required_score_states () const |
Return whether score states are computed. More... | |
ModelObjectsTemp | get_inputs () const |
ModelObjectsTemps | get_interactions () const |
Get the interacting sets induced by this ModelObject. More... | |
Model * | get_model () const |
ModelObjectsTemp | get_outputs () const |
const ScoreStatesTemp & | get_required_score_states () const |
Get the score states that are ancestors of this in the dependency graph. More... | |
void | set_has_dependencies (bool tf) |
Either invalidate the dependencies or ensure they are correct. More... | |
void | set_has_required_score_states (bool tf) |
Compute the required score states. 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) |
Methods to control the set of filters | |
PairPredicate objects can be added as filters to prevent the addition of pairs to the container output list. Pairs for which the predicates evaluate to a non-zero value are excluded from the list. | |
list | pair_filters |
A Python list of PairPredicates 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 () |
PairPredicate * | get_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 | |
Public Types inherited from IMP::PairContainer | |
typedef ParticleIndexPair | ContainedIndexType |
typedef ParticleIndexPairs | ContainedIndexTypes |
typedef ParticlePair | ContainedType |
typedef ParticlePairsTemp | ContainedTypes |
typedef PairModifier | Modifier |
typedef const ParticleIndexPair & | PassContainedIndexType |
Protected Member Functions inherited from IMP::PairContainer | |
PairContainer (Model *m, std::string name="PairContainer %1%") | |
virtual void | do_apply_moved (const PairModifier *sm, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const |
virtual bool | do_get_provides_access () const |
Protected Member Functions inherited from IMP::Container | |
Container (Model *m, std::string name="Container %1%") | |
Protected Member Functions inherited from IMP::ModelObject | |
virtual ModelObjectsTemps | do_get_interactions () const |
virtual void | handle_set_has_required_score_states (bool) |
Protected Member Functions inherited from IMP::Object | |
Object (std::string name) | |
Construct an object with the given name. More... | |
virtual void | do_destroy () |
IMP::container::CloseBipartitePairContainer::CloseBipartitePairContainer | ( | SingletonContainerAdaptor | a, |
SingletonContainerAdaptor | b, | ||
double | distance, | ||
double | slack = 1 , |
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std::string | name = "CloseBipartitePairContainer%1%" |
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Get the individual particles from the passed SingletonContainer.
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Get any Particle, Container or other ModelObjects read by this during evaluation. If you read everything in a container, you can just return that container.
Implements IMP::ModelObject.
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Get contained particles.
Get a list of all particles contained in this one, given that the input containers are up to date.
Implements IMP::Container.
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Get all the indexes contained in the container.
This should be protected but isn't for compatibility reasons.
External callers should use get_contents().
Implements IMP::PairContainer.
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Get all the indexes that might possibly be contained in the container, useful with dynamic containers. For example, with a container::ClosePairContainer, this is the list of all pairs taken from the input list (those that are far apart in addition to those that are close).
Implements IMP::PairContainer.
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overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 92 of file CloseBipartitePairContainer.h.
list IMP::container::CloseBipartitePairContainer::pair_filters |
A Python list of PairPredicates
Definition at line 81 of file CloseBipartitePairContainer.h.