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IMP Reference Guide
develop.63b38c487d,2024/12/21
The Integrative Modeling Platform
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A container which keeps a set of pairs that connect a set of spheres. More...
#include <IMP/container/ConnectingPairContainer.h>
Inheritance diagram for IMP::container::ConnectingPairContainer:A container which keeps a set of pairs that connect a set of spheres.
This container is for implementing connectivity when
The contents of this container are a set of pairs defining a tree over the spheres in the supplied SingletonContainer. This set of edges has the property that
It is significantly more efficient than the ConnectivityRestraint but less flexible.
Definition at line 40 of file ConnectingPairContainer.h.
Public Member Functions | |
| ConnectingPairContainer (SingletonContainer *sc, double error) | |
| 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) |
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::ConnectingPairContainer::ConnectingPairContainer | ( | SingletonContainer * | sc, |
| double | error | ||
| ) |
For efficiency, the set of edges is only updated occasionally. The error parameter determines how far particles need to move before the set of edges is updated.
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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 67 of file ConnectingPairContainer.h.