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IMP Reference Guide
2.16.0
The Integrative Modeling Platform
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#include <IMP/core/NeighborsTable.h>
Inheritance diagram for IMP::core::NeighborsTable:Maintain a table that can be used to look up the neighbors of particles. That is, you can efficiently find all particles that are within a certain distance of a passed one.
As with the container::ClosePairContainer, there may be some neighbors returned that are not close neighbors, but all close neighbors will be returned.
Definition at line 28 of file NeighborsTable.h.
Public Member Functions | |
| NeighborsTable (PairContainer *input, std::string name="CloseNeighborsTable%1%") | |
| const ParticleIndexes & | get_neighbors (ParticleIndex pi) const |
| 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... | |
| Public Member Functions inherited from IMP::ScoreState | |
| ScoreState (Model *m, std::string name) | |
| void | after_evaluate (DerivativeAccumulator *accpt) |
| Do post evaluation work if needed. More... | |
| void | before_evaluate () |
| Force update of the structure. More... | |
| bool | get_can_skip () const |
| Get whether this state can be skipped if its inputs/outputs didn't move. More... | |
| 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) |
Protected Member Functions | |
| virtual void | do_after_evaluate (DerivativeAccumulator *) |
| Do any necessary updates after the model score is calculated. More... | |
| virtual void | do_before_evaluate () |
| Update the state given the current state of the model. More... | |
| virtual ModelObjectsTemp | do_get_inputs () const |
| virtual ModelObjectsTemp | do_get_outputs () const |
| Protected Member Functions inherited from IMP::ScoreState | |
| void | set_can_skip (bool can_skip) |
| Set whether we can skip during model evaluation if appropriate. More... | |
| 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 () |
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protectedvirtual |
Do any necessary updates after the model score is calculated.
| [in] | accpt | The object used to scale derivatives in the score calculation, or nullptr if derivatives were not requested. |
Implements IMP::ScoreState.
Definition at line 41 of file NeighborsTable.h.
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protectedvirtual |
Update the state given the current state of the model.
This is also called prior to every calculation of the model score. It should be implemented by ScoreStates in order to provide functionality.
Implements IMP::ScoreState.
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protectedvirtual |
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.
Definition at line 34 of file NeighborsTable.h.
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protectedvirtual |
Get any Particle, Container or other ModelObjects changed by this during evaluation. This is only useful for ScoreStates, at the moment.
Implements IMP::ModelObject.
Definition at line 37 of file NeighborsTable.h.
| const ParticleIndexes& IMP::core::NeighborsTable::get_neighbors | ( | ParticleIndex | pi | ) | const |
Return all ParticleIndexes that are within the distance threshold of this one (plus some that are aren't, for efficiency).
Definition at line 48 of file NeighborsTable.h.
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virtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 52 of file NeighborsTable.h.