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IMP Reference Guide
develop.63b38c487d,2024/12/24
The Integrative Modeling Platform
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Return all close unordered pairs of particles taken from the SingletonContainer. More...
#include <IMP/container/ClosePairContainer.h>
Inheritance diagram for IMP::container::ClosePairContainer:Return all close unordered pairs of particles taken from the SingletonContainer.
The ClosePairContainer class maintains a list of particle pairs whose distance (opportunely defined by the decorator, eg., sphere surface distance for XYZR, and center-to-center distance for XYZ) is smaller than the distance_cutoff parameter. It is generally used to construct the non-bonded list for the excluded volume score, as well as electrostatic and van der Waals potential terms.
To increase the efficiency, the stored list actually includes all pairs that are closer than distance_cutoff + 2 * slack. This allows us to reuse the list and only recompute it when a particle moves more than slack. The class keeps track internally of how far the particles have moved using a score state, and is also updated via a score state. Too small a slack value can slow things down because the non-bonded list will be updated frequently. Also, too large a slack value generates many particle pairs whose score is zero, thereby unnecessarily slowing down the score calculation. As a result, it may be useful to experiment with the parameter. You may wish to use the get_slack_estimate() function to help with this experimentation.
distance_cutoff apart. If you use an IMP::PairScore with the generated list of pairs, make sure the IMP::PairScore is 0 for distances beyond the distance_cutoff. One way to accomplish this is to use a smoothing function (see IMP::atom::SmoothingFunction).IMP, the contents of the container will only be valid during restraint evaluation, or immediately following a call to Model::update().Here is a simple example of using this for a nonbonded list
Definition at line 66 of file ClosePairContainer.h.
Public Member Functions | |
| ClosePairContainer (SingletonContainerAdaptor c, double distance_cutoff, double slack=1, std::string name="ClosePairContainer%1%") | |
| Get the individual particles from the passed SingletonContainer. More... | |
| ClosePairContainer (SingletonContainerAdaptor c, double distance_cutoff, core::ClosePairsFinder *cpf, double slack=1, std::string name="ClosePairContainer%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 |
| unsigned int | get_number_of_full_rebuilds () const |
| unsigned int | get_number_of_partial_rebuilds () const |
| unsigned int | get_number_of_update_calls () const |
| ParticleIndexPairs | get_range_indexes () const |
| double | get_slack () 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... | |
| void | set_slack (double s) |
| 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::ClosePairContainer::ClosePairContainer | ( | SingletonContainerAdaptor | c, |
| double | distance_cutoff, | ||
| double | slack = 1, |
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| std::string | name = "ClosePairContainer%1%" |
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Get the individual particles from the passed SingletonContainer.
Creates a close pair container associated with c.
| IMP::container::ClosePairContainer::ClosePairContainer | ( | SingletonContainerAdaptor | c, |
| double | distance_cutoff, | ||
| core::ClosePairsFinder * | cpf, | ||
| double | slack = 1, |
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| std::string | name = "ClosePairContainer%1%" |
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| ) |
Get the individual particles from the passed SingletonContainer.
Creates a close pair container associated with c. The passed core::ClosePairsFinder is used to generate the list of close pairs, instead of the default.
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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.
| unsigned int IMP::container::ClosePairContainer::get_number_of_full_rebuilds | ( | ) | const |
Get the number of times this container has computed its contents from scratch.
| unsigned int IMP::container::ClosePairContainer::get_number_of_partial_rebuilds | ( | ) | const |
Get the number of times this container has performed a partial recomputation of its contents.
| unsigned int IMP::container::ClosePairContainer::get_number_of_update_calls | ( | ) | const |
Get the number of times this container has been asked to update its contents.
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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 137 of file ClosePairContainer.h.
| list IMP::container::ClosePairContainer::pair_filters |
A Python list of PairPredicates
Definition at line 114 of file ClosePairContainer.h.