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IMP
2.1.1
The Integrative Modeling Platform
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IMP
2.1.1
The Integrative Modeling Platform
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Ensure that a set of particles remains connected with one another. More...
#include <IMP/core/MSConnectivityRestraint.h>
Inheritance diagram for IMP::core::MSConnectivityRestraint:Public Member Functions | |
| MSConnectivityRestraint (PairScore *ps, double eps=0.1) | |
| Use the given PairScore. More... | |
| kernel::Restraints | do_create_current_decomposition () const |
| kernel::ModelObjectsTemp | do_get_inputs () const |
| kernel::ParticlePairsTemp | get_connected_pairs () const |
| Return the set of pairs which are connected by the restraint. More... | |
| PairScore * | get_pair_score () const |
| Return the pair score used for scoring. | |
| virtual std::string | get_type_name () const |
| virtual ::IMP::base::VersionInfo | get_version_info () const |
| Get information about the module and version of the object. | |
| double | unprotected_evaluate (IMP::kernel::DerivativeAccumulator *accum) const |
| Public Member Functions inherited from IMP::kernel::Restraint | |
| Restraint (kernel::Model *m, std::string name) | |
| Restraint (std::string name="Restraint %1%") | |
| void | add_score_and_derivatives (ScoreAccumulator sa) const |
| Restraint * | create_current_decomposition () const |
| Decompose this restraint into constituent terms for the current conf. More... | |
| Restraint * | create_decomposition () const |
| Decompose this restraint into constituent terms. More... | |
| virtual ScoringFunction * | create_scoring_function (double weight=1.0, double max=NO_MAX) const |
| ContainersTemp | get_input_containers () const |
| ParticlesTemp | get_input_particles () const |
| virtual double | get_last_score () const |
| double | get_score () const |
| bool | get_was_good () const |
| void | set_weight (Float weight) |
| Float | get_weight () const |
| double | get_maximum_score () const |
| void | set_maximum_score (double s) |
| Public Member Functions inherited from IMP::kernel::ModelObject | |
| ModelObject (kernel::Model *m, std::string name) | |
| ModelObject (std::string name) | |
| virtual void | do_set_model (kernel::Model *) |
| bool | get_has_dependencies () const |
| Return whether this object has dependencies computed. | |
| bool | get_has_required_score_states () const |
| ModelObjectsTemp | get_inputs () const |
| ModelObjectsTemps | get_interactions () const |
| bool | get_is_part_of_model () const |
| Model * | get_model () const |
| ModelObjectsTemp | get_outputs () const |
| const ScoreStatesTemp & | get_required_score_states () const |
| void | set_has_dependencies (bool tf) |
| void | set_has_required_score_states (bool tf) |
| virtual void | set_model (kernel::Model *m) |
| Public Member Functions inherited from IMP::base::Object | |
| virtual void | clear_caches () |
| virtual void | do_destroy () |
| 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) |
kernel::Particles to be connected | |
The following methods are used to manipulate the list of particles that are to be connected. Each particle should have all the attributes expected by the PairScore used. Ideally, one should pass a singleton container instead. These can only be used if none is passed. | |
| unsigned int | add_type (const kernel::ParticlesTemp &ps) |
| unsigned int | add_composite (const Ints &components) |
| unsigned int | add_composite (const Ints &components, unsigned int parent) |
Additional Inherited Members | |
| Protected Member Functions inherited from IMP::kernel::Restraint | |
| virtual void | do_add_score_and_derivatives (ScoreAccumulator sa) const |
| virtual Restraints | do_create_decomposition () const |
| ModelObjectsTemp | do_get_outputs () const |
| Protected Member Functions inherited from IMP::kernel::ModelObject | |
| virtual ModelObjectsTemps | do_get_interactions () const |
| virtual void | handle_set_has_required_score_states (bool) |
| Protected Member Functions inherited from IMP::base::Object | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
| Object () | |
The restraint implements ambiguous connectivity. That is, it takes several particles including multiple copies and ensures that they remain connected, but allows how they are connected to change. If you wish to restrain the connectivity of sets of particles (i.e. each protein is represented using a set of balls) use an appropriate PairScore which calls a Refiner (such as ClosePairsPairScore).
More precisely, the restraint scores by computing the MST on the complete graph connecting all the particles. The edge weights are given by the value of the PairScore for the two endpoints of the edge.
Definition at line 54 of file MSConnectivityRestraint.h.
| IMP::core::MSConnectivityRestraint::MSConnectivityRestraint | ( | PairScore * | ps, |
| double | eps = 0.1 |
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If sc is nullptr, a ListSingletonContainer is created internally. eps is set to 0.1 by default.
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virtual |
A Restraint should override this if they want to decompose themselves for display and other purposes. The returned restraints will be made in to a RestraintSet, if needed and the weight and maximum score set for the restraint set.
The returned restraints should be only the non-zero terms and should have their last scores set appropriately;
Reimplemented from IMP::kernel::Restraint.
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virtual |
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::kernel::ModelObject.
| kernel::ParticlePairsTemp IMP::core::MSConnectivityRestraint::get_connected_pairs | ( | ) | const |
This set of pairs reflects the current configuration at the time of the get_connected_pairs() call, not the set at the time of the last evaluate() call.