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IMP
2.2.0
The Integrative Modeling Platform
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IMP
2.2.0
The Integrative Modeling Platform
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Prevent a set of particles and rigid bodies from inter-penetrating. More...
#include <IMP/core/ExcludedVolumeRestraint.h>
Inheritance diagram for IMP::core::ExcludedVolumeRestraint:Public Member Functions | |
| ExcludedVolumeRestraint (SingletonContainerAdaptor sc, double k=1, double slack=10, std::string name="ExcludedVolumeRestraint%1%") | |
| unsigned int | add_pair_filter (PairPredicate *obj) |
| void | add_pair_filters (const PairPredicates &objs) |
| void | clear_caches () |
| void | clear_pair_filters () |
| kernel::Restraints | do_create_current_decomposition () const |
| kernel::Restraints | do_create_decomposition () const |
| IMP::kernel::ModelObjectsTemp | do_get_inputs () const |
| bool | get_has_pair_filters () |
| unsigned int | get_number_of_pair_filters () const |
| PairPredicate * | get_pair_filter (unsigned int i) const |
| PairPredicates | get_pair_filters () const |
| 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. | |
| void | remove_pair_filter (PairPredicate *d) |
| void | remove_pair_filters (const PairPredicates &d) |
| void | reserve_pair_filters (unsigned int sz) |
| void | set_pair_filters (const PairPredicates &ps) |
| void | set_pair_filters_order (const PairPredicates &objs) |
| double | unprotected_evaluate (IMP::DerivativeAccumulator *accum) const |
| Public Member Functions inherited from IMP::kernel::Restraint | |
| Restraint (kernel::Model *m, std::string name) | |
| 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 |
| 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) | |
| 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 |
| 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) |
| Public Member Functions inherited from IMP::base::Object | |
| 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) |
Additional Inherited Members | |
| Protected Member Functions inherited from IMP::kernel::Restraint | |
| virtual void | do_add_score_and_derivatives (ScoreAccumulator sa) 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... | |
Given an arbitrary collection of particles and rigid bodies, this restraint prevents the particles from interpenetrating. Such restraints are also known as steric clash restraints.
IMP.Definition at line 40 of file ExcludedVolumeRestraint.h.
| IMP::core::ExcludedVolumeRestraint::ExcludedVolumeRestraint | ( | SingletonContainerAdaptor | sc, |
| double | k = 1, |
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| double | slack = 10, |
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| std::string | name = "ExcludedVolumeRestraint%1%" |
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| ) |
The SingletonContainer contains a set of XYZR particles and RigidMembers.
The slack is how far the particles must move before the list of close pairs is computed. It does not matter for correctness, just running time. You may want to fiddle with it or use the IMP::container::get_slack_estimate() function.
The spring constant used is k.
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Objects can have internal caches. This method resets them returning the object to its just-initialized state.
Reimplemented from IMP::base::Object.
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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 |
A Restraint should override this if they want to decompose themselves for domino 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.
Reimplemented from IMP::kernel::Restraint.
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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::kernel::ModelObject.