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 () |
| Restraints | do_create_current_decomposition () const |
| Restraints | do_create_decomposition () const |
| IMP::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 |
| 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 (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 |
| 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 (Model *m, std::string name) | |
| ModelObjectsTemp | get_inputs () const |
| ModelObjectsTemps | get_interactions () const |
| Model * | get_model () const |
| ModelObjectsTemp | get_outputs () const |
| Public Member Functions inherited from IMP::base::Object | |
| virtual IMP::base::VersionInfo | get_version_info () const =0 |
| Get information about the module and version of the object. | |
| 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 |
| virtual void | do_update_dependencies () |
| Related Functions inherited from IMP::kernel::Restraint | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < Restraint > > | RestraintsTemp |
Detailed Description
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.
- Note
- See IMP::container::ClosePairContainer for more information about close pair based scoring functions and
IMP. - Changing the set of particles in the SingletonContainer is not currently supported after the first evaluate call.
- Currently the radius of all particles is assumed to be constant
Definition at line 40 of file ExcludedVolumeRestraint.h.
Constructor & Destructor Documentation
| 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.
Member Function Documentation
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virtual |
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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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 |
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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virtual |
Override if this reads other objects during evaluate.
Implements IMP::kernel::ModelObject.
The documentation for this class was generated from the following file: