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IMP Reference Guide
2.19.0
The Integrative Modeling Platform
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Abstract class for scoring object(s) of type ParticleIndex. More...
#include <IMP/SingletonScore.h>
Inheritance diagram for IMP::SingletonScore:Abstract class for scoring object(s) of type ParticleIndex.
SingletonScore will evaluate the score and derivatives for passed object(s) of type ParticleIndex.
Use in conjunction with various restraints such as IMP::container::SingletonsRestraint or IMP::core::SingletonRestraint. The restraints couple the score functions with appropriate lists of object(s) of type ParticleIndex.
It is possible to call the various evaluate* methods directly, but this is not recommended as they do not ensure that Model invariants (e.g. ScoreStates) are preserved. Use a Restraint or ScoringFunction to score the model instead.
Implementers should check out IMP_SINGLETON_SCORE().
Definition at line 44 of file SingletonScore.h.
Public Types | |
| typedef Particle * | Argument |
| typedef ParticleIndex | IndexArgument |
| typedef SingletonModifier | Modifier |
| typedef Particle * | PassArgument |
| typedef ParticleIndex | PassIndexArgument |
Public Member Functions | |
| SingletonScore (std::string name="SingletonScore %1%") | |
| Restraints | create_current_decomposition (Model *m, ParticleIndex vt) const |
| virtual double | evaluate_if_good_index (Model *m, ParticleIndex vt, DerivativeAccumulator *da, double max) const |
| Compute the score and the derivative if needed, only if "good". More... | |
| virtual double | evaluate_if_good_indexes (Model *m, const ParticleIndexes &o, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const |
| virtual double | evaluate_index (Model *m, ParticleIndex vt, DerivativeAccumulator *da) const =0 |
| Compute the score and the derivative if needed. More... | |
| virtual double | evaluate_indexes (Model *m, const ParticleIndexes &o, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound) const |
| Compute the score and the derivative if needed over a set. More... | |
| virtual double | evaluate_indexes_delta (Model *m, const ParticleIndexes &o, DerivativeAccumulator *da, const std::vector< unsigned > &indexes, std::vector< double > &score) const |
| Compute the change in score and the derivative if needed over a set. More... | |
| virtual double | evaluate_indexes_scores (Model *m, const ParticleIndexes &o, DerivativeAccumulator *da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double > &score) const |
| Compute the score and the derivative if needed over a set. More... | |
| Public Member Functions inherited from IMP::ParticleInputs | |
| ModelObjectsTemp | get_inputs (Model *m, const ParticleIndexes &pis) const |
| Get the ModelObjects read when the given list of particles is used. More... | |
| Public Member Functions inherited from IMP::Object | |
| virtual void | clear_caches () |
| CheckLevel | get_check_level () const |
| LogLevel | get_log_level () const |
| virtual VersionInfo | get_version_info () const |
| Get information about the module and version of the object. More... | |
| 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) |
| virtual std::string | get_type_name () const |
Protected Member Functions | |
| virtual Restraints | do_create_current_decomposition (Model *m, ParticleIndex vt) const |
| Override this to return your own decomposition. More... | |
| Protected Member Functions inherited from IMP::ParticleInputs | |
| virtual ModelObjectsTemp | do_get_inputs (Model *m, const ParticleIndexes &pis) const =0 |
| Overload this method to specify the inputs. More... | |
| Protected Member Functions inherited from IMP::Object | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
| virtual void | do_destroy () |
| Restraints IMP::SingletonScore::create_current_decomposition | ( | Model * | m, |
| ParticleIndex | vt | ||
| ) | const |
Decompose this SingletonScore into a set of currently positive restraints over vt. The scoring function and derivatives should be equal to the current score. The default implementation returns a single restraint with this score bound to vt, or zero restraints if the score equals zero.
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protectedvirtual |
Override this to return your own decomposition.
Reimplemented in IMP::container::MinimumSingletonScore.
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virtual |
Compute the score and the derivative if needed, only if "good".
This functions similarly to evaluate_index(), but may terminate the computation early if the score is higher than max.
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Compute the score and the derivative if needed over a set, only if "good". This functions similarly to evaluate_indexes(), but may terminate the computation early if the total score is higher than max.
Reimplemented in IMP::core::PredicateSingletonScore< Predicate, Score >, IMP::core::SphereDistanceToSingletonScore, IMP::npctransport::ZBiasSingletonScore, IMP::npctransport::HarmonicSpringSingletonScore, IMP::core::GenericDistanceToSingletonScore< UF >, IMP::atom::ImproperSingletonScore, IMP::npctransport::ExcludeZRangeSingletonScore, IMP::core::GenericBoundingSphere3DSingletonScore< UF >, IMP::spb::TiltSingletonScore, IMP::core::GenericBoundingBox3DSingletonScore< UF >, IMP::atom::AngleSingletonScore, IMP::atom::DihedralSingletonScore, IMP::core::GenericAttributeSingletonScore< UF >, IMP::core::GenericAttributeSingletonScore< core::Harmonic >, IMP::atom::BondSingletonScore, and IMP::container::MinimumSingletonScore.
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pure virtual |
Compute the score and the derivative if needed.
| m | the model of vt |
| vt | the index in m of an object of type Particle |
| da | a DerivativeAccumulator that weights computed derivatives. If nullptr, derivatives will not be computed. |
Implemented in IMP::core::PredicateSingletonScore< Predicate, Score >, IMP::core::SphereDistanceToSingletonScore, IMP::npctransport::HarmonicSpringSingletonScore, IMP::npctransport::ZBiasSingletonScore, IMP::core::GenericDistanceToSingletonScore< UF >, IMP::atom::ImproperSingletonScore, IMP::npctransport::ExcludeZRangeSingletonScore, IMP::core::GenericBoundingSphere3DSingletonScore< UF >, IMP::spb::TiltSingletonScore, IMP::core::GenericBoundingBox3DSingletonScore< UF >, IMP::atom::AngleSingletonScore, IMP::atom::DihedralSingletonScore, IMP::atom::BondSingletonScore, IMP::container::MinimumSingletonScore, IMP::core::GenericAttributeSingletonScore< UF >, and IMP::core::GenericAttributeSingletonScore< core::Harmonic >.
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virtual |
Compute the score and the derivative if needed over a set.
| m | the model of o |
| o | objects of type Particle, specified by index |
| da | a derivative accumulator that weights computed derivatives. If nullptr, derivatives will not be computed. |
| lower_bound | index of first item in o to evaluate |
| upper_bound | index one past last item in o to evaluate |
Reimplemented in IMP::core::PredicateSingletonScore< Predicate, Score >, IMP::core::SphereDistanceToSingletonScore, IMP::npctransport::ZBiasSingletonScore, IMP::npctransport::HarmonicSpringSingletonScore, IMP::core::GenericDistanceToSingletonScore< UF >, IMP::atom::ImproperSingletonScore, IMP::npctransport::ExcludeZRangeSingletonScore, IMP::core::GenericBoundingSphere3DSingletonScore< UF >, IMP::spb::TiltSingletonScore, IMP::core::GenericBoundingBox3DSingletonScore< UF >, IMP::atom::AngleSingletonScore, IMP::atom::DihedralSingletonScore, IMP::core::GenericAttributeSingletonScore< UF >, IMP::core::GenericAttributeSingletonScore< core::Harmonic >, IMP::atom::BondSingletonScore, and IMP::container::MinimumSingletonScore.
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Compute the change in score and the derivative if needed over a set.
The score for each o[indexes[x]] is updated in score[indexes[x]] and the total difference between the old and new score values (over the set) is returned.
Reimplemented in IMP::core::PredicateSingletonScore< Predicate, Score >, IMP::core::SphereDistanceToSingletonScore, IMP::npctransport::ZBiasSingletonScore, IMP::npctransport::HarmonicSpringSingletonScore, IMP::core::GenericDistanceToSingletonScore< UF >, IMP::atom::ImproperSingletonScore, IMP::npctransport::ExcludeZRangeSingletonScore, IMP::core::GenericBoundingSphere3DSingletonScore< UF >, IMP::spb::TiltSingletonScore, IMP::core::GenericBoundingBox3DSingletonScore< UF >, IMP::atom::AngleSingletonScore, IMP::atom::DihedralSingletonScore, IMP::core::GenericAttributeSingletonScore< UF >, IMP::core::GenericAttributeSingletonScore< core::Harmonic >, IMP::atom::BondSingletonScore, and IMP::container::MinimumSingletonScore.
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virtual |
Compute the score and the derivative if needed over a set.
Like regular evaluate_indexes(), but the score for each o[x] is also returned as score[x].
Reimplemented in IMP::core::PredicateSingletonScore< Predicate, Score >, IMP::core::SphereDistanceToSingletonScore, IMP::npctransport::ZBiasSingletonScore, IMP::npctransport::HarmonicSpringSingletonScore, IMP::core::GenericDistanceToSingletonScore< UF >, IMP::atom::ImproperSingletonScore, IMP::npctransport::ExcludeZRangeSingletonScore, IMP::core::GenericBoundingSphere3DSingletonScore< UF >, IMP::spb::TiltSingletonScore, IMP::core::GenericBoundingBox3DSingletonScore< UF >, IMP::atom::AngleSingletonScore, IMP::atom::DihedralSingletonScore, IMP::core::GenericAttributeSingletonScore< UF >, IMP::core::GenericAttributeSingletonScore< core::Harmonic >, IMP::atom::BondSingletonScore, and IMP::container::MinimumSingletonScore.