IMP Reference Guide
2.21.0
The Integrative Modeling Platform
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Abstract class for scoring object(s) of type ParticleIndexPair. More...
#include <IMP/PairScore.h>
Inherits IMP::ParticleInputs, and IMP::Object.
Inherited by IMP::score_functor::DistancePairScore< LinearInteractionScore >, IMP::score_functor::DistancePairScore< LinearSoftSphereScore >, IMP::score_functor::DistancePairScore< score_functor::Dope >, IMP::score_functor::DistancePairScore< score_functor::LoopStatistical >, IMP::score_functor::DistancePairScore< score_functor::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE > >, IMP::score_functor::DistancePairScore< score_functor::Statistical< ProteinLigandType, BIPARTITE, INTERPOLATE, false > >, IMP::score_functor::DistancePairScoreWithCache< score_functor::OrientedSoap >, IMP::atom::CoulombPairScore, IMP::atom::LennardJonesPairScore, IMP::container::MinimumPairScore, IMP::core::ClosePairsPairScore, IMP::core::DistancePairScore, IMP::core::HarmonicDistancePairScore, IMP::core::HarmonicSphereDistancePairScore, IMP::core::HarmonicSurfaceDepthPairScore, IMP::core::HarmonicSurfaceDistancePairScore, IMP::core::HarmonicSurfaceHeightPairScore, IMP::core::HarmonicUpperBoundSphereDiameterPairScore, IMP::core::HarmonicUpperBoundSphereDistancePairScore, IMP::core::KClosePairsPairScore, IMP::core::NormalizedSphereDistancePairScore, IMP::core::RefinedPairsPairScore, IMP::core::RigidBodyAnglePairScore, IMP::core::SoftSpherePairScore, IMP::core::SoftSubSurfacePairScore, IMP::core::SoftSuperSurfacePairScore, IMP::core::SphereDistancePairScore, IMP::core::SurfaceDepthPairScore, IMP::core::SurfaceDistancePairScore, IMP::core::SurfaceHeightPairScore, IMP::core::TransformedDistancePairScore, IMP::core::TypedPairScore, IMP::core::WeightedSphereDistancePairScore, IMP::example::ExamplePairScore, IMP.example.PythonExamplePairScore, IMP::isd::RepulsiveDistancePairScore, IMP::misc::LogPairScore, IMP::misc::LowestRefinedPairScore, IMP::misc::SoftCylinderPairScore, IMP::npc::MinimumSphereDistancePairScore, IMP::npc::SlabWithSphericalIndentMBMScore, IMP::npc::SlabWithToroidalPoreGoPairScore, IMP::npc::SlabWithToroidalPoreMBMScore, IMP::npc::SphericalIndentSurfaceDepthPairScore, IMP::npc::ToroidalPoreSurfaceDepthPairScore, IMP::npctransport::AnchorToCylidnricalPorePairScore, IMP::npctransport::HarmonicWellPairScore, IMP::npctransport::LinearInteractionPairScore, IMP::npctransport::LinearSoftSpherePairScore, IMP::npctransport::LinearWellPairScore, IMP::npctransport::SlabWithCylindricalPorePairScore, IMP::npctransport::SlabWithToroidalPorePairScore, IMP::score_functor::DistancePairScore< DistanceScoreT >, IMP::score_functor::DistancePairScoreWithCache< DistanceScoreT >, IMP::score_functor::SurfaceDepthPairScore< DistanceScoreT >, IMP::score_functor::SurfaceDistancePairScore< DistanceScoreT >, IMP::score_functor::SurfaceHeightPairScore< DistanceScoreT >, IMP::spb::AttributeDistancePairScore, IMP::spb::KinkPairScore, IMP::spb::RigidBodyPackingScore, and marina_party.SumPricePairScore.
Abstract class for scoring object(s) of type ParticleIndexPair.
PairScore will evaluate the score and derivatives for passed object(s) of type ParticleIndexPair.
Use in conjunction with various restraints such as IMP::container::PairsRestraint or IMP::core::PairRestraint. The restraints couple the score functions with appropriate lists of object(s) of type ParticleIndexPair.
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_PAIR_SCORE_METHODS().
Definition at line 44 of file PairScore.h.
Public Types | |
typedef ParticlePair | Argument |
typedef ParticleIndexPair | IndexArgument |
typedef PairModifier | Modifier |
typedef const ParticlePair & | PassArgument |
typedef const ParticleIndexPair & | PassIndexArgument |
Public Member Functions | |
PairScore (std::string name="PairScore %1%") | |
Restraints | create_current_decomposition (Model *m, const ParticleIndexPair &vt) const |
virtual double | evaluate_if_good_index (Model *m, const ParticleIndexPair &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 ParticleIndexPairs &o, DerivativeAccumulator *da, double max, unsigned int lower_bound, unsigned int upper_bound) const |
virtual double | evaluate_index (Model *m, const ParticleIndexPair &vt, DerivativeAccumulator *da) const =0 |
Compute the score and the derivative if needed. More... | |
virtual double | evaluate_indexes (Model *m, const ParticleIndexPairs &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 ParticleIndexPairs &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 ParticleIndexPairs &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, const ParticleIndexPair &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::PairScore::create_current_decomposition | ( | Model * | m, |
const ParticleIndexPair & | vt | ||
) | const |
Decompose this PairScore 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::MinimumPairScore.
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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.
Reimplemented in IMP::core::ClosePairsPairScore, and IMP::core::KClosePairsPairScore.
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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::npctransport::LinearWellPairScore, IMP::core::WeightedSphereDistancePairScore, IMP::core::NormalizedSphereDistancePairScore, IMP::npctransport::SitesPairScore, IMP::core::ClosePairsPairScore, IMP::npctransport::LinearSoftSpherePairScore, IMP::npctransport::HarmonicWellPairScore, IMP::npctransport::SlabWithCylindricalPorePairScore, IMP::npctransport::AnchorToCylidnricalPorePairScore, IMP::atom::LennardJonesPairScore, IMP::core::HarmonicUpperBoundSphereDiameterPairScore, IMP::npctransport::SlabWithToroidalPorePairScore, IMP::core::TypedPairScore, IMP::score_functor::SurfaceDistancePairScore< DistanceScoreT >, IMP::core::KClosePairsPairScore, IMP::score_functor::DistancePairScore< DistanceScoreT >, IMP::score_functor::DistancePairScore< LinearInteractionScore >, IMP::score_functor::DistancePairScore< LinearSoftSphereScore >, IMP::score_functor::DistancePairScore< score_functor::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE > >, IMP::score_functor::DistancePairScore< score_functor::LoopStatistical >, IMP::score_functor::DistancePairScore< score_functor::Statistical< ProteinLigandType, BIPARTITE, INTERPOLATE, false > >, IMP::score_functor::DistancePairScore< score_functor::Dope >, IMP::npc::MinimumSphereDistancePairScore, IMP::atom::CoulombPairScore, IMP::npc::SlabWithSphericalIndentMBMScore, IMP::npc::SphericalIndentSurfaceDepthPairScore, IMP::npc::SlabWithToroidalPoreGoPairScore, IMP::npc::SlabWithToroidalPoreMBMScore, IMP::npc::ToroidalPoreSurfaceDepthPairScore, IMP::core::TransformedDistancePairScore, IMP::isd::RepulsiveDistancePairScore, IMP::spb::AttributeDistancePairScore, IMP::core::RefinedPairsPairScore, IMP::example::ExamplePairScore, IMP::spb::RigidBodyPackingScore, IMP::container::MinimumPairScore, IMP::misc::LowestRefinedPairScore, IMP::spb::KinkPairScore, IMP::misc::SoftCylinderPairScore, and IMP::core::RigidBodyAnglePairScore.
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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 ParticlePair |
da | a DerivativeAccumulator that weights computed derivatives. If nullptr, derivatives will not be computed. |
Implemented in IMP::npctransport::LinearWellPairScore, IMP::core::SoftSpherePairScore, IMP::core::WeightedSphereDistancePairScore, IMP::npctransport::SitesPairScore, IMP::core::SoftSubSurfacePairScore, IMP::core::NormalizedSphereDistancePairScore, IMP::core::SoftSuperSurfacePairScore, IMP::core::HarmonicSurfaceDepthPairScore, IMP::core::HarmonicSphereDistancePairScore, IMP::core::HarmonicSurfaceHeightPairScore, IMP::core::ClosePairsPairScore, IMP::npctransport::HarmonicWellPairScore, IMP::npctransport::LinearSoftSpherePairScore, IMP::core::HarmonicSurfaceDistancePairScore, IMP::atom::LennardJonesPairScore, IMP::core::HarmonicUpperBoundSphereDiameterPairScore, IMP::npctransport::AnchorToCylidnricalPorePairScore, IMP::core::TypedPairScore, IMP::core::SurfaceDepthPairScore, IMP::npctransport::SlabWithCylindricalPorePairScore, IMP::core::HarmonicUpperBoundSphereDistancePairScore, IMP::score_functor::SurfaceDistancePairScore< DistanceScoreT >, IMP::core::KClosePairsPairScore, IMP::core::HarmonicDistancePairScore, IMP::npctransport::SlabWithToroidalPorePairScore, IMP::core::SurfaceHeightPairScore, IMP::score_functor::DistancePairScore< DistanceScoreT >, IMP::score_functor::DistancePairScore< LinearInteractionScore >, IMP::score_functor::DistancePairScore< LinearSoftSphereScore >, IMP::score_functor::DistancePairScore< score_functor::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE > >, IMP::score_functor::DistancePairScore< score_functor::LoopStatistical >, IMP::score_functor::DistancePairScore< score_functor::Statistical< ProteinLigandType, BIPARTITE, INTERPOLATE, false > >, IMP::score_functor::DistancePairScore< score_functor::Dope >, IMP::atom::CoulombPairScore, IMP::npc::MinimumSphereDistancePairScore, IMP::core::SphereDistancePairScore, IMP::npc::SlabWithSphericalIndentMBMScore, IMP::npc::SphericalIndentSurfaceDepthPairScore, IMP::core::TransformedDistancePairScore, IMP::npc::SlabWithToroidalPoreGoPairScore, IMP::npc::SlabWithToroidalPoreMBMScore, IMP::npc::ToroidalPoreSurfaceDepthPairScore, IMP::score_functor::DistancePairScoreWithCache< DistanceScoreT >, IMP::score_functor::DistancePairScoreWithCache< score_functor::OrientedSoap >, IMP::core::SurfaceDistancePairScore, IMP::isd::RepulsiveDistancePairScore, IMP::core::RefinedPairsPairScore, IMP::container::MinimumPairScore, IMP::example::ExamplePairScore, IMP::misc::LowestRefinedPairScore, IMP::spb::AttributeDistancePairScore, IMP::core::DistancePairScore, IMP::spb::RigidBodyPackingScore, IMP::misc::SoftCylinderPairScore, IMP::core::RigidBodyAnglePairScore, IMP::misc::LogPairScore, and IMP::spb::KinkPairScore.
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Compute the score and the derivative if needed over a set.
m | the model of o |
o | objects of type ParticlePair, 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::npctransport::LinearWellPairScore, IMP::npctransport::LinearInteractionPairScore, IMP::core::WeightedSphereDistancePairScore, IMP::core::NormalizedSphereDistancePairScore, IMP::npctransport::SitesPairScore, IMP::core::ClosePairsPairScore, IMP::npctransport::HarmonicWellPairScore, IMP::npctransport::LinearSoftSpherePairScore, IMP::npctransport::AnchorToCylidnricalPorePairScore, IMP::atom::LennardJonesPairScore, IMP::core::HarmonicUpperBoundSphereDiameterPairScore, IMP::npctransport::SlabWithCylindricalPorePairScore, IMP::core::TypedPairScore, IMP::score_functor::SurfaceDistancePairScore< DistanceScoreT >, IMP::npctransport::SlabWithToroidalPorePairScore, IMP::core::KClosePairsPairScore, IMP::score_functor::DistancePairScore< DistanceScoreT >, IMP::score_functor::DistancePairScore< LinearInteractionScore >, IMP::score_functor::DistancePairScore< LinearSoftSphereScore >, IMP::score_functor::DistancePairScore< score_functor::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE > >, IMP::score_functor::DistancePairScore< score_functor::LoopStatistical >, IMP::score_functor::DistancePairScore< score_functor::Statistical< ProteinLigandType, BIPARTITE, INTERPOLATE, false > >, IMP::score_functor::DistancePairScore< score_functor::Dope >, IMP::score_functor::DistancePairScoreWithCache< DistanceScoreT >, IMP::score_functor::DistancePairScoreWithCache< score_functor::OrientedSoap >, IMP::npc::MinimumSphereDistancePairScore, IMP::atom::CoulombPairScore, IMP::npc::SlabWithSphericalIndentMBMScore, IMP::npc::SphericalIndentSurfaceDepthPairScore, IMP::npc::SlabWithToroidalPoreGoPairScore, IMP::npc::SlabWithToroidalPoreMBMScore, IMP::npc::ToroidalPoreSurfaceDepthPairScore, IMP::core::TransformedDistancePairScore, IMP::isd::RepulsiveDistancePairScore, IMP::spb::AttributeDistancePairScore, IMP::core::RefinedPairsPairScore, IMP::example::ExamplePairScore, IMP::spb::RigidBodyPackingScore, IMP::container::MinimumPairScore, IMP::misc::LowestRefinedPairScore, IMP::spb::KinkPairScore, IMP::misc::SoftCylinderPairScore, and IMP::core::RigidBodyAnglePairScore.
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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::npctransport::LinearWellPairScore, IMP::core::WeightedSphereDistancePairScore, IMP::core::NormalizedSphereDistancePairScore, IMP::core::ClosePairsPairScore, IMP::npctransport::HarmonicWellPairScore, IMP::npctransport::AnchorToCylidnricalPorePairScore, IMP::atom::LennardJonesPairScore, IMP::core::HarmonicUpperBoundSphereDiameterPairScore, IMP::core::TypedPairScore, IMP::score_functor::SurfaceDistancePairScore< DistanceScoreT >, IMP::score_functor::DistancePairScoreWithCache< DistanceScoreT >, IMP::score_functor::DistancePairScoreWithCache< score_functor::OrientedSoap >, IMP::core::KClosePairsPairScore, IMP::score_functor::DistancePairScore< DistanceScoreT >, IMP::score_functor::DistancePairScore< LinearInteractionScore >, IMP::score_functor::DistancePairScore< LinearSoftSphereScore >, IMP::score_functor::DistancePairScore< score_functor::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE > >, IMP::score_functor::DistancePairScore< score_functor::LoopStatistical >, IMP::score_functor::DistancePairScore< score_functor::Statistical< ProteinLigandType, BIPARTITE, INTERPOLATE, false > >, IMP::score_functor::DistancePairScore< score_functor::Dope >, IMP::npc::MinimumSphereDistancePairScore, IMP::atom::CoulombPairScore, IMP::npc::SlabWithSphericalIndentMBMScore, IMP::npc::SphericalIndentSurfaceDepthPairScore, IMP::npc::SlabWithToroidalPoreGoPairScore, IMP::npc::SlabWithToroidalPoreMBMScore, IMP::npc::ToroidalPoreSurfaceDepthPairScore, IMP::core::TransformedDistancePairScore, IMP::isd::RepulsiveDistancePairScore, IMP::spb::AttributeDistancePairScore, IMP::core::RefinedPairsPairScore, IMP::example::ExamplePairScore, IMP::spb::RigidBodyPackingScore, IMP::container::MinimumPairScore, IMP::misc::LowestRefinedPairScore, IMP::spb::KinkPairScore, IMP::misc::SoftCylinderPairScore, and IMP::core::RigidBodyAnglePairScore.
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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::npctransport::LinearWellPairScore, IMP::core::WeightedSphereDistancePairScore, IMP::core::NormalizedSphereDistancePairScore, IMP::core::ClosePairsPairScore, IMP::npctransport::HarmonicWellPairScore, IMP::npctransport::AnchorToCylidnricalPorePairScore, IMP::atom::LennardJonesPairScore, IMP::core::HarmonicUpperBoundSphereDiameterPairScore, IMP::core::TypedPairScore, IMP::score_functor::SurfaceDistancePairScore< DistanceScoreT >, IMP::core::KClosePairsPairScore, IMP::score_functor::DistancePairScore< DistanceScoreT >, IMP::score_functor::DistancePairScore< LinearInteractionScore >, IMP::score_functor::DistancePairScore< LinearSoftSphereScore >, IMP::score_functor::DistancePairScore< score_functor::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE > >, IMP::score_functor::DistancePairScore< score_functor::LoopStatistical >, IMP::score_functor::DistancePairScore< score_functor::Statistical< ProteinLigandType, BIPARTITE, INTERPOLATE, false > >, IMP::score_functor::DistancePairScore< score_functor::Dope >, IMP::score_functor::DistancePairScoreWithCache< DistanceScoreT >, IMP::score_functor::DistancePairScoreWithCache< score_functor::OrientedSoap >, IMP::npc::MinimumSphereDistancePairScore, IMP::atom::CoulombPairScore, IMP::npc::SlabWithSphericalIndentMBMScore, IMP::npc::SphericalIndentSurfaceDepthPairScore, IMP::npc::SlabWithToroidalPoreGoPairScore, IMP::npc::SlabWithToroidalPoreMBMScore, IMP::npc::ToroidalPoreSurfaceDepthPairScore, IMP::core::TransformedDistancePairScore, IMP::isd::RepulsiveDistancePairScore, IMP::spb::AttributeDistancePairScore, IMP::core::RefinedPairsPairScore, IMP::example::ExamplePairScore, IMP::spb::RigidBodyPackingScore, IMP::container::MinimumPairScore, IMP::misc::LowestRefinedPairScore, IMP::spb::KinkPairScore, IMP::misc::SoftCylinderPairScore, and IMP::core::RigidBodyAnglePairScore.