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IMP Reference Guide
2.20.2
The Integrative Modeling Platform
IMP Manual
Reference Guide
Tutorial Index
Modules
Classes
Examples
Class List
Class Index
Class Hierarchy
Class Members
All
Functions
Variables
Enumerations
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Em2DRestraint() :
IMP::em2d::Em2DRestraint
EM2DRestraint() :
IMP::spb::EM2DRestraint
enable_all_movers() :
IMP.pmi.dof.DegreesOfFreedom
EnvelopeFitRestraint() :
IMP::em::EnvelopeFitRestraint
EnvelopePenetrationRestraint() :
IMP::em::EnvelopePenetrationRestraint
estimate_cv_constant() :
IMP.isd.TuneRex.CvEstimator
estimate_cv_interpolate() :
IMP.isd.TuneRex.CvEstimator
estimate_cv_mbar() :
IMP.isd.TuneRex.CvEstimator
evaluate() :
IMP::core::ClosedCubicSpline
,
IMP::core::Cosine
,
IMP::core::Harmonic
,
IMP::core::HarmonicLowerBound
,
IMP::core::HarmonicUpperBound
,
IMP::core::HarmonicWell
,
IMP::core::Linear
,
IMP::core::SurfaceTetheredChain
,
IMP::core::TruncatedHarmonic< DIRECTION >
,
IMP::core::WeightedSum
,
IMP::core::WeightedSumOfExponential
,
IMP::em::CoarseCCatIntervals
,
IMP::example::ExampleUnaryFunction
,
IMP::isd::MultivariateFNormalSufficient
,
IMP::isd::OneDimensionalDistribution
,
IMP::isd::OneDimensionalSufficientDistribution
,
IMP::misc::FreelyJointedChain
,
IMP::misc::WormLikeChain
,
IMP.pmi1.restraints.RestraintBase
,
IMP::Restraint
,
IMP::score_functor::ScoreUnaryFunction< Score, D >
,
IMP::ScoringFunction
,
IMP::spb::Gaussian
,
IMP::UnaryFunction
evaluate_derivative_alpha() :
IMP::isd::PenalizedComplexityPrior
evaluate_derivative_Dxi() :
IMP::isd::PenalizedComplexityPrior
evaluate_derivative_factor() :
IMP::isd::MultivariateFNormalSufficient
evaluate_derivative_FM() :
IMP::isd::FStudentT
,
IMP::isd::MultivariateFNormalSufficient
evaluate_derivative_Fx() :
IMP::isd::FStudentT
evaluate_derivative_FX() :
IMP::isd::FStudentT
evaluate_derivative_Jxi() :
IMP::isd::PenalizedComplexityPrior
evaluate_derivative_LogJX() :
IMP::isd::FStudentT
evaluate_derivative_nu() :
IMP::isd::FStudentT
evaluate_derivative_sigma() :
IMP::isd::FStudentT
evaluate_derivative_Sigma() :
IMP::isd::MultivariateFNormalSufficient
evaluate_derivative_xi() :
IMP::isd::PenalizedComplexityPrior
evaluate_for_contributions() :
IMP::isd::AtomicCrossLinkMSRestraint
,
IMP::isd::ResidueProteinProximityRestraint
evaluate_if_below() :
IMP::Restraint
evaluate_if_good() :
IMP::Restraint
evaluate_if_good_index() :
IMP::core::ClosePairsPairScore
,
IMP::core::KClosePairsPairScore
,
IMP::PairScore
,
IMP::QuadScore
,
IMP::SingletonScore
,
IMP::TripletScore
evaluate_if_good_indexes() :
IMP::atom::AngleSingletonScore
,
IMP::atom::BondSingletonScore
,
IMP::atom::CoulombPairScore
,
IMP::atom::DihedralSingletonScore
,
IMP::atom::ImproperSingletonScore
,
IMP::atom::LennardJonesPairScore
,
IMP::container::MinimumPairScore
,
IMP::container::MinimumQuadScore
,
IMP::container::MinimumSingletonScore
,
IMP::container::MinimumTripletScore
,
IMP::core::AngleTripletScore
,
IMP::core::ClosePairsPairScore
,
IMP::core::GenericAttributeSingletonScore< UF >
,
IMP::core::GenericBoundingBox3DSingletonScore< UF >
,
IMP::core::GenericBoundingSphere3DSingletonScore< UF >
,
IMP::core::GenericDistanceToSingletonScore< UF >
,
IMP::core::HarmonicUpperBoundSphereDiameterPairScore
,
IMP::core::KClosePairsPairScore
,
IMP::core::NormalizedSphereDistancePairScore
,
IMP::core::PredicateSingletonScore< Predicate, Score >
,
IMP::core::RefinedPairsPairScore
,
IMP::core::RigidBodyAnglePairScore
,
IMP::core::SphereDistanceToSingletonScore
,
IMP::core::TransformedDistancePairScore
,
IMP::core::TypedPairScore
,
IMP::core::WeightedSphereDistancePairScore
,
IMP::example::ExamplePairScore
,
IMP::isd::RepulsiveDistancePairScore
,
IMP::misc::LowestRefinedPairScore
,
IMP::misc::SoftCylinderPairScore
,
IMP::npc::MinimumSphereDistancePairScore
,
IMP::npctransport::AnchorToCylidnricalPorePairScore
,
IMP::npctransport::ExcludeZRangeSingletonScore
,
IMP::npctransport::HarmonicSpringSingletonScore
,
IMP::npctransport::HarmonicWellPairScore
,
IMP::npctransport::LinearSoftSpherePairScore
,
IMP::npctransport::LinearWellPairScore
,
IMP::npctransport::SitesPairScore
,
IMP::npctransport::SlabWithCylindricalPorePairScore
,
IMP::npctransport::SlabWithToroidalPorePairScore
,
IMP::npctransport::ZBiasSingletonScore
,
IMP::PairScore
,
IMP::QuadScore
,
IMP::score_functor::DistancePairScore< DistanceScoreT >
,
IMP::score_functor::SurfaceDistancePairScore< DistanceScoreT >
,
IMP::SingletonScore
,
IMP::spb::AttributeDistancePairScore
,
IMP::spb::KinkPairScore
,
IMP::spb::RigidBodyPackingScore
,
IMP::spb::TiltSingletonScore
,
IMP::TripletScore
evaluate_index() :
IMP::atom::AngleSingletonScore
,
IMP::atom::BondSingletonScore
,
IMP::atom::CoulombPairScore
,
IMP::atom::DihedralSingletonScore
,
IMP::atom::ImproperSingletonScore
,
IMP::atom::LennardJonesPairScore
,
IMP::container::MinimumPairScore
,
IMP::container::MinimumQuadScore
,
IMP::container::MinimumSingletonScore
,
IMP::container::MinimumTripletScore
,
IMP::core::AngleTripletScore
,
IMP::core::ClosePairsPairScore
,
IMP::core::DistancePairScore
,
IMP::core::GenericAttributeSingletonScore< UF >
,
IMP::core::GenericBoundingBox3DSingletonScore< UF >
,
IMP::core::GenericBoundingSphere3DSingletonScore< UF >
,
IMP::core::GenericDistanceToSingletonScore< UF >
,
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::PredicateSingletonScore< Predicate, Score >
,
IMP::core::RefinedPairsPairScore
,
IMP::core::RigidBodyAnglePairScore
,
IMP::core::SoftSpherePairScore
,
IMP::core::SoftSubSurfacePairScore
,
IMP::core::SoftSuperSurfacePairScore
,
IMP::core::SphereDistancePairScore
,
IMP::core::SphereDistanceToSingletonScore
,
IMP::core::SurfaceDepthPairScore
,
IMP::core::SurfaceDistancePairScore
,
IMP::core::SurfaceHeightPairScore
,
IMP::core::TransformedDistancePairScore
,
IMP::core::TypedPairScore
,
IMP::core::WeightedSphereDistancePairScore
,
IMP::example::ExamplePairScore
,
IMP::isd::RepulsiveDistancePairScore
,
IMP::misc::LogPairScore
,
IMP::misc::LowestRefinedPairScore
,
IMP::misc::SoftCylinderPairScore
,
IMP::npc::MinimumSphereDistancePairScore
,
IMP::npctransport::AnchorToCylidnricalPorePairScore
,
IMP::npctransport::ExcludeZRangeSingletonScore
,
IMP::npctransport::HarmonicSpringSingletonScore
,
IMP::npctransport::HarmonicWellPairScore
,
IMP::npctransport::LinearInteractionPairScore
,
IMP::npctransport::LinearSoftSpherePairScore
,
IMP::npctransport::LinearWellPairScore
,
IMP::npctransport::SitesPairScore
,
IMP::npctransport::SlabWithCylindricalPorePairScore
,
IMP::npctransport::SlabWithToroidalPorePairScore
,
IMP::npctransport::ZBiasSingletonScore
,
IMP::PairScore
,
IMP::QuadScore
,
IMP::score_functor::DistancePairScore< DistanceScoreT >
,
IMP::score_functor::DistancePairScoreWithCache< DistanceScoreT >
,
IMP::score_functor::SurfaceDistancePairScore< DistanceScoreT >
,
IMP::SingletonScore
,
IMP::spb::AttributeDistancePairScore
,
IMP::spb::KinkPairScore
,
IMP::spb::RigidBodyPackingScore
,
IMP::spb::TiltSingletonScore
,
IMP::TripletScore
evaluate_indexes() :
IMP::atom::AngleSingletonScore
,
IMP::atom::BondSingletonScore
,
IMP::atom::CoulombPairScore
,
IMP::atom::DihedralSingletonScore
,
IMP::atom::ImproperSingletonScore
,
IMP::atom::LennardJonesPairScore
,
IMP::container::MinimumPairScore
,
IMP::container::MinimumQuadScore
,
IMP::container::MinimumSingletonScore
,
IMP::container::MinimumTripletScore
,
IMP::core::AngleTripletScore
,
IMP::core::ClosePairsPairScore
,
IMP::core::GenericAttributeSingletonScore< UF >
,
IMP::core::GenericBoundingBox3DSingletonScore< UF >
,
IMP::core::GenericBoundingSphere3DSingletonScore< UF >
,
IMP::core::GenericDistanceToSingletonScore< UF >
,
IMP::core::HarmonicUpperBoundSphereDiameterPairScore
,
IMP::core::KClosePairsPairScore
,
IMP::core::NormalizedSphereDistancePairScore
,
IMP::core::PredicateSingletonScore< Predicate, Score >
,
IMP::core::RefinedPairsPairScore
,
IMP::core::RigidBodyAnglePairScore
,
IMP::core::SphereDistanceToSingletonScore
,
IMP::core::TransformedDistancePairScore
,
IMP::core::TypedPairScore
,
IMP::core::WeightedSphereDistancePairScore
,
IMP::example::ExamplePairScore
,
IMP::isd::RepulsiveDistancePairScore
,
IMP::misc::LowestRefinedPairScore
,
IMP::misc::SoftCylinderPairScore
,
IMP::npc::MinimumSphereDistancePairScore
,
IMP::npctransport::AnchorToCylidnricalPorePairScore
,
IMP::npctransport::ExcludeZRangeSingletonScore
,
IMP::npctransport::HarmonicSpringSingletonScore
,
IMP::npctransport::HarmonicWellPairScore
,
IMP::npctransport::LinearInteractionPairScore
,
IMP::npctransport::LinearSoftSpherePairScore
,
IMP::npctransport::LinearWellPairScore
,
IMP::npctransport::SitesPairScore
,
IMP::npctransport::SlabWithCylindricalPorePairScore
,
IMP::npctransport::SlabWithToroidalPorePairScore
,
IMP::npctransport::ZBiasSingletonScore
,
IMP::PairScore
,
IMP::QuadScore
,
IMP::score_functor::DistancePairScore< DistanceScoreT >
,
IMP::score_functor::DistancePairScoreWithCache< DistanceScoreT >
,
IMP::score_functor::SurfaceDistancePairScore< DistanceScoreT >
,
IMP::SingletonScore
,
IMP::spb::AttributeDistancePairScore
,
IMP::spb::KinkPairScore
,
IMP::spb::RigidBodyPackingScore
,
IMP::spb::TiltSingletonScore
,
IMP::TripletScore
evaluate_indexes_delta() :
IMP::atom::AngleSingletonScore
,
IMP::atom::BondSingletonScore
,
IMP::atom::CoulombPairScore
,
IMP::atom::DihedralSingletonScore
,
IMP::atom::ImproperSingletonScore
,
IMP::atom::LennardJonesPairScore
,
IMP::container::MinimumPairScore
,
IMP::container::MinimumQuadScore
,
IMP::container::MinimumSingletonScore
,
IMP::container::MinimumTripletScore
,
IMP::core::AngleTripletScore
,
IMP::core::ClosePairsPairScore
,
IMP::core::GenericAttributeSingletonScore< UF >
,
IMP::core::GenericBoundingBox3DSingletonScore< UF >
,
IMP::core::GenericBoundingSphere3DSingletonScore< UF >
,
IMP::core::GenericDistanceToSingletonScore< UF >
,
IMP::core::HarmonicUpperBoundSphereDiameterPairScore
,
IMP::core::KClosePairsPairScore
,
IMP::core::NormalizedSphereDistancePairScore
,
IMP::core::PredicateSingletonScore< Predicate, Score >
,
IMP::core::RefinedPairsPairScore
,
IMP::core::RigidBodyAnglePairScore
,
IMP::core::SphereDistanceToSingletonScore
,
IMP::core::TransformedDistancePairScore
,
IMP::core::TypedPairScore
,
IMP::core::WeightedSphereDistancePairScore
,
IMP::example::ExamplePairScore
,
IMP::isd::RepulsiveDistancePairScore
,
IMP::misc::LowestRefinedPairScore
,
IMP::misc::SoftCylinderPairScore
,
IMP::npc::MinimumSphereDistancePairScore
,
IMP::npctransport::AnchorToCylidnricalPorePairScore
,
IMP::npctransport::ExcludeZRangeSingletonScore
,
IMP::npctransport::HarmonicSpringSingletonScore
,
IMP::npctransport::HarmonicWellPairScore
,
IMP::npctransport::LinearWellPairScore
,
IMP::npctransport::ZBiasSingletonScore
,
IMP::PairScore
,
IMP::QuadScore
,
IMP::score_functor::DistancePairScore< DistanceScoreT >
,
IMP::score_functor::DistancePairScoreWithCache< DistanceScoreT >
,
IMP::score_functor::SurfaceDistancePairScore< DistanceScoreT >
,
IMP::SingletonScore
,
IMP::spb::AttributeDistancePairScore
,
IMP::spb::KinkPairScore
,
IMP::spb::RigidBodyPackingScore
,
IMP::spb::TiltSingletonScore
,
IMP::TripletScore
evaluate_indexes_scores() :
IMP::atom::AngleSingletonScore
,
IMP::atom::BondSingletonScore
,
IMP::atom::CoulombPairScore
,
IMP::atom::DihedralSingletonScore
,
IMP::atom::ImproperSingletonScore
,
IMP::atom::LennardJonesPairScore
,
IMP::container::MinimumPairScore
,
IMP::container::MinimumQuadScore
,
IMP::container::MinimumSingletonScore
,
IMP::container::MinimumTripletScore
,
IMP::core::AngleTripletScore
,
IMP::core::ClosePairsPairScore
,
IMP::core::GenericAttributeSingletonScore< UF >
,
IMP::core::GenericBoundingBox3DSingletonScore< UF >
,
IMP::core::GenericBoundingSphere3DSingletonScore< UF >
,
IMP::core::GenericDistanceToSingletonScore< UF >
,
IMP::core::HarmonicUpperBoundSphereDiameterPairScore
,
IMP::core::KClosePairsPairScore
,
IMP::core::NormalizedSphereDistancePairScore
,
IMP::core::PredicateSingletonScore< Predicate, Score >
,
IMP::core::RefinedPairsPairScore
,
IMP::core::RigidBodyAnglePairScore
,
IMP::core::SphereDistanceToSingletonScore
,
IMP::core::TransformedDistancePairScore
,
IMP::core::TypedPairScore
,
IMP::core::WeightedSphereDistancePairScore
,
IMP::example::ExamplePairScore
,
IMP::isd::RepulsiveDistancePairScore
,
IMP::misc::LowestRefinedPairScore
,
IMP::misc::SoftCylinderPairScore
,
IMP::npc::MinimumSphereDistancePairScore
,
IMP::npctransport::AnchorToCylidnricalPorePairScore
,
IMP::npctransport::ExcludeZRangeSingletonScore
,
IMP::npctransport::HarmonicSpringSingletonScore
,
IMP::npctransport::HarmonicWellPairScore
,
IMP::npctransport::LinearWellPairScore
,
IMP::npctransport::ZBiasSingletonScore
,
IMP::PairScore
,
IMP::QuadScore
,
IMP::score_functor::DistancePairScore< DistanceScoreT >
,
IMP::score_functor::DistancePairScoreWithCache< DistanceScoreT >
,
IMP::score_functor::SurfaceDistancePairScore< DistanceScoreT >
,
IMP::SingletonScore
,
IMP::spb::AttributeDistancePairScore
,
IMP::spb::KinkPairScore
,
IMP::spb::RigidBodyPackingScore
,
IMP::spb::TiltSingletonScore
,
IMP::TripletScore
evaluate_moved() :
IMP::Restraint
,
IMP::ScoringFunction
evaluate_moved_if_below() :
IMP::Restraint
evaluate_moved_if_good() :
IMP::Restraint
evaluate_second_derivative_FM_FM() :
IMP::isd::MultivariateFNormalSufficient
evaluate_second_derivative_FM_Sigma() :
IMP::isd::MultivariateFNormalSufficient
evaluate_second_derivative_Sigma_Sigma() :
IMP::isd::MultivariateFNormalSufficient
evaluate_site_contributions() :
IMP::npctransport::SitesPairScore
evaluate_site_contributions_with_internal_tables() :
IMP::npctransport::SitesPairScore
evaluate_with_derivative() :
IMP::core::ClosedCubicSpline
,
IMP::core::Cosine
,
IMP::core::Harmonic
,
IMP::core::HarmonicLowerBound
,
IMP::core::HarmonicUpperBound
,
IMP::core::HarmonicWell
,
IMP::core::Linear
,
IMP::core::SurfaceTetheredChain
,
IMP::core::TruncatedHarmonic< DIRECTION >
,
IMP::core::WeightedSum
,
IMP::core::WeightedSumOfExponential
,
IMP::example::ExampleUnaryFunction
,
IMP::misc::FreelyJointedChain
,
IMP::misc::WormLikeChain
,
IMP::score_functor::ScoreUnaryFunction< Score, D >
,
IMP::spb::Gaussian
,
IMP::UnaryFunction
EventException() :
IMP::EventException
ExampleComplexRestraint() :
IMP::example::ExampleComplexRestraint
ExampleRestraint() :
IMP::example::ExampleRestraint
ExampleTemplateClassD() :
IMP::example::ExampleTemplateClassD< D >
ExampleUnaryFunction() :
IMP::example::ExampleUnaryFunction
exclude_coordinates() :
IMP.pmi.mmcif.ProtocolOutput
,
IMP.pmi1.mmcif.ProtocolOutput
ExcludedVolumeRestraint() :
IMP::core::ExcludedVolumeRestraint
ExcludeZRangeSingletonScore() :
IMP::npctransport::ExcludeZRangeSingletonScore
execute() :
IMP::kmeans::KMeans
execute_macro() :
IMP.pmi.macros.BuildSystem
ExtendedGridIndexD() :
IMP::algebra::ExtendedGridIndexD< D >