- d -

• DeltaDistributionFunction() : IMP::saxs::DeltaDistributionFunction
• density() : IMP::isd::MultivariateFNormalSufficient
• DensityFillingRestraint() : IMP::em::DensityFillingRestraint
• DensityMap() : IMP::em::DensityMap
• DerivativeAccumulator() : IMP::DerivativeAccumulator
• DerivativesFromRefined() : IMP::core::DerivativesFromRefined
• DerivativesToRefined() : IMP::core::DerivativesToRefined
• destroy() : IMP::atom::Hierarchy
• detect_top_fits() : IMP::multifit::FFTFitting
• determine_grid_size() : IMP::em::SampledDensityMap
• DiameterRestraint() : IMP::core::DiameterRestraint
• DihedralAngleRevoluteJoint() : IMP::kinematics::DihedralAngleRevoluteJoint
• DihedralRestraint() : IMP::core::DihedralRestraint
• DistanceFilter() : IMP::em2d::DistanceFilter
• DistanceRestraint() : IMP::core::DistanceRestraint
• Distribution() : IMP::saxs::Distribution< ValueT >
• distribution_2_profile() : IMP::saxs::Profile
• do_accept() : IMP::core::MonteCarloMover , IMP::core::SerialMover
• do_accept_or_reject_move() : IMP::core::MonteCarlo
• do_add_score_and_derivatives() : IMP::container::PredicatePairsRestraint , IMP::container::PredicateQuadsRestraint , IMP::container::PredicateSingletonsRestraint , IMP::container::PredicateTripletsRestraint , IMP::core::IncrementalScoringFunction , IMP::example::ExampleRestraint , IMP::Restraint , IMP::ScoringFunction
• do_advance_chunk() : IMP::atom::BrownianDynamics , IMP::atom::BrownianDynamicsTAMD
• do_close() : IMP::display::PymolWriter , IMP::display::Writer
• do_cluster() : IMP.pmi.analysis.Clustering
• do_clustering() : IMP.multifit.cluster.AlignmentClustering
• do_create_current_decomposition() : IMP::container::MinimumPairScore , IMP::container::MinimumQuadScore , IMP::container::MinimumSingletonScore , IMP::container::MinimumTripletScore , IMP::core::ConnectivityRestraint , IMP::core::ExcludedVolumeRestraint , IMP::core::MSConnectivityRestraint , IMP::PairScore , IMP::QuadScore , IMP::Restraint , IMP::SingletonScore , IMP::TripletScore
• do_create_decomposition() : IMP::core::ExcludedVolumeRestraint , IMP::Restraint
• do_destroy() : IMP::container::ExclusiveConsecutivePairContainer , IMP::display::PymolWriter , IMP::Object
• do_evaluate() : IMP::core::MonteCarlo , IMP::isd::HybridMonteCarlo
• do_exchange() : IMP::mpi::ReplicaExchange
• do_get_inputs() : IMP::atom::AngleSingletonScore , IMP::atom::BondedPairFilter , IMP::atom::BondEndpointsRefiner , IMP::atom::BondPairContainer , IMP::atom::BondSingletonScore , IMP::atom::CAAngleRestraint , IMP::atom::CADihedralRestraint , IMP::atom::CHARMMStereochemistryRestraint , IMP::atom::CoulombPairScore , IMP::atom::CoverBond , IMP::atom::DihedralSingletonScore , IMP::atom::EzRestraint , IMP::atom::ImproperSingletonScore , IMP::atom::LennardJonesPairScore , IMP::atom::SameResiduePairFilter , IMP::atom::SoapPairFilter , IMP::atom::StereochemistryPairFilter , IMP::atom::WritePDBOptimizerState , IMP::container::AllBipartitePairContainer , IMP::container::AllPairContainer , IMP::container::CloseBipartitePairContainer , IMP::container::ClosePairContainer , IMP::container::ConnectingPairContainer , IMP::container::ConsecutivePairContainer , IMP::container::ConsecutivePairFilter , IMP::container::DistributePairsScoreState , IMP::container::DistributeQuadsScoreState , IMP::container::DistributeSingletonsScoreState , IMP::container::DistributeTripletsScoreState , IMP::container::ExclusiveConsecutivePairContainer , IMP::container::ExclusiveConsecutivePairFilter , IMP::container::InContainerPairFilter , IMP::container::InContainerQuadFilter , IMP::container::InContainerSingletonFilter , IMP::container::InContainerTripletFilter , IMP::container::MinimumPairRestraint , IMP::container::MinimumPairScore , IMP::container::MinimumQuadRestraint , IMP::container::MinimumQuadScore , IMP::container::MinimumSingletonRestraint , IMP::container::MinimumSingletonScore , IMP::container::MinimumTripletRestraint , IMP::container::MinimumTripletScore , IMP::container::PairContainerStatistics , IMP::container::PairsConstraint , IMP::container::PairsRestraint , IMP::container::PredicatePairsRestraint , IMP::container::PredicateQuadsRestraint , IMP::container::PredicateSingletonsRestraint , IMP::container::PredicateTripletsRestraint , IMP::container::QuadContainerStatistics , IMP::container::QuadsConstraint , IMP::container::QuadsRestraint , IMP::container::SingletonContainerStatistics , IMP::container::SingletonsConstraint , IMP::container::SingletonsRestraint , IMP::container::TripletContainerStatistics , IMP::container::TripletsConstraint , IMP::container::TripletsRestraint , IMP::core::AllSamePairPredicate , IMP::core::AllSameQuadPredicate , IMP::core::AllSameSingletonPredicate , IMP::core::AllSameTripletPredicate , IMP::core::AngleTripletScore , IMP::core::AttributeSingletonPredicate , IMP::core::BallMover , IMP::core::BoxSweepClosePairsFinder , IMP::core::CentroidOfRefined , IMP::core::ChecksScoreState , IMP::core::ChildrenRefiner , IMP::core::ClosePairsPairScore , IMP::core::CoinFlipPairPredicate , IMP::core::CoinFlipQuadPredicate , IMP::core::CoinFlipSingletonPredicate , IMP::core::CoinFlipTripletPredicate , IMP::core::ConnectivityRestraint , IMP::core::ConstantPairPredicate , IMP::core::ConstantQuadPredicate , IMP::core::ConstantRestraint , IMP::core::ConstantSingletonPredicate , IMP::core::ConstantTripletPredicate , IMP::core::CoverRefined , IMP::core::DerivativesFromRefined , IMP::core::DerivativesToRefined , IMP::core::DiameterRestraint , IMP::core::DihedralRestraint , IMP::core::DistancePairScore , IMP::core::ExcludedVolumeRestraint , IMP::core::FixedRefiner , IMP::core::GenericAttributeSingletonScore< UF > , IMP::core::GenericBoundingBox3DSingletonScore< UF > , IMP::core::GenericDistanceToSingletonScore< UF > , IMP::core::GridClosePairsFinder , IMP::core::HarmonicDistancePairScore , IMP::core::HarmonicSphereDistancePairScore , IMP::core::HarmonicUpperBoundSphereDiameterPairScore , IMP::core::HarmonicUpperBoundSphereDistancePairScore , IMP::core::InBoundingBox3DSingletonPredicate , IMP::core::IncrementalScoringFunction , IMP::core::IsCollisionPairPredicate , IMP::core::KClosePairsPairScore , IMP::core::LeavesRefiner , IMP::core::MinimumRestraint , IMP::core::MoveStatisticsScoreState , IMP::core::MSConnectivityRestraint , IMP::core::NearestNeighborsClosePairsFinder , IMP::core::NeighborsTable , IMP::core::NormalizedSphereDistancePairScore , IMP::core::NormalMover , IMP::core::OrderedTypePairPredicate , IMP::core::OrderedTypeQuadPredicate , IMP::core::OrderedTypeSingletonPredicate , IMP::core::OrderedTypeTripletPredicate , IMP::core::PairConstraint , IMP::core::PairRestraint , IMP::core::PredicateSingletonScore< Predicate, Score > , IMP::core::QuadConstraint , IMP::core::QuadraticClosePairsFinder , IMP::core::QuadRestraint , IMP::core::RefinedPairsPairScore , IMP::core::RigidBodyAnglePairScore , IMP::core::RigidBodyMover , IMP::core::RigidBodyTunneler , IMP::core::RigidBodyUmbrella , IMP::core::RigidClosePairsFinder , IMP::core::SerialMover , IMP::core::SingletonConstraint , IMP::core::SingletonRestraint , IMP::core::SoftSpherePairScore , IMP::core::SphereDistancePairScore , IMP::core::SphereDistanceToSingletonScore , IMP::core::TableRefiner , IMP::core::Transform , IMP::core::TransformationAndReflectionSymmetry , IMP::core::TransformationSymmetry , IMP::core::TransformationSymmetryMover , IMP::core::TransformedDistancePairScore , IMP::core::TripletConstraint , IMP::core::TripletRestraint , IMP::core::TypedPairScore , IMP::core::UnorderedTypePairPredicate , IMP::core::UnorderedTypeQuadPredicate , IMP::core::UnorderedTypeSingletonPredicate , IMP::core::UnorderedTypeTripletPredicate , IMP::core::VolumeRestraint , IMP::core::WeightedDerivativesToRefined , IMP::core::WeightedSphereDistancePairScore , IMP::domino::DependencyScoreState , IMP::em2d::DummyRestraint , IMP::em2d::Em2DRestraint , IMP::em2d::Fine2DRegistrationRestraint , IMP::em2d::ParticlesDummyRestraint , IMP::em2d::PCAFitRestraint , IMP::em2d::ProjectionParametersScoreState , IMP::em::DensityFillingRestraint , IMP::em::EnvelopeFitRestraint , IMP::em::EnvelopePenetrationRestraint , IMP::em::FitRestraint , IMP::em::PCAFitRestraint , IMP::example::ExampleComplexRestraint , IMP::example::ExampleConstraint , IMP::example::ExamplePairScore , IMP::example::ExampleRestraint , IMP::example::ExampleSingletonModifier , IMP::isd::AmbiguousNOERestraint , IMP::isd::AmbiguousRestraint , IMP::isd::AtomicCrossLinkMSRestraint , IMP::isd::CrossLinkMSRestraint , IMP::isd::CysteineCrossLinkRestraint , IMP::isd::FretRestraint , IMP::isd::GaussianEMRestraint , IMP::isd::GaussianProcessInterpolationRestraint , IMP::isd::GaussianRestraint , IMP::isd::ISDRestraint , IMP::isd::JeffreysRestraint , IMP::isd::LognormalAmbiguousRestraint , IMP::isd::LognormalRestraint , IMP::isd::LogWrapper , IMP::isd::MarginalHBondRestraint , IMP::isd::MarginalNOERestraint , IMP::isd::MolecularDynamicsMover , IMP::isd::NOERestraint , IMP::isd::RepulsiveDistancePairScore , IMP::isd::TALOSRestraint , IMP::isd::UniformPrior , IMP::isd::vonMisesKappaConjugateRestraint , IMP::isd::vonMisesKappaJeffreysRestraint , IMP::isd::WeightMover , IMP::isd::WeightRestraint , IMP::kinematics::KinematicForestScoreState , IMP::kinematics::RevoluteJointMover , IMP::misc::CommonEndpointPairFilter , IMP::misc::LogPairScore , IMP::misc::LowestRefinedPairScore , IMP::misc::MetricClosePairsFinder< LowerBound, UpperBound > , IMP::misc::SoftCylinderPairScore , IMP::misc::StateAdaptor , IMP::modeller::MultipleBinormalRestraint , IMP::ModelObject , IMP::multifit::ComplementarityRestraint , IMP::multifit::DummyRestraint , IMP::multifit::RadiusOfGyrationRestraint , IMP::multifit::WeightedExcludedVolumeRestraint , IMP::Optimizer , IMP::OptimizerState , IMP::Particle , IMP::ParticleInputs , IMP::pmi::CompositeRestraint , IMP::pmi::MembraneRestraint , IMP::pmi::SigmoidRestraintSphere , IMP::pmi::TransformMover , IMP::saxs::RadiusOfGyrationRestraint , IMP::saxs::Restraint , IMP::score_functor::DistancePairScore< DistanceScoreT > , IMP::symmetry::BallMover , IMP::symmetry::RigidBodyMover
• do_get_interactions() : IMP::ModelObject
• do_get_outputs() : IMP::atom::CoverBond , IMP::container::DistributePairsScoreState , IMP::container::DistributeQuadsScoreState , IMP::container::DistributeSingletonsScoreState , IMP::container::DistributeTripletsScoreState , IMP::Container , IMP::container::PairContainerStatistics , IMP::container::PairsConstraint , IMP::container::QuadContainerStatistics , IMP::container::QuadsConstraint , IMP::container::SingletonContainerStatistics , IMP::container::SingletonsConstraint , IMP::container::TripletContainerStatistics , IMP::container::TripletsConstraint , IMP::core::CentroidOfRefined , IMP::core::ChecksScoreState , IMP::core::CoverRefined , IMP::core::DerivativesFromRefined , IMP::core::DerivativesToRefined , IMP::core::MonteCarloMover , IMP::core::MoveStatisticsScoreState , IMP::core::NeighborsTable , IMP::core::PairConstraint , IMP::core::QuadConstraint , IMP::core::SingletonConstraint , IMP::core::Transform , IMP::core::TransformationAndReflectionSymmetry , IMP::core::TransformationSymmetry , IMP::core::TripletConstraint , IMP::core::WeightedDerivativesToRefined , IMP::domino::DependencyScoreState , IMP::em2d::ProjectionParametersScoreState , IMP::example::ExampleConstraint , IMP::example::ExampleSingletonModifier , IMP::kinematics::KinematicForestScoreState , IMP::misc::StateAdaptor , IMP::ModelObject , IMP::Optimizer , IMP::OptimizerState , IMP::Particle , IMP::ParticleOutputs , IMP::Restraint , IMP::ScoringFunction
• do_get_weight() : IMP::statistics::ChiSquareMetric , IMP::statistics::Embedding , IMP::statistics::Metric
• do_global_fitting() : IMP::multifit::FFTFitting
• do_join_clusters() : IMP::em2d::ClusterSet
• do_link_particle() : IMP::rmf::HierarchyLoadLink
• do_load_hierarchy() : IMP::rmf::HierarchyLoadLink
• do_local_fitting() : IMP::multifit::FFTFitting
• do_md_protein_statistics() : IMP.isd.shared_functions.sfo_common
• do_open() : IMP::display::PymolWriter , IMP::display::Writer
• do_optimize() : IMP::atom::Simulator , IMP::core::ConjugateGradients , IMP::core::MonteCarlo , IMP::core::SteepestDescent , IMP::gsl::ConjugateGradients , IMP::gsl::QuasiNewton , IMP::gsl::Simplex , IMP::Optimizer
• do_preprocess_for_fast_coarse_registration() : IMP::em2d::ProjectionFinder
• do_propose() : IMP::core::BallMover , IMP::core::MonteCarloMover , IMP::core::NormalMover , IMP::core::RigidBodyMover , IMP::core::RigidBodyTunneler , IMP::core::SerialMover , IMP::core::TransformationSymmetryMover , IMP::em2d::RelativePositionMover , IMP::isd::MolecularDynamicsMover , IMP::isd::WeightMover , IMP::kinematics::RevoluteJointMover , IMP::pmi::TransformMover , IMP::symmetry::BallMover , IMP::symmetry::RigidBodyMover
• do_reject() : IMP::core::BallMover , IMP::core::MonteCarloMover , IMP::core::NormalMover , IMP::core::RigidBodyMover , IMP::core::RigidBodyTunneler , IMP::core::SerialMover , IMP::core::TransformationSymmetryMover , IMP::em2d::RelativePositionMover , IMP::isd::MolecularDynamicsMover , IMP::isd::WeightMover , IMP::kinematics::RevoluteJointMover , IMP::pmi::TransformMover , IMP::symmetry::BallMover , IMP::symmetry::RigidBodyMover
• do_sampling() : IMP.EMageFit.domino_model.DominoModel
• do_save_hierarchy() : IMP::rmf::HierarchySaveLink
• do_set_frame() : IMP::display::TextWriter , IMP::display::Writer
• do_setup_node() : IMP::rmf::HierarchySaveLink
• do_setup_particle() : IMP::rmf::HierarchyLoadLink
• do_show() : IMP::em2d::CenteredMat
• do_simulate() : IMP::atom::Simulator
• do_simulate_wave() : IMP::atom::Simulator
• do_step() : IMP::atom::BrownianDynamics , IMP::atom::MolecularDynamics , IMP::atom::Simulator , IMP::core::MonteCarlo , IMP::core::MonteCarloWithBasinHopping , IMP::core::MonteCarloWithLocalOptimization , IMP::isd::HybridMonteCarlo
• do_update() : IMP::atom::BerendsenThermostatOptimizerState , IMP::atom::LangevinThermostatOptimizerState , IMP::atom::RemoveRigidMotionOptimizerState , IMP::atom::RemoveTranslationOptimizerState , IMP::atom::VelocityScalingOptimizerState , IMP::atom::WritePDBOptimizerState , IMP::core::WriteRestraintScoresOptimizerState , IMP::display::WriteOptimizerState , IMP::misc::DecayPairContainerOptimizerState , IMP::OptimizerState , IMP::rmf::SaveOptimizerState , IMP::SaveToConfigurationSetOptimizerState
• DOFsSampler() : IMP::kinematics::DOFsSampler
• downsample() : IMP::saxs::Profile
• drop_table() : IMP.EMageFit.database.Database2
• drop_view() : IMP.EMageFit.database.Database2
• DummyRestraint() : IMP::em2d::DummyRestraint
• dump() : IMP.isd.Analysis.Analysis
• DynamicListPairContainer() : IMP::container::DynamicListPairContainer
• DynamicListQuadContainer() : IMP::container::DynamicListQuadContainer
• DynamicListSingletonContainer() : IMP::container::DynamicListSingletonContainer
• DynamicListTripletContainer() : IMP::container::DynamicListTripletContainer