- d -

• decorate_particle() : IMP::atom::Angle , IMP::atom::Dihedral , IMP::atom::Bond , IMP::atom::CHARMMAtom , IMP::atom::Molecule , IMP::em2d::ProjectionParameters , IMP::example::ExampleDecorator , IMP::atom::Residue , IMP::isd::Nuisance , IMP::isd::Scale , IMP::atom::Copy , IMP::atom::SecondaryStructureResidue , IMP::isd::Switching , IMP::isd::Weight , IMP::core::Centroid , IMP::kinematics::KinematicNode , IMP::misc::CustomXYZR , IMP::atom::Bonded , IMP::atom::Diffusion , IMP::core::Cover , IMP::core::Hierarchy , IMP::atom::RigidBodyDiffusion , IMP::core::RigidBody , IMP::core::RigidBodyMember , IMP::atom::Atom , IMP::atom::Chain , IMP::atom::Domain , IMP::core::RigidMember , IMP::core::NonRigidMember , IMP::atom::Fragment , IMP::core::Reference , IMP::core::Typed , IMP::atom::Charged , IMP::atom::LennardJones , IMP::core::XYZ , IMP::core::XYZR , IMP::atom::Mass , IMP::display::Colored , IMP::em::Voxel
• Decorator() : IMP::kernel::Decorator
• DeltaDistributionFunction() : IMP::saxs::DeltaDistributionFunction
• DensityFillingRestraint() : IMP::em::DensityFillingRestraint
• DensityMap() : IMP::em::DensityMap
• DerivativeAccumulator() : IMP::kernel::DerivativeAccumulator
• DerivativesFromRefined() : IMP::core::DerivativesFromRefined
• DerivativesToRefined() : IMP::core::DerivativesToRefined
• 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::PredicateTripletsRestraint , IMP::example::ExampleRestraint , IMP::kernel::Restraint , IMP::kernel::ScoringFunction , IMP::container::PredicatePairsRestraint , IMP::container::PredicateQuadsRestraint , IMP::container::PredicateSingletonsRestraint
• do_after_evaluate() : IMP::kernel::Container
• do_close() : IMP::display::BildWriter , IMP::display::ChimeraWriter , IMP::display::CMMWriter , IMP::display::PymolWriter , IMP::display::Writer
• do_clustering() : IMP.multifit.cluster.AlignmentClustering
• do_create_current_decomposition() : IMP::container::MinimumSingletonScore , IMP::core::ConnectivityRestraint , IMP::core::ExcludedVolumeRestraint , IMP::core::MSConnectivityRestraint , IMP::kernel::Restraint , IMP::kernel::PairScore , IMP::kernel::QuadScore , IMP::kernel::SingletonScore , IMP::kernel::TripletScore
• do_create_decomposition() : IMP::core::ExcludedVolumeRestraint , IMP::kernel::Restraint
• do_destroy() : IMP::base::Object , IMP::display::BildWriter , IMP::display::ChimeraWriter , IMP::display::CMMWriter , IMP::display::PymolWriter
• do_evaluate() : IMP::core::MonteCarlo , IMP::isd::HybridMonteCarlo
• do_exchange() : IMP::mpi::ReplicaExchange
• do_get_inputs() : IMP::container::MinimumQuadRestraint , IMP::isd::MarginalHBondRestraint , IMP::isd::MarginalNOERestraint , IMP::container::MinimumQuadScore , IMP::isd::MolecularDynamicsMover , IMP::isd::NOERestraint , IMP::container::MinimumSingletonRestraint , IMP::isd::RepulsiveDistancePairScore , IMP::isd::TALOSRestraint , IMP::container::MinimumSingletonScore , IMP::isd::vonMisesKappaConjugateRestraint , IMP::isd::vonMisesKappaJeffreysRestraint , IMP::container::MinimumTripletRestraint , IMP::isd::WeightMover , IMP::isd::WeightRestraint , IMP::container::MinimumTripletScore , IMP::kernel::Particle , IMP::kernel::ParticleInputs , IMP::container::PairContainerStatistics , IMP::kernel::ModelObject , IMP::kernel::Optimizer , IMP::container::PairsConstraint , IMP::symmetry::RigidBodyMover , IMP::symmetry::BallMover , IMP::score_functor::DistancePairScore< DistanceScoreT > , IMP::kernel::OptimizerState , IMP::saxs::RadiusOfGyrationRestraint , IMP::multifit::WeightedExcludedVolumeRestraint , IMP::kinematics::KinematicForestScoreState , IMP::container::PairsRestraint , IMP::multifit::ComplementarityRestraint , IMP::modeller::MultipleBinormalRestraint , IMP::misc::StateAdaptor , IMP::misc::CommonEndpointPairFilter , IMP::misc::LogPairScore , IMP::container::PredicatePairsRestraint , IMP::misc::LowestRefinedPairScore , IMP::misc::MetricClosePairsFinder< LowerBound, UpperBound > , IMP::container::PredicateQuadsRestraint , IMP::misc::SoftCylinderPairScore , IMP::container::PredicateSingletonsRestraint , IMP::container::PredicateTripletsRestraint , IMP::multifit::DummyRestraint , IMP::multifit::RadiusOfGyrationRestraint , IMP::container::QuadContainerStatistics , IMP::container::QuadsConstraint , IMP::saxs::Restraint , IMP::container::QuadsRestraint , IMP::container::SingletonContainerStatistics , IMP::container::SingletonsConstraint , IMP::container::SingletonsRestraint , IMP::container::TripletContainerStatistics , IMP::container::TripletsConstraint , IMP::container::TripletsRestraint , IMP::isd::LognormalRestraint , IMP::isd::JeffreysRestraint , IMP::isd::GaussianRestraint , IMP::core::AngleTripletScore , IMP::isd::FretRestraint , IMP::isd::CysteineCrossLinkRestraint , IMP::core::GenericAttributeSingletonScore< UF > , IMP::core::BallMover , IMP::example::ExampleSingletonModifier , IMP::example::ExampleRestraint , IMP::example::ExamplePairScore , IMP::core::GenericBoundingBox3DSingletonScore< UF > , IMP::example::ExampleComplexRestraint , IMP::em2d::ProjectionParametersScoreState , IMP::core::BoxSweepClosePairsFinder , IMP::core::CentroidOfRefined , IMP::em2d::ParticlesDummyRestraint , IMP::em2d::DummyRestraint , IMP::em::PCAFitRestraint , IMP::core::ChecksScoreState , IMP::em::EnvelopePenetrationRestraint , IMP::em::EnvelopeFitRestraint , IMP::core::ChildrenRefiner , IMP::core::KClosePairsPairScore , IMP::core::VolumeRestraint , IMP::core::TypedPairScore , IMP::core::TripletRestraint , IMP::core::ClosePairsPairScore , IMP::core::CoinFlipTripletPredicate , IMP::core::ConnectivityRestraint , IMP::core::ConstantRestraint , IMP::core::CoverRefined , IMP::core::ConstantTripletPredicate , IMP::core::TransformedDistancePairScore , IMP::core::Transform , IMP::core::DiameterRestraint , IMP::core::TransformationSymmetry , IMP::core::TransformationAndReflectionSymmetry , IMP::core::DihedralRestraint , IMP::core::DistancePairScore , IMP::core::NormalizedSphereDistancePairScore , IMP::core::HarmonicSphereDistancePairScore , IMP::core::HarmonicUpperBoundSphereDiameterPairScore , IMP::core::HarmonicDistancePairScore , IMP::core::SphereDistancePairScore , IMP::core::SingletonRestraint , IMP::core::GenericDistanceToSingletonScore< UF > , IMP::core::SphereDistanceToSingletonScore , IMP::core::AllSameSingletonPredicate , IMP::core::OrderedTypeSingletonPredicate , IMP::core::UnorderedTypeSingletonPredicate , IMP::core::ExcludedVolumeRestraint , IMP::core::SerialMover , IMP::core::RigidClosePairsFinder , IMP::core::FixedRefiner , IMP::core::GridClosePairsFinder , IMP::core::QuadRestraint , IMP::core::QuadraticClosePairsFinder , IMP::core::QuadConstraint , IMP::core::IncrementalScoringFunction , IMP::core::LeavesRefiner , IMP::core::MinimumRestraint , IMP::core::Mover , IMP::core::MoveStatisticsScoreState , IMP::core::PredicateSingletonScore< Predicate, Score > , IMP::core::IsCollisionPairPredicate , IMP::core::AttributeSingletonPredicate , IMP::core::MSConnectivityRestraint , IMP::core::PairRestraint , IMP::core::NearestNeighborsClosePairsFinder , IMP::core::NeighborsTable , IMP::core::NormalMover , IMP::core::ConstantPairPredicate , IMP::core::UnorderedTypePairPredicate , IMP::core::OrderedTypePairPredicate , IMP::core::AllSamePairPredicate , IMP::core::CoinFlipPairPredicate , IMP::core::PairConstraint , IMP::atom::AngleSingletonScore , IMP::core::InBoundingBox3DSingletonPredicate , IMP::atom::BondedPairFilter , IMP::atom::BondEndpointsRefiner , IMP::core::ConstantQuadPredicate , IMP::core::UnorderedTypeQuadPredicate , IMP::atom::BondPairContainer , IMP::core::OrderedTypeQuadPredicate , IMP::core::AllSameQuadPredicate , IMP::atom::BondSingletonScore , IMP::core::CoinFlipQuadPredicate , IMP::atom::CHARMMStereochemistryRestraint , IMP::atom::CoulombPairScore , IMP::core::RefinedPairsPairScore , IMP::core::RigidBodyMover , IMP::atom::CoverBond , IMP::atom::DihedralSingletonScore , IMP::core::ConstantSingletonPredicate , IMP::atom::EzRestraint , IMP::atom::ImproperSingletonScore , IMP::core::CoinFlipSingletonPredicate , IMP::core::SingletonConstraint , IMP::atom::LennardJonesPairScore , IMP::atom::WritePDBOptimizerState , IMP::core::HarmonicUpperBoundSphereDistancePairScore , IMP::atom::SameResiduePairFilter , IMP::atom::StereochemistryPairFilter , IMP::core::WeightedSphereDistancePairScore , IMP::core::SoftSpherePairScore , IMP::container::AllBipartitePairContainer , IMP::container::AllPairContainer , IMP::core::TableRefiner , IMP::container::CloseBipartitePairContainer , IMP::container::ClosePairContainer , IMP::core::UnorderedTypeTripletPredicate , IMP::core::OrderedTypeTripletPredicate , IMP::container::ConnectingPairContainer , IMP::core::AllSameTripletPredicate , IMP::container::ConsecutivePairContainer , IMP::core::TripletConstraint , IMP::container::ConsecutivePairFilter , IMP::container::ExclusiveConsecutivePairContainer , IMP::domino::DependencyScoreState , IMP::em::DensityFillingRestraint , IMP::container::ExclusiveConsecutivePairFilter , IMP::container::DistributePairsScoreState , IMP::em::FitRestraint , IMP::container::DistributeQuadsScoreState , IMP::container::DistributeSingletonsScoreState , IMP::em2d::Em2DRestraint , IMP::container::MinimumPairScore , IMP::isd::GaussianProcessInterpolationRestraint , IMP::container::InContainerTripletFilter , IMP::isd::AmbiguousRestraint , IMP::em2d::Fine2DRegistrationRestraint , IMP::container::DistributeTripletsScoreState , IMP::container::InContainerPairFilter , IMP::example::ExampleConstraint , IMP::container::InContainerQuadFilter , IMP::container::InContainerSingletonFilter , IMP::isd::AmbiguousNOERestraint , IMP::container::MinimumPairRestraint
• do_get_interactions() : IMP::kernel::ModelObject
• do_get_outputs() : IMP::core::CentroidOfRefined , IMP::core::QuadConstraint , IMP::core::SingletonConstraint , IMP::kernel::Optimizer , IMP::core::ChecksScoreState , IMP::container::QuadsConstraint , IMP::container::TripletsConstraint , IMP::container::DistributeQuadsScoreState , IMP::container::DistributeTripletsScoreState , IMP::atom::CoverBond , IMP::container::DistributePairsScoreState , IMP::container::DistributeSingletonsScoreState , IMP::kernel::OptimizerState , IMP::container::QuadContainerStatistics , IMP::container::SingletonContainerStatistics , IMP::container::TripletContainerStatistics , IMP::kinematics::KinematicForestScoreState , IMP::core::CoverRefined , IMP::core::MoveStatisticsScoreState , IMP::core::PairConstraint , IMP::core::TransformationSymmetry , IMP::core::TripletConstraint , IMP::em2d::ProjectionParametersScoreState , IMP::kernel::ParticleOutputs , IMP::kernel::Particle , IMP::kernel::ScoringFunction , IMP::core::TransformationAndReflectionSymmetry , IMP::kernel::ModelObject , IMP::misc::StateAdaptor , IMP::kernel::Container , IMP::kernel::Restraint , IMP::domino::DependencyScoreState , IMP::example::ExampleConstraint , IMP::core::Transform , IMP::example::ExampleSingletonModifier , IMP::container::SingletonsConstraint , IMP::container::PairsConstraint , IMP::container::PairContainerStatistics , IMP::core::NeighborsTable , IMP::core::MonteCarloMover
• do_get_weight() : IMP::statistics::Metric , IMP::statistics::Embedding , IMP::statistics::ChiSquareMetric
• do_global_fitting() : IMP::multifit::FFTFitting
• 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_move() : IMP::core::MoverBase
• do_open() : IMP::display::PymolWriter , IMP::display::CMMWriter , IMP::display::ChimeraWriter , IMP::display::Writer , IMP::display::BildWriter
• do_optimize() : IMP::core::MonteCarlo , IMP::kernel::Optimizer , IMP::atom::Simulator
• do_preprocess_for_fast_coarse_registration() : IMP::em2d::ProjectionFinder
• do_propose() : IMP::symmetry::RigidBodyMover , IMP::core::RigidBodyMover , IMP::isd::MolecularDynamicsMover , IMP::core::Mover , IMP::core::SerialMover , IMP::isd::WeightMover , IMP::em2d::RelativePositionMover , IMP::symmetry::BallMover , IMP::core::NormalMover , IMP::core::MonteCarloMover , IMP::core::BallMover
• do_reject() : IMP::core::SerialMover , IMP::symmetry::RigidBodyMover , IMP::core::Mover , IMP::core::RigidBodyMover , IMP::core::BallMover , IMP::isd::MolecularDynamicsMover , IMP::isd::WeightMover , IMP::symmetry::BallMover , IMP::core::MonteCarloMover , IMP::core::NormalMover , IMP::em2d::RelativePositionMover
• do_sampling() : IMP.em2d.DominoModel.DominoModel
• do_save_hierarchy() : IMP::rmf::HierarchySaveLink
• do_set_frame() : IMP::display::TextWriter , IMP::display::Writer
• do_set_model() : IMP::isd::GaussianProcessInterpolationRestraint , IMP::kernel::ModelObject
• do_setup_node() : IMP::rmf::HierarchySaveLink
• do_setup_particle() : IMP::rmf::HierarchyLoadLink
• do_show() : IMP::em2d::CenteredMat
• do_step() : IMP::atom::Simulator , IMP::core::MonteCarloWithLocalOptimization , IMP::atom::MolecularDynamics , IMP::core::MonteCarlo , IMP::isd::HybridMonteCarlo , IMP::core::MonteCarloWithBasinHopping
• do_update() : IMP::atom::VelocityScalingOptimizerState , IMP::display::WriteOptimizerState , IMP::atom::RemoveTranslationOptimizerState , IMP::core::WriteRestraintScoresOptimizerState , IMP::atom::RemoveRigidMotionOptimizerState , IMP::atom::WritePDBOptimizerState , IMP::misc::DecayPairContainerOptimizerState , IMP::atom::LangevinThermostatOptimizerState , IMP::rmf::SaveOptimizerState , IMP::kernel::OptimizerState , IMP::kernel::SaveToConfigurationSetOptimizerState , IMP::atom::BerendsenThermostatOptimizerState
• DOFsSampler() : IMP::kinematics::DOFsSampler
• downsample() : IMP::saxs::Profile
• drop_table() : IMP.em2d.Database.Database2
• drop_view() : IMP.em2d.Database.Database2
• DummyRestraint() : IMP::em2d::DummyRestraint
• dump() : IMP.isd.Analysis.Analysis