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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
Related Functions
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- 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
disable_movers() :
IMP.pmi.dof.DegreesOfFreedom
DistanceFilter() :
IMP::em2d::DistanceFilter
DistanceRestraint() :
IMP::core::DistanceRestraint
DistanceTerminiRestraint() :
IMP::spb::DistanceTerminiRestraint
Distribution() :
IMP::saxs::Distribution< ValueT >
distribution_2_profile() :
IMP::saxs::Profile
do_accept() :
IMP::core::MonteCarloMover
,
IMP::core::SerialMover
,
IMP::core::SubsetMover
do_accept_or_reject_move() :
IMP::core::MonteCarlo
do_add_score_and_derivatives() :
IMP::ScoringFunction
do_add_score_and_derivatives_moved() :
IMP::ScoringFunction
do_advance_chunk() :
IMP::atom::BrownianDynamics
,
IMP::atom::BrownianDynamicsTAMD
,
IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport
do_after_evaluate() :
IMP::Constraint
,
IMP::container::DistributePairsScoreState
,
IMP::container::DistributeQuadsScoreState
,
IMP::container::DistributeSingletonsScoreState
,
IMP::container::DistributeTripletsScoreState
,
IMP::container::PairContainerStatistics
,
IMP::container::QuadContainerStatistics
,
IMP::container::SingletonContainerStatistics
,
IMP::container::TripletContainerStatistics
,
IMP::core::ChecksScoreState
,
IMP::core::LateralSurfaceConstraint
,
IMP::core::MoveStatisticsScoreState
,
IMP::core::NeighborsTable
,
IMP::core::SurfaceGeometryConstraint
,
IMP::domino::DependencyScoreState
,
IMP::em2d::ProjectionParametersScoreState
,
IMP::kinematics::KinematicForestScoreState
,
IMP::misc::StateAdaptor
,
IMP::ScoreState
do_before_evaluate() :
IMP::Constraint
,
IMP::container::DistributePairsScoreState
,
IMP::container::DistributeQuadsScoreState
,
IMP::container::DistributeSingletonsScoreState
,
IMP::container::DistributeTripletsScoreState
,
IMP::container::PairContainerStatistics
,
IMP::container::QuadContainerStatistics
,
IMP::container::SingletonContainerStatistics
,
IMP::container::TripletContainerStatistics
,
IMP::core::ChecksScoreState
,
IMP::core::LateralSurfaceConstraint
,
IMP::core::MoveStatisticsScoreState
,
IMP::core::NeighborsTable
,
IMP::core::SurfaceGeometryConstraint
,
IMP::domino::DependencyScoreState
,
IMP::em2d::ProjectionParametersScoreState
,
IMP::kinematics::KinematicForestScoreState
,
IMP::misc::StateAdaptor
,
IMP::ScoreState
do_close() :
IMP::display::PymolWriter
,
IMP::display::Writer
do_cluster() :
IMP.pmi.analysis.Clustering
,
IMP.pmi1.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::HelixRestraint
,
IMP::atom::ImproperSingletonScore
,
IMP::atom::LennardJonesPairScore
,
IMP::atom::SameResiduePairFilter
,
IMP::atom::SoapPairFilter
,
IMP::atom::StereochemistryPairFilter
,
IMP::atom::WritePDBOptimizerState
,
IMP::bayesianem::GaussianEMRestraint
,
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::DirectionMover
,
IMP::core::DistancePairScore
,
IMP::core::ExcludedVolumeRestraint
,
IMP::core::FixedRefiner
,
IMP::core::GenericAttributeSingletonScore< UF >
,
IMP::core::GenericBoundingBox3DSingletonScore< UF >
,
IMP::core::GenericBoundingSphere3DSingletonScore< UF >
,
IMP::core::GenericDistanceToSingletonScore< UF >
,
IMP::core::GridClosePairsFinder
,
IMP::core::HarmonicDistancePairScore
,
IMP::core::HarmonicSphereDistancePairScore
,
IMP::core::HarmonicSurfaceDepthPairScore
,
IMP::core::HarmonicSurfaceDistancePairScore
,
IMP::core::HarmonicSurfaceHeightPairScore
,
IMP::core::HarmonicUpperBoundSphereDiameterPairScore
,
IMP::core::HarmonicUpperBoundSphereDistancePairScore
,
IMP::core::InBoundingBox3DSingletonPredicate
,
IMP::core::IsCollisionPairPredicate
,
IMP::core::KClosePairsPairScore
,
IMP::core::LateralSurfaceConstraint
,
IMP::core::LeavesRefiner
,
IMP::core::LogNormalMover
,
IMP::core::MinimumRestraint
,
IMP::core::MoveStatisticsScoreState
,
IMP::core::MSConnectivityRestraint
,
IMP::core::MultipleBinormalRestraint
,
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::SoftSubSurfacePairScore
,
IMP::core::SoftSuperSurfacePairScore
,
IMP::core::SphereDistancePairScore
,
IMP::core::SphereDistanceToSingletonScore
,
IMP::core::SubsetMover
,
IMP::core::SurfaceDepthPairScore
,
IMP::core::SurfaceDistancePairScore
,
IMP::core::SurfaceGeometryConstraint
,
IMP::core::SurfaceHeightPairScore
,
IMP::core::SurfaceMover
,
IMP::core::SurfaceSymmetryConstraint
,
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::ParticlesDummyRestraint
,
IMP::em2d::PCAFitRestraint
,
IMP::em2d::ProjectionParametersScoreState
,
IMP::em::DensityFillingRestraint
,
IMP::em::EnvelopeFitRestraint
,
IMP::em::EnvelopePenetrationRestraint
,
IMP::em::FitRestraint
,
IMP::em::FitRestraintBayesEM3D
,
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::GammaPrior
,
IMP::isd::GaussianAnchorEMRestraint
,
IMP::isd::GaussianEMRestraint
,
IMP::isd::GaussianProcessInterpolationRestraint
,
IMP::isd::GaussianRestraint
,
IMP::isd::ISDRestraint
,
IMP::isd::JeffreysRestraint
,
IMP::isd::LognormalAmbiguousRestraint
,
IMP::isd::LognormalRestraint
,
IMP::isd::MarginalHBondRestraint
,
IMP::isd::MarginalNOERestraint
,
IMP::isd::MolecularDynamicsMover
,
IMP::isd::NOERestraint
,
IMP::isd::NormalSigmaPCRestraint
,
IMP::isd::RepulsiveDistancePairScore
,
IMP::isd::ResidueProteinProximityRestraint
,
IMP::isd::StudentTRestraint
,
IMP::isd::TALOSRestraint
,
IMP::isd::UniformPrior
,
IMP::isd::vonMisesKappaConjugateRestraint
,
IMP::isd::vonMisesKappaJeffreysRestraint
,
IMP::isd::WeightMover
,
IMP::isd::WeightRestraint
,
IMP::kinematics::DihedralMover
,
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::ModelObject
,
IMP::multifit::ComplementarityRestraint
,
IMP::multifit::DummyRestraint
,
IMP::multifit::RadiusOfGyrationRestraint
,
IMP::multifit::RigidLeavesRefiner
,
IMP::multifit::WeightedExcludedVolumeRestraint
,
IMP::npc::AssemblySymmetryByDihedralRestraint
,
IMP::npc::AssemblySymmetryByDistanceRestraint
,
IMP::npc::CompositeRestraint
,
IMP::npc::MembraneExclusionRestraint
,
IMP::npc::MembraneSurfaceLocationConditionalRestraint
,
IMP::npc::MembraneSurfaceLocationRestraint
,
IMP::npc::MinimumSphereDistancePairScore
,
IMP::npc::PerinuclearVolumeLocationRestraint
,
IMP::npc::PoreSideVolumeLocationRestraint
,
IMP::npc::ProteinChainRestraint
,
IMP::npc::ProteinContactRestraint
,
IMP::npc::ProteinProximityRestraint
,
IMP::npc::XYRadialPositionLowerRestraint
,
IMP::npc::XYRadialPositionRestraint
,
IMP::npc::XYRadialPositionUpperRestraint
,
IMP::npc::YAxialPositionLowerRestraint
,
IMP::npc::YAxialPositionRestraint
,
IMP::npc::YAxialPositionUpperRestraint
,
IMP::npc::ZAxialPositionLowerRestraint
,
IMP::npc::ZAxialPositionRestraint
,
IMP::npc::ZAxialPositionUpperRestraint
,
IMP::npctransport::AnchorToCylidnricalPorePairScore
,
IMP::npctransport::ExcludeZRangeSingletonScore
,
IMP::npctransport::HarmonicSpringSingletonScore
,
IMP::npctransport::HarmonicWellPairScore
,
IMP::npctransport::LinearInteractionPairScore
,
IMP::npctransport::LinearSoftSpherePairScore
,
IMP::npctransport::LinearWellPairScore
,
IMP::npctransport::PoreRadiusSingletonScore
,
IMP::npctransport::SitesPairScore
,
IMP::npctransport::SlabWithCylindricalPorePairScore
,
IMP::npctransport::SlabWithToroidalPorePairScore
,
IMP::npctransport::ZBiasSingletonScore
,
IMP::Optimizer
,
IMP::OptimizerState
,
IMP::Particle
,
IMP::ParticleInputs
,
IMP::pmi1::CompositeRestraint
,
IMP::pmi1::InternalCoordinatesConstraint
,
IMP::pmi1::MembraneRestraint
,
IMP::pmi1::SigmoidRestraintSphere
,
IMP::pmi1::TransformMover
,
IMP::pmi::CompositeRestraint
,
IMP::pmi::MembraneRestraint
,
IMP::pmi::TransformMover
,
IMP::saxs::RadiusOfGyrationRestraint
,
IMP::saxs::Restraint
,
IMP::score_functor::DistancePairScore< DistanceScoreT >
,
IMP::score_functor::DistancePairScoreWithCache< DistanceScoreT >
,
IMP::score_functor::SurfaceDistancePairScore< DistanceScoreT >
,
IMP::spb::AttributeDistancePairScore
,
IMP::spb::BoxedMover
,
IMP::spb::CellMover
,
IMP::spb::DiameterRgyrRestraint
,
IMP::spb::DistanceTerminiRestraint
,
IMP::spb::EM2DRestraint
,
IMP::spb::KinkPairScore
,
IMP::spb::NuisanceRangeModifier
,
IMP::spb::PbcBoxedMover
,
IMP::spb::PbcBoxedRigidBodyMover
,
IMP::spb::RigidBodyNewMover
,
IMP::spb::RigidBodyPackingScore
,
IMP::spb::SameParticlePairFilter
,
IMP::spb::SameRigidBodyPairFilter
,
IMP::spb::TiltSingletonScore
,
IMP::spb::TransformationSymmetry
,
IMP::spb::TwoStateGoModelRestraint
,
IMP::spb::UniformBoundedRestraint
,
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::LateralSurfaceConstraint
,
IMP::core::MonteCarloMover
,
IMP::core::MoveStatisticsScoreState
,
IMP::core::NeighborsTable
,
IMP::core::PairConstraint
,
IMP::core::QuadConstraint
,
IMP::core::SingletonConstraint
,
IMP::core::SurfaceGeometryConstraint
,
IMP::core::SurfaceSymmetryConstraint
,
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::pmi1::InternalCoordinatesConstraint
,
IMP::Restraint
,
IMP::ScoringFunction
,
IMP::spb::NuisanceRangeModifier
,
IMP::spb::TransformationSymmetry
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::npctransport::HierarchyWithSitesLoadLink
,
IMP::rmf::HierarchyLoadLink
do_load_hierarchy() :
IMP::npctransport::HierarchyWithSitesLoadLink
,
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::DirectionMover
,
IMP::core::LogNormalMover
,
IMP::core::MonteCarloMover
,
IMP::core::NormalMover
,
IMP::core::RigidBodyMover
,
IMP::core::RigidBodyTunneler
,
IMP::core::SerialMover
,
IMP::core::SubsetMover
,
IMP::core::SurfaceMover
,
IMP::core::TransformationSymmetryMover
,
IMP::em2d::RelativePositionMover
,
IMP::isd::MolecularDynamicsMover
,
IMP::isd::WeightMover
,
IMP::kinematics::DihedralMover
,
IMP::kinematics::RevoluteJointMover
,
IMP::pmi1::TransformMover
,
IMP::pmi::TransformMover
,
IMP::spb::BoxedMover
,
IMP::spb::CellMover
,
IMP::spb::PbcBoxedMover
,
IMP::spb::PbcBoxedRigidBodyMover
,
IMP::spb::RigidBodyNewMover
,
IMP::symmetry::BallMover
,
IMP::symmetry::RigidBodyMover
do_reject() :
IMP::core::BallMover
,
IMP::core::DirectionMover
,
IMP::core::LogNormalMover
,
IMP::core::MonteCarloMover
,
IMP::core::NormalMover
,
IMP::core::RigidBodyMover
,
IMP::core::RigidBodyTunneler
,
IMP::core::SerialMover
,
IMP::core::SubsetMover
,
IMP::core::SurfaceMover
,
IMP::core::TransformationSymmetryMover
,
IMP::em2d::RelativePositionMover
,
IMP::isd::MolecularDynamicsMover
,
IMP::isd::WeightMover
,
IMP::kinematics::DihedralMover
,
IMP::kinematics::RevoluteJointMover
,
IMP::pmi1::TransformMover
,
IMP::pmi::TransformMover
,
IMP::spb::BoxedMover
,
IMP::spb::CellMover
,
IMP::spb::PbcBoxedMover
,
IMP::spb::PbcBoxedRigidBodyMover
,
IMP::spb::RigidBodyNewMover
,
IMP::symmetry::BallMover
,
IMP::symmetry::RigidBodyMover
do_sampling() :
IMP.EMageFit.domino_model.DominoModel
do_save_hierarchy() :
IMP::npctransport::HierarchyWithSitesSaveLink
,
IMP::rmf::HierarchySaveLink
do_set_frame() :
IMP::display::TextWriter
,
IMP::display::Writer
do_setup_node() :
IMP::npctransport::HierarchyWithSitesSaveLink
,
IMP::rmf::HierarchySaveLink
do_setup_particle() :
IMP::npctransport::HierarchyWithSitesLoadLink
,
IMP::rmf::HierarchyLoadLink
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
,
IMP::spb::MolecularDynamicsWithWte
,
IMP::spb::MonteCarloWithWte
do_update() :
IMP::atom::BerendsenThermostatOptimizerState
,
IMP::atom::LangevinThermostatOptimizerState
,
IMP::atom::RemoveRigidMotionOptimizerState
,
IMP::atom::RemoveTranslationOptimizerState
,
IMP::atom::VelocityScalingOptimizerState
,
IMP::atom::WritePDBOptimizerState
,
IMP::container::EventPairsOptimizerState
,
IMP::container::EventQuadsOptimizerState
,
IMP::container::EventSingletonsOptimizerState
,
IMP::container::EventTripletsOptimizerState
,
IMP::container::PairsOptimizerState
,
IMP::container::QuadsOptimizerState
,
IMP::container::SingletonsOptimizerState
,
IMP::container::TripletsOptimizerState
,
IMP::core::WriteRestraintScoresOptimizerState
,
IMP::display::WriteOptimizerState
,
IMP::misc::DecayPairContainerOptimizerState
,
IMP::npctransport::BipartitePairsStatisticsOptimizerState
,
IMP::npctransport::BodyStatisticsOptimizerState
,
IMP::npctransport::ChainStatisticsOptimizerState
,
IMP::npctransport::GlobalStatisticsOptimizerState
,
IMP::npctransport::ParticleTransportStatisticsOptimizerState
,
IMP::OptimizerState
,
IMP::rmf::SaveOptimizerState
,
IMP::SaveToConfigurationSetOptimizerState
DOFsSampler() :
IMP::kinematics::DOFsSampler
DOFValues() :
IMP::kinematics::DOFValues
downsample() :
IMP::saxs::Profile
draw_gamma() :
IMP.pmi.restraints.saxs.SAXSISDRestraint
,
IMP.pmi1.restraints.saxs.SAXSISDRestraint
draw_sigma() :
IMP.pmi.restraints.saxs.SAXSISDRestraint
,
IMP.pmi1.restraints.saxs.SAXSISDRestraint
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