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IMP Reference Guide
develop.4f1ba46383,2024/09/07
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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GammaPrior() :
IMP::isd::GammaPrior
Gaussian() :
IMP::spb::Gaussian
GaussianAnchorEMRestraint() :
IMP::isd::GaussianAnchorEMRestraint
GaussianEMRestraint() :
IMP::bayesianem::GaussianEMRestraint
,
IMP::isd::GaussianEMRestraint
GaussianProcessInterpolation() :
IMP::isd::GaussianProcessInterpolation
GaussianProcessInterpolationRestraint() :
IMP::isd::GaussianProcessInterpolationRestraint
GaussianRestraint() :
IMP::isd::GaussianRestraint
GenericAttributeSingletonScore() :
IMP::core::GenericAttributeSingletonScore< UF >
GenericBoundingBox3DSingletonScore() :
IMP::core::GenericBoundingBox3DSingletonScore< UF >
get() :
IMP.isd.utils.Pipe
,
IMP::Pointer< O >
,
IMP::PointerMember< O >
get_a() :
IMP::algebra::LinearFit2D
,
IMP::algebra::ParabolicFit2D
get_abort_evaluation() :
IMP::ScoreAccumulator
get_age() :
IMP::Model
get_all_chain_restraints() :
IMP::npctransport::Scoring
get_all_possible_indexes() :
IMP::atom::BondPairContainer
,
IMP::container::AllBipartitePairContainer
,
IMP::container::AllPairContainer
,
IMP::container::CloseBipartitePairContainer
,
IMP::container::ClosePairContainer
,
IMP::container::ConnectingPairContainer
,
IMP::container::ConsecutivePairContainer
,
IMP::container::ExclusiveConsecutivePairContainer
,
IMP::Container
,
IMP::container::PairContainerSet
,
IMP::container::QuadContainerSet
,
IMP::container::SingletonContainerSet
,
IMP::container::TripletContainerSet
get_all_probabilities() :
IMP::atom::SecondaryStructureResidue
get_all_strings() :
IMP::Key< ID >
get_alpha() :
IMP::isd::PenalizedComplexityPrior
get_alt_loc_indicator() :
IMP::atom::PDBRecord
get_angle() :
IMP::algebra::Cone3D
,
IMP::algebra::Rotation2D
,
IMP::core::DirectionAngle
,
IMP::kinematics::RevoluteJoint
get_angle_derivative() :
IMP::core::DirectionAngle
get_angle_key() :
IMP::core::DirectionAngle
get_angle_parameters() :
IMP::atom::CHARMMParameters
get_angle_step() :
IMP::em2d::PolarResamplingParameters
get_angular_d_factor() :
IMP::npctransport::SimulationData
get_are_close_and_filtered() :
IMP::core::QuadraticClosePairsFinder
get_are_floaters_on_one_slab_side() :
IMP::npctransport::SimulationData
get_area() :
IMP::algebra::Plane3D
,
IMP::algebra::SpherePatch3D
get_assignment_and_RFs() :
IMP.EMageFit.domino_model.DominoModel
get_assignment_info() :
IMP.EMageFit.domino_model.DominoModel
get_assignment_scores() :
IMP.EMageFit.domino_model.DominoModel
get_assignment_text() :
IMP.EMageFit.domino_model.DominoModel
get_assignments() :
IMP::kmeans::KMeans
get_assignments_with_heap() :
IMP.EMageFit.domino_model.DominoModel
get_atom() :
IMP::atom::CHARMMBondEndpoint
get_atom_exists() :
IMP::rotamer::ResidueRotamer
get_atomic_residues() :
IMP.pmi.topology.Molecule
get_atoms() :
IMP::atom::CHARMMConnection< D >
get_attribute() :
IMP::Model
get_average_distance() :
IMP::core::SurfaceTetheredChain
,
IMP::misc::FreelyJointedChain
get_average_distance_wrt_reference_structure() :
IMP.pmi.analysis.Precision
,
IMP.pmi1.analysis.Precision
get_average_fraction_bound_particle_sites_I() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_fraction_bound_particle_sites_II() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_fraction_bound_particles_I() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_fraction_bound_particles_II() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_fraction_nonspecific_interactions_I() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_fraction_nonspecific_interactions_II() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_number_of_contacts() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_off_per_bound_I_per_ns() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_off_per_bound_II_per_ns() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_off_per_contact_per_ns() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_on_per_missing_contact_per_ns() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_on_per_unbound_I_per_ns() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_on_per_unbound_II_per_ns() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_b() :
IMP::algebra::LinearFit2D
,
IMP::algebra::ParabolicFit2D
get_backbone_k() :
IMP::npctransport::FGChain
get_backward_converter() :
IMP.pmi.io.crosslink.CrossLinkDataBaseKeywordsConverter
,
IMP.pmi1.io.crosslink.CrossLinkDataBaseKeywordsConverter
get_barycenter() :
IMP::algebra::UnitSimplexBaseD< D >
get_base_plane() :
IMP::algebra::Cone3D
get_bd() :
IMP::npctransport::SimulationData
get_bead() :
IMP::npctransport::FGChain
get_bead_index() :
IMP::npctransport::FGChain
get_beads() :
IMP::npctransport::FGChain
,
IMP::npctransport::SimulationData
get_beads_byref() :
IMP::npctransport::SimulationData
get_begin() :
IMP::spb::HelixDecorator
get_best_accepted_energy() :
IMP::core::MonteCarlo
get_best_stats() :
IMP.pmi.restraints.crosslinking.AtomicCrossLinkMSRestraint
,
IMP.pmi1.restraints.crosslinking.AtomicCrossLinkMSRestraint
get_bin_size() :
IMP::saxs::Distribution< ValueT >
get_binarized_interior() :
IMP::em::DensityMap
get_body_member_particle_indexes() :
IMP::core::RigidBody
get_bond() :
IMP::atom::Bonded
get_bond_parameters() :
IMP::atom::CHARMMParameters
get_bonded() :
IMP::atom::Bond
,
IMP::atom::Bonded
get_bottom_z() :
IMP::npctransport::ExcludeZRangeSingletonScore
get_boundary_point() :
IMP::algebra::SpherePatch3D
get_bounding_box() :
IMP::algebra::Cone3D
,
IMP::algebra::Cylinder3D
,
IMP::algebra::Ellipsoid3D
,
IMP::algebra::Line3D
,
IMP::algebra::Plane3D
,
IMP::algebra::Segment3D
,
IMP::algebra::SpherePatch3D
,
IMP::algebra::Torus3D
,
IMP::atom::Hierarchy
get_bounding_box_size() :
IMP::npctransport::SimulationData
get_bounding_sphere() :
IMP::atom::Hierarchy
get_bounding_sphere_radius() :
IMP::npctransport::SimulationData
get_bounding_volume_restraint() :
IMP::npctransport::Scoring
get_buckets() :
IMP::multifit::GeometricHash< T, D >
get_by_type() :
IMP::atom::Hierarchy
get_by_unique_id() :
IMP::Model
get_c() :
IMP::algebra::ParabolicFit2D
get_can_refine() :
IMP::atom::BondEndpointsRefiner
,
IMP::core::ChildrenRefiner
,
IMP::core::FixedRefiner
,
IMP::core::LeavesRefiner
,
IMP::core::TableRefiner
,
IMP::multifit::RigidLeavesRefiner
,
IMP::Refiner
get_can_skip() :
IMP::ScoreState
get_cartesian_coordinates() :
IMP::algebra::SphericalVector3D
get_cc() :
IMP.multifit.cluster.AlignmentClustering
get_ccc() :
IMP::em2d::RegistrationResult
,
IMP.EMageFit.solutions_io.ResultsDB
get_ccs() :
IMP::em2d::CollisionCrossSection
get_center() :
IMP::kmeans::KMeans
get_center_of_mass() :
IMP.bayesianem.restraint.GaussianEMRestraintWrapper
,
IMP.pmi.restraints.em.GaussianEMRestraint
,
IMP.pmi1.restraints.em.GaussianEMRestraint
get_centroid() :
IMP::em::DensityMap
get_chain_id() :
IMP::atom::PDBRecord
,
IMP::core::StructureProvenance
get_chain_restraints() :
IMP::npctransport::FGChain
get_chain_restraints_on() :
IMP::npctransport::Scoring
get_chain_type() :
IMP::atom::Chain
,
IMP.pmi.alphabets.ResidueAlphabet
get_chain_type_key() :
IMP::atom::Chain
get_chains_of_super_rigid_bodies() :
IMP.pmi.topology.TopologyReader
,
IMP.pmi1.topology.TopologyReader
get_changed_key() :
IMP::core::Hierarchy
get_charge() :
IMP::atom::Charged
get_charmm_type() :
IMP::atom::CHARMMAtom
get_chi1() :
IMP::rotamer::RotamerAngleTuple
get_chi2() :
IMP::rotamer::RotamerAngleTuple
get_chi3() :
IMP::rotamer::RotamerAngleTuple
get_chi4() :
IMP::rotamer::RotamerAngleTuple
get_chi_square_experimental() :
IMP::statistics::ChiSquareMetric
get_child() :
IMP::atom::Hierarchy
get_child_index() :
IMP::core::Hierarchy
get_children() :
IMP::atom::Hierarchy
get_close_beads_container() :
IMP::npctransport::Scoring
get_close_pairs() :
IMP::core::BoxSweepClosePairsFinder
,
IMP::core::ClosePairsFinder
,
IMP::core::GridClosePairsFinder
,
IMP::core::NearestNeighborsClosePairsFinder
,
IMP::core::QuadraticClosePairsFinder
,
IMP::core::RigidClosePairsFinder
,
IMP::misc::MetricClosePairsFinder< LowerBound, UpperBound >
get_cluster() :
IMP::statistics::PartitionalClustering
,
IMP::statistics::PartitionalClusteringWithCenter
get_cluster_data() :
IMP.pmi.macros.AnalysisReplicaExchange
,
IMP.pmi1.macros.AnalysisReplicaExchange
get_cluster_elements() :
IMP::em2d::ClusterSet
get_cluster_formed_at_step() :
IMP::em2d::ClusterSet
get_cluster_representative() :
IMP::statistics::PartitionalClustering
,
IMP::statistics::PartitionalClusteringWithCenter
get_clusters_below_cutoff() :
IMP::em2d::ClusterSet
get_coarse_registration() :
IMP::em2d::ProjectionFinder
get_coarse_registration_time() :
IMP::em2d::ProjectionFinder
get_coarse_registrations_for_subject() :
IMP::em2d::ProjectionFinder
get_complete_registration() :
IMP::em2d::ProjectionFinder
get_components() :
IMP::atom::BondsGeometry
,
IMP::atom::HierarchiesGeometry
,
IMP::atom::HierarchyGeometry
,
IMP::atom::SelectionGeometry
,
IMP::core::EdgePairGeometry
,
IMP::core::EdgePairsGeometry
,
IMP::core::RigidBodyDerivativesGeometry
,
IMP::core::RigidBodyFramesGeometry
,
IMP::core::RigidBodyHierarchyGeometry
,
IMP::core::SurfaceGeometry
,
IMP::core::XYZDerivativesGeometry
,
IMP::core::XYZRsGeometry
,
IMP::display::BoundingBoxGeometry
,
IMP::display::CylinderGeometry
,
IMP::display::EllipsoidGeometry
,
IMP::display::FilterGeometry
,
IMP::display::Geometry
,
IMP::display::GeometrySet
,
IMP::display::LabelGeometry
,
IMP::display::PlaneGeometry
,
IMP::display::PointGeometry
,
IMP::display::PolygonGeometry
,
IMP::display::ReferenceFrameGeometry
,
IMP::display::RestraintGeometry
,
IMP::display::RestraintSetGeometry
,
IMP::display::SegmentGeometry
,
IMP::display::SphereGeometry
,
IMP::display::SurfaceMeshGeometry
,
IMP::display::TriangleGeometry
,
IMP::npc::SlabWithSphericalIndentGeometry
,
IMP::npc::SlabWithToroidalPoreWireGeometry
,
IMP::npctransport::SitesGeometry
,
IMP::npctransport::SlabWithCylindricalPoreWireGeometry
,
IMP::npctransport::SlabWithToroidalPoreWireGeometry
,
IMP::npctransport::TypedSitesGeometry
,
IMP.pmi.topology.TopologyReader
,
IMP.pmi1.topology.TopologyReader
get_condition_string() :
IMP.EMageFit.database.Database2
get_cone_3d_geometry() :
IMP::algebra::Cone3D
get_connected_index_pairs() :
IMP::core::ConnectivityRestraint
get_connected_pairs() :
IMP::core::MSConnectivityRestraint
,
IMP::npc::CompositeRestraint
get_container_pairs() :
IMP.pmi.restraints.basic.ResidueProteinProximityRestraint
get_contains() :
IMP::algebra::BoundingBoxD< D >
,
IMP::algebra::Cone3D
,
IMP::algebra::SphereD< D >
,
IMP::algebra::SpherePatch3D
,
IMP::algebra::UnitSimplexBaseD< D >
,
IMP::misc::LogPairScore
get_contains_any_sorted_residue() :
IMP::atom::Fragment
get_contains_atom() :
IMP::atom::CHARMMConnection< D >
get_contains_residue() :
IMP::atom::Fragment
get_contents_hash() :
IMP::Container
get_context() :
IMP.parallel.Manager
get_contribution() :
IMP::isd::AtomicCrossLinkMSRestraint
get_contribution_particle_indexes() :
IMP::isd::CrossLinkMSRestraint
get_contribution_psi_index() :
IMP::isd::CrossLinkMSRestraint
get_contribution_sigma_indexes() :
IMP::isd::CrossLinkMSRestraint
get_contribution_sigmas() :
IMP::isd::AtomicCrossLinkMSRestraint
get_converter() :
IMP.pmi.io.crosslink.CrossLinkDataBaseKeywordsConverter
,
IMP.pmi1.io.crosslink.CrossLinkDataBaseKeywordsConverter
get_coordinate() :
IMP::core::XYZ
get_coordinates() :
IMP::core::RigidBody
,
IMP::core::XYZ
,
IMP::rotamer::ResidueRotamer
get_coordinates_are_optimized() :
IMP::core::RigidBody
,
IMP::core::XYZ
get_corner() :
IMP::algebra::BoundingBoxD< D >
get_count() :
IMP::core::HierarchyCounter
get_cropped() :
IMP::em::DensityMap
get_cross_correlation_coefficient() :
IMP::em2d::PCAFitRestraint
,
IMP::isd::GaussianEMRestraint
get_current_angle_from_cartesian_witnesses() :
IMP::kinematics::BondAngleRevoluteJoint
,
IMP::kinematics::DihedralAngleRevoluteJoint
,
IMP::kinematics::RevoluteJoint
get_current_file_name() :
IMP::display::TextWriter
get_current_time() :
IMP::atom::Simulator
get_custom_scoring_function() :
IMP::npctransport::Scoring
get_cylinder_3d_geometry() :
IMP::algebra::Cylinder3D
get_cylindrical_pore_key() :
IMP::npctransport::SlabWithCylindricalPore
get_data() :
IMP::algebra::VectorBaseD< D >
,
IMP::em2d::Image
,
IMP::Model
,
IMP::statistics::ChiSquareMetric
get_data_point() :
IMP::kmeans::KMeans
get_data_type() :
IMP::em::DensityHeader
get_decorator_name() :
IMP::example::ExampleDecorator
,
IMP::npc::SlabWithSphericalIndent
get_default_backbone_k() :
IMP::npctransport::Scoring
get_default_radius_key() :
IMP::misc::CustomXYZR
get_default_traits() :
IMP::core::Hierarchy
get_delta_q() :
IMP::saxs::Profile
get_denominator() :
IMP::core::WeightedSumOfExponential
get_density() :
IMP::core::ClusterProvenance
,
IMP::em::DensityMap
,
IMP::em::Voxel
,
IMP::isd::OneDimensionalDistribution
,
IMP::isd::OneDimensionalSufficientDistribution
,
IMP.pmi.analysis.GetModelDensity
,
IMP.pmi1.analysis.GetModelDensity
,
IMP.sampcon.precision_rmsd.GetModelDensity
get_density_as_hierarchy() :
IMP.bayesianem.restraint.GaussianEMRestraintWrapper
get_dependencies_updated() :
IMP::Model
get_depth() :
IMP::core::Surface
get_derivative() :
IMP::core::XYZ
get_derivative_matrix() :
IMP::isd::BivariateFunction
,
IMP::isd::Covariance1DFunction
,
IMP::isd::GeneralizedGuinierPorodFunction
,
IMP::isd::Linear1DFunction
,
IMP::isd::UnivariateFunction
get_derivative_vector() :
IMP::isd::GeneralizedGuinierPorodFunction
,
IMP::isd::Linear1DFunction
,
IMP::isd::UnivariateFunction
get_derivatives() :
IMP::core::XYZ
get_derivatives_numpy() :
IMP::Model
get_diffusion_coefficient() :
IMP::atom::Diffusion
,
IMP::npctransport::ChainStatisticsOptimizerState
get_diffusion_coefficient_key() :
IMP::atom::Diffusion
get_dihedral_parameters() :
IMP::atom::CHARMMParameters
get_dim_index_by_location() :
IMP::em::DensityMap
get_dimension() :
IMP::algebra::UnitSimplexBaseD< D >
,
IMP::algebra::UnitSimplexD< D >
,
IMP::algebra::UnitSimplexD<-1 >
get_direction() :
IMP::algebra::Cone3D
,
IMP::algebra::Line3D
,
IMP::algebra::Segment3D
,
IMP::core::Direction
,
IMP::core::DirectionMover
get_direction_derivative() :
IMP::core::Direction
get_direction_derivatives() :
IMP::core::Direction
get_direction_is_optimized() :
IMP::core::Direction
get_direction_key() :
IMP::core::Direction
get_displacement_direction() :
IMP::npctransport::SlabWithCylindricalPorePairScore
get_displacement_magnitude() :
IMP::npctransport::SlabWithCylindricalPorePairScore
get_distance() :
IMP::algebra::VectorBaseD< D >
get_distance_at_minimum() :
IMP::core::SurfaceTetheredChain
,
IMP::misc::FreelyJointedChain
get_distance_at_step() :
IMP::em2d::ClusterSet
get_distance_from_envelope() :
IMP::em::MapDistanceTransform
get_distance_to() :
IMP::core::Surface
get_distance_to_center() :
IMP::core::Surface
get_docking_order() :
IMP.EMageFit.buildxlinks.DockOrder
get_dof() :
IMP::kinematics::DOFsSampler
get_dofs() :
IMP::kinematics::DOFsSampler
get_dummy_form_factor() :
IMP::saxs::FormFactorTable
get_dummy_form_factors() :
IMP::saxs::FormFactorTable
get_dummy_water_form_factor() :
IMP::saxs::FormFactorTable
get_Dxi() :
IMP::isd::PenalizedComplexityPrior
get_dynamic_info() :
IMP::bayesianem::GaussianEMRestraint
,
IMP::em2d::PCAFitRestraint
,
IMP::isd::GaussianEMRestraint
,
IMP::isd::UniformPrior
,
IMP::Restraint
get_edges() :
IMP.spatiotemporal.graphNode.graphNode
get_element() :
IMP::atom::Atom
,
IMP::atom::ElementTable
,
IMP::atom::PDBRecord
get_ellipsoid_3d_geometry() :
IMP::algebra::Ellipsoid3D
get_embedding() :
IMP::domino::NestedRigidBodyStates
,
IMP::domino::ParticleStates
,
IMP::domino::RigidBodyStates
,
IMP::domino::XYZStates
get_end() :
IMP::spb::HelixDecorator
get_end_index() :
IMP::algebra::BoundedGridRangeD< D >
get_ending_radius() :
IMP::em2d::PolarResamplingParameters
get_epsilon() :
IMP::atom::ForceFieldParameters
get_equilibrium_rest_length_factor() :
IMP::npctransport::RelaxingSpring
get_equilibrium_rest_length_factor_key() :
IMP::npctransport::RelaxingSpring
get_exchange_array() :
IMP::mpi::ReplicaExchange
get_excluded_volume_k() :
IMP::npctransport::Scoring
get_extended_index() :
IMP::algebra::DefaultEmbeddingD< D >
,
IMP::algebra::GridD< D, StorageT, Value, EmbeddingT >
,
IMP::algebra::LogEmbeddingD< D >
get_fAngle1() :
IMP::em::ImageHeader
get_fFlag() :
IMP::em::ImageHeader
get_fg_bead_types() :
IMP::npctransport::SimulationData
get_fg_chain_roots() :
IMP::npctransport::SimulationData
get_fg_chain_types() :
IMP::npctransport::SimulationData
get_fg_chains() :
IMP::npctransport::Scoring
,
IMP::npctransport::SimulationData
get_fields() :
IMP.pmi.output.ProcessOutput
,
IMP.pmi1.output.ProcessOutput
get_file_dataset() :
IMP.pmi1.representation.Representation
get_filename() :
IMP::core::ScriptProvenance
,
IMP::core::StructureProvenance
get_filename_key() :
IMP::RestraintInfo
get_filename_value() :
IMP::RestraintInfo
get_filenames_key() :
IMP::RestraintInfo
get_filenames_value() :
IMP::RestraintInfo
get_fine_registration_time() :
IMP::em2d::ProjectionFinder
get_fit_error() :
IMP::algebra::LinearFit2D
,
IMP::algebra::ParabolicFit2D
get_flatten() :
IMP.pmi.tools.Segments
,
IMP.pmi1.tools.Segments
get_flexible_beads() :
IMP.pmi.dof.DegreesOfFreedom
get_float_key() :
IMP::RestraintInfo
get_float_value() :
IMP::RestraintInfo
get_floater_types() :
IMP::npctransport::SimulationData
get_floats_key() :
IMP::RestraintInfo
get_floats_numpy() :
IMP::Model
get_floats_value() :
IMP::RestraintInfo
get_floppy_body_movers() :
IMP.pmi.dof.DegreesOfFreedom
get_force() :
IMP::atom::BrownianDynamics
get_forces() :
IMP::atom::BrownianDynamics
get_form_factor() :
IMP::saxs::FormFactorTable
get_form_factors() :
IMP::saxs::FormFactorTable
get_friction_scale_factor() :
IMP::atom::TAMDParticle
get_friction_scale_factor_key() :
IMP::atom::TAMDParticle
get_friend_index() :
IMP::mpi::ReplicaExchange
get_friend_parameter() :
IMP::mpi::ReplicaExchange
get_full_graph() :
IMP.pmi.restraints.proteomics.ConnectivityNetworkRestraint
,
IMP.pmi1.restraints.proteomics.ConnectivityNetworkRestraint
get_full_pair_filter() :
IMP::atom::CHARMMStereochemistryRestraint
get_function() :
IMP::core::WeightedSum
,
IMP::core::WeightedSumOfExponential
get_function_number() :
IMP::core::WeightedSum
,
IMP::core::WeightedSumOfExponential
get_gamma_value() :
IMP.pmi.restraints.saxs.SAXSISDRestraint
,
IMP.pmi1.restraints.saxs.SAXSISDRestraint
get_gaussian() :
IMP::core::Gaussian
get_global_coordinates() :
IMP::algebra::ReferenceFrame3D
get_global_covariance() :
IMP::core::Gaussian
get_global_reference_frame() :
IMP::algebra::ReferenceFrame3D
get_global_score() :
IMP::em2d::ProjectionFinder
get_good_scoring_models() :
IMP.sampcon.good_scoring_model_selector.GoodScoringModelSelector
get_gradient_of_rotated() :
IMP::algebra::Rotation3D
get_had_good_score() :
IMP::ScoringFunction
get_has_attribute() :
IMP::Model
get_has_bounding_box() :
IMP::npctransport::Scoring
,
IMP::npctransport::SimulationData
get_has_bounding_sphere() :
IMP::npctransport::Scoring
,
IMP::npctransport::SimulationData
get_has_bounding_volume() :
IMP::npctransport::Scoring
,
IMP::npctransport::SimulationData
get_has_data() :
IMP::Model
get_has_dependencies() :
IMP::ModelObject
get_has_index() :
IMP::algebra::BoundedGridRangeD< D >
,
IMP::algebra::SparseGridStorageD< D, VT, Base, Map >
get_has_lower() :
IMP::isd::Nuisance
get_has_particle() :
IMP::Model
get_has_required_score_states() :
IMP::ModelObject
get_has_resolution() :
IMP::em::DensityHeader
get_has_slope() :
IMP::isd::CrossLinkMSRestraint
get_header() :
IMP::em2d::Image
,
IMP::em::DensityMap
get_header_writable() :
IMP::em::DensityMap
get_height() :
IMP::core::Surface
get_hessian() :
IMP::isd::GaussianProcessInterpolationRestraint
get_hierarchies() :
IMP::atom::Selection
,
IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
get_hierarchies_at_given_resolution() :
IMP.pmi1.representation.Representation
get_hierarchy() :
IMP.pmi.topology.Molecule
,
IMP.pmi.topology.State
,
IMP.pmi.topology.System
get_id() :
IMP::atom::Chain
get_id_key() :
IMP::atom::Chain
get_ideal() :
IMP::atom::Angle
,
IMP::atom::Dihedral
get_ideal_helices() :
IMP.pmi.topology.Molecule
get_image_index() :
IMP::em2d::RegistrationResult
get_improper_parameters() :
IMP::atom::CHARMMParameters
get_in_ball() :
IMP::algebra::NearestNeighborD< D >
get_index() :
IMP::algebra::BoundedGridRangeD< D >
,
IMP::algebra::SparseGridStorageD< D, VT, Base, Map >
,
IMP::atom::Residue
,
IMP::Particle
,
IMP.spatiotemporal.graphNode.graphNode
get_index_range() :
IMP::atom::Domain
get_indexes() :
IMP::atom::BondPairContainer
,
IMP::container::AllBipartitePairContainer
,
IMP::container::AllPairContainer
,
IMP::container::CloseBipartitePairContainer
,
IMP::container::ClosePairContainer
,
IMP::container::ConnectingPairContainer
,
IMP::container::ConsecutivePairContainer
,
IMP::container::ExclusiveConsecutivePairContainer
,
IMP::container::PredicatePairsRestraint
,
IMP::container::PredicateQuadsRestraint
,
IMP::container::PredicateSingletonsRestraint
,
IMP::container::PredicateTripletsRestraint
,
IMP::PairContainer
,
IMP::QuadContainer
,
IMP::SingletonContainer
,
IMP::TripletContainer
get_indexes_in_place() :
IMP::container::PairContainerSet
,
IMP::container::QuadContainerSet
,
IMP::container::SingletonContainerSet
,
IMP::container::TripletContainerSet
get_individual_placement_statistics() :
IMP.EMageFit.solutions_io.ResultsDB
get_initial_simulation_time_ns() :
IMP::npctransport::SimulationData
get_inner_joints() :
IMP::kinematics::CompositeJoint
get_inner_point_at() :
IMP::algebra::Cylinder3D
get_inner_state() :
IMP::domino::PermutationStates
get_input_file_name() :
IMP.test.TestCase
get_input_index() :
IMP::atom::Atom
get_inputs() :
IMP::isd::BivariateFunction
,
IMP::isd::Covariance1DFunction
,
IMP::isd::GeneralizedGuinierPorodFunction
,
IMP::isd::Linear1DFunction
,
IMP::isd::UnivariateFunction
,
IMP::ModelObject
,
IMP::ParticleInputs
,
IMP::score_functor::Score
,
IMP::score_functor::ScoreWithCache
get_int_key() :
IMP::RestraintInfo
get_int_value() :
IMP::RestraintInfo
get_interaction_k() :
IMP::npctransport::Scoring
get_interaction_range_for() :
IMP::npctransport::Scoring
get_interaction_type() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_interactions() :
IMP::ModelObject
get_internal_bonds() :
IMP::atom::Hierarchy
get_internal_coordinates() :
IMP::core::RigidBodyMember
get_internal_derivatives() :
IMP::core::NonRigidMember
get_internal_rotational_derivatives() :
IMP::core::NonRigidMember
get_internal_transformation() :
IMP::core::RigidBodyMember
get_interp() :
IMP.isd.TuneRex.CvEstimator
get_ints_key() :
IMP::RestraintInfo
get_ints_numpy() :
IMP::Model
get_ints_value() :
IMP::RestraintInfo
get_inv_rsigsq() :
IMP::em::KernelParameters
get_inverse() :
IMP::algebra::Rotation2D
,
IMP::algebra::Rotation3D
,
IMP::algebra::Transformation2D
get_is_activated() :
IMP::npctransport::Statistics
get_is_aggregate() :
IMP::Restraint
get_is_atom() :
IMP::atom::PDBRecord
get_is_by_ref_supported() :
IMP::Refiner
get_is_decomposable() :
IMP::Container
get_is_evaluate_if_below() :
IMP::ScoreAccumulator
get_is_evaluate_if_good() :
IMP::ScoreAccumulator
get_is_exclude_floaters_from_slab_initially() :
IMP::npctransport::SimulationData
get_is_fg_bead() :
IMP::npctransport::SimulationData
get_is_fg_chain() :
IMP::npctransport::SimulationData
get_is_heterogen() :
IMP::atom::Hierarchy
get_is_last_entry_from_top() :
IMP::npctransport::Transporting
get_is_last_entry_from_top_key() :
IMP::npctransport::Transporting
get_is_length_variable() :
IMP::isd::CrossLinkMSRestraint
get_is_ok() :
IMP::domino::SubsetFilter
,
IMP::em2d::DistanceFilter
get_is_pore_radius_dynamic() :
IMP::npctransport::SimulationData
get_is_selected() :
IMP::atom::AllPDBSelector
,
IMP::atom::AndPDBSelector
,
IMP::atom::ATOMPDBSelector
,
IMP::atom::AtomTypePDBSelector
,
IMP::atom::BackbonePDBSelector
,
IMP::atom::CAlphaPDBSelector
,
IMP::atom::CBetaPDBSelector
,
IMP::atom::ChainPDBSelector
,
IMP::atom::CPDBSelector
,
IMP::atom::HydrogenPDBSelector
,
IMP::atom::NonAlternativePDBSelector
,
IMP::atom::NonHydrogenPDBSelector
,
IMP::atom::NonWaterNonHydrogenPDBSelector
,
IMP::atom::NonWaterPDBSelector
,
IMP::atom::NotPDBSelector
,
IMP::atom::NPDBSelector
,
IMP::atom::OrPDBSelector
,
IMP::atom::PDBSelector
,
IMP::atom::PPDBSelector
,
IMP::atom::ResidueTypePDBSelector
,
IMP::atom::WaterPDBSelector
,
IMP::atom::XorPDBSelector
get_is_setup() :
IMP::atom::Angle
,
IMP::atom::Atom
,
IMP::atom::Charged
,
IMP::atom::CHARMMAtom
,
IMP::atom::Diffusion
,
IMP::atom::Hierarchy
,
IMP::atom::LennardJones
,
IMP::atom::RigidBodyDiffusion
,
IMP::atom::SecondaryStructureResidue
,
IMP::atom::TAMDParticle
,
IMP::core::Direction
,
IMP::core::DirectionAngle
,
IMP::core::Hierarchy
,
IMP::core::NonRigidMember
,
IMP::core::RigidBody
,
IMP::core::RigidBodyMember
,
IMP::core::RigidMember
,
IMP::core::Surface
,
IMP::core::XYZR
,
IMP::em2d::ProjectionParameters
,
IMP::example::ExampleDecorator
,
IMP::kinematics::KinematicNode
,
IMP::misc::CustomXYZR
,
IMP::npc::SlabWithPore
,
IMP::npc::SlabWithSphericalIndent
,
IMP::npc::SlabWithToroidalPore
,
IMP::npctransport::RelaxingSpring
,
IMP::npctransport::SlabWithCylindricalPore
,
IMP::npctransport::SlabWithPore
,
IMP::npctransport::SlabWithToroidalPore
,
IMP::npctransport::Transporting
get_is_simulation_particle() :
IMP::atom::BrownianDynamics
,
IMP::atom::MolecularDynamics
,
IMP::atom::Simulator
,
IMP::isd::MolecularDynamics
,
IMP::spb::MolecularDynamicsWithWte
get_is_slab_with_cylindrical_pore() :
IMP::npctransport::SimulationData
get_is_slab_with_toroidal_pore() :
IMP::npctransport::SimulationData
get_is_srk() :
IMP::atom::BrownianDynamics
get_is_trivially_zero() :
IMP::score_functor::Score
get_is_trivially_zero_with_cache() :
IMP::score_functor::ScoreWithCache
get_is_valid() :
IMP::algebra::Rotation3D
,
IMP::algebra::Transformation3D
,
IMP::atom::Hierarchy
,
IMP::Decorator
get_is_xyz_hist_stats() :
IMP::npctransport::SimulationData
get_jacobian_of_rotated() :
IMP::algebra::Rotation3D
get_joints() :
IMP::kinematics::ProteinKinematics
get_Jxi() :
IMP::isd::PenalizedComplexityPrior
get_k() :
IMP::core::Harmonic
,
IMP::npctransport::ExcludeZRangeSingletonScore
,
IMP::npctransport::LinearSoftSpherePairScore
,
IMP::npctransport::ZBiasSingletonScore
get_k1() :
IMP::npctransport::HarmonicSpringSingletonScore
get_k2() :
IMP::npctransport::HarmonicSpringSingletonScore
get_k_attraction() :
IMP::npctransport::LinearInteractionPairScore
get_k_from_standard_deviation() :
IMP::core::Harmonic
get_k_repulsion() :
IMP::npctransport::LinearInteractionPairScore
get_key_exists() :
IMP::Key< ID >
get_keys() :
IMP::em2d::ProjectionParameters
get_kinematic_forest() :
IMP::kinematics::ProteinKinematics
get_kinetic_energy() :
IMP::atom::MolecularDynamics
,
IMP::isd::MolecularDynamics
,
IMP::spb::MolecularDynamicsWithWte
get_kinetic_temperature() :
IMP::atom::MolecularDynamics
,
IMP::spb::MolecularDynamicsWithWte
get_label() :
IMP.spatiotemporal.graphNode.graphNode
get_label_asym_id() :
IMP::atom::Chain
get_label_asym_id_key() :
IMP::atom::Chain
get_last_accepted_energy() :
IMP::core::MonteCarlo
get_last_last_score() :
IMP::Restraint
get_last_score() :
IMP::Optimizer
,
IMP::Restraint
,
IMP::RestraintSet
,
IMP::ScoringFunction
get_last_time_step() :
IMP::atom::Simulator
get_last_tracked_z() :
IMP::npctransport::Transporting
get_last_tracked_z_key() :
IMP::npctransport::Transporting
get_leaves() :
IMP::atom::Hierarchy
get_left_join_command() :
IMP.EMageFit.solutions_io.ResultsDB
get_length() :
IMP::atom::Bond
,
IMP::isd::CrossLinkMSRestraint
,
IMP::kinematics::PrismaticJoint
get_likelihood() :
IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi.restraints.em.GaussianEMRestraint
get_lim() :
IMP::em::KernelParameters
get_line_3d_geometry() :
IMP::algebra::Line3D
get_link_length() :
IMP::core::SurfaceTetheredChain
,
IMP::misc::FreelyJointedChain
get_link_number() :
IMP::core::SurfaceTetheredChain
,
IMP::misc::FreelyJointedChain
get_linkage_matrix() :
IMP::em2d::ClusterSet
get_linkage_matrix_in_matlab_format() :
IMP::em2d::ClusterSet
get_list() :
IMP.pmi.io.crosslink.ResiduePairListParser
,
IMP.pmi1.io.crosslink.ResiduePairListParser
get_local_coordinates() :
IMP::algebra::ReferenceFrame3D
get_local_covariance() :
IMP::core::Gaussian
get_local_diffusion_coefficients() :
IMP::npctransport::ChainStatisticsOptimizerState
get_local_reference_frame() :
IMP::algebra::ReferenceFrame3D
get_location() :
IMP::core::SoftwareProvenance
get_location_by_voxel() :
IMP::em::DensityMap
get_location_in_dim_by_voxel() :
IMP::em::DensityMap
get_locations_string() :
IMP::em::DensityMap
get_log_generalized_variance() :
IMP::isd::MultivariateFNormalSufficient
get_logdet_hessian() :
IMP::isd::GaussianProcessInterpolationRestraint
get_magnitude() :
IMP.test.TestCase
get_mass() :
IMP::atom::ElementTable
get_mass_key() :
IMP::atom::Mass
get_max_distance() :
IMP::saxs::Distribution< ValueT >
get_max_q() :
IMP::saxs::Profile
get_max_step() :
IMP::atom::BrownianDynamics
get_max_value() :
IMP::em::DensityMap
get_maximum() :
IMP::ScoreAccumulator
get_maximum_extended_index() :
IMP::algebra::BoundedGridRangeD< D >
get_maximum_number_of_minutes() :
IMP::npctransport::SimulationData
get_maximum_range() :
IMP::score_functor::AddScores< BaseDistanceScore0, BaseDistanceScore1 >
,
IMP::score_functor::Score
,
IMP::score_functor::ScoreWithCache
get_maximum_rotation() :
IMP::core::DirectionMover
,
IMP::core::SurfaceMover
get_maximum_time_step() :
IMP::atom::Simulator
get_maximum_translation() :
IMP::core::SurfaceMover
get_maximum_value_in_xy_plane() :
IMP::em::DensityMap
get_maximum_value_in_xz_plane() :
IMP::em::DensityMap
get_maximum_value_in_yz_plane() :
IMP::em::DensityMap
get_mbar() :
IMP.isd.TuneRex.CvEstimator
get_mean() :
IMP::core::Harmonic
get_mean_bond_distance() :
IMP::npctransport::ChainStatisticsOptimizerState
get_mean_end_to_end_distance() :
IMP::npctransport::ChainStatisticsOptimizerState
get_mean_radius_of_gyration() :
IMP::npctransport::ChainStatisticsOptimizerState
get_mean_square_bond_distance() :
IMP::npctransport::ChainStatisticsOptimizerState
get_mean_square_end_to_end_distance() :
IMP::npctransport::ChainStatisticsOptimizerState
get_mean_square_radius_of_gyration() :
IMP::npctransport::ChainStatisticsOptimizerState
get_mean_square_residuals() :
IMP::isd::MultivariateFNormalSufficient
get_member_indexes() :
IMP::core::RigidBody
get_member_particle_indexes() :
IMP::core::RigidBody
get_method() :
IMP::core::FilterProvenance
,
IMP::core::SampleProvenance
get_min_and_max_values() :
IMP::em2d::Image
get_min_q() :
IMP::saxs::Profile
get_min_value() :
IMP::em::DensityMap
get_minimum_extended_index() :
IMP::algebra::BoundedGridRangeD< D >
get_minimum_resampled_value() :
IMP::em::SampledDensityMap
get_minimum_spanning_tree() :
IMP.pmi.restraints.proteomics.ConnectivityNetworkRestraint
,
IMP.pmi1.restraints.proteomics.ConnectivityNetworkRestraint
get_minor_radius_h2v_aspect_ratio_key() :
IMP::npc::SlabWithToroidalPore
,
IMP::npctransport::SlabWithToroidalPore
get_minus_exponent() :
IMP::isd::MultivariateFNormalSufficient
get_minus_log_normalization() :
IMP::isd::GaussianProcessInterpolationRestraint
,
IMP::isd::MultivariateFNormalSufficient
get_model() :
IMP::Decorator
,
IMP::npctransport::ParticleFactory
,
IMP::npctransport::Scoring
,
IMP::npctransport::Statistics
get_model_dens_map() :
IMP::em::FitRestraint
get_model_objects() :
IMP::Model
get_modeling_trajectory() :
IMP.pmi.macros.AnalysisReplicaExchange0
,
IMP.pmi1.macros.AnalysisReplicaExchange0
get_moldict_coorddict() :
IMP.pmi.analysis.RMSD
,
IMP.pmi1.analysis.RMSD
get_molecule() :
IMP.pmi.topology.State
get_molecules() :
IMP.pmi.macros.BuildSystem
,
IMP.pmi.topology.State
get_moment() :
IMP::algebra::Line3D
get_movable_particles() :
IMP::core::MonteCarlo
get_movers() :
IMP.pmi.dof.DegreesOfFreedom
,
IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
get_multiplicity() :
IMP::atom::Dihedral
get_my_index() :
IMP::mpi::ReplicaExchange
get_my_parameter() :
IMP::mpi::ReplicaExchange
get_n_entries_bottom() :
IMP::npctransport::Transporting
get_n_entries_bottom_key() :
IMP::npctransport::Transporting
get_n_entries_top() :
IMP::npctransport::Transporting
get_n_entries_top_key() :
IMP::npctransport::Transporting
get_n_transports_down() :
IMP::npctransport::ParticleTransportStatisticsOptimizerState
get_n_transports_up() :
IMP::npctransport::ParticleTransportStatisticsOptimizerState
get_name() :
IMP::atom::ElementTable
,
IMP::em2d::Image
,
IMP::em2d::RegistrationResult
,
IMP.EMageFit.buildxlinks.Xlink
,
IMP.pmi.topology.Molecule
get_native_rank() :
IMP.EMageFit.solutions_io.ResultsDB
get_native_solution() :
IMP.EMageFit.solutions_io.ResultsDB
get_ndims_x() :
IMP::isd::GeneralizedGuinierPorodFunction
,
IMP::isd::Linear1DFunction
,
IMP::isd::UnivariateFunction
get_ndims_x1() :
IMP::isd::BivariateFunction
,
IMP::isd::Covariance1DFunction
get_ndims_y() :
IMP::isd::BivariateFunction
,
IMP::isd::Covariance1DFunction
,
IMP::isd::GeneralizedGuinierPorodFunction
,
IMP::isd::Linear1DFunction
,
IMP::isd::UnivariateFunction
get_nearest_neighbor() :
IMP::algebra::NearestNeighborD< D >
get_nearest_neighbors() :
IMP::algebra::NearestNeighborD< D >
get_nearest_state() :
IMP::domino::NestedRigidBodyStates
,
IMP::domino::ParticleStates
,
IMP::domino::RigidBodyStates
,
IMP::domino::XYZStates
get_neighbors() :
IMP::core::NeighborsTable
get_next_state() :
IMP::domino::SubsetFilter
get_non_atomic_residues() :
IMP.pmi.topology.Molecule
get_non_optimizable_beads() :
IMP::npctransport::SimulationData
get_non_sets_and_sets() :
IMP::RestraintSet
get_normal() :
IMP::core::Surface
get_normal_derivative() :
IMP::core::Surface
get_normal_derivatives() :
IMP::core::Surface
get_normal_is_optimized() :
IMP::core::Surface
get_normal_x() :
IMP::core::Surface
get_normal_y() :
IMP::core::Surface
get_normal_z() :
IMP::core::Surface
get_nth_largest_cluster() :
IMP.EMageFit.solutions_io.ResultsDB
get_nuisance_movers_parameters() :
IMP.pmi.samplers.MonteCarlo
,
IMP.pmi1.samplers.MonteCarlo
get_nuisances_from_restraint() :
IMP.pmi.dof.DegreesOfFreedom
get_num_restraints() :
IMP.pmi.restraints.stereochemistry.ConnectivityRestraint
,
IMP.pmi1.restraints.stereochemistry.ConnectivityRestraint
get_number_of_accepted_steps() :
IMP::core::MonteCarlo
get_number_of_angles() :
IMP::em2d::PolarResamplingParameters
get_number_of_assignments_for_vertex() :
IMP::domino::DominoSampler
get_number_of_beads() :
IMP::npctransport::FGChain
get_number_of_bonds() :
IMP::atom::HelixRestraint
get_number_of_cases() :
IMP::rotamer::ResidueRotamer
get_number_of_centers() :
IMP::kmeans::KMeans
get_number_of_contributions() :
IMP::isd::AtomicCrossLinkMSRestraint
,
IMP::isd::ResidueProteinProximityRestraint
get_number_of_copies() :
IMP.pmi.topology.State
get_number_of_data_points() :
IMP::kmeans::KMeans
get_number_of_dihedrals() :
IMP::atom::HelixRestraint
get_number_of_downward_steps() :
IMP::core::MonteCarlo
get_number_of_entries() :
IMP::domino::RestraintCache
get_number_of_filename() :
IMP::RestraintInfo
get_number_of_filenames() :
IMP::RestraintInfo
get_number_of_float() :
IMP::RestraintInfo
get_number_of_floats() :
IMP::RestraintInfo
get_number_of_frames() :
IMP::core::CombineProvenance
,
IMP::core::FilterProvenance
,
IMP::core::SampleProvenance
get_number_of_full_rebuilds() :
IMP::container::ClosePairContainer
get_number_of_int() :
IMP::RestraintInfo
get_number_of_ints() :
IMP::RestraintInfo
get_number_of_iterations() :
IMP::core::SampleProvenance
get_number_of_masks() :
IMP::em2d::RigidBodiesImageFitRestraint
get_number_of_members() :
IMP::core::ClusterProvenance
get_number_of_optimized_particles() :
IMP::isd::BivariateFunction
,
IMP::isd::Covariance1DFunction
,
IMP::isd::GeneralizedGuinierPorodFunction
,
IMP::isd::Linear1DFunction
,
IMP::isd::UnivariateFunction
get_number_of_partial_rebuilds() :
IMP::container::ClosePairContainer
get_number_of_particle_indexes() :
IMP::RestraintInfo
get_number_of_particles() :
IMP::isd::BivariateFunction
,
IMP::isd::Covariance1DFunction
,
IMP::isd::GeneralizedGuinierPorodFunction
,
IMP::isd::Linear1DFunction
,
IMP::isd::UnivariateFunction
get_number_of_particles_1() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_number_of_particles_2() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_number_of_proposed_steps() :
IMP::core::MonteCarlo
get_number_of_refined() :
IMP::Refiner
get_number_of_replicas() :
IMP::core::SampleProvenance
,
IMP::mpi::ReplicaExchange
get_number_of_rings() :
IMP::em2d::PolarResamplingParameters
get_number_of_runs() :
IMP::core::CombineProvenance
get_number_of_solutions() :
IMP::em::FittingSolutions
get_number_of_states() :
IMP.pmi.topology.System
get_number_of_steps() :
IMP::em2d::ClusterSet
,
IMP::kinematics::DOF
get_number_of_string() :
IMP::RestraintInfo
get_number_of_strings() :
IMP::RestraintInfo
get_number_of_unique_crosslinked_sites() :
IMP.pmi.io.crosslink.CrossLinkDataBase
get_number_of_update_calls() :
IMP::container::ClosePairContainer
get_number_of_updates() :
IMP::OptimizerState
get_number_of_upward_steps() :
IMP::core::MonteCarlo
get_number_of_voxels() :
IMP::algebra::BoundedGridRangeD< D >
,
IMP::em::DensityMap
get_number_of_weights() :
IMP::isd::Weight
get_number_of_weights_key() :
IMP::isd::Weight
get_number_unique() :
IMP::Key< ID >
get_nx() :
IMP::em::DensityHeader
get_ny() :
IMP::em::DensityHeader
get_nz() :
IMP::em::DensityHeader
get_obstacle_particles() :
IMP::npctransport::SimulationData
get_obstacle_types() :
IMP::npctransport::SimulationData
get_old_rot() :
IMP::em::ImageHeader
get_one_letter_code_from_residue_type() :
IMP.pmi.alphabets.ResidueAlphabet
get_opposite() :
IMP::algebra::Line3D
,
IMP::algebra::Plane3D
get_optimizable_beads() :
IMP::npctransport::SimulationData
get_order() :
IMP::atom::Bond
get_ordered_joints() :
IMP::kinematics::KinematicForest
,
IMP::kinematics::ProteinKinematics
get_orientation() :
IMP::em2d::GridStates
get_origin() :
IMP::em::DensityHeader
get_output() :
IMP.pmi.analysis.RMSD
,
IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi1.analysis.RMSD
,
IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi1.restraints.RestraintBase
get_outputs() :
IMP::ModelObject
,
IMP::ParticleOutputs
get_owner() :
IMP::npctransport::ParticleTransportStatisticsOptimizerState
get_padded_atom_name() :
IMP::atom::PDBRecord
get_pair_filter() :
IMP::atom::CHARMMStereochemistryRestraint
,
IMP::atom::OrientedSoapPairScore
get_pair_score() :
IMP::core::ConnectivityRestraint
,
IMP::core::MSConnectivityRestraint
get_parameters_optimized() :
IMP::em2d::ProjectionParameters
get_parent() :
IMP::atom::Hierarchy
,
IMP::core::Hierarchy
get_particle() :
IMP::atom::Angle
,
IMP::atom::Dihedral
,
IMP::core::DirectionAngle
,
IMP::Decorator
,
IMP::Model
get_particle_assignments() :
IMP::domino::AssignmentContainer
,
IMP::domino::CappedAssignmentContainer
,
IMP::domino::HeapAssignmentContainer
,
IMP::domino::ListAssignmentContainer
,
IMP::domino::PackedAssignmentContainer
,
IMP::domino::RangeViewAssignmentContainer
,
IMP::domino::ReadAssignmentContainer
,
IMP::domino::ReadHDF5AssignmentContainer
,
IMP::domino::SampleAssignmentContainer
,
IMP::domino::WriteAssignmentContainer
,
IMP::domino::WriteHDF5AssignmentContainer
get_particle_index() :
IMP::core::DirectionAngle
,
IMP::Decorator
get_particle_indexes() :
IMP::Model
get_particle_indexes_key() :
IMP::RestraintInfo
get_particle_indexes_value() :
IMP::RestraintInfo
get_particle_is_optimized() :
IMP::isd::BivariateFunction
,
IMP::isd::Covariance1DFunction
,
IMP::isd::GeneralizedGuinierPorodFunction
,
IMP::isd::Linear1DFunction
,
IMP::isd::UnivariateFunction
get_particle_key() :
IMP::core::DirectionAngle
get_particle_name() :
IMP::Model
get_particle_pairs() :
IMP::misc::LogPairScore
,
IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi.restraints.stereochemistry.ConnectivityRestraint
,
IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi1.restraints.stereochemistry.ConnectivityRestraint
get_particles_at_all_resolutions() :
IMP.pmi.topology.Molecule
get_particles_from_selection_tuples() :
IMP.pmi1.representation.Representation
get_particles_size() :
IMP::Model
get_particles_to_sample() :
IMP.pmi.restraints.crosslinking.AtomicCrossLinkMSRestraint
,
IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi1.restraints.crosslinking.AtomicCrossLinkMSRestraint
,
IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi1.restraints.RestraintBase
get_pdb() :
IMP.isd.shared_functions.sfo_common
get_pdb_names() :
IMP.pmi.output.Output
get_period() :
IMP::OptimizerState
get_phi() :
IMP::kinematics::ProteinKinematics
get_placement_fields() :
IMP.EMageFit.solutions_io.ResultsDB
get_placement_score_from_coordinates() :
IMP.multifit.cluster.AlignmentClustering
get_placement_statistics() :
IMP.EMageFit.solutions_io.ResultsDB
get_plane() :
IMP::core::Surface
get_plane_3d_geometry() :
IMP::algebra::Plane3D
get_point() :
IMP::algebra::Segment3D
,
IMP::algebra::Triangle3D
,
IMP::example::ExampleTemplateClassD< D >
get_point_on_line() :
IMP::algebra::Line3D
get_pore_radius() :
IMP::npc::SlabWithPore
,
IMP::npctransport::SimulationData
,
IMP::npctransport::SlabWithPore
get_pore_radius_k() :
IMP::npctransport::SimulationData
get_pore_radius_key() :
IMP::npc::SlabWithPore
,
IMP::npctransport::SlabWithPore
get_position() :
IMP::em2d::GridStates
get_posterior_mean() :
IMP::isd::GaussianProcessInterpolation
get_precision() :
IMP::core::ClusterProvenance
,
IMP.pmi.analysis.Precision
,
IMP.pmi1.analysis.Precision
get_predicate_pair_score() :
IMP::npctransport::Scoring
get_predicates_pair_restraint() :
IMP::npctransport::Scoring
get_preprocessing_time() :
IMP::em2d::ProjectionFinder
get_previous() :
IMP::core::Provenance
get_prob_coil() :
IMP::atom::SecondaryStructureResidue
get_prob_helix() :
IMP::atom::SecondaryStructureResidue
get_prob_strand() :
IMP::atom::SecondaryStructureResidue
get_probability() :
IMP::bayesianem::GaussianEMRestraint
,
IMP::isd::GaussianEMRestraint
,
IMP::isd::GaussianProcessInterpolationRestraint
,
IMP::isd::StudentTRestraint
,
IMP::isd::TALOSRestraint
,
IMP::rotamer::ResidueRotamer
,
IMP::rotamer::RotamerAngleTuple
get_probability_distribution_function() :
IMP::statistics::HistogramD< D, Grid >
get_profile() :
IMP::saxs::ProfileFitter< ScoringFunctionT >
get_projected() :
IMP::algebra::Plane3D
get_projected_area() :
IMP::em2d::CollisionCrossSection
get_projection() :
IMP::em2d::ProjectionStates
get_projection_index() :
IMP::em2d::RegistrationResult
get_prot_name_from_particle() :
IMP.pmi.output.Output
,
IMP.pmi1.output.Output
get_psi() :
IMP::isd::AtomicCrossLinkMSRestraint
,
IMP::kinematics::ProteinKinematics
get_quaternion() :
IMP::algebra::Rotation3D
get_quaternion_1() :
IMP::em2d::ProjectionParameters
get_quaternion_2() :
IMP::em2d::ProjectionParameters
get_quaternion_3() :
IMP::em2d::ProjectionParameters
get_quaternion_4() :
IMP::em2d::ProjectionParameters
get_radius() :
IMP::algebra::Cone3D
,
IMP::atom::ForceFieldParameters
,
IMP::em2d::PolarResamplingParameters
,
IMP::misc::CustomXYZR
,
IMP::npctransport::ParticleFactory
,
IMP::saxs::FormFactorTable
get_radius_key() :
IMP::core::XYZR
get_radius_of_gyration() :
IMP::multifit::RadiusOfGyrationRestraint
get_radius_step() :
IMP::em2d::PolarResamplingParameters
get_range() :
IMP::npctransport::SimulationData
get_range_attraction() :
IMP::npctransport::LinearInteractionPairScore
get_range_indexes() :
IMP::atom::BondPairContainer
,
IMP::container::AllBipartitePairContainer
,
IMP::container::AllPairContainer
,
IMP::container::CloseBipartitePairContainer
,
IMP::container::ClosePairContainer
,
IMP::container::ConnectingPairContainer
,
IMP::container::ConsecutivePairContainer
,
IMP::container::ExclusiveConsecutivePairContainer
,
IMP::PairContainer
,
IMP::QuadContainer
,
IMP::SingletonContainer
,
IMP::TripletContainer
get_reciprocal_product() :
IMP::algebra::Line3D
get_reduced_coordinates() :
IMP::core::RigidBodyTunneler
get_reference_frame() :
IMP::core::RigidBody
,
IMP::core::Surface
get_reference_particle_index() :
IMP::atom::TAMDParticle
get_reference_particle_index_key() :
IMP::atom::TAMDParticle
get_refined() :
IMP::atom::BondEndpointsRefiner
,
IMP::core::ChildrenRefiner
,
IMP::core::FixedRefiner
,
IMP::core::LeavesRefiner
,
IMP::core::TableRefiner
,
IMP::multifit::RigidLeavesRefiner
,
IMP::Refiner
get_refined_indexes() :
IMP::core::FixedRefiner
,
IMP::Refiner
get_refined_indexes_by_ref() :
IMP::core::FixedRefiner
,
IMP::Refiner
get_reflect_probability() :
IMP::core::DirectionMover
,
IMP::core::SurfaceMover
get_registration_results() :
IMP::em2d::Em2DRestraint
,
IMP::em2d::ProjectionFinder
get_representation() :
IMP::atom::Representation
,
IMP.pmi1.macros.BuildModel
get_representations() :
IMP::atom::Representation
get_represented() :
IMP.pmi.topology.Molecule
get_required_score_states() :
IMP::ModelObject
get_resampled() :
IMP::em::DensityMap
get_resampling_map() :
IMP::em2d::PolarResamplingParameters
get_resampling_maps() :
IMP::em2d::PolarResamplingParameters
get_residue() :
IMP::atom::Hierarchy
get_residue_coordinates() :
IMP.EMageFit.buildxlinks.InitialDockingFromXlinks
get_residue_name() :
IMP::atom::PDBRecord
get_residue_offset() :
IMP::core::StructureProvenance
get_residue_particle() :
IMP.EMageFit.buildxlinks.InitialDockingFromXlinks
get_residue_type_from_one_letter_code() :
IMP.pmi.alphabets.ResidueAlphabet
get_residues() :
IMP.pmi.topology.Molecule
get_resolution() :
IMP::em::DensityHeader
get_resolutions() :
IMP::atom::Representation
get_rest_length() :
IMP::npctransport::RelaxingSpring
get_rest_length_diffusion_coefficient() :
IMP::npctransport::RelaxingSpring
get_rest_length_diffusion_coefficient_key() :
IMP::npctransport::RelaxingSpring
get_rest_length_factor() :
IMP::npctransport::FGChain
get_rest_length_key() :
IMP::npctransport::RelaxingSpring
get_restraint() :
IMP.pmi1.restraints.RestraintBase
get_restraint_for_rmf() :
IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi1.restraints.RestraintBase
get_restraint_set() :
IMP::multifit::ProteomicsEMAlignmentAtomic
,
IMP.pmi1.restraints.RestraintBase
get_restraint_sets() :
IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
get_restraint_value_for_assignment() :
IMP.EMageFit.domino_model.DominoModel
get_restraints() :
IMP::domino::RestraintCache
,
IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
get_restraints_for_native() :
IMP.EMageFit.domino_model.DominoModel
get_restraints_names_used() :
IMP.EMageFit.domino_model.DominoModel
get_results_unordered() :
IMP.parallel.Context
get_reversed() :
IMP::em::ImageHeader
get_rigid_bodies() :
IMP::kinematics::ProteinKinematics
,
IMP.pmi.dof.DegreesOfFreedom
,
IMP.pmi.topology.TopologyReader
,
IMP.pmi1.topology.TopologyReader
get_rkdist() :
IMP::em::KernelParameters
get_rkdistsq() :
IMP::em::KernelParameters
get_rmf_sos_writer() :
IMP::npctransport::SimulationData
get_rmsd_wrt_reference_structure_with_alignment() :
IMP.pmi.analysis.Precision
,
IMP.pmi1.analysis.Precision
get_rmsf() :
IMP.pmi.analysis.Precision
,
IMP.pmi1.analysis.Precision
get_rnormfac() :
IMP::em::KernelParameters
get_root() :
IMP::atom::Hierarchy
get_root_of_type() :
IMP::npctransport::SimulationData
get_rotamer() :
IMP::rotamer::RotamerCalculator
get_rotamers() :
IMP::rotamer::RotamerLibrary
get_rotamers_fast() :
IMP::rotamer::RotamerLibrary
get_rotated() :
IMP::algebra::Rotation2D
,
IMP::algebra::Rotation3D
get_rotated_adjoint() :
IMP::algebra::Rotation3D
get_rotated_one_coordinate() :
IMP::algebra::Rotation3D
get_rotation() :
IMP::algebra::Transformation2D
,
IMP::algebra::Transformation3D
,
IMP::core::RigidBody
,
IMP::em2d::RegistrationResult
get_rotation_about_joint_in_parent_coordinates() :
IMP::kinematics::RevoluteJoint
get_rotation_keys() :
IMP::core::RigidBody
get_rotational_derivatives() :
IMP::core::RigidBody
get_rotational_diffusion_coefficient() :
IMP::atom::RigidBodyDiffusion
get_rotational_diffusion_coefficient_key() :
IMP::atom::RigidBodyDiffusion
get_rsig() :
IMP::em::KernelParameters
get_rsigsq() :
IMP::em::KernelParameters
get_sample() :
IMP::atom::BrownianDynamics
,
IMP::kinematics::DOFsSampler
get_sample_assignments() :
IMP::domino::DiscreteSampler
get_sample_assignments_for_vertex() :
IMP::domino::DominoSampler
get_score() :
IMP::domino::RestraintCache
,
IMP::em2d::RegistrationResult
,
IMP::em2d::ScoreFunction
,
IMP::em::FittingSolutions
,
IMP::Restraint
,
IMP::score_functor::Score
get_score_and_derivative() :
IMP::score_functor::Score
get_score_and_derivative_with_cache() :
IMP::score_functor::ScoreWithCache
get_score_functor() :
IMP::score_functor::DistancePairScore< DistanceScoreT >
,
IMP::score_functor::DistancePairScoreWithCache< DistanceScoreT >
get_score_threshold() :
IMP::core::MonteCarlo
get_score_with_cache() :
IMP::score_functor::ScoreWithCache
get_scores() :
IMP.spatiotemporal.graphNode.graphNode
get_scoring() :
IMP::npctransport::SimulationData
get_scoring_function() :
IMP.EMageFit.domino_model.DominoModel
,
IMP::npctransport::Scoring
,
IMP::Optimizer
,
IMP::Sampler
get_scoring_function_restraints() :
IMP::npctransport::Scoring
get_sd() :
IMP::npctransport::Scoring
,
IMP::npctransport::Statistics
get_second_derivative_matrix() :
IMP::isd::BivariateFunction
,
IMP::isd::Covariance1DFunction
get_second_derivative_vector() :
IMP::isd::GeneralizedGuinierPorodFunction
,
IMP::isd::Linear1DFunction
,
IMP::isd::UnivariateFunction
get_secondary_structure_is_set() :
IMP::multifit::AnchorsData
get_segment_3d_geometry() :
IMP::algebra::Segment3D
get_segment_starting_at() :
IMP::algebra::Line3D
get_selected_particle_indexes() :
IMP::atom::Selection
get_selected_particles() :
IMP::atom::Selection
get_sequence() :
IMP::atom::Chain
get_sequence_key() :
IMP::atom::Chain
get_sequence_offset() :
IMP::atom::Chain
get_sequence_offset_key() :
IMP::atom::Chain
get_setup_keys() :
IMP.pmi.io.crosslink.CrossLinkDataBaseKeywordsConverter
,
IMP.pmi1.io.crosslink.CrossLinkDataBaseKeywordsConverter
get_Sigma_condition_number() :
IMP::isd::MultivariateFNormalSufficient
get_Sigma_eigenvalues() :
IMP::isd::MultivariateFNormalSufficient
get_simulation_data() :
IMP::npctransport::ParticleFactory
get_simulation_particle_indexes() :
IMP::atom::Simulator
get_simulation_particles() :
IMP::atom::Simulator
get_site_centers() :
IMP::npctransport::SimulationData
get_site_display_radius() :
IMP::npctransport::SimulationData
get_site_interactions_statistics() :
IMP::npctransport::Scoring
get_sites() :
IMP::npctransport::SimulationData
get_sites_k() :
IMP::npctransport::SitesPairScore
get_sites_range() :
IMP::npctransport::SitesPairScore
get_size() :
IMP::rotamer::ResidueRotamer
get_slab_particle() :
IMP::npctransport::SimulationData
get_slab_restraint() :
IMP::npctransport::Scoring
get_slice() :
IMP::domino::RestraintCache
get_slope() :
IMP::bayesianem::GaussianEMRestraint
,
IMP::isd::GaussianEMRestraint
get_software_name() :
IMP::core::SoftwareProvenance
get_solutions() :
IMP.EMageFit.solutions_io.ResultsDB
get_solutions_from_list() :
IMP.EMageFit.solutions_io.ResultsDB
get_solutions_results_table() :
IMP.EMageFit.solutions_io.ResultsDB
get_solvent_accessibility() :
IMP::saxs::SolventAccessibleSurface
get_source_chain_id() :
IMP::atom::StructureSource
get_source_id() :
IMP::atom::StructureSource
get_source_protein1() :
IMP::isd::CrossLinkMSRestraint
get_source_protein2() :
IMP::isd::CrossLinkMSRestraint
get_source_residue1() :
IMP::isd::CrossLinkMSRestraint
get_source_residue2() :
IMP::isd::CrossLinkMSRestraint
get_spacing() :
IMP::em::DensityHeader
,
IMP::em::DensityMap
get_sphere() :
IMP::core::XYZR
,
IMP::misc::CustomXYZR
get_sphere_depth() :
IMP::npc::SlabWithSphericalIndent
get_sphere_depth_key() :
IMP::npc::SlabWithSphericalIndent
get_sphere_derivatives_numpy() :
IMP::Model
get_sphere_patch_3d_geometry() :
IMP::algebra::SpherePatch3D
get_sphere_radius() :
IMP::npc::SlabWithSphericalIndent
get_sphere_radius_key() :
IMP::npc::SlabWithSphericalIndent
get_spheres_numpy() :
IMP::Model
get_sq2pi3() :
IMP::em::KernelParameters
get_square_root_distances() :
IMP::saxs::RadialDistributionFunction
get_squared_distance_to_centers() :
IMP::kmeans::KMeans
get_standard_deviation() :
IMP::statistics::ChiSquareMetric
get_starting_radius() :
IMP::em2d::PolarResamplingParameters
get_state() :
IMP.pmi.topology.Molecule
get_states() :
IMP.pmi.topology.System
get_static_info() :
IMP::bayesianem::GaussianEMRestraint
,
IMP::em2d::PCAFitRestraint
,
IMP::isd::CrossLinkMSRestraint
,
IMP::isd::GaussianEMRestraint
,
IMP::isd::UniformPrior
,
IMP::npc::MembraneExclusionRestraint
,
IMP::npc::MembraneSurfaceLocationConditionalRestraint
,
IMP::npc::MembraneSurfaceLocationRestraint
,
IMP::npc::OverallPositionRestraint
,
IMP::npc::XAxialPositionLowerRestraint
,
IMP::npc::XAxialPositionRestraint
,
IMP::npc::XAxialPositionUpperRestraint
,
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::pmi::CrossLinkRestraintSet
,
IMP::Restraint
,
IMP::saxs::Restraint
get_statistics() :
IMP::npctransport::SimulationData
get_statistics_fraction() :
IMP::npctransport::SimulationData
get_step_size() :
IMP::kinematics::DOF
get_stiffness() :
IMP::atom::Angle
,
IMP::atom::Bond
,
IMP::atom::Dihedral
get_stream() :
IMP::display::TextWriter
get_strength() :
IMP::domino::EqualitySubsetFilterTable
,
IMP::domino::EquivalenceAndExclusionSubsetFilterTable
,
IMP::domino::EquivalenceSubsetFilterTable
,
IMP::domino::ExclusionSubsetFilterTable
,
IMP::domino::ListSubsetFilterTable
,
IMP::domino::MinimumRestraintScoreSubsetFilterTable
,
IMP::domino::PairListSubsetFilterTable
,
IMP::domino::ProbabilisticSubsetFilterTable
,
IMP::domino::RestraintScoreSubsetFilterTable
,
IMP::domino::SubsetFilterTable
,
IMP::em2d::DistanceFilterTable
,
IMP::example::ExampleSubsetFilterTable
get_string() :
IMP::Key< ID >
get_string_key() :
IMP::RestraintInfo
get_string_value() :
IMP::RestraintInfo
get_strings_key() :
IMP::RestraintInfo
get_strings_value() :
IMP::RestraintInfo
get_subcomplex_components() :
IMP.spatiotemporal.graphNode.graphNode
get_subset() :
IMP::domino::ParticleStatesTable
get_subset_filter() :
IMP::domino::EqualitySubsetFilterTable
,
IMP::domino::EquivalenceAndExclusionSubsetFilterTable
,
IMP::domino::EquivalenceSubsetFilterTable
,
IMP::domino::ExclusionSubsetFilterTable
,
IMP::domino::ListSubsetFilterTable
,
IMP::domino::MinimumRestraintScoreSubsetFilterTable
,
IMP::domino::PairListSubsetFilterTable
,
IMP::domino::ProbabilisticSubsetFilterTable
,
IMP::domino::RestraintScoreSubsetFilterTable
,
IMP::domino::SubsetFilterTable
,
IMP::em2d::DistanceFilterTable
,
IMP::example::ExampleSubsetFilterTable
get_sufficient_statistics() :
IMP::isd::vonMisesSufficient
get_sumFX() :
IMP::isd::FStudentT
get_super_rigid_bodies() :
IMP.pmi.topology.TopologyReader
,
IMP.pmi1.topology.TopologyReader
get_surface() :
IMP::core::SurfaceMover
get_surface_area() :
IMP::algebra::Cone3D
,
IMP::algebra::Cylinder3D
,
IMP::algebra::Ellipsoid3D
,
IMP::algebra::Torus3D
get_surface_point_at() :
IMP::algebra::Cylinder3D
get_symm_axis_alignments_from_model_to_density() :
IMP::cnmultifit::AlignSymmetric
get_table() :
IMP.EMageFit.database.Database2
get_table_column_names() :
IMP.EMageFit.database.Database2
get_table_types() :
IMP.EMageFit.database.Database2
get_temperature() :
IMP::atom::Simulator
get_temperature_scale_factor() :
IMP::atom::TAMDParticle
get_temperature_scale_factor_key() :
IMP::atom::TAMDParticle
get_thickness() :
IMP::npc::SlabWithPore
,
IMP::npctransport::SlabWithPore
get_thickness_key() :
IMP::npc::SlabWithPore
,
IMP::npctransport::SlabWithPore
get_threshold() :
IMP::core::FilterProvenance
get_time() :
IMP.spatiotemporal.graphNode.graphNode
get_timessig() :
IMP::em::KernelParameters
get_tip() :
IMP::algebra::Cone3D
get_tmp_file_name() :
IMP.test.TestCase
get_top() :
IMP::em::DensityHeader
get_top_z() :
IMP::npctransport::ExcludeZRangeSingletonScore
get_toroidal_pore_key() :
IMP::npc::SlabWithToroidalPore
,
IMP::npctransport::SlabWithToroidalPore
get_torque() :
IMP::core::RigidBody
get_torus_3d_geometry() :
IMP::algebra::Torus3D
get_torus_distance() :
IMP::algebra::Torus3D
get_total_count() :
IMP::statistics::HistogramD< D, Grid >
get_total_n_transports() :
IMP::npctransport::ParticleTransportStatisticsOptimizerState
get_traits() :
IMP::atom::Hierarchy
get_transformation() :
IMP::em2d::PCAFitRestraint
,
IMP::em::FittingSolutions
get_transformation_child_to_parent() :
IMP::kinematics::Joint
get_transformation_child_to_parent_no_checks() :
IMP::kinematics::Joint
get_transformation_from() :
IMP::algebra::ReferenceFrame3D
get_transformation_to() :
IMP::algebra::ReferenceFrame3D
get_transformed() :
IMP::algebra::Transformation2D
,
IMP::algebra::Transformation3D
,
IMP::em::DensityMap
get_transformed_adjoint() :
IMP::algebra::Transformation3D
get_transformed_into() :
IMP::em::DensityMap
get_translation() :
IMP::algebra::Transformation2D
,
IMP::algebra::Transformation3D
get_translation_x() :
IMP::em2d::ProjectionParameters
get_translation_y() :
IMP::em2d::ProjectionParameters
get_transport_time_points_in_ns() :
IMP::npctransport::ParticleTransportStatisticsOptimizerState
get_trigger_last_updated() :
IMP::Model
get_trimmed_atom_name() :
IMP::atom::PDBRecord
get_tunnel_radius() :
IMP::npctransport::SimulationData
get_tunnel_radius_k() :
IMP::npctransport::SimulationData
get_type() :
IMP::atom::Bond
get_type_changed_key() :
IMP::atom::Residue
get_type_name() :
IMP::em2d::Image
,
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_unary_function() :
IMP::core::GenericAttributeSingletonScore< UF >
get_uniprot_accession() :
IMP::atom::Chain
get_uniprot_accession_key() :
IMP::atom::Chain
get_unique_id() :
IMP::Model
get_unit_cell() :
IMP::algebra::DefaultEmbeddingD< D >
,
IMP::algebra::LogEmbeddingD< D >
get_unit_simplex() :
IMP::isd::Weight
get_vacuum_form_factor() :
IMP::saxs::FormFactorTable
get_vacuum_form_factors() :
IMP::saxs::FormFactorTable
get_vacuum_water_form_factor() :
IMP::saxs::FormFactorTable
get_value() :
IMP::core::OrderedTypePairPredicate
,
IMP::core::OrderedTypeQuadPredicate
,
IMP::core::OrderedTypeSingletonPredicate
,
IMP::core::OrderedTypeTripletPredicate
,
IMP::em::DensityMap
get_value_index() :
IMP::atom::BondedPairFilter
,
IMP::atom::SameResiduePairFilter
,
IMP::atom::SoapPairFilter
,
IMP::atom::StereochemistryPairFilter
,
IMP::container::ConsecutivePairFilter
,
IMP::container::ExclusiveConsecutivePairFilter
,
IMP::container::InContainerPairFilter
,
IMP::container::InContainerQuadFilter
,
IMP::container::InContainerSingletonFilter
,
IMP::container::InContainerTripletFilter
,
IMP::core::AllSamePairPredicate
,
IMP::core::AllSameQuadPredicate
,
IMP::core::AllSameSingletonPredicate
,
IMP::core::AllSameTripletPredicate
,
IMP::core::AttributeSingletonPredicate
,
IMP::core::CoinFlipPairPredicate
,
IMP::core::CoinFlipQuadPredicate
,
IMP::core::CoinFlipSingletonPredicate
,
IMP::core::CoinFlipTripletPredicate
,
IMP::core::ConstantPairPredicate
,
IMP::core::ConstantQuadPredicate
,
IMP::core::ConstantSingletonPredicate
,
IMP::core::ConstantTripletPredicate
,
IMP::core::InBoundingBox3DSingletonPredicate
,
IMP::core::IsCollisionPairPredicate
,
IMP::core::OrderedTypePairPredicate
,
IMP::core::OrderedTypeQuadPredicate
,
IMP::core::OrderedTypeSingletonPredicate
,
IMP::core::OrderedTypeTripletPredicate
,
IMP::core::UnorderedTypePairPredicate
,
IMP::core::UnorderedTypeQuadPredicate
,
IMP::core::UnorderedTypeSingletonPredicate
,
IMP::core::UnorderedTypeTripletPredicate
,
IMP::misc::CommonEndpointPairFilter
,
IMP::PairPredicate
,
IMP::QuadPredicate
,
IMP::SingletonPredicate
,
IMP::spb::SameParticlePairFilter
,
IMP::spb::SameRigidBodyPairFilter
,
IMP::TripletPredicate
get_value_index_in_batch() :
IMP::core::OrderedTypePairPredicate
,
IMP::core::OrderedTypeQuadPredicate
,
IMP::core::OrderedTypeSingletonPredicate
,
IMP::core::OrderedTypeTripletPredicate
,
IMP::PairPredicate
,
IMP::QuadPredicate
,
IMP::SingletonPredicate
,
IMP::TripletPredicate
get_values() :
IMP.pmi.io.crosslink.CrossLinkDataBase
get_variances() :
IMP::core::Gaussian
get_vector_to() :
IMP::core::XYZ
get_version() :
IMP::core::SoftwareProvenance
get_version_info() :
IMP::algebra::DynamicNearestNeighbor3D
,
IMP::algebra::EuclideanVectorKDMetric
,
IMP::algebra::MaxVectorKDMetric
,
IMP::algebra::NearestNeighborD< D >
,
IMP::atom::AllPDBSelector
,
IMP::atom::AndPDBSelector
,
IMP::atom::AngleSingletonScore
,
IMP::atom::ATOMPDBSelector
,
IMP::atom::AtomTypePDBSelector
,
IMP::atom::BackbonePDBSelector
,
IMP::atom::BerendsenThermostatOptimizerState
,
IMP::atom::BondedPairFilter
,
IMP::atom::BondEndpointsRefiner
,
IMP::atom::BondGeometry
,
IMP::atom::BondPairContainer
,
IMP::atom::BondsGeometry
,
IMP::atom::BondSingletonScore
,
IMP::atom::BrownianDynamics
,
IMP::atom::CAAngleRestraint
,
IMP::atom::CADihedralRestraint
,
IMP::atom::CAlphaPDBSelector
,
IMP::atom::CBetaPDBSelector
,
IMP::atom::ChainPDBSelector
,
IMP::atom::CHARMMIdealResidueTopology
,
IMP::atom::CHARMMParameters
,
IMP::atom::CHARMMPatch
,
IMP::atom::CHARMMResidueTopology
,
IMP::atom::CHARMMResidueTopologyBase
,
IMP::atom::CHARMMSegmentTopology
,
IMP::atom::CHARMMStereochemistryRestraint
,
IMP::atom::CHARMMTopology
,
IMP::atom::CoulombPairScore
,
IMP::atom::CoverBond
,
IMP::atom::CPDBSelector
,
IMP::atom::DihedralSingletonScore
,
IMP::atom::EzRestraint
,
IMP::atom::ForceSwitch
,
IMP::atom::HelixRestraint
,
IMP::atom::HierarchiesGeometry
,
IMP::atom::HierarchyGeometry
,
IMP::atom::HydrogenPDBSelector
,
IMP::atom::ImproperSingletonScore
,
IMP::atom::LangevinThermostatOptimizerState
,
IMP::atom::LennardJonesPairScore
,
IMP::atom::MolecularDynamics
,
IMP::atom::NonAlternativePDBSelector
,
IMP::atom::NonHydrogenPDBSelector
,
IMP::atom::NonWaterNonHydrogenPDBSelector
,
IMP::atom::NonWaterPDBSelector
,
IMP::atom::NotPDBSelector
,
IMP::atom::NPDBSelector
,
IMP::atom::OrPDBSelector
,
IMP::atom::PPDBSelector
,
IMP::atom::RemoveRigidMotionOptimizerState
,
IMP::atom::RemoveTranslationOptimizerState
,
IMP::atom::ResidueTypePDBSelector
,
IMP::atom::SameResiduePairFilter
,
IMP::atom::SelectionGeometry
,
IMP::atom::SoapPairFilter
,
IMP::atom::StereochemistryPairFilter
,
IMP::atom::VelocityScalingOptimizerState
,
IMP::atom::WaterPDBSelector
,
IMP::atom::WritePDBOptimizerState
,
IMP::atom::XorPDBSelector
,
IMP::bayesianem::GaussianEMRestraint
,
IMP::Configuration
,
IMP::ConfigurationSet
,
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::DynamicListPairContainer
,
IMP::container::DynamicListQuadContainer
,
IMP::container::DynamicListSingletonContainer
,
IMP::container::DynamicListTripletContainer
,
IMP::container::EventPairsOptimizerState
,
IMP::container::EventQuadsOptimizerState
,
IMP::container::EventSingletonsOptimizerState
,
IMP::container::EventTripletsOptimizerState
,
IMP::container::ExclusiveConsecutivePairContainer
,
IMP::container::ExclusiveConsecutivePairFilter
,
IMP::container::InContainerPairFilter
,
IMP::container::InContainerQuadFilter
,
IMP::container::InContainerSingletonFilter
,
IMP::container::InContainerTripletFilter
,
IMP::container::ListPairContainer
,
IMP::container::ListQuadContainer
,
IMP::container::ListSingletonContainer
,
IMP::container::ListTripletContainer
,
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::PairContainerSet
,
IMP::container::PairContainerStatistics
,
IMP::container::PairsConstraint
,
IMP::container::PairsOptimizerState
,
IMP::container::PairsRestraint
,
IMP::container::PredicatePairsRestraint
,
IMP::container::PredicateQuadsRestraint
,
IMP::container::PredicateSingletonsRestraint
,
IMP::container::PredicateTripletsRestraint
,
IMP::container::QuadContainerSet
,
IMP::container::QuadContainerStatistics
,
IMP::container::QuadsConstraint
,
IMP::container::QuadsOptimizerState
,
IMP::container::QuadsRestraint
,
IMP::container::SingletonContainerSet
,
IMP::container::SingletonContainerStatistics
,
IMP::container::SingletonsConstraint
,
IMP::container::SingletonsOptimizerState
,
IMP::container::SingletonsRestraint
,
IMP::container::TripletContainerSet
,
IMP::container::TripletContainerStatistics
,
IMP::container::TripletsConstraint
,
IMP::container::TripletsOptimizerState
,
IMP::container::TripletsRestraint
,
IMP::core::AllSamePairPredicate
,
IMP::core::AllSameQuadPredicate
,
IMP::core::AllSameSingletonPredicate
,
IMP::core::AllSameTripletPredicate
,
IMP::core::AngleRestraint
,
IMP::core::AngleTripletScore
,
IMP::core::AttributeSingletonPredicate
,
IMP::core::BallMover
,
IMP::core::BoxSweepClosePairsFinder
,
IMP::core::CentroidOfRefined
,
IMP::core::ChecksScoreState
,
IMP::core::ChildrenRefiner
,
IMP::core::ClosedCubicSpline
,
IMP::core::ClosePairsPairScore
,
IMP::core::CoinFlipPairPredicate
,
IMP::core::CoinFlipQuadPredicate
,
IMP::core::CoinFlipSingletonPredicate
,
IMP::core::CoinFlipTripletPredicate
,
IMP::core::ConjugateGradients
,
IMP::core::ConnectivityRestraint
,
IMP::core::ConstantPairPredicate
,
IMP::core::ConstantQuadPredicate
,
IMP::core::ConstantRestraint
,
IMP::core::ConstantSingletonPredicate
,
IMP::core::ConstantTripletPredicate
,
IMP::core::Cosine
,
IMP::core::CoverRefined
,
IMP::core::DerivativesFromRefined
,
IMP::core::DerivativesToRefined
,
IMP::core::DiameterRestraint
,
IMP::core::DihedralRestraint
,
IMP::core::DirectionMover
,
IMP::core::DistancePairScore
,
IMP::core::EdgePairGeometry
,
IMP::core::EdgePairsGeometry
,
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::Harmonic
,
IMP::core::HarmonicDistancePairScore
,
IMP::core::HarmonicLowerBound
,
IMP::core::HarmonicSphereDistancePairScore
,
IMP::core::HarmonicSurfaceDepthPairScore
,
IMP::core::HarmonicSurfaceDistancePairScore
,
IMP::core::HarmonicSurfaceHeightPairScore
,
IMP::core::HarmonicUpperBound
,
IMP::core::HarmonicUpperBoundSphereDiameterPairScore
,
IMP::core::HarmonicUpperBoundSphereDistancePairScore
,
IMP::core::HarmonicWell
,
IMP::core::InBoundingBox3DSingletonPredicate
,
IMP::core::IsCollisionPairPredicate
,
IMP::core::KClosePairsPairScore
,
IMP::core::LateralSurfaceConstraint
,
IMP::core::LeavesRefiner
,
IMP::core::Linear
,
IMP::core::LogNormalMover
,
IMP::core::MCCGSampler
,
IMP::core::MinimumRestraint
,
IMP::core::MonteCarlo
,
IMP::core::MonteCarloWithBasinHopping
,
IMP::core::MonteCarloWithLocalOptimization
,
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::RigidBodyDerivativeGeometry
,
IMP::core::RigidBodyDerivativesGeometry
,
IMP::core::RigidBodyFrameGeometry
,
IMP::core::RigidBodyFramesGeometry
,
IMP::core::RigidBodyHierarchyGeometry
,
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::SteepestDescent
,
IMP::core::SubsetMover
,
IMP::core::SurfaceDepthPairScore
,
IMP::core::SurfaceDistancePairScore
,
IMP::core::SurfaceGeometry
,
IMP::core::SurfaceGeometryConstraint
,
IMP::core::SurfaceHeightPairScore
,
IMP::core::SurfaceMover
,
IMP::core::SurfaceSymmetryConstraint
,
IMP::core::SurfaceTetheredChain
,
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::TruncatedHarmonic< DIRECTION >
,
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::core::WeightedSum
,
IMP::core::WeightedSumOfExponential
,
IMP::core::WriteRestraintScoresOptimizerState
,
IMP::core::XYZDerivativeGeometry
,
IMP::core::XYZDerivativesGeometry
,
IMP::core::XYZRGeometry
,
IMP::core::XYZRsGeometry
,
IMP::display::BoundingBoxGeometry
,
IMP::display::CylinderGeometry
,
IMP::display::EllipsoidGeometry
,
IMP::display::FilterGeometry
,
IMP::display::GeometrySet
,
IMP::display::LabelGeometry
,
IMP::display::PlaneGeometry
,
IMP::display::PointGeometry
,
IMP::display::PolygonGeometry
,
IMP::display::PymolWriter
,
IMP::display::ReferenceFrameGeometry
,
IMP::display::RestraintGeometry
,
IMP::display::RestraintSetGeometry
,
IMP::display::SegmentGeometry
,
IMP::display::SphereGeometry
,
IMP::display::SurfaceMeshGeometry
,
IMP::display::TriangleGeometry
,
IMP::display::WriteOptimizerState
,
IMP::domino::BranchAndBoundAssignmentsTable
,
IMP::domino::BranchAndBoundSampler
,
IMP::domino::CappedAssignmentContainer
,
IMP::domino::CompoundStates
,
IMP::domino::DependencyScoreState
,
IMP::domino::DominoSampler
,
IMP::domino::EqualitySubsetFilterTable
,
IMP::domino::EquivalenceAndExclusionSubsetFilterTable
,
IMP::domino::EquivalenceSubsetFilterTable
,
IMP::domino::ExclusionSubsetFilterTable
,
IMP::domino::HeapAssignmentContainer
,
IMP::domino::IndexStates
,
IMP::domino::ListAssignmentContainer
,
IMP::domino::ListAssignmentsTable
,
IMP::domino::ListSubsetFilterTable
,
IMP::domino::MinimumRestraintScoreSubsetFilterTable
,
IMP::domino::NestedRigidBodyStates
,
IMP::domino::PackedAssignmentContainer
,
IMP::domino::PairListSubsetFilterTable
,
IMP::domino::ParticleStatesTable
,
IMP::domino::PermutationStates
,
IMP::domino::ProbabilisticSubsetFilterTable
,
IMP::domino::RangeViewAssignmentContainer
,
IMP::domino::ReadAssignmentContainer
,
IMP::domino::ReadHDF5AssignmentContainer
,
IMP::domino::RecursiveAssignmentsTable
,
IMP::domino::RecursiveStates
,
IMP::domino::RestraintCache
,
IMP::domino::RestraintScoreSubsetFilterTable
,
IMP::domino::RigidBodyStates
,
IMP::domino::SampleAssignmentContainer
,
IMP::domino::SimpleAssignmentsTable
,
IMP::domino::WriteAssignmentContainer
,
IMP::domino::WriteHDF5AssignmentContainer
,
IMP::domino::XYZStates
,
IMP::em2d::CollisionCrossSection
,
IMP::em2d::DistanceFilter
,
IMP::em2d::DistanceFilterTable
,
IMP::em2d::DummyRestraint
,
IMP::em2d::Em2DRestraint
,
IMP::em2d::GridStates
,
IMP::em2d::Image
,
IMP::em2d::ImageReaderWriter
,
IMP::em2d::JPGImageReaderWriter
,
IMP::em2d::ParticlesDummyRestraint
,
IMP::em2d::PCAFitRestraint
,
IMP::em2d::ProjectionFinder
,
IMP::em2d::ProjectionParametersScoreState
,
IMP::em2d::ProjectionStates
,
IMP::em2d::RelativePositionMover
,
IMP::em2d::RigidBodiesImageFitRestraint
,
IMP::em2d::ScoreFunction
,
IMP::em2d::SpiderImageReaderWriter
,
IMP::em2d::TIFFImageReaderWriter
,
IMP::em::CoarseCCatIntervals
,
IMP::em::DensityFillingRestraint
,
IMP::em::DensityMap
,
IMP::em::EMReaderWriter
,
IMP::em::EnvelopeFitRestraint
,
IMP::em::EnvelopePenetrationRestraint
,
IMP::em::EnvelopeScore
,
IMP::em::FitRestraint
,
IMP::em::FitRestraintBayesEM3D
,
IMP::em::HighDensityEmbedding
,
IMP::em::MapReaderWriter
,
IMP::em::MRCReaderWriter
,
IMP::em::PCAAligner
,
IMP::em::PCAFitRestraint
,
IMP::em::SpiderMapReaderWriter
,
IMP::em::XplorReaderWriter
,
IMP::example::ExampleComplexRestraint
,
IMP::example::ExampleConstraint
,
IMP::example::ExampleObject
,
IMP::example::ExamplePairScore
,
IMP::example::ExampleRestraint
,
IMP::example::ExampleSingletonModifier
,
IMP::example::ExampleSubsetFilterTable
,
IMP::example::ExampleUnaryFunction
,
IMP::gsl::ConjugateGradients
,
IMP::gsl::QuasiNewton
,
IMP::gsl::Simplex
,
IMP::isd::AmbiguousNOERestraint
,
IMP::isd::AmbiguousRestraint
,
IMP::isd::AtomicCrossLinkMSRestraint
,
IMP::isd::Covariance1DFunction
,
IMP::isd::CrossLinkData
,
IMP::isd::CrossLinkMSRestraint
,
IMP::isd::CysteineCrossLinkData
,
IMP::isd::CysteineCrossLinkRestraint
,
IMP::isd::Distribution
,
IMP::isd::FNormal
,
IMP::isd::FretData
,
IMP::isd::FretRestraint
,
IMP::isd::FStudentT
,
IMP::isd::GammaPrior
,
IMP::isd::GaussianAnchorEMRestraint
,
IMP::isd::GaussianEMRestraint
,
IMP::isd::GaussianProcessInterpolation
,
IMP::isd::GaussianProcessInterpolationRestraint
,
IMP::isd::GaussianRestraint
,
IMP::isd::GeneralizedGuinierPorodFunction
,
IMP::isd::HybridMonteCarlo
,
IMP::isd::ISDRestraint
,
IMP::isd::JeffreysRestraint
,
IMP::isd::Linear1DFunction
,
IMP::isd::LognormalAmbiguousRestraint
,
IMP::isd::LognormalRestraint
,
IMP::isd::LogWrapper
,
IMP::isd::MarginalHBondRestraint
,
IMP::isd::MarginalNOERestraint
,
IMP::isd::MolecularDynamicsMover
,
IMP::isd::MultivariateFNormalSufficient
,
IMP::isd::NOERestraint
,
IMP::isd::NormalSigmaPCRestraint
,
IMP::isd::OneDimensionalDistribution
,
IMP::isd::OneDimensionalSufficientDistribution
,
IMP::isd::PenalizedComplexityPrior
,
IMP::isd::RepulsiveDistancePairScore
,
IMP::isd::ResidueProteinProximityRestraint
,
IMP::isd::StudentTRestraint
,
IMP::isd::TALOSRestraint
,
IMP::isd::UniformPrior
,
IMP::isd::vonMises
,
IMP::isd::vonMisesKappaConjugateRestraint
,
IMP::isd::vonMisesKappaJeffreysRestraint
,
IMP::isd::vonMisesSufficient
,
IMP::isd::WeightMover
,
IMP::isd::WeightRestraint
,
IMP::kinematics::DihedralMover
,
IMP::kinematics::DirectionalDOF
,
IMP::kinematics::DOF
,
IMP::kinematics::DOFsSampler
,
IMP::kinematics::Joint
,
IMP::kinematics::KinematicForest
,
IMP::kinematics::KinematicForestScoreState
,
IMP::kinematics::LocalPlanner
,
IMP::kinematics::ProteinKinematics
,
IMP::kinematics::RevoluteJointMover
,
IMP::kinematics::RRT
,
IMP::kmeans::KMeans
,
IMP::misc::CommonEndpointPairFilter
,
IMP::misc::DecayPairContainerOptimizerState
,
IMP::misc::FreelyJointedChain
,
IMP::misc::LogPairScore
,
IMP::misc::LowestRefinedPairScore
,
IMP::misc::MetricClosePairsFinder< LowerBound, UpperBound >
,
IMP::misc::SoftCylinderPairScore
,
IMP::misc::StateAdaptor
,
IMP::misc::WormLikeChain
,
IMP::Model
,
IMP::mpi::ReplicaExchange
,
IMP::multifit::AssemblyHeader
,
IMP::multifit::ComplementarityRestraint
,
IMP::multifit::ComponentHeader
,
IMP::multifit::DummyRestraint
,
IMP::multifit::Ensemble
,
IMP::multifit::FFTFitting
,
IMP::multifit::FFTFittingOutput
,
IMP::multifit::FittingStates
,
IMP::multifit::ProbabilisticAnchorGraph
,
IMP::multifit::ProteomicsData
,
IMP::multifit::ProteomicsEMAlignmentAtomic
,
IMP::multifit::RadiusOfGyrationRestraint
,
IMP::multifit::RigidLeavesRefiner
,
IMP::multifit::SettingsData
,
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::OverallPositionRestraint
,
IMP::npc::PerinuclearVolumeLocationRestraint
,
IMP::npc::PoreSideVolumeLocationRestraint
,
IMP::npc::ProteinChainRestraint
,
IMP::npc::ProteinContactRestraint
,
IMP::npc::ProteinProximityRestraint
,
IMP::npc::SlabWithSphericalIndentGeometry
,
IMP::npc::SlabWithSphericalIndentMBMScore
,
IMP::npc::SlabWithToroidalPoreGoPairScore
,
IMP::npc::SlabWithToroidalPoreMBMScore
,
IMP::npc::SlabWithToroidalPoreWireGeometry
,
IMP::npc::SphericalIndentSurfaceDepthPairScore
,
IMP::npc::ToroidalPoreSurfaceDepthPairScore
,
IMP::npc::XAxialPositionLowerRestraint
,
IMP::npc::XAxialPositionRestraint
,
IMP::npc::XAxialPositionUpperRestraint
,
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::BipartitePairsStatisticsOptimizerState
,
IMP::npctransport::BodyStatisticsOptimizerState
,
IMP::npctransport::ChainStatisticsOptimizerState
,
IMP::npctransport::ExcludeZRangeSingletonScore
,
IMP::npctransport::FGChain
,
IMP::npctransport::FunctorLinearInteractionPairScore
,
IMP::npctransport::FunctorLinearSoftSpherePairScore
,
IMP::npctransport::GlobalStatisticsOptimizerState
,
IMP::npctransport::HarmonicSpringSingletonScore
,
IMP::npctransport::HarmonicWellPairScore
,
IMP::npctransport::LinearInteractionPairScore
,
IMP::npctransport::LinearSoftSpherePairScore
,
IMP::npctransport::LinearWellPairScore
,
IMP::npctransport::ParticleFactory
,
IMP::npctransport::ParticleTransportStatisticsOptimizerState
,
IMP::npctransport::Scoring
,
IMP::npctransport::SimulationData
,
IMP::npctransport::SitesGeometry
,
IMP::npctransport::SitesPairScore
,
IMP::npctransport::SlabWithCylindricalPorePairScore
,
IMP::npctransport::SlabWithCylindricalPoreWireGeometry
,
IMP::npctransport::SlabWithToroidalPorePairScore
,
IMP::npctransport::SlabWithToroidalPoreWireGeometry
,
IMP::npctransport::Statistics
,
IMP::npctransport::TypedSitesGeometry
,
IMP::npctransport::ZBiasSingletonScore
,
IMP::Object
,
IMP::Particle
,
IMP::pmi1::CompositeRestraint
,
IMP::pmi1::InternalCoordinatesConstraint
,
IMP::pmi1::MembraneRestraint
,
IMP::pmi1::SigmoidRestraintSphere
,
IMP::pmi1::TransformMover
,
IMP::pmi::CompositeRestraint
,
IMP::pmi::CrossLinkRestraintSet
,
IMP::pmi::MembraneRestraint
,
IMP::pmi::TransformMover
,
IMP::RestraintInfo
,
IMP::RestraintSet
,
IMP::rmf::HierarchyLoadLink
,
IMP::rmf::HierarchySaveLink
,
IMP::rmf::SaveOptimizerState
,
IMP::rotamer::RotamerCalculator
,
IMP::rotamer::RotamerLibrary
,
IMP::SaveToConfigurationSetOptimizerState
,
IMP::saxs::ChiScore
,
IMP::saxs::ChiScoreLog
,
IMP::saxs::Profile
,
IMP::saxs::RadiusOfGyrationRestraint
,
IMP::saxs::RatioVolatilityScore
,
IMP::saxs::Restraint
,
IMP::saxs::RigidBodiesProfileHandler
,
IMP::score_functor::DistancePairScore< DistanceScoreT >
,
IMP::score_functor::DistancePairScoreWithCache< DistanceScoreT >
,
IMP::score_functor::ScoreUnaryFunction< Score, D >
,
IMP::score_functor::SurfaceDistancePairScore< DistanceScoreT >
,
IMP::spb::AttributeDistancePairScore
,
IMP::spb::BoxedMover
,
IMP::spb::CellMover
,
IMP::spb::ChiSquareMetric
,
IMP::spb::ContactMapMetric
,
IMP::spb::DiameterRgyrRestraint
,
IMP::spb::DistanceRMSDMetric
,
IMP::spb::DistanceTerminiRestraint
,
IMP::spb::EM2DRestraint
,
IMP::spb::Gaussian
,
IMP::spb::KinkPairScore
,
IMP::spb::MonteCarloWithWte
,
IMP::spb::NuisanceRangeModifier
,
IMP::spb::PbcBoxedMover
,
IMP::spb::PbcBoxedRigidBodyMover
,
IMP::spb::RigidBodyNewMover
,
IMP::spb::RMSDMetric
,
IMP::spb::SameParticlePairFilter
,
IMP::spb::SameRigidBodyPairFilter
,
IMP::spb::TiltSingletonScore
,
IMP::spb::TransformationSymmetry
,
IMP::spb::TwoStateGoModelRestraint
,
IMP::spb::UniformBoundedRestraint
,
IMP::statistics::ChiSquareMetric
,
IMP::statistics::ConfigurationSetRMSDMetric
,
IMP::statistics::ConfigurationSetXYZEmbedding
,
IMP::statistics::EuclideanMetric
,
IMP::statistics::ParticleEmbedding
,
IMP::statistics::PartitionalClusteringWithCenter
,
IMP::statistics::RecursivePartitionalClusteringEmbedding
,
IMP::statistics::RecursivePartitionalClusteringMetric
,
IMP::statistics::VectorDEmbedding
,
IMP::symmetry::BallMover
,
IMP::symmetry::RigidBodyMover
get_vertex_assignments() :
IMP::domino::DominoSampler
get_volume() :
IMP::algebra::Cone3D
,
IMP::algebra::Cylinder3D
,
IMP::algebra::Ellipsoid3D
,
IMP::algebra::Torus3D
,
IMP::saxs::FormFactorTable
get_voxel_by_location() :
IMP::em::DensityMap
get_was_good() :
IMP::Restraint
get_water_dummy_form_factors() :
IMP::saxs::FormFactorTable
get_water_form_factor() :
IMP::saxs::FormFactorTable
get_water_form_factors() :
IMP::saxs::FormFactorTable
get_water_vacuum_form_factors() :
IMP::saxs::FormFactorTable
get_weight() :
IMP::core::WeightedSum
,
IMP::core::WeightedSumOfExponential
,
IMP::isd::Weight
,
IMP.spatiotemporal.graphNode.graphNode
,
IMP::statistics::Embedding
,
IMP::statistics::Metric
get_weight_derivative() :
IMP::isd::Weight
get_weight_key() :
IMP::isd::Weight
get_weight_keys() :
IMP::isd::Weight
get_weights() :
IMP::core::WeightedSum
,
IMP::core::WeightedSumOfExponential
,
IMP::isd::Weight
get_weights_are_optimized() :
IMP::isd::Weight
get_weights_derivatives() :
IMP::isd::Weight
get_x() :
IMP::core::XYZ
get_xlinks_for_pair() :
IMP.EMageFit.buildxlinks.XlinksDict
get_xorigin() :
IMP::em::DensityHeader
get_xyz_keys() :
IMP::core::XYZ
get_xyz_stats_crop_factor() :
IMP::npctransport::SimulationData
get_xyz_stats_max_box_size_A() :
IMP::npctransport::SimulationData
get_xyz_stats_voxel_size_A() :
IMP::npctransport::SimulationData
get_y() :
IMP::core::XYZ
get_yorigin() :
IMP::em::DensityHeader
get_z() :
IMP::core::XYZ
get_z_bias_restraints() :
IMP::npctransport::Scoring
get_zorigin() :
IMP::em::DensityHeader
GlobalStatisticsOptimizerState() :
IMP::npctransport::GlobalStatisticsOptimizerState
GridD() :
IMP::algebra::GridD< D, StorageT, Value, EmbeddingT >
GridStates() :
IMP::em2d::GridStates