- g -

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 >
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_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_c() : IMP::algebra::ParabolicFit2D
get_calls() : IMP::em2d::Fine2DRegistrationRestraint
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::core::StructureProvenance
get_chain_restraints() : IMP::npctransport::FGChain
get_chain_restraints_on() : IMP::npctransport::Scoring
get_chain_type() : IMP::atom::Chain
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::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
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_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_element() : IMP::atom::Atom , IMP::atom::ElementTable
get_ellipsoid_3d_geometry() : IMP::algebra::Ellipsoid3D
get_embedding() : IMP::domino::NestedRigidBodyStates , IMP::domino::ParticleStates , IMP::domino::RigidBodyStates , IMP::domino::XYZStates
get_end() : IMP::em2d::CenteredMat , 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_final_registration() : IMP::em2d::Fine2DRegistrationRestraint
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_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
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_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_in_range() : IMP::em2d::CenteredMat
get_is_last_entry_from_top() : IMP::npctransport::Transporting
get_is_last_entry_from_top_key() : IMP::npctransport::Transporting
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::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_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_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_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::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_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::npctransport::SimulationData , IMP::npctransport::SlabWithPore
get_pore_radius_k() : IMP::npctransport::SimulationData
get_pore_radius_key() : 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_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_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_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_spacing() : IMP::em::DensityHeader , IMP::em::DensityMap
get_sphere() : IMP::core::XYZR , IMP::misc::CustomXYZR
get_sphere_derivatives_numpy() : IMP::Model
get_sphere_patch_3d_geometry() : IMP::algebra::SpherePatch3D
get_spheres_numpy() : IMP::Model
get_sq2pi3() : IMP::em::KernelParameters
get_squared_distance_to_centers() : IMP::kmeans::KMeans
get_standard_deviation() : IMP::statistics::ChiSquareMetric
get_start() : IMP::em2d::CenteredMat
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::GaussianEMRestraint , IMP::isd::UniformPrior , 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_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::npctransport::SlabWithPore
get_thickness_key() : IMP::npctransport::SlabWithPore
get_threshold() : IMP::core::FilterProvenance
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::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_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_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::IncrementalScoringFunction , 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::Fine2DRegistrationRestraint , 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::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::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::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::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_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