- g -

• Gaussian() : IMP::spb::Gaussian
• GaussianAnchorEMRestraint() : IMP::isd::GaussianAnchorEMRestraint
• 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_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_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_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.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_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_contains() : IMP::algebra::BoundingBoxD< D > , IMP::algebra::Cone3D , IMP::algebra::SphereD< D > , IMP::algebra::SpherePatch3D , IMP::misc::LogPairScore
• 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_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::em::DensityMap , IMP::em::Voxel , IMP::isd::OneDimensionalDistribution , IMP::isd::OneDimensionalSufficientDistribution , IMP.pmi.analysis.GetModelDensity , IMP.pmi1.analysis.GetModelDensity
• get_depth() : IMP::core::Surface
• get_derivative() : IMP::algebra::Rotation3D , 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_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_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() : write_a_metric.MyMetric
• 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::em2d::PCAFitRestraint , IMP::isd::GaussianEMRestraint , 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_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_gradient() : 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.pmi.representation.Representation , IMP.pmi1.representation.Representation
• get_hierarchy() : IMP.pmi.topology.Molecule
• 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
• 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_inv_rsigsq() : IMP::em::KernelParameters
• get_inverse() : IMP::algebra::Rotation2D , IMP::algebra::Rotation3D , IMP::algebra::Transformation2D
• get_is_activated() : IMP::npctransport::Statistics
• 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_valid() : IMP::algebra::Rotation3D , IMP::algebra::Transformation3D , IMP::atom::Hierarchy , IMP::Decorator
• 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_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_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::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
• 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_nstates_key() : IMP::isd::Weight
• 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
• 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_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_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::isd::Weight , IMP.pmi.topology.System
• get_number_of_steps() : IMP::em2d::ClusterSet , IMP::kinematics::DOF
• get_number_of_string() : 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_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_opposite() : IMP::algebra::Line3D , IMP::algebra::Plane3D
• get_optimizable_beads() : IMP::npctransport::SimulationData
• get_order() : IMP::atom::Bond
• get_ordered_joints() : IMP::kinematics::KinematicForest
• get_orientation() : IMP::em2d::GridStates
• get_origin() : IMP::em::DensityHeader
• get_output() : IMP.pmi.analysis.RMSD , IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint , IMP.pmi.restraints.RestraintBase , 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 , IMP::SingletonContainer
• 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_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_pair() : IMP::PairContainer
• get_particle_pairs() : IMP::misc::LogPairScore , IMP::PairContainer , IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint , IMP.pmi.restraints.stereochemistry.ConnectivityRestraint , IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint , IMP.pmi1.restraints.stereochemistry.ConnectivityRestraint
• get_particle_quad() : IMP::QuadContainer
• get_particle_quads() : IMP::QuadContainer
• get_particle_triplet() : IMP::TripletContainer
• get_particle_triplets() : IMP::TripletContainer
• get_particles() : IMP::SingletonContainer
• get_particles_at_all_resolutions() : IMP.pmi.topology.Molecule
• get_particles_from_selection_tuples() : IMP.pmi.representation.Representation , IMP.pmi1.representation.Representation
• get_particles_to_sample() : IMP.pmi.restraints.crosslinking.AtomicCrossLinkMSRestraint , IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint , IMP.pmi.restraints.RestraintBase , 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_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.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::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_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
• 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_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.pmi.restraints.RestraintBase , IMP.pmi1.restraints.RestraintBase
• get_restraint_for_rmf() : IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint , IMP.pmi.restraints.RestraintBase , IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint , IMP.pmi1.restraints.RestraintBase
• get_restraint_set() : IMP::multifit::ProteomicsEMAlignmentAtomic , IMP.pmi.restraints.RestraintBase , 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_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_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_functor() : IMP::score_functor::DistancePairScore< DistanceScoreT >
• get_score_threshold() : IMP::core::MonteCarlo
• 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::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_patch_3d_geometry() : IMP::algebra::SpherePatch3D
• 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_static_info() : IMP::em2d::PCAFitRestraint , IMP::isd::GaussianEMRestraint , IMP::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_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_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_tunnel_radius() : IMP::npctransport::SimulationData
• get_tunnel_radius_k() : IMP::npctransport::SimulationData
• get_type() : IMP::atom::Bond
• 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_vacuum_form_factor() : IMP::saxs::FormFactorTable
• get_vacuum_form_factors() : IMP::saxs::FormFactorTable
• get_vacuum_water_form_factor() : IMP::saxs::FormFactorTable
• get_value() : 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::OrderedTypePairPredicate , IMP::core::OrderedTypeQuadPredicate , IMP::core::OrderedTypeSingletonPredicate , IMP::core::OrderedTypeTripletPredicate , IMP::core::UnorderedTypePairPredicate , IMP::core::UnorderedTypeQuadPredicate , IMP::core::UnorderedTypeSingletonPredicate , IMP::core::UnorderedTypeTripletPredicate , IMP::em::DensityMap , IMP::misc::CommonEndpointPairFilter , IMP::PairPredicate , IMP::QuadPredicate , IMP::SingletonPredicate , IMP::spb::SameParticlePairFilter , IMP::spb::SameRigidBodyPairFilter , IMP::TripletPredicate
• 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::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::CoarseCC , 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::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::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::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::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::InternalCoordinatesConstraint , IMP::pmi::MembraneRestraint , IMP::pmi::SigmoidRestraintSphere , 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::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_key() : IMP::isd::Weight
• get_weights() : IMP::core::WeightedSum , IMP::core::WeightedSumOfExponential , 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