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• same_dimensions() : IMP::em::DensityMap
• same_origin() : IMP::em::DensityMap
• same_voxel_size() : IMP::em::DensityMap
• SampledDensityMap() : IMP::em::SampledDensityMap
• sanity_check() : IMP.isd.History.History
• save_cache() : IMP::domino::RestraintCache
• save_configuration() : IMP::kernel::ConfigurationSet
• scale() : IMP::saxs::RadialDistributionFunction , IMP::saxs::Profile
• score() : IMP::em::EnvelopeScore
• score_alignment() : IMP::cnmultifit::AlignSymmetric
• ScoreAccumulator() : IMP::kernel::ScoreAccumulator
• select_table() : IMP.em2d.Database.Database2
• Selection() : IMP::atom::Selection
• SerialMover() : IMP::core::SerialMover
• set() : IMP::base::Memoizer< Generator, Checker >
• set_angle() : IMP::algebra::Rotation2D
• set_assembly() : IMP.em2d.DominoModel.DominoModel
• set_assembly_components() : IMP.em2d.DominoModel.DominoModel
• set_assignments() : IMP::domino::ListAssignmentsTable
• set_atom_type() : IMP::atom::Atom , IMP::atom::Selection
• set_atom_types() : IMP::atom::Selection
• set_attribute() : IMP::kernel::Model
• set_bounding_box() : IMP::algebra::GridD< D, Storage, Value, EmbeddingT > , IMP::core::MCCGSampler
• set_chain() : IMP::atom::Selection
• set_chains() : IMP::atom::Selection
• set_check_level() : IMP::base::Object
• set_close_pairs_excluded_volume_restraint() : IMP.em2d.DominoModel.DominoModel
• set_coarse_registration_mode() : IMP::em2d::Em2DRestraint
• set_complementarity_restraint() : IMP.em2d.DominoModel.DominoModel
• set_complementarity_thickness() : IMP::multifit::ComplementarityRestraint
• set_complementarity_value() : IMP::multifit::ComplementarityRestraint
• set_components_and_connections() : IMP.em2d.buildxlinks.DockOrder
• set_cone_3d_geometry() : IMP::algebra::Cone3D
• set_connectivity_restraint() : IMP.em2d.DominoModel.DominoModel
• set_coordinate() : IMP::core::XYZ
• set_coordinates() : IMP::core::RigidMember , IMP::core::NonRigidMember , IMP::core::XYZ
• set_coordinates_are_optimized() : IMP::core::RigidBody , IMP::core::XYZ
• set_copy_index() : IMP::atom::Selection
• set_copy_indexes() : IMP::atom::Selection
• set_current_time() : IMP::atom::Simulator
• set_cylinder_3d_geometry() : IMP::algebra::Cylinder3D
• set_data() : IMP::em2d::Image
• set_decorator_name() : IMP::example::ExampleDecorator
• set_domain() : IMP::atom::Selection
• set_domains() : IMP::atom::Selection
• set_ellipsoid_3d_geometry() : IMP::algebra::Ellipsoid3D
• set_em2d_restraint() : IMP.em2d.DominoModel.DominoModel
• set_enclosing_radius() : IMP::core::XYZR
• set_enclosing_sphere() : IMP::core::XYZR
• set_estimated_number_of_angles() : IMP::em2d::PolarResamplingParameters
• set_fAngle1() : IMP::em::ImageHeader
• set_fast_mode() : IMP::em2d::ProjectionFinder , IMP::em2d::Em2DRestraint
• set_ff_table() : IMP::saxs::Profile
• set_gradient_threshold() : IMP::core::ConjugateGradients
• set_header() : IMP::em::ImageHeader
• set_hierarchies() : IMP.em2d.buildxlinks.InitialDockingFromXlinks
• set_hierarchy_types() : IMP::atom::Selection
• set_id() : IMP::atom::Chain
• set_image_index() : IMP::em2d::RegistrationResult
• set_image_type() : IMP::em::ImageHeader
• set_images() : IMP::em2d::Em2DRestraint
• set_in_image() : IMP::em2d::RegistrationResult
• set_incremental_scoring_function() : IMP::core::MonteCarlo
• set_interior_layer_thickness() : IMP::multifit::ComplementarityRestraint
• set_internal_coordinates() : IMP::core::RigidMember , IMP::core::NonRigidMember
• set_internal_transformation() : IMP::core::RigidMember , IMP::core::NonRigidMember
• set_is_changed() : IMP::kernel::Container
• set_is_complete() : IMP::container::PredicatePairsRestraint , IMP::container::PredicateQuadsRestraint , IMP::container::PredicateSingletonsRestraint , IMP::container::PredicateTripletsRestraint
• set_is_optimized() : IMP::kernel::Model
• set_is_optimizing() : IMP::kernel::OptimizerState
• set_is_refining() : IMP::core::MCCGSampler
• set_is_rigid_member() : IMP::core::RigidBody
• set_k() : IMP::core::Harmonic , IMP::restrainer::SimpleConnectivity , IMP::restrainer::SimpleDistance , IMP::restrainer::SimpleDiameter
• set_loader() : IMP.isd.AbstractGrid.AbstractGrid
• set_local_optimizer() : IMP::core::MCCGSampler
• set_log_level() : IMP::base::Object
• set_lower() : IMP::isd::Nuisance
• set_max_change() : IMP::core::ConjugateGradients
• set_max_monte_carlo_step_size() : IMP::core::MCCGSampler
• set_maximum_difference() : IMP::core::MonteCarlo
• set_maximum_number_of_assignments() : IMP::domino::DiscreteSampler
• set_maximum_penetration() : IMP::multifit::ComplementarityRestraint
• set_maximum_penetration_score() : IMP::multifit::ComplementarityRestraint
• set_maximum_separation() : IMP::multifit::ComplementarityRestraint
• set_maximum_step_size() : IMP::core::SteepestDescent
• set_mean() : IMP::core::Harmonic , IMP::restrainer::SimpleConnectivity , IMP::restrainer::SimpleDistance , IMP::restrainer::SimpleDiameter
• set_merge_tree() : IMP::domino::DominoSampler
• set_model() : IMP::kernel::Optimizer
• set_model_particles() : IMP::em2d::ProjectionFinder
• set_molecule() : IMP::atom::Selection
• set_molecules() : IMP::atom::Selection
• set_moved_particles() : IMP::core::IncrementalScoringFunction
• set_n() : IMP::container::MinimumPairRestraint , IMP::container::MinimumQuadRestraint , IMP::container::MinimumSingletonRestraint , IMP::container::MinimumTripletRestraint
• set_name() : IMP::em2d::Image
• set_native_assembly_for_benchmark() : IMP.em2d.DominoModel.DominoModel
• set_no_tracker() : IMP::base::TrackedObject< Type, Tracker >
• set_not_optimized() : IMP.em2d.DominoModel.DominoModel
• set_number_of_attempts() : IMP::core::MCCGSampler
• set_number_of_conjugate_gradient_steps() : IMP::core::MCCGSampler
• set_number_of_monte_carlo_steps() : IMP::core::MCCGSampler
• set_number_of_updates() : IMP::core::PeriodicOptimizerState
• set_old_rot() : IMP::em::ImageHeader
• set_origin() : IMP::em::DensityMap
• set_pair_score() : IMP::core::TypedPairScore
• set_pair_score_restraint() : IMP.em2d.DominoModel.DominoModel
• set_parameters_optimized() : IMP::em2d::ProjectionParameters
• set_params() : IMP::em::KernelParameters
• set_particle() : IMP::core::TableRefiner
• set_particle_states() : IMP::domino::DiscreteSampler , IMP::domino::ParticleStatesTable
• set_particle_type() : IMP::atom::Selection , IMP::core::TypedPairScore
• set_particle_types() : IMP::atom::Selection
• set_particles() : IMP::atom::BerendsenThermostatOptimizerState , IMP::atom::LangevinThermostatOptimizerState , IMP::atom::RemoveRigidMotionOptimizerState , IMP::atom::RemoveTranslationOptimizerState , IMP::atom::VelocityScalingOptimizerState , IMP::em::SampledDensityMap , IMP::em2d::Em2DRestraint
• set_pdbs() : IMP.em2d.buildxlinks.InitialDockingFromXlinks
• set_period() : IMP::core::PeriodicOptimizerState
• set_plane_3d_geometry() : IMP::algebra::Plane3D
• set_projections() : IMP::em2d::ProjectionFinder
• set_proper_ranges_for_keys() : IMP::em2d::ProjectionParameters
• set_query_log() : IMP::algebra::NearestNeighborD< D >
• set_radius_of_gyration() : IMP::multifit::RadiusOfGyrationRestraint
• set_random_registration() : IMP::em2d::RegistrationResult
• set_rb_states() : IMP.em2d.DominoModel.DominoModel
• set_reference_frame() : IMP::core::RigidBody
• set_reference_frame_from_members() : IMP::core::RigidBody
• set_reference_frame_lazy() : IMP::core::RigidBody
• set_relative_movers() : IMP.em2d.MonteCarloRelativeMoves.MonteCarloRelativeMoves
• set_residue_index() : IMP::atom::Selection
• set_residue_indexes() : IMP::atom::Fragment , IMP::atom::Selection
• set_residue_type() : IMP::atom::Residue , IMP::atom::Selection
• set_residue_types() : IMP::atom::Selection
• set_resolution() : IMP::em::DensityHeader
• set_return_best() : IMP::core::MonteCarlo
• set_rigid_bodies() : IMP.em2d.buildxlinks.InitialDockingFromXlinks
• set_rotation() : IMP::em2d::RegistrationResult
• set_save_match_images() : IMP::em2d::ProjectionFinder
• set_save_rejected_configurations() : IMP::core::MCCGSampler
• set_score() : IMP::container::PredicateQuadsRestraint , IMP::container::PredicatePairsRestraint , IMP::container::PredicateSingletonsRestraint , IMP::container::PredicateTripletsRestraint
• set_scoring_function() : IMP::kernel::Optimizer
• set_shift() : IMP::em2d::RegistrationResult
• set_simulator() : IMP::rmf::SaveOptimizerState
• set_size() : IMP::em2d::Image
• set_skip_steps() : IMP::atom::RemoveRigidMotionOptimizerState , IMP::atom::RemoveTranslationOptimizerState , IMP::atom::VelocityScalingOptimizerState
• set_slack() : IMP::core::CoverRefined
• set_sphere() : IMP::core::XYZR , IMP::misc::CustomXYZR
• set_sphere_patch_3d_geometry() : IMP::algebra::SpherePatch3D
• set_standard_deviation() : IMP::restrainer::SimpleDistance , IMP::restrainer::SimpleConnectivity , IMP::restrainer::SimpleDiameter
• set_starts_and_ends() : IMP::em2d::CenteredMat
• set_step_size() : IMP::core::SteepestDescent
• set_stop_on_good_score() : IMP::kernel::Optimizer
• set_stop_score() : IMP::gsl::GSLOptimizer
• set_subject_image() : IMP::em2d::Fine2DRegistrationRestraint
• set_subjects() : IMP::em2d::ProjectionFinder
• set_subset_graph() : IMP::domino::DominoSampler
• set_surface_shell() : IMP::em::SurfaceShellDensityMap
• set_target_radius() : IMP::atom::Selection
• set_temperature() : IMP::atom::VelocityScalingOptimizerState
• set_temperature_pattern() : IMP.em2d.MonteCarloRelativeMoves.MonteCarloRelativeMoves
• set_terminus() : IMP::atom::Selection
• set_threshold() : IMP::core::SteepestDescent , IMP::gsl::ConjugateGradients
• set_title() : IMP::em::ImageHeader
• set_track_unique() : IMP::container::PairContainerStatistics , IMP::container::QuadContainerStatistics , IMP::container::SingletonContainerStatistics , IMP::container::TripletContainerStatistics
• set_transformation() : IMP::core::TransformedDistancePairScore
• set_translation() : IMP::algebra::Transformation2D
• set_unknown_score() : IMP::container::PredicateQuadsRestraint , IMP::container::PredicatePairsRestraint , IMP::container::PredicateSingletonsRestraint , IMP::container::PredicateTripletsRestraint
• set_use_cross_subset_filtering() : IMP::domino::DominoSampler
• set_value() : IMP::em::DensityMap , IMP::em2d::Image , IMP::em::DensityMap
• set_variance_images() : IMP::em2d::ProjectionFinder , IMP::em2d::Em2DRestraint
• set_vector_d_geometry() : IMP::algebra::VectorD< D >
• set_velocity_cap() : IMP::atom::MolecularDynamics
• set_void_map() : IMP::em::DensityMap
• set_was_used() : IMP::base::Object
• set_xlink_restraint() : IMP.em2d.DominoModel.DominoModel
• set_xlinks() : IMP.em2d.buildxlinks.InitialDockingFromXlinks , IMP.em2d.buildxlinks.DockOrder
• set_xorigin() : IMP::em::DensityHeader
• set_yorigin() : IMP::em::DensityHeader
• set_zeros() : IMP::em2d::Image
• set_zorigin() : IMP::em::DensityHeader
• SetCheckState() : IMP::base::SetCheckState
• SetLogState() : IMP::base::SetLogState
• setup() : IMP::em2d::Em2DRestraint , IMP::em2d::PolarResamplingParameters , IMP::atom::Simulator , IMP::em2d::Fine2DRegistrationRestraint , IMP::em2d::ProjectionFinder
• setup_as_approximation() : IMP::atom::Hierarchy
• setup_domino_sampler() : IMP.em2d.DominoModel.DominoModel
• setup_hierarchy() : IMP::atom::CHARMMTopology
• setup_kernel() : IMP::em2d::MasksManager
• setup_particle() : IMP::atom::Diffusion , IMP::atom::Molecule , IMP::misc::CustomXYZR , IMP::atom::LennardJones , IMP::atom::Residue , IMP::core::Reference , IMP::core::Hierarchy , IMP::core::XYZR , IMP::core::Typed , IMP::core::XYZR , IMP::core::XYZ , IMP::core::Hierarchy , IMP::core::XYZR , IMP::core::RigidBody , IMP::atom::CHARMMAtom , IMP::atom::Residue , IMP::atom::SecondaryStructureResidue , IMP::atom::Charged , IMP::atom::SecondaryStructureResidue , IMP::atom::Hierarchy , IMP::atom::Atom , IMP::atom::RigidBodyDiffusion , IMP::atom::Fragment , IMP::atom::Domain , IMP::atom::Copy , IMP::atom::Atom , IMP::atom::Charged , IMP::atom::Angle , IMP::misc::CustomXYZR , IMP::core::RigidBody , IMP::atom::Molecule , IMP::em::Voxel , IMP::em2d::ProjectionParameters , IMP::atom::Domain , IMP::core::XYZR , IMP::atom::Dihedral , IMP::example::ExampleDecorator
• show() : IMP::saxs::DeltaDistributionFunction , IMP::atom::Hierarchy , IMP::algebra::LinearFit2D , IMP::display::PivyWriter , IMP::saxs::RadialDistributionFunction , IMP::em2d::Image , IMP::saxs::FormFactorTable , IMP::core::Hierarchy , IMP::multifit::FittingSolutionRecord , IMP::em2d::DummyRestraint , IMP::kernel::PythonDirectedGraph , IMP::em2d::ParticlesDummyRestraint , IMP::algebra::Rotation2D , IMP::kernel::Optimizer , IMP::em::RadiusDependentKernelParameters
• show_all() : IMP::kernel::Key< ID, LazyAdd >
• show_all_restraints() : IMP.restrainer.Restraint
• show_histogram() : IMP::statistics::HistogramD< D, Grid >
• show_projection_params() : IMP::em::ImageHeader
• show_restraint_information() : IMP::domino::RestraintCache
• simulate() : IMP::atom::Simulator
• Simulator() : IMP::atom::Simulator
• SingletonConstraint() : IMP::core::SingletonConstraint
• SingletonContainerSet() : IMP::container::SingletonContainerSet
• SingletonRestraint() : IMP::core::SingletonRestraint
• SingletonsConstraint() : IMP::container::SingletonsConstraint
• SingletonsOptimizerState() : IMP::container::SingletonsOptimizerState
• SingletonsRestraint() : IMP::container::SingletonsRestraint
• size() : IMP::saxs::Profile
• SlidingPriorRestraint() : IMP::isd::SlidingPriorRestraint
• sort() : IMP::em::FittingSolutions
• SpherePatch3D() : IMP::algebra::SpherePatch3D
• SphericalVector3D() : IMP::algebra::SphericalVector3D
• SpiderImageReaderWriter() : IMP::em2d::SpiderImageReaderWriter
• SpiderMapReaderWriter() : IMP::em::SpiderMapReaderWriter
• StateAdaptor() : IMP::misc::StateAdaptor
• Statistical() : IMP::score_functor::Statistical< Key, BIPARTITE, INTERPOLATE, SPARSE >
• StatisticalPairScore() : IMP::core::StatisticalPairScore< Key, BIPARTITE, INTERPOLATE, SPARSE >
• std_normalize() : IMP::em::DensityMap
• store_cluster_data() : IMP.em2d.solutions_io.ResultsDB
• store_data() : IMP.em2d.Database.Database2
• store_dataV1() : IMP.em2d.Database.Database2
• Subset() : IMP::domino::Subset
• sum_partial_profiles() : IMP::saxs::Profile
• SurfaceShellDensityMap() : IMP::em::SurfaceShellDensityMap
• swap() : IMP.em2d.buildxlinks.Xlink
• swap_configuration() : IMP::kernel::Configuration