Here is a list of all documented class members with links to the class documentation for each member:
- s -
- same_dimensions()
: IMP::em::DensityMap
- same_origin()
: IMP::em::DensityMap
- same_voxel_size()
: IMP::em::DensityMap
- SampledDensityMap()
: IMP::em::SampledDensityMap
- SampledDensityMapsTemp
: IMP::em::SampledDensityMap
- SamplersTemp
: IMP::kernel::Sampler
- sanity_check()
: IMP.isd.History.History
- save_cache()
: IMP::domino::RestraintCache
- save_configuration()
: IMP::kernel::ConfigurationSet
- SaveLinksTemp
: IMP::rmf::SaveLink
- scale()
: IMP::saxs::RadialDistributionFunction
, IMP::saxs::Profile
- score()
: IMP::em::EnvelopeScore
- Score_
: IMP::em2d::RegistrationResult
- score_alignment()
: IMP::cnmultifit::AlignSymmetric
- ScoreAccumulator()
: IMP::kernel::ScoreAccumulator
- ScoreFunctionsTemp
: IMP::em2d::ScoreFunction
- ScoreStatesTemp
: IMP::kernel::ScoreState
- ScoringFunctionsTemp
: IMP::kernel::ScoringFunction
- 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::Em2DRestraint
, IMP::em2d::ProjectionFinder
- 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::PredicatePairsRestraint
, IMP::container::PredicateQuadsRestraint
, 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::RemoveTranslationOptimizerState
, IMP::atom::RemoveRigidMotionOptimizerState
, 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::SimpleDiameter
, IMP::restrainer::SimpleConnectivity
, IMP::restrainer::SimpleDistance
- 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::PredicateSingletonsRestraint
, IMP::container::PredicatePairsRestraint
, IMP::container::PredicateQuadsRestraint
, IMP::container::PredicateTripletsRestraint
- set_use_cross_subset_filtering()
: IMP::domino::DominoSampler
- set_value()
: IMP::em::DensityMap
, IMP::em2d::Image
- 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.DockOrder
, IMP.em2d.buildxlinks.InitialDockingFromXlinks
- 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::ProjectionFinder
, IMP::em2d::Em2DRestraint
, IMP::em2d::Fine2DRegistrationRestraint
, IMP::em2d::PolarResamplingParameters
, IMP::atom::Simulator
- 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::RigidBodyDiffusion
, IMP::atom::Atom
, IMP::atom::Charged
, IMP::example::ExampleDecorator
, IMP::atom::Diffusion
, IMP::atom::Domain
, IMP::atom::Molecule
, IMP::atom::Residue
, IMP::atom::SecondaryStructureResidue
, IMP::core::RigidBody
, IMP::core::Reference
, IMP::core::XYZ
, IMP::core::XYZR
, IMP::em::Voxel
, IMP::em2d::ProjectionParameters
, IMP::misc::CustomXYZR
, IMP::atom::Charged
, IMP::misc::CustomXYZR
, IMP::atom::Diffusion
, IMP::core::Typed
, IMP::atom::Fragment
, IMP::atom::Hierarchy
, IMP::core::XYZR
, IMP::atom::Residue
, IMP::core::RigidBody
, IMP::atom::SecondaryStructureResidue
, IMP::core::Hierarchy
, IMP::atom::Domain
, IMP::atom::LennardJones
, IMP::misc::CustomXYZR
, IMP::atom::Diffusion
, IMP::atom::Dihedral
, IMP::atom::Angle
, IMP::atom::CHARMMAtom
, IMP::atom::Copy
- shift_
: IMP::em2d::RegistrationResult
- show()
: IMP::atom::Hierarchy
, IMP::algebra::LinearFit2D
, IMP::algebra::Rotation2D
, IMP::display::PivyWriter
, IMP::em2d::ParticlesDummyRestraint
, IMP::kernel::PythonDirectedGraph
, IMP::kernel::Optimizer
, IMP::em2d::Image
, IMP::multifit::FittingSolutionRecord
, IMP::em::RadiusDependentKernelParameters
, IMP::saxs::RadialDistributionFunction
, IMP::core::Hierarchy
, IMP::saxs::FormFactorTable
, IMP::saxs::DeltaDistributionFunction
, IMP::em2d::DummyRestraint
- 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
- sig_
: IMP::em::RadiusDependentKernelParameters
- simulate()
: IMP::atom::Simulator
- Simulator()
: IMP::atom::Simulator
- SimulatorsTemp
: IMP::atom::Simulator
- SingletonConstraint()
: IMP::core::SingletonConstraint
- SingletonContainerSet()
: IMP::container::SingletonContainerSet
- SingletonContainersTemp
: IMP::kernel::SingletonContainer
- SingletonModifiersTemp
: IMP::kernel::SingletonModifier
- SingletonPredicatesTemp
: IMP::kernel::SingletonPredicate
- SingletonRestraint()
: IMP::core::SingletonRestraint
- SingletonsConstraint()
: IMP::container::SingletonsConstraint
- SingletonsConstraintsTemp
: IMP::container::SingletonsConstraint
- SingletonScoresTemp
: IMP::kernel::SingletonScore
- SingletonsOptimizerState()
: IMP::container::SingletonsOptimizerState
- SingletonsOptimizerStatesTemp
: 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
- stored_cc_
: IMP::em::CoarseCCatIntervals
- stored_dvx_
: IMP::em::CoarseCCatIntervals
- subjects_
: IMP::em2d::ProjectionFinder
- Subset()
: IMP::domino::Subset
- SubsetFiltersTemp
: IMP::domino::SubsetFilter
- SubsetFilterTablesTemp
: IMP::domino::SubsetFilterTable
- sum_partial_profiles()
: IMP::saxs::Profile
- SurfaceShellDensityMap()
: IMP::em::SurfaceShellDensityMap
- SurfaceShellDensityMapsTemp
: IMP::em::SurfaceShellDensityMap
- swap()
: IMP.em2d.buildxlinks.Xlink
- swap_configuration()
: IMP::kernel::Configuration
- szIDat
: IMP::em::SpiderHeader
- szITim
: IMP::em::SpiderHeader
- szITit
: IMP::em::SpiderHeader