- s -

• same_dimensions() : IMP::em::DensityMap
• same_origin() : IMP::em::DensityMap
• same_voxel_size() : IMP::em::DensityMap
• sample_and_apply() : IMP::kinematics::DOFsSampler
• SampledDensityMap() : IMP::em::SampledDensityMap
• sanity_check() : IMP.isd.History.History
• save_cache() : IMP::domino::RestraintCache
• save_configuration() : IMP::ConfigurationSet
• scale() : IMP::saxs::Profile , IMP::saxs::RadialDistributionFunction
• ScopedAddCacheAttribute() : IMP::ScopedAddCacheAttribute< Key, Value >
• ScopedSetAttribute() : IMP::ScopedSetAttribute< Key, Value >
• score() : IMP::em::EnvelopeScore
• score_alignment() : IMP::cnmultifit::AlignSymmetric
• ScoreAccumulator() : IMP::ScoreAccumulator
• select_table() : IMP.EMageFit.database.Database2
• Selection() : IMP::atom::Selection
• SerialMover() : IMP::core::SerialMover
• set() : IMP::benchmark::Profiler , IMP::container::DynamicListPairContainer , IMP::container::DynamicListQuadContainer , IMP::container::DynamicListSingletonContainer , IMP::container::DynamicListTripletContainer , IMP::container::ListPairContainer , IMP::container::ListQuadContainer , IMP::container::ListSingletonContainer , IMP::container::ListTripletContainer , IMP::CreateLogContext , IMP::Memoizer< Generator, Checker > , IMP::ScopedAddCacheAttribute< Key, Value > , IMP::ScopedSetAttribute< Key, Value > , IMP::SetCheckState , IMP::SetLogState , IMP::SetLogTarget , IMP::SetNumberOfThreads
• set_angle() : IMP::algebra::Rotation2D , IMP::kinematics::RevoluteJoint
• set_assembly() : IMP.EMageFit.domino_model.DominoModel
• set_assembly_components() : IMP.EMageFit.domino_model.DominoModel
• set_assignments() : IMP::domino::ListAssignmentsTable
• set_atom_type() : IMP::atom::Atom , IMP::atom::Selection
• set_atom_types() : IMP::atom::Selection
• set_attribute() : IMP::Model
• set_bounding_box() : IMP::algebra::GridD< D, StorageT, Value, EmbeddingT > , IMP::core::MCCGSampler
• set_chain_id() : IMP::atom::Selection
• set_chain_ids() : IMP::atom::Selection
• set_chain_of_super_rigid_bodies() : IMP.pmi.representation.Representation
• set_check_level() : IMP::Object
• set_close_pairs_excluded_volume_restraint() : IMP.EMageFit.domino_model.DominoModel
• set_coarse_registration_mode() : IMP::em2d::Em2DRestraint
• set_complementarity_restraint() : IMP.EMageFit.domino_model.DominoModel
• set_complementarity_thickness() : IMP::multifit::ComplementarityRestraint
• set_complementarity_value() : IMP::multifit::ComplementarityRestraint
• set_components_and_connections() : IMP.EMageFit.buildxlinks.DockOrder
• set_cone_3d_geometry() : IMP::algebra::Cone3D
• set_connectivity_restraint() : IMP.EMageFit.domino_model.DominoModel
• set_coordinate() : IMP::core::XYZ
• set_coordinates() : IMP::core::RigidBodyMember , IMP::core::XYZ
• set_coordinates_are_optimized() : IMP::core::RigidBody , IMP::core::XYZ
• set_coordinates_from_rmf() : IMP.pmi.representation.Representation
• set_coordinates_safe() : IMP::kinematics::KinematicForest
• 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_difference() : IMP::atom::Selection
• set_dir() : IMP.pmi.topology.TopologyReader
• set_domain() : IMP::atom::Selection
• set_domains() : IMP::atom::Selection
• set_element() : IMP::atom::Selection
• set_ellipsoid_3d_geometry() : IMP::algebra::Ellipsoid3D
• set_em2d_restraint() : IMP.EMageFit.domino_model.DominoModel
• set_estimated_number_of_angles() : IMP::em2d::PolarResamplingParameters
• set_fAngle1() : IMP::em::ImageHeader
• set_fast_mode() : IMP::em2d::Em2DRestraint , IMP::em2d::ProjectionFinder
• set_fast_scoring() : IMP::multifit::ProteomicsEMAlignmentAtomic
• set_fasta_dir() : IMP.pmi.topology.TopologyReader
• set_ff_table() : IMP::saxs::Profile
• set_floppy_bodies_as_fixed() : IMP.pmi.representation.Representation
• set_force() : IMP::atom::BrownianDynamics
• set_friction_scale_factor() : IMP::atom::TAMDParticle
• set_gaussian() : IMP::core::Gaussian
• set_global_covariance() : IMP::core::Gaussian
• set_gmm_dir() : IMP.pmi.topology.TopologyReader
• set_gradient_threshold() : IMP::core::ConjugateGradients
• set_has_dependencies() : IMP::ModelObject
• set_has_required_score_states() : IMP::ModelObject
• set_header() : IMP::em::ImageHeader
• set_hierarchies() : IMP.EMageFit.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::RigidBodyMember
• set_internal_transformation() : IMP::core::RigidBodyMember
• set_intersection() : IMP::atom::Selection
• set_is_complete() : IMP::container::PredicatePairsRestraint , IMP::container::PredicateQuadsRestraint , IMP::container::PredicateSingletonsRestraint , IMP::container::PredicateTripletsRestraint
• set_is_optimized() : IMP::Model
• set_is_optimizing() : IMP::OptimizerState
• set_is_refining() : IMP::core::MCCGSampler
• set_is_rigid_member() : IMP::core::RigidBody
• set_joints() : IMP::kinematics::CompositeJoint
• set_k() : IMP::core::Harmonic
• set_label() : IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
• set_length() : IMP::kinematics::PrismaticJoint
• set_local_covariance() : IMP::core::Gaussian
• set_local_optimizer() : IMP::core::MCCGSampler
• set_log_level() : IMP::Object
• 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
• set_merge_tree() : IMP::domino::DominoSampler
• set_model_particles() : IMP::em2d::CollisionCrossSection , IMP::em2d::ProjectionFinder
• set_molecule() : IMP::atom::Selection
• set_molecules() : IMP::atom::Selection
• set_moved_particles() : IMP::core::IncrementalScoringFunction
• set_my_parameter() : IMP::mpi::ReplicaExchange
• set_n() : IMP::container::MinimumPairRestraint , IMP::container::MinimumQuadRestraint , IMP::container::MinimumSingletonRestraint , IMP::container::MinimumTripletRestraint
• set_name() : IMP::em2d::Image
• set_name_if_default() : IMP::PairContainerAdaptor , IMP::QuadContainerAdaptor , IMP::SingletonContainerAdaptor , IMP::TripletContainerAdaptor
• set_native_assembly_for_benchmark() : IMP.EMageFit.domino_model.DominoModel
• set_not_optimized() : IMP.EMageFit.domino_model.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::OptimizerState
• set_old_rot() : IMP::em::ImageHeader
• set_orientations() : IMP::em2d::RigidBodiesImageFitRestraint
• set_origin() : IMP::em::DensityMap
• set_output_level() : IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
• set_owner_kf() : IMP::kinematics::Joint
• set_pair_score() : IMP::core::TypedPairScore
• set_pair_score_restraint() : IMP.EMageFit.domino_model.DominoModel
• set_parameters_optimized() : IMP::em2d::ProjectionParameters
• set_particle() : IMP::core::TableRefiner
• set_particle_pairs() : IMP::container::DynamicListPairContainer , IMP::container::ListPairContainer
• set_particle_probabilities_on_anchors() : IMP::multifit::ProbabilisticAnchorGraph
• set_particle_quads() : IMP::container::DynamicListQuadContainer , IMP::container::ListQuadContainer
• set_particle_states() : IMP::domino::DiscreteSampler , IMP::domino::ParticleStatesTable
• set_particle_triplets() : IMP::container::DynamicListTripletContainer , IMP::container::ListTripletContainer
• 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::container::DynamicListSingletonContainer , IMP::container::ListSingletonContainer , IMP::em2d::Em2DRestraint , IMP::em::SampledDensityMap
• set_pdb_dir() : IMP.pmi.topology.TopologyReader
• set_pdbs() : IMP.EMageFit.buildxlinks.InitialDockingFromXlinks
• set_period() : IMP::OptimizerState
• set_plane_3d_geometry() : IMP::algebra::Plane3D
• set_projections() : IMP::em2d::ProjectionFinder
• set_proper_ranges_for_keys() : IMP::em2d::ProjectionParameters
• set_psi_is_sampled() : IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
• set_query_log() : IMP::algebra::NearestNeighborD< D >
• set_radius_of_gyration() : IMP::multifit::RadiusOfGyrationRestraint
• set_random_move_probability() : IMP::em2d::RelativePositionMover
• set_random_registration() : IMP::em2d::RegistrationResult
• set_rb_states() : IMP.EMageFit.domino_model.DominoModel
• set_reduced_coordinates() : IMP::core::RigidBodyTunneler
• set_reference_frame() : IMP::core::RigidBody
• set_reference_frame_from_members() : IMP::core::RigidBody
• set_reference_frame_lazy() : IMP::core::RigidBody
• set_reference_frame_safe() : IMP::kinematics::KinematicForest
• set_reference_structure() : IMP.pmi.analysis.Precision
• set_relative_movers() : IMP.EMageFit.monte_carlo.MonteCarloRelativeMoves
• set_representation_type() : IMP::atom::Selection
• set_residue_index() : IMP::atom::Selection
• set_residue_indexes() : IMP::atom::Fragment , IMP::atom::Selection
• set_residue_pairs_to_display() : IMP.pmi.io.xltable.XLTable
• set_residue_type() : IMP::atom::Residue , IMP::atom::Selection
• set_residue_types() : IMP::atom::Selection
• set_resolution() : IMP::atom::Selection , IMP::em::DensityHeader
• set_restraints() : IMP::domino::DiscreteSampler
• set_return_best() : IMP::core::MonteCarlo
• set_rigid_bodies() : IMP.EMageFit.buildxlinks.InitialDockingFromXlinks , IMP.pmi.representation.Representation
• set_rigid_bodies_as_fixed() : IMP.pmi.representation.Representation
• set_rigid_body_from_hierarchies() : IMP.pmi.representation.Representation
• 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_score_threshold() : IMP::core::MonteCarlo
• set_scoring_function() : IMP.EMageFit.monte_carlo.MonteCarloRelativeMoves , IMP::Optimizer
• set_secondary_structure_probabilities() : IMP::multifit::AnchorsData
• set_shift() : IMP::em2d::RegistrationResult
• set_sigma_is_sampled() : IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
• set_simulator() : IMP::rmf::SaveOptimizerState
• set_size() : IMP::em2d::Image
• set_slack() : IMP::core::CoverRefined
• set_slope() : IMP::isd::GaussianEMRestraint
• set_source_chain_id() : IMP::atom::StructureSource
• set_source_id() : IMP::atom::StructureSource
• set_sphere() : IMP::core::XYZR , IMP::misc::CustomXYZR
• set_sphere_patch_3d_geometry() : IMP::algebra::SpherePatch3D
• set_starts_and_ends() : IMP::em2d::CenteredMat
• set_state_index() : IMP::atom::Selection
• set_state_indexes() : IMP::atom::Selection
• set_step_size() : IMP::core::SteepestDescent
• set_stop_on_good_score() : IMP::Optimizer
• set_stop_score() : IMP::gsl::GSLOptimizer
• set_subject_image() : IMP::em2d::Fine2DRegistrationRestraint
• set_subjects() : IMP::em2d::ProjectionFinder
• set_surface_shell() : IMP::em::SurfaceShellDensityMap
• set_symmetric_difference() : IMP::atom::Selection
• set_temperature() : IMP::atom::VelocityScalingOptimizerState
• set_temperature_pattern() : IMP.EMageFit.monte_carlo.MonteCarloRelativeMoves
• set_temperature_scale_factor() : IMP::atom::TAMDParticle
• 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::TransformationSymmetry , IMP::core::TransformedDistancePairScore
• set_transformation_child_to_parent() : IMP::kinematics::TransformationJoint
• set_transformation_child_to_parent_no_checks() : IMP::kinematics::Joint
• set_translation() : IMP::algebra::Transformation2D
• set_union() : IMP::atom::Selection
• set_unknown_score() : IMP::container::PredicatePairsRestraint , IMP::container::PredicateQuadsRestraint , IMP::container::PredicateSingletonsRestraint , IMP::container::PredicateTripletsRestraint
• set_use_cg() : IMP::isd::GaussianProcessInterpolationRestraint , IMP::isd::MultivariateFNormalSufficient
• set_use_cross_subset_filtering() : IMP::domino::DominoSampler
• set_value() : IMP::em2d::Image , IMP::em::DensityMap
• set_variance_images() : IMP::em2d::Em2DRestraint , IMP::em2d::ProjectionFinder
• set_variances() : IMP::core::Gaussian
• set_velocity_cap() : IMP::atom::MolecularDynamics
• set_void_map() : IMP::em::DensityMap
• set_was_used() : IMP::Object
• set_weights() : IMP::isd::Weight
• set_weights_are_optimized() : IMP::isd::Weight
• set_xlink_restraint() : IMP.EMageFit.domino_model.DominoModel
• set_xlinks() : IMP.EMageFit.buildxlinks.DockOrder , IMP.EMageFit.buildxlinks.InitialDockingFromXlinks
• set_xorigin() : IMP::em::DensityHeader
• set_yorigin() : IMP::em::DensityHeader
• set_zeros() : IMP::em2d::Image
• set_zorigin() : IMP::em::DensityHeader
• SetCheckState() : IMP::SetCheckState
• SetLogState() : IMP::SetLogState
• SetLogTarget() : IMP::SetLogTarget
• SetNumberOfThreads() : IMP::SetNumberOfThreads
• setup() : IMP::atom::BrownianDynamics , IMP::atom::MolecularDynamics , IMP::atom::Simulator , IMP::em2d::Em2DRestraint , IMP::em2d::Fine2DRegistrationRestraint , IMP::em2d::PolarResamplingParameters , IMP::em2d::ProjectionFinder
• setup_component_sequence_connectivity() : IMP.pmi.representation.Representation
• setup_contact_map() : IMP.pmi.io.xltable.XLTable
• setup_domino_sampler() : IMP.EMageFit.domino_model.DominoModel
• setup_hierarchy() : IMP::atom::CHARMMTopology
• setup_kernel() : IMP::em2d::MasksManager
• setup_md() : IMP.pmi.dof.DegreesOfFreedom
• setup_particle() : IMP::atom::Angle , IMP::atom::Atom , IMP::atom::Bonded , IMP::atom::CenterOfMass , IMP::atom::Chain , IMP::atom::Charged , IMP::atom::CHARMMAtom , IMP::atom::Copy , IMP::atom::Diffusion , IMP::atom::Dihedral , IMP::atom::Domain , IMP::atom::Fragment , IMP::atom::Hierarchy , IMP::atom::LennardJones , IMP::atom::Mass , IMP::atom::Molecule , IMP::atom::Representation , IMP::atom::Residue , IMP::atom::RigidBodyDiffusion , IMP::atom::SecondaryStructureResidue , IMP::atom::State , IMP::atom::StructureSource , IMP::atom::TAMDCentroid , IMP::atom::TAMDParticle , IMP::core::Centroid , IMP::core::Cover , IMP::core::Gaussian , IMP::core::Hierarchy , IMP::core::Reference , IMP::core::RigidBody , IMP::core::Typed , IMP::core::XYZ , IMP::core::XYZR , IMP::display::Colored , IMP::em2d::ProjectionParameters , IMP::em::Voxel , IMP::example::ExampleDecorator , IMP::isd::Nuisance , IMP::isd::Scale , IMP::isd::Switching , IMP::isd::Weight , IMP::kinematics::KinematicNode , IMP::misc::CustomXYZR , IMP::pmi::Resolution , IMP::pmi::Symmetric , IMP::pmi::Uncertainty
• setup_secondary_structure() : IMP::multifit::AnchorsData
• show() : IMP::algebra::LinearFit2D , IMP::algebra::Rotation2D , IMP::atom::Hierarchy , IMP::display::PivyWriter , IMP::em2d::CollisionCrossSection , IMP::em2d::DummyRestraint , IMP::em2d::Image , IMP::em2d::ParticlesDummyRestraint , IMP::em2d::ProjectingOptions , IMP::em2d::ProjectingParameters , IMP::multifit::FittingSolutionRecord , IMP::PythonDirectedGraph , IMP::saxs::DeltaDistributionFunction , IMP::saxs::FormFactorTable , IMP::saxs::RadialDistributionFunction
• show_all() : IMP::Key< ID, LazyAdd >
• show_projection_params() : IMP::em::ImageHeader
• show_restraint_information() : IMP::domino::RestraintCache
• shuffle_configuration() : IMP.pmi.representation.Representation
• sigmoid() : IMP.pmi.restraints.proteomics.ConnectivityNetworkRestraint
• SigmoidRestraintSphere() : IMP::pmi::SigmoidRestraintSphere
• simulate() : IMP::atom::Simulator
• simulate_wave() : IMP::atom::Simulator
• Simulator() : IMP::atom::Simulator
• SingletonConstraint() : IMP::core::SingletonConstraint
• SingletonContainerAdaptor() : IMP::SingletonContainerAdaptor
• SingletonContainerSet() : IMP::container::SingletonContainerSet
• SingletonRestraint() : IMP::core::SingletonRestraint
• SingletonsConstraint() : IMP::container::SingletonsConstraint
• SingletonsOptimizerState() : IMP::container::SingletonsOptimizerState
• SingletonsRestraint() : IMP::container::SingletonsRestraint
• size() : IMP::saxs::Profile
• solve() : IMP::isd::MultivariateFNormalSufficient
• 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 >
• stats() : IMP::isd::MultivariateFNormalSufficient
• std_normalize() : IMP::em::DensityMap
• store_cluster_data() : IMP.EMageFit.solutions_io.ResultsDB
• store_data() : IMP.EMageFit.database.Database2
• store_dataV1() : IMP.EMageFit.database.Database2
• Subset() : IMP::domino::Subset
• sum_partial_profiles() : IMP::saxs::Profile
• SurfaceShellDensityMap() : IMP::em::SurfaceShellDensityMap
• swap() : IMP.EMageFit.buildxlinks.Xlink
• swap_configuration() : IMP::Configuration