- 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_clusters() : IMP.pmi.macros.AnalysisReplicaExchange , IMP.pmi1.macros.AnalysisReplicaExchange
• save_configuration() : IMP::ConfigurationSet
• save_coordinates() : IMP.pmi.macros.AnalysisReplicaExchange , IMP.pmi1.macros.AnalysisReplicaExchange
• save_data() : IMP.pmi.macros.AnalysisReplicaExchange , IMP.pmi1.macros.AnalysisReplicaExchange
• 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
• Scoring() : IMP::npctransport::Scoring
• 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_actual_tree_size() : IMP::kinematics::RRT
• set_alignment_selection() : IMP.pmi.macros.AnalysisReplicaExchange , IMP.pmi1.macros.AnalysisReplicaExchange
• set_alpha() : IMP::isd::PenalizedComplexityPrior
• 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_backbone_k() : IMP::npctransport::FGChain
• set_begin() : IMP::spb::HelixDecorator
• set_bounding_box() : IMP::algebra::GridD< D, StorageT, Value, EmbeddingT > , IMP::core::MCCGSampler
• set_bounding_box_size() : IMP::npctransport::SimulationData
• set_bounding_sphere_radius() : IMP::npctransport::SimulationData
• set_bounding_volume() : IMP::npctransport::SimulationData
• set_chain_id() : IMP::atom::Selection , IMP::core::StructureProvenance
• set_chain_ids() : IMP::atom::Selection
• set_chain_of_super_rigid_bodies() : IMP.pmi1.representation.Representation
• set_chain_type() : IMP::atom::Chain
• set_charge() : IMP::atom::Charged
• set_charmm_type() : IMP::atom::CHARMMAtom
• 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.pmi1.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 , IMP.pmi.macros.AnalysisReplicaExchange , IMP.pmi1.macros.AnalysisReplicaExchange
• set_decorator_name() : IMP::example::ExampleDecorator
• set_denominator() : IMP::core::WeightedSumOfExponential
• set_density() : IMP::em::Voxel
• set_density_filename() : IMP::bayesianem::GaussianEMRestraint , IMP::isd::GaussianEMRestraint
• set_difference() : IMP::atom::Selection
• set_diffusion_coefficient() : IMP::atom::Diffusion
• set_direction() : IMP::core::Direction
• set_direction_is_optimized() : IMP::core::Direction
• set_domain() : IMP::atom::Selection
• set_domains() : IMP::atom::Selection
• set_Dxi() : IMP::isd::PenalizedComplexityPrior
• set_element() : IMP::atom::Selection
• set_ellipsoid_3d_geometry() : IMP::algebra::Ellipsoid3D
• set_em2d_restraint() : IMP.EMageFit.domino_model.DominoModel
• set_end() : IMP::spb::HelixDecorator
• set_ensemble_file() : IMP.pmi.mmcif.ProtocolOutput , IMP.pmi1.mmcif.ProtocolOutput
• set_equilibrium_rest_length_factor() : IMP::npctransport::RelaxingSpring
• 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 , IMP.pmi1.topology.TopologyReader
• set_ff_table() : IMP::saxs::Profile
• set_file_dataset() : IMP.pmi1.representation.Representation
• set_filename() : IMP::core::ScriptProvenance , IMP::core::StructureProvenance
• set_floppy_bodies_as_fixed() : IMP.pmi1.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 , IMP.pmi1.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_ideal() : IMP::atom::Angle , IMP::atom::Dihedral
• 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_index() : IMP::atom::Residue
• set_input_index() : IMP::atom::Atom
• set_interaction_k_factor() : IMP::npctransport::Scoring
• set_interaction_range_factor() : IMP::npctransport::Scoring
• set_interior_layer_thickness() : IMP::multifit::ComplementarityRestraint
• set_internal_coordinates() : IMP::core::RigidBodyMember
• set_internal_transformation() : IMP::core::RigidBodyMember
• set_interrupted() : IMP::npctransport::Statistics
• set_intersection() : IMP::atom::Selection
• set_is_complete() : IMP::container::PredicatePairsRestraint , IMP::container::PredicateQuadsRestraint , IMP::container::PredicateSingletonsRestraint , IMP::container::PredicateTripletsRestraint
• set_is_get_inputs_ignores_individual_scores() : IMP::container::PredicatePairsRestraint , IMP::container::PredicateQuadsRestraint , IMP::container::PredicateSingletonsRestraint , IMP::container::PredicateTripletsRestraint
• set_is_last_entry_from_top() : IMP::npctransport::Transporting
• 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_Jxi() : IMP::isd::PenalizedComplexityPrior
• set_k() : IMP::core::Harmonic , IMP::npctransport::PoreRadiusSingletonScore , IMP::npctransport::ZBiasSingletonScore
• set_k1() : IMP::npctransport::HarmonicSpringSingletonScore
• set_k2() : IMP::npctransport::HarmonicSpringSingletonScore
• set_k_attraction() : IMP::npctransport::LinearInteractionPairScore
• set_k_repulsion() : IMP::npctransport::LinearInteractionPairScore
• set_label() : IMP.pmi1.restraints.RestraintBase
• set_last_tracked_z() : IMP::npctransport::Transporting
• set_length() : IMP::atom::Bond , IMP::kinematics::PrismaticJoint
• set_link_length() : IMP::core::SurfaceTetheredChain , IMP::misc::FreelyJointedChain
• set_link_number() : IMP::core::SurfaceTetheredChain , IMP::misc::FreelyJointedChain
• set_local_covariance() : IMP::core::Gaussian
• set_local_optimizer() : IMP::core::MCCGSampler
• set_location() : IMP::core::SoftwareProvenance
• 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_move() : IMP::atom::BrownianDynamics
• set_maximum_number_of_assignments() : IMP::domino::DiscreteSampler
• set_maximum_penetration() : IMP::multifit::ComplementarityRestraint
• set_maximum_penetration_score() : IMP::multifit::ComplementarityRestraint
• set_maximum_rotation() : IMP::core::DirectionMover , IMP::core::SurfaceMover
• set_maximum_separation() : IMP::multifit::ComplementarityRestraint
• set_maximum_step_size() : IMP::core::SteepestDescent
• set_maximum_translation() : IMP::core::SurfaceMover
• set_mean() : IMP::core::Harmonic
• set_merge_tree() : IMP::domino::DominoSampler
• set_method() : IMP::core::FilterProvenance , IMP::core::SampleProvenance
• 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_multiplicity() : IMP::atom::Dihedral
• set_my_parameter() : IMP::mpi::ReplicaExchange
• set_n() : IMP::container::MinimumPairRestraint , IMP::container::MinimumQuadRestraint , IMP::container::MinimumSingletonRestraint , IMP::container::MinimumTripletRestraint
• set_n_entries_bottom() : IMP::npctransport::Transporting
• set_n_entries_top() : IMP::npctransport::Transporting
• 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_normal() : IMP::core::Surface
• set_normal_is_optimized() : IMP::core::Surface
• set_normal_x() : IMP::core::Surface
• set_normal_y() : IMP::core::Surface
• set_normal_z() : IMP::core::Surface
• set_not_optimized() : IMP.EMageFit.domino_model.DominoModel
• set_number_of_attempts() : IMP::core::MCCGSampler
• set_number_of_collisions() : IMP::kinematics::RRT
• set_number_of_conjugate_gradient_steps() : IMP::core::MCCGSampler
• set_number_of_frames() : IMP::core::CombineProvenance , IMP::core::FilterProvenance , IMP::core::SampleProvenance
• set_number_of_iterations() : IMP::core::SampleProvenance , IMP::kinematics::RRT
• set_number_of_members() : IMP::core::ClusterProvenance
• set_number_of_monte_carlo_steps() : IMP::core::MCCGSampler
• set_number_of_replicas() : IMP::core::SampleProvenance
• set_number_of_runs() : IMP::core::CombineProvenance
• set_number_of_updates() : IMP::OptimizerState
• set_number_of_weights() : IMP::isd::Weight
• set_number_of_weights_lazy() : IMP::isd::Weight
• set_old_rot() : IMP::em::ImageHeader
• set_order() : IMP::atom::Bond
• set_orientations() : IMP::em2d::RigidBodiesImageFitRestraint
• set_origin() : IMP::em::DensityMap
• set_output_level() : IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint , IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
• set_owner() : IMP::npctransport::ParticleTransportStatisticsOptimizerState
• 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_probabilities_on_anchors() : IMP::multifit::ProbabilisticAnchorGraph
• 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::em2d::Em2DRestraint , IMP::em::SampledDensityMap
• set_pdb_dir() : IMP.pmi.topology.TopologyReader , IMP.pmi1.topology.TopologyReader
• set_pdbs() : IMP.EMageFit.buildxlinks.InitialDockingFromXlinks
• set_period() : IMP::OptimizerState
• set_plane_3d_geometry() : IMP::algebra::Plane3D
• set_pore_radius() : IMP::npctransport::SlabWithPore
• set_pore_radius_is_optimized() : IMP::npctransport::SlabWithPore
• set_previous() : IMP::core::Provenance
• set_prob_coil() : IMP::atom::SecondaryStructureResidue
• set_prob_helix() : IMP::atom::SecondaryStructureResidue
• set_prob_strand() : IMP::atom::SecondaryStructureResidue
• set_projections() : IMP::em2d::ProjectionFinder
• set_proper_ranges_for_keys() : IMP::em2d::ProjectionParameters
• set_psi_is_sampled() : IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint , IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
• set_quaternion_1() : IMP::em2d::ProjectionParameters
• set_quaternion_2() : IMP::em2d::ProjectionParameters
• set_quaternion_3() : IMP::em2d::ProjectionParameters
• set_quaternion_4() : IMP::em2d::ProjectionParameters
• set_query_log() : IMP::algebra::NearestNeighborD< D >
• set_radius() : IMP::misc::CustomXYZR
• 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() : IMP.pmi.macros.AnalysisReplicaExchange , IMP.pmi1.macros.AnalysisReplicaExchange
• set_reference_frame() : IMP::core::RigidBody , IMP::core::Surface
• 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 , IMP.pmi1.analysis.Precision
• set_reflect_probability() : IMP::core::DirectionMover , IMP::core::SurfaceMover
• 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_offset() : IMP::core::StructureProvenance
• set_residue_pairs_to_display() : IMP.pmi1.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_rest_length() : IMP::npctransport::RelaxingSpring
• set_rest_length_diffusion_coefficient() : IMP::npctransport::RelaxingSpring
• set_rest_length_factor() : IMP::npctransport::FGChain
• set_restraints() : IMP::domino::DiscreteSampler
• set_return_best() : IMP::core::MonteCarlo
• set_rigid_bodies() : IMP.EMageFit.buildxlinks.InitialDockingFromXlinks , IMP.pmi1.representation.Representation
• set_rigid_bodies_as_fixed() : IMP.pmi1.representation.Representation
• set_rigid_body_from_hierarchies() : IMP.pmi1.representation.Representation
• set_rmf_file() : IMP::npctransport::SimulationData
• set_rmsd_selection() : IMP.pmi.macros.AnalysisReplicaExchange , IMP.pmi1.macros.AnalysisReplicaExchange
• set_root() : IMP::npctransport::FGChain
• set_rotation() : IMP::em2d::RegistrationResult
• set_rotational_diffusion_coefficient() : IMP::atom::RigidBodyDiffusion
• 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_sequence() : IMP::atom::Chain
• set_shift() : IMP::em2d::RegistrationResult
• set_sigma_is_sampled() : IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint , IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
• set_simulator() : IMP::rmf::SaveOptimizerState
• set_sites() : IMP::npctransport::SimulationData
• set_size() : IMP::em2d::Image
• set_slack() : IMP::core::CoverRefined
• set_slope() : IMP::bayesianem::GaussianEMRestraint , IMP::isd::GaussianEMRestraint
• set_software_name() : IMP::core::SoftwareProvenance
• 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_standard_keys() : IMP.pmi.io.crosslink.CrossLinkDataBaseKeywordsConverter , IMP.pmi1.io.crosslink.CrossLinkDataBaseKeywordsConverter
• 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_stiffness() : IMP::atom::Angle , IMP::atom::Bond , IMP::atom::Dihedral
• 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() : IMP.pmi.macros.AnalysisReplicaExchange , IMP.pmi1.macros.AnalysisReplicaExchange
• set_symmetric_difference() : IMP::atom::Selection
• set_temperature() : IMP::atom::Simulator , IMP::atom::VelocityScalingOptimizerState
• set_temperature_pattern() : IMP.EMageFit.monte_carlo.MonteCarloRelativeMoves
• set_temperature_scale_factor() : IMP::atom::TAMDParticle
• set_terminus() : IMP::atom::Selection
• set_thickness() : IMP::npctransport::SlabWithPore
• set_threshold() : IMP::core::FilterProvenance , IMP::core::SteepestDescent , IMP::gsl::ConjugateGradients
• set_title() : IMP::em::ImageHeader
• set_torus_3d_geometry() : IMP::algebra::Torus3D
• 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_translation_x() : IMP::em2d::ProjectionParameters
• set_translation_y() : IMP::em2d::ProjectionParameters
• set_tree_size() : IMP::kinematics::RRT
• set_type() : IMP::atom::Bond
• 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_use_stochastic_runge_kutta() : IMP::atom::BrownianDynamics
• set_value() : IMP::em2d::Image , IMP::em::DensityMap , IMP.pmi.io.crosslink.CrossLinkDataBase
• set_variance_images() : IMP::em2d::Em2DRestraint , IMP::em2d::ProjectionFinder
• set_variances() : IMP::core::Gaussian
• set_velocity_cap() : IMP::atom::MolecularDynamics , IMP::spb::MolecularDynamicsWithWte
• set_version() : IMP::core::SoftwareProvenance
• set_void_map() : IMP::em::DensityMap
• set_was_used() : IMP::Object
• set_weight() : IMP.bayesianem.restraint.GaussianEMRestraintWrapper , IMP.pmi1.restraints.RestraintBase
• set_weight_lazy() : IMP::isd::Weight
• set_weights() : IMP::core::WeightedSum , IMP::core::WeightedSumOfExponential , IMP::isd::Weight
• set_weights_are_optimized() : IMP::isd::Weight
• set_weights_lazy() : IMP::isd::Weight
• set_x() : IMP::core::XYZ
• set_xlink_restraint() : IMP.EMageFit.domino_model.DominoModel
• set_xlinks() : IMP.EMageFit.buildxlinks.DockOrder , IMP.EMageFit.buildxlinks.InitialDockingFromXlinks
• set_xorigin() : IMP::em::DensityHeader
• set_y() : IMP::core::XYZ
• set_yorigin() : IMP::em::DensityHeader
• set_z() : IMP::core::XYZ
• 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 , IMP::spb::MolecularDynamicsWithWte
• setup_component_sequence_connectivity() : IMP.pmi1.representation.Representation
• setup_contact_map() : IMP.pmi1.io.xltable.XLTable
• setup_domino_sampler() : IMP.EMageFit.domino_model.DominoModel
• setup_for_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
• 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::ClusterProvenance , IMP::core::CombineProvenance , IMP::core::Cover , IMP::core::Direction , IMP::core::DirectionAngle , IMP::core::FilterProvenance , IMP::core::Gaussian , IMP::core::Hierarchy , IMP::core::Provenance , IMP::core::Provenanced , IMP::core::Reference , IMP::core::RigidBody , IMP::core::SampleProvenance , IMP::core::ScriptProvenance , IMP::core::SoftwareProvenance , IMP::core::StructureProvenance , IMP::core::Surface , 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::npctransport::RelaxingSpring , IMP::npctransport::SlabWithCylindricalPore , IMP::npctransport::SlabWithPore , IMP::npctransport::SlabWithToroidalPore , IMP::npctransport::Transporting , IMP::pmi1::Resolution , IMP::pmi1::Symmetric , IMP::pmi1::Uncertainty , 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 >
• show_projection_params() : IMP::em::ImageHeader
• show_restraint_information() : IMP::domino::RestraintCache
• shuffle_configuration() : IMP.pmi1.representation.Representation
• sigmoid() : IMP.pmi.restraints.proteomics.ConnectivityNetworkRestraint , IMP.pmi1.restraints.proteomics.ConnectivityNetworkRestraint
• SigmoidRestraintSphere() : IMP::pmi1::SigmoidRestraintSphere
• simulate() : IMP::atom::Simulator
• simulate_wave() : IMP::atom::Simulator
• SimulationData() : IMP::npctransport::SimulationData
• 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
• SitesPairScore() : IMP::npctransport::SitesPairScore
• SitesPairScoreParameters() : IMP::npctransport::SitesPairScoreParameters
• size() : IMP::saxs::Profile
• SlabWithCylindricalPorePairScore() : IMP::npctransport::SlabWithCylindricalPorePairScore
• SlabWithCylindricalPoreWireGeometry() : IMP::npctransport::SlabWithCylindricalPoreWireGeometry
• SlabWithToroidalPorePairScore() : IMP::npctransport::SlabWithToroidalPorePairScore
• SlabWithToroidalPoreWireGeometry() : IMP::npctransport::SlabWithToroidalPoreWireGeometry
• Soap() : IMP::score_functor::Soap
• 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 >
• Statistics() : IMP::npctransport::Statistics
• 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
• SubsetMover() : IMP::core::SubsetMover
• sum_partial_profiles() : IMP::saxs::Profile
• SurfaceShellDensityMap() : IMP::em::SurfaceShellDensityMap
• SurfaceSymmetryConstraint() : IMP::core::SurfaceSymmetryConstraint
• swap() : IMP.EMageFit.buildxlinks.Xlink
• swap_configuration() : IMP::Configuration