- s -

same_dimensions() : IMP::em::DensityMap
same_origin() : IMP::em::DensityMap
same_voxel_size() : IMP::em::DensityMap
sample_and_apply() : IMP::kinematics::DOFsSampler
sample_obstacles() : IMP::bff::PathMap
SampledDensityMap() : IMP::em::SampledDensityMap
sanity_check() : IMP.isd.History.History
save_cache() : IMP::domino::RestraintCache
save_clusters() : IMP.pmi.macros.AnalysisReplicaExchange
save_configuration() : IMP::ConfigurationSet
save_coordinates() : IMP.pmi.macros.AnalysisReplicaExchange
save_data() : IMP.pmi.macros.AnalysisReplicaExchange
save_dependencies() : IMP::Model
scale() : IMP::saxs::Profile , IMP::saxs::RadialDistributionFunction
ScopedAddCacheAttribute() : IMP::ScopedAddCacheAttribute< Key, Value >
ScopedSetAttribute() : IMP::ScopedSetAttribute< Key, Value >
score() : IMP::bff::DecayScore , IMP::em::EnvelopeScore
score_alignment() : IMP::cnmultifit::AlignSymmetric
score_model() : IMP::bff::AVPairDistanceMeasurement
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::bff::DecayModifier , IMP::bff::DecayRange , IMP::bff::DecayScale , IMP::bff::DecayScore , 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_abs_lifetime_spectrum() : IMP::bff::DecayLifetimeHandler
set_acquisition_time() : IMP::bff::DecayCurve
set_active() : IMP::bff::DecayModifier
set_actual_tree_size() : IMP::kinematics::RRT
set_alignment_selection() : IMP.pmi.macros.AnalysisReplicaExchange
set_allowed_sphere_radius() : IMP::bff::AV
set_alpha() : IMP::isd::PenalizedComplexityPrior
set_amplitude_threshold() : IMP::bff::DecayLifetimeHandler
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_av_parameter() : IMP::bff::AV
set_av_parameters_are_optimized() : IMP::bff::AV
set_backbone_k() : IMP::npctransport::FGChain
set_begin() : IMP::spb::HelixDecorator
set_blank_outside() : IMP::bff::DecayScale
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_can_skip() : IMP::ScoreState
set_chain_id() : IMP::atom::Selection , IMP::core::StructureProvenance
set_chain_ids() : IMP::atom::Selection
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_constant_background() : IMP::bff::DecayScale
set_constant_offset() : IMP::bff::DecayPattern
set_contact_volume_thickness() : IMP::bff::AV
set_contact_volume_trapped_fraction() : IMP::bff::AV
set_convolution_method() : IMP::bff::DecayConvolution
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_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::bff::DecayModifier , IMP::bff::DecayScore , IMP::bff::PathMap , IMP::em2d::Image , IMP.pmi.macros.AnalysisReplicaExchange
set_decorator_name() : IMP::example::ExampleDecorator , IMP::npc::SlabWithSphericalIndent
set_denominator() : IMP::core::WeightedSumOfExponential
set_density() : IMP::core::ClusterProvenance , 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
set_equilibrium_rest_length_factor() : IMP::npctransport::RelaxingSpring
set_estimated_number_of_angles() : IMP::em2d::PolarResamplingParameters
set_expected_subcomplexes() : IMP.spatiotemporal.graphNode.graphNode
set_ey() : IMP::bff::DecayCurve
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_filename() : IMP::core::ScriptProvenance , IMP::core::StructureProvenance
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_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_index() : IMP::atom::Residue , IMP.spatiotemporal.graphNode.graphNode
set_input_index() : IMP::atom::Atom
set_instrument_dead_time() : IMP::bff::DecayPileup
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_keywords() : IMP::atom::PDBRecord
set_label() : IMP.spatiotemporal.graphNode.graphNode
set_label_asym_id() : IMP::atom::Chain
set_last_tracked_z() : IMP::npctransport::Transporting
set_length() : IMP::atom::Bond , IMP::kinematics::PrismaticJoint
set_lifetime_spectrum() : IMP::bff::DecayLifetimeHandler
set_line() : IMP::atom::PDBRecord
set_linearization_table() : IMP::bff::DecayLinearization
set_link_length() : IMP::core::SurfaceTetheredChain , IMP::misc::FreelyJointedChain
set_link_number() : IMP::core::SurfaceTetheredChain , IMP::misc::FreelyJointedChain
set_linker_length() : IMP::bff::AV
set_linker_width() : IMP::bff::AV
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() : IMP::bff::DecayScore
set_model_particles() : IMP::em2d::CollisionCrossSection , IMP::em2d::ProjectionFinder
set_molecule() : IMP::atom::Selection
set_molecules() : IMP::atom::Selection
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_neighbor_radius() : IMP::bff::PathMapHeader
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_obstacle_threshold() : IMP::bff::PathMapHeader
set_old_rot() : IMP::em::ImageHeader
set_order() : IMP::atom::Bond
set_orientations() : IMP::em2d::RigidBodiesImageFitRestraint
set_origin() : IMP::bff::PathMapHeader , IMP::em::DensityMap
set_output_level() : IMP.pmi.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_path_map_header() : IMP::bff::PathMap
set_path_origin() : IMP::bff::PathMapHeader
set_pattern() : IMP::bff::DecayPattern
set_pattern_fraction() : IMP::bff::DecayPattern
set_pdb_dir() : IMP.pmi.topology.TopologyReader
set_pdbs() : IMP.EMageFit.buildxlinks.InitialDockingFromXlinks
set_period() : IMP::OptimizerState
set_pile_up_model() : IMP::bff::DecayPileup
set_plane_3d_geometry() : IMP::algebra::Plane3D
set_pore_radius() : IMP::npc::SlabWithPore , IMP::npctransport::SlabWithPore
set_pore_radius_is_optimized() : IMP::npc::SlabWithPore , IMP::npctransport::SlabWithPore
set_precision() : IMP::core::ClusterProvenance
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
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_radius1() : IMP::bff::AV
set_radius2() : IMP::bff::AV
set_radius3() : IMP::bff::AV
set_radius_of_gyration() : IMP::multifit::RadiusOfGyrationRestraint
set_random_move_probability() : IMP::em2d::RelativePositionMover
set_random_registration() : IMP::em2d::RegistrationResult
set_range() : IMP::bff::DecayRange
set_rb_states() : IMP.EMageFit.domino_model.DominoModel
set_reduced_coordinates() : IMP::core::RigidBodyTunneler
set_reference() : IMP.pmi.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
set_reflect_probability() : IMP::core::DirectionMover , IMP::core::SurfaceMover
set_relative_movers() : IMP.EMageFit.monte_carlo.MonteCarloRelativeMoves
set_repetition_rate() : IMP::bff::DecayPileup
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_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
set_rmf_file() : IMP::npctransport::SimulationData
set_rmsd_selection() : IMP.pmi.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_moved() : IMP::core::MonteCarlo
set_score_threshold() : IMP::core::MonteCarlo
set_score_type() : IMP::bff::DecayScore
set_scores() : IMP.spatiotemporal.graphNode.graphNode
set_scoring_function() : IMP.EMageFit.monte_carlo.MonteCarloRelativeMoves , IMP::Optimizer
set_secondary_structure_probabilities() : IMP::multifit::AnchorsData
set_sequence() : IMP::atom::Chain
set_sequence_offset() : IMP::atom::Chain
set_shift() : IMP::bff::DecayCurve , IMP::em2d::RegistrationResult
set_sigma_is_sampled() : IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
set_simulation_grid_resolution() : IMP::bff::AV
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_source_protein1() : IMP::isd::CrossLinkMSRestraint
set_source_protein2() : IMP::isd::CrossLinkMSRestraint
set_source_residue1() : IMP::isd::CrossLinkMSRestraint
set_source_residue2() : IMP::isd::CrossLinkMSRestraint
set_sphere() : IMP::core::XYZR , IMP::misc::CustomXYZR
set_sphere_patch_3d_geometry() : IMP::algebra::SpherePatch3D
set_standard_keys() : IMP.pmi.io.crosslink.CrossLinkDataBaseKeywordsConverter
set_start() : IMP::bff::DecayRange
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() : IMP::bff::DecayRange
set_stop_on_good_score() : IMP::Optimizer
set_stop_score() : IMP::gsl::GSLOptimizer
set_subcomplex_components() : IMP.spatiotemporal.graphNode.graphNode
set_subjects() : IMP::em2d::ProjectionFinder
set_surface_shell() : IMP::em::SurfaceShellDensityMap
set_symmetric() : IMP.pmi.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::npc::SlabWithPore , IMP::npctransport::SlabWithPore
set_threshold() : IMP::core::FilterProvenance , IMP::core::SteepestDescent , IMP::gsl::ConjugateGradients
set_time() : IMP.spatiotemporal.graphNode.graphNode
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_trigger_updated() : IMP::Model
set_type() : IMP::atom::Bond
set_union() : IMP::atom::Selection
set_uniprot_accession() : IMP::atom::Chain
set_unknown_score() : IMP::container::PredicatePairsRestraint , IMP::container::PredicateQuadsRestraint , IMP::container::PredicateSingletonsRestraint , IMP::container::PredicateTripletsRestraint
set_use_amplitude_threshold() : IMP::bff::DecayLifetimeHandler
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::bff::PathMapTile , 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
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::bff::DecayCurve , 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::bff::DecayCurve , 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::PolarResamplingParameters , IMP::em2d::ProjectionFinder , IMP::spb::MolecularDynamicsWithWte
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::bff::AV , 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::npc::SlabWithPore , IMP::npc::SlabWithSphericalIndent , IMP::npc::SlabWithToroidalPore , IMP::npctransport::RelaxingSpring , IMP::npctransport::SlabWithCylindricalPore , IMP::npctransport::SlabWithPore , IMP::npctransport::SlabWithToroidalPore , IMP::npctransport::Transporting , IMP::pmi::Resolution , IMP::pmi::Symmetric , IMP::pmi::Uncertainty
setup_secondary_structure() : IMP::multifit::AnchorsData
shift_array() : IMP::bff::DecayCurve
show() : IMP::algebra::LinearFit2D , IMP::algebra::Rotation2D , IMP::atom::Hierarchy , IMP::bff::AVNetworkRestraint , 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
sigmoid() : IMP.pmi.restraints.proteomics.ConnectivityNetworkRestraint
simulate() : IMP::atom::Simulator
simulate_wave() : IMP::atom::Simulator
SimulationData() : IMP::npctransport::SimulationData
Simulator() : IMP::atom::Simulator
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::bff::DecayCurve , IMP::saxs::Profile
SlabWithCylindricalPorePairScore() : IMP::npctransport::SlabWithCylindricalPorePairScore
SlabWithCylindricalPoreWireGeometry() : IMP::npctransport::SlabWithCylindricalPoreWireGeometry
SlabWithSphericalIndentMBMScore() : IMP::npc::SlabWithSphericalIndentMBMScore
SlabWithToroidalPoreGoPairScore() : IMP::npc::SlabWithToroidalPoreGoPairScore
SlabWithToroidalPoreMBMScore() : IMP::npc::SlabWithToroidalPoreMBMScore
SlabWithToroidalPorePairScore() : IMP::npctransport::SlabWithToroidalPorePairScore
SlabWithToroidalPoreWireGeometry() : IMP::npc::SlabWithToroidalPoreWireGeometry , IMP::npctransport::SlabWithToroidalPoreWireGeometry
Soap() : IMP::score_functor::Soap
solve() : IMP::isd::MultivariateFNormalSufficient
sort() : IMP::em::FittingSolutions
SpherePatch3D() : IMP::algebra::SpherePatch3D
SphericalIndentSurfaceDepthPairScore() : IMP::npc::SphericalIndentSurfaceDepthPairScore
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() : IMP::bff::DecayCurve
sum_partial_profiles() : IMP::saxs::Profile
SurfaceShellDensityMap() : IMP::em::SurfaceShellDensityMap
SurfaceSymmetryConstraint() : IMP::core::SurfaceSymmetryConstraint
swap() : IMP.EMageFit.buildxlinks.Xlink
swap_configuration() : IMP::Configuration