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
- 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_
: IMP::em2d::RegistrationResult
- 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
- 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
- shift_
: IMP::em2d::RegistrationResult
- 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
- 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.EMageFit.solutions_io.ResultsDB
- store_data()
: IMP.EMageFit.database.Database2
- store_dataV1()
: IMP.EMageFit.database.Database2
- stored_cc_
: IMP::em::CoarseCCatIntervals
- stored_dvx_
: IMP::em::CoarseCCatIntervals
- subjects_
: IMP::em2d::ProjectionFinder
- Subset()
: IMP::domino::Subset
- sum_partial_profiles()
: IMP::saxs::Profile
- SurfaceShellDensityMap()
: IMP::em::SurfaceShellDensityMap
- swap()
: IMP.EMageFit.buildxlinks.Xlink
- swap_configuration()
: IMP::Configuration
- szIDat
: IMP::em::SpiderHeader
- szITim
: IMP::em::SpiderHeader
- szITit
: IMP::em::SpiderHeader