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IMP Reference Guide
2.20.2
The Integrative Modeling Platform
IMP Manual
Reference Guide
Tutorial Index
Modules
Classes
Examples
Class List
Class Index
Class Hierarchy
Class Members
All
Functions
Variables
Enumerations
Related Functions
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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
save_dependencies() :
IMP::Model
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_can_skip() :
IMP::ScoreState
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::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
,
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_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_keywords() :
IMP::atom::PDBRecord
set_label() :
IMP.pmi1.restraints.RestraintBase
set_last_tracked_z() :
IMP::npctransport::Transporting
set_length() :
IMP::atom::Bond
,
IMP::kinematics::PrismaticJoint
set_line() :
IMP::atom::PDBRecord
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_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_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
,
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_moved() :
IMP::core::MonteCarlo
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_sequence_offset() :
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_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
,
IMP.pmi1.io.crosslink.CrossLinkDataBaseKeywordsConverter
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_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_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_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::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
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