IMP
2.1.0
The Integrative Modeling Platform
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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_configuration() :
IMP::kernel::ConfigurationSet
SaveOptimizerState() :
IMP::rmf::SaveOptimizerState
scale() :
IMP::saxs::RadialDistributionFunction
,
IMP::saxs::Profile
ScopedAddCacheAttribute() :
IMP::kernel::ScopedAddCacheAttribute< Key, Value >
ScopedSetAttribute() :
IMP::kernel::ScopedSetAttribute< Key, Value >
score() :
IMP::em::EnvelopeScore
score_alignment() :
IMP::cnmultifit::AlignSymmetric
ScoreAccumulator() :
IMP::kernel::ScoreAccumulator
ScoreState() :
IMP::kernel::ScoreState
select_table() :
IMP.em2d.Database.Database2
Selection() :
IMP::atom::Selection
SerialMover() :
IMP::core::SerialMover
set() :
IMP::benchmark::Profiler
,
IMP::kernel::ScopedAddCacheAttribute< Key, Value >
,
IMP::kernel::ScopedSetAttribute< Key, Value >
,
IMP::base::Memoizer< Generator, Checker >
,
IMP::base::CreateLogContext
,
IMP::base::SetCheckState
,
IMP::base::SetLogState
,
IMP::base::SetNumberOfThreads
set_angle() :
IMP::algebra::Rotation2D
,
IMP::kinematics::RevoluteJoint
set_assembly() :
IMP.em2d.DominoModel.DominoModel
set_assembly_components() :
IMP.em2d.DominoModel.DominoModel
set_assignments() :
IMP::domino::ListAssignmentsTable
set_atom_type() :
IMP::atom::Atom
,
IMP::atom::Selection
set_atom_types() :
IMP::atom::Selection
set_attribute() :
IMP::kernel::Model
set_bounding_box() :
IMP::algebra::GridD< D, Storage, Value, EmbeddingT >
,
IMP::core::MCCGSampler
set_chain() :
IMP::atom::Selection
set_chains() :
IMP::atom::Selection
set_check_level() :
IMP::base::Object
set_close_pairs_excluded_volume_restraint() :
IMP.em2d.DominoModel.DominoModel
set_coarse_registration_mode() :
IMP::em2d::Em2DRestraint
set_complementarity_restraint() :
IMP.em2d.DominoModel.DominoModel
set_complementarity_thickness() :
IMP::multifit::ComplementarityRestraint
set_complementarity_value() :
IMP::multifit::ComplementarityRestraint
set_components_and_connections() :
IMP.em2d.buildxlinks.DockOrder
set_connectivity_restraint() :
IMP.em2d.DominoModel.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_safe() :
IMP::kinematics::KinematicForest
set_copy_index() :
IMP::atom::Selection
set_copy_indexes() :
IMP::atom::Selection
set_current_time() :
IMP::atom::Simulator
set_d() :
IMP::atom::Diffusion
set_data() :
IMP::em2d::Image
set_decorator_name() :
IMP::example::ExampleDecorator
set_domain() :
IMP::atom::Selection
set_domains() :
IMP::atom::Selection
set_em2d_restraint() :
IMP.em2d.DominoModel.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_ff_table() :
IMP::saxs::Profile
set_gradient_threshold() :
IMP::core::ConjugateGradients
set_has_dependencies() :
IMP::kernel::ModelObject
set_has_required_score_states() :
IMP::kernel::ModelObject
set_header() :
IMP::em::ImageHeader
set_hierarchies() :
IMP.em2d.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_is_changed() :
IMP::kernel::Container
set_is_complete() :
IMP::container::PredicatePairsRestraint
,
IMP::container::PredicateQuadsRestraint
,
IMP::container::PredicateSingletonsRestraint
,
IMP::container::PredicateTripletsRestraint
set_is_optimized() :
IMP::kernel::Model
set_is_optimizing() :
IMP::kernel::OptimizerState
set_is_refining() :
IMP::core::MCCGSampler
set_is_rigid_member() :
IMP::core::RigidBody
set_joints() :
IMP::kinematics::CompositeJoint
set_k() :
IMP::core::Harmonic
,
IMP::restrainer::SimpleConnectivity
,
IMP::restrainer::SimpleDistance
,
IMP::restrainer::SimpleDiameter
set_length() :
IMP::kinematics::PrismaticJoint
set_local_optimizer() :
IMP::core::MCCGSampler
set_log_level() :
IMP::base::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_score() :
IMP::kernel::Model
set_maximum_separation() :
IMP::multifit::ComplementarityRestraint
set_maximum_step_size() :
IMP::core::SteepestDescent
set_mean() :
IMP::core::Harmonic
,
IMP::restrainer::SimpleConnectivity
,
IMP::restrainer::SimpleDistance
,
IMP::restrainer::SimpleDiameter
set_merge_tree() :
IMP::domino::DominoSampler
set_model() :
IMP::core::MinimumRestraint
,
IMP::kernel::ModelObject
set_model_particles() :
IMP::em2d::ProjectionFinder
,
IMP::em2d::CollisionCrossSection
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_native_assembly_for_benchmark() :
IMP.em2d.DominoModel.DominoModel
set_not_optimized() :
IMP.em2d.DominoModel.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::kernel::OptimizerState
set_old_rot() :
IMP::em::ImageHeader
set_orientations() :
IMP::em2d::RigidBodiesImageFitRestraint
set_origin() :
IMP::em::DensityMap
set_owner_kf() :
IMP::kinematics::Joint
set_pair_score() :
IMP::core::TypedPairScore
set_pair_score_restraint() :
IMP.em2d.DominoModel.DominoModel
set_parameters_optimized() :
IMP::em2d::ProjectionParameters
set_params() :
IMP::em::KernelParameters
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::em::SampledDensityMap
,
IMP::em2d::Em2DRestraint
set_pdbs() :
IMP.em2d.buildxlinks.InitialDockingFromXlinks
set_period() :
IMP::kernel::OptimizerState
set_projections() :
IMP::em2d::ProjectionFinder
set_proper_ranges_for_keys() :
IMP::em2d::ProjectionParameters
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.em2d.DominoModel.DominoModel
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_relative_movers() :
IMP.em2d.MonteCarloRelativeMoves.MonteCarloRelativeMoves
set_residue_index() :
IMP::atom::Selection
set_residue_indexes() :
IMP::atom::Fragment
,
IMP::atom::Selection
set_residue_type() :
IMP::atom::Residue
,
IMP::atom::Selection
set_residue_types() :
IMP::atom::Selection
set_resolution() :
IMP::em::DensityHeader
set_restraints() :
IMP::kernel::Optimizer
set_return_best() :
IMP::core::MonteCarlo
set_rigid_bodies() :
IMP.em2d.buildxlinks.InitialDockingFromXlinks
set_rotation() :
IMP::em2d::RegistrationResult
set_save_match_images() :
IMP::em2d::ProjectionFinder
set_save_rejected_configurations() :
IMP::core::MCCGSampler
set_scaled_value() :
IMP::kernel::Optimizer
set_score() :
IMP::container::PredicatePairsRestraint
,
IMP::container::PredicateQuadsRestraint
,
IMP::container::PredicateSingletonsRestraint
,
IMP::container::PredicateTripletsRestraint
set_score_threshold() :
IMP::kernel::Optimizer
set_scoring_function() :
IMP::kernel::Optimizer
set_secondary_structure_probabilities() :
IMP::multifit::AnchorsData
set_shift() :
IMP::em2d::RegistrationResult
set_simulator() :
IMP::rmf::SaveOptimizerState
set_size() :
IMP::em2d::Image
set_slack() :
IMP::core::CoverRefined
set_sphere() :
IMP::core::XYZR
,
IMP::misc::CustomXYZR
set_standard_deviation() :
IMP::restrainer::SimpleConnectivity
,
IMP::restrainer::SimpleDistance
,
IMP::restrainer::SimpleDiameter
set_starts_and_ends() :
IMP::em2d::CenteredMat
set_step_size() :
IMP::core::SteepestDescent
set_stop_on_good_score() :
IMP::kernel::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_target_radius() :
IMP::atom::Selection
set_temperature() :
IMP::atom::VelocityScalingOptimizerState
set_temperature_pattern() :
IMP.em2d.MonteCarloRelativeMoves.MonteCarloRelativeMoves
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::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_unknown_score() :
IMP::container::PredicateQuadsRestraint
,
IMP::container::PredicatePairsRestraint
,
IMP::container::PredicateSingletonsRestraint
,
IMP::container::PredicateTripletsRestraint
set_use_cross_subset_filtering() :
IMP::domino::DominoSampler
set_value() :
IMP::em::DensityMap
,
IMP::em2d::Image
,
IMP::kernel::Optimizer
set_variance_images() :
IMP::em2d::Em2DRestraint
,
IMP::em2d::ProjectionFinder
set_velocity_cap() :
IMP::atom::MolecularDynamics
set_void_map() :
IMP::em::DensityMap
set_was_used() :
IMP::base::Object
set_weights() :
IMP::isd::Weight
set_weights_are_optimized() :
IMP::isd::Weight
set_xlink_restraint() :
IMP.em2d.DominoModel.DominoModel
set_xlinks() :
IMP.em2d.buildxlinks.DockOrder
,
IMP.em2d.buildxlinks.InitialDockingFromXlinks
set_xorigin() :
IMP::em::DensityHeader
set_yorigin() :
IMP::em::DensityHeader
set_zeros() :
IMP::em2d::Image
set_zorigin() :
IMP::em::DensityHeader
SetCheckState() :
IMP::base::SetCheckState
SetLogState() :
IMP::base::SetLogState
SetNumberOfThreads() :
IMP::base::SetNumberOfThreads
setup() :
IMP::em2d::PolarResamplingParameters
,
IMP::atom::Simulator
,
IMP::em2d::Em2DRestraint
,
IMP::em2d::Fine2DRegistrationRestraint
,
IMP::em2d::ProjectionFinder
,
IMP::atom::MolecularDynamics
setup_domino_sampler() :
IMP.em2d.DominoModel.DominoModel
setup_hierarchy() :
IMP::atom::CHARMMTopology
setup_kernel() :
IMP::em2d::MasksManager
setup_particle() :
IMP::atom::Bonded
,
IMP::atom::Chain
,
IMP::atom::Residue
,
IMP::isd::Scale
,
IMP::isd::Weight
,
IMP::atom::Angle
,
IMP::atom::Dihedral
,
IMP::core::XYZR
,
IMP::atom::Charged
,
IMP::isd::Switching
,
IMP::atom::Domain
,
IMP::atom::Atom
,
IMP::atom::LennardJones
,
IMP::isd::Nuisance
,
IMP::display::Colored
,
IMP::atom::SecondaryStructureResidue
,
IMP::atom::Chain
,
IMP::atom::Copy
,
IMP::core::RigidBody
,
IMP::core::XYZ
,
IMP::atom::CHARMMAtom
,
IMP::core::XYZR
,
IMP::em::Voxel
,
IMP::atom::Residue
,
IMP::atom::Domain
,
IMP::example::ExampleDecorator
,
IMP::atom::Fragment
,
IMP::isd::Scale
,
IMP::core::Hierarchy
,
IMP::core::XYZ
,
IMP::kinematics::KinematicNode
,
IMP::core::Typed
,
IMP::atom::Diffusion
,
IMP::kinematics::KinematicNode
,
IMP::core::RigidBody
,
IMP::core::Reference
,
IMP::atom::Mass
,
IMP::atom::Residue
,
IMP::core::Cover
,
IMP::atom::Molecule
,
IMP::core::Centroid
,
IMP::atom::Charged
,
IMP::atom::Residue
,
IMP::atom::RigidBodyDiffusion
,
IMP::atom::LennardJones
,
IMP::kinematics::KinematicNode
,
IMP::atom::Molecule
,
IMP::atom::Hierarchy
,
IMP::atom::Fragment
,
IMP::atom::Diffusion
,
IMP::core::Hierarchy
,
IMP::em2d::ProjectionParameters
,
IMP::misc::CustomXYZR
,
IMP::core::Cover
,
IMP::atom::Fragment
,
IMP::atom::Atom
,
IMP::core::XYZR
setup_secondary_structure() :
IMP::multifit::AnchorsData
show() :
IMP::algebra::LinearFit2D
,
IMP::saxs::DeltaDistributionFunction
,
IMP::saxs::RadialDistributionFunction
,
IMP::em2d::DummyRestraint
,
IMP::em2d::ProjectingParameters
,
IMP::display::PivyWriter
,
IMP::saxs::FormFactorTable
,
IMP::kernel::PythonDirectedGraph
,
IMP::multifit::FittingSolutionRecord
,
IMP::em2d::ProjectingOptions
,
IMP::em2d::ParticlesDummyRestraint
,
IMP::em::RadiusDependentKernelParameters
,
IMP::em2d::Image
,
IMP::em2d::CollisionCrossSection
,
IMP::algebra::Rotation2D
show_all() :
IMP::kernel::Key< ID, LazyAdd >
show_all_restraints() :
IMP.restrainer.Restraint
show_projection_params() :
IMP::em::ImageHeader
show_restraint_information() :
IMP::domino::RestraintCache
Simplex() :
IMP::gsl::Simplex
simulate() :
IMP::atom::Simulator
simulate_wave() :
IMP::atom::Simulator
Simulator() :
IMP::atom::Simulator
SingletonConstraint() :
IMP::core::SingletonConstraint
SingletonContainerAdaptor() :
IMP::kernel::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
SteepestDescent() :
IMP::core::SteepestDescent
store_cluster_data() :
IMP.em2d.solutions_io.ResultsDB
store_data() :
IMP.em2d.Database.Database2
store_dataV1() :
IMP.em2d.Database.Database2
Subset() :
IMP::domino::Subset
sum_partial_profiles() :
IMP::saxs::Profile
SurfaceShellDensityMap() :
IMP::em::SurfaceShellDensityMap
swap() :
IMP.em2d.buildxlinks.Xlink
swap_configuration() :
IMP::kernel::Configuration