home
about
news
download
doc
source
systems
tests
bugs
contact
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
_
a
b
c
d
e
f
g
h
i
j
k
l
m
n
o
p
q
r
s
t
u
v
w
x
z
~
- g -
GammaPrior() :
IMP::isd::GammaPrior
Gaussian() :
IMP::spb::Gaussian
GaussianAnchorEMRestraint() :
IMP::isd::GaussianAnchorEMRestraint
GaussianEMRestraint() :
IMP::bayesianem::GaussianEMRestraint
,
IMP::isd::GaussianEMRestraint
GaussianProcessInterpolation() :
IMP::isd::GaussianProcessInterpolation
GaussianProcessInterpolationRestraint() :
IMP::isd::GaussianProcessInterpolationRestraint
GaussianRestraint() :
IMP::isd::GaussianRestraint
GenericAttributeSingletonScore() :
IMP::core::GenericAttributeSingletonScore< UF >
GenericBoundingBox3DSingletonScore() :
IMP::core::GenericBoundingBox3DSingletonScore< UF >
get() :
IMP.isd.utils.Pipe
,
IMP::Pointer< O >
,
IMP::PointerMember< O >
get_a() :
IMP::algebra::LinearFit2D
,
IMP::algebra::ParabolicFit2D
get_abort_evaluation() :
IMP::ScoreAccumulator
get_age() :
IMP::Model
get_all_chain_restraints() :
IMP::npctransport::Scoring
get_all_possible_indexes() :
IMP::atom::BondPairContainer
,
IMP::container::AllBipartitePairContainer
,
IMP::container::AllPairContainer
,
IMP::container::CloseBipartitePairContainer
,
IMP::container::ClosePairContainer
,
IMP::container::ConnectingPairContainer
,
IMP::container::ConsecutivePairContainer
,
IMP::container::ExclusiveConsecutivePairContainer
,
IMP::Container
,
IMP::container::PairContainerSet
,
IMP::container::QuadContainerSet
,
IMP::container::SingletonContainerSet
,
IMP::container::TripletContainerSet
get_all_probabilities() :
IMP::atom::SecondaryStructureResidue
get_all_strings() :
IMP::Key< ID >
get_alpha() :
IMP::isd::PenalizedComplexityPrior
get_alt_loc_indicator() :
IMP::atom::PDBRecord
get_angle() :
IMP::algebra::Cone3D
,
IMP::algebra::Rotation2D
,
IMP::core::DirectionAngle
,
IMP::kinematics::RevoluteJoint
get_angle_derivative() :
IMP::core::DirectionAngle
get_angle_key() :
IMP::core::DirectionAngle
get_angle_parameters() :
IMP::atom::CHARMMParameters
get_angle_step() :
IMP::em2d::PolarResamplingParameters
get_angular_d_factor() :
IMP::npctransport::SimulationData
get_are_close_and_filtered() :
IMP::core::QuadraticClosePairsFinder
get_are_floaters_on_one_slab_side() :
IMP::npctransport::SimulationData
get_area() :
IMP::algebra::Plane3D
,
IMP::algebra::SpherePatch3D
get_assignment_and_RFs() :
IMP.EMageFit.domino_model.DominoModel
get_assignment_info() :
IMP.EMageFit.domino_model.DominoModel
get_assignment_scores() :
IMP.EMageFit.domino_model.DominoModel
get_assignment_text() :
IMP.EMageFit.domino_model.DominoModel
get_assignments() :
IMP::kmeans::KMeans
get_assignments_with_heap() :
IMP.EMageFit.domino_model.DominoModel
get_atom() :
IMP::atom::CHARMMBondEndpoint
get_atom_exists() :
IMP::rotamer::ResidueRotamer
get_atomic_residues() :
IMP.pmi.topology.Molecule
get_atoms() :
IMP::atom::CHARMMConnection< D >
get_attribute() :
IMP::Model
get_average_distance() :
IMP::core::SurfaceTetheredChain
,
IMP::misc::FreelyJointedChain
get_average_distance_wrt_reference_structure() :
IMP.pmi.analysis.Precision
,
IMP.pmi1.analysis.Precision
get_average_fraction_bound_particle_sites_I() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_fraction_bound_particle_sites_II() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_fraction_bound_particles_I() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_fraction_bound_particles_II() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_fraction_nonspecific_interactions_I() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_fraction_nonspecific_interactions_II() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_number_of_contacts() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_off_per_bound_I_per_ns() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_off_per_bound_II_per_ns() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_off_per_contact_per_ns() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_on_per_missing_contact_per_ns() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_on_per_unbound_I_per_ns() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_average_on_per_unbound_II_per_ns() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_b() :
IMP::algebra::LinearFit2D
,
IMP::algebra::ParabolicFit2D
get_backbone_k() :
IMP::npctransport::FGChain
get_backward_converter() :
IMP.pmi.io.crosslink.CrossLinkDataBaseKeywordsConverter
,
IMP.pmi1.io.crosslink.CrossLinkDataBaseKeywordsConverter
get_barycenter() :
IMP::algebra::UnitSimplexBaseD< D >
get_base_plane() :
IMP::algebra::Cone3D
get_bd() :
IMP::npctransport::SimulationData
get_bead() :
IMP::npctransport::FGChain
get_bead_index() :
IMP::npctransport::FGChain
get_beads() :
IMP::npctransport::FGChain
,
IMP::npctransport::SimulationData
get_beads_byref() :
IMP::npctransport::SimulationData
get_begin() :
IMP::spb::HelixDecorator
get_best_accepted_energy() :
IMP::core::MonteCarlo
get_best_stats() :
IMP.pmi.restraints.crosslinking.AtomicCrossLinkMSRestraint
,
IMP.pmi1.restraints.crosslinking.AtomicCrossLinkMSRestraint
get_bin_size() :
IMP::saxs::Distribution< ValueT >
get_binarized_interior() :
IMP::em::DensityMap
get_body_member_particle_indexes() :
IMP::core::RigidBody
get_bond() :
IMP::atom::Bonded
get_bond_parameters() :
IMP::atom::CHARMMParameters
get_bonded() :
IMP::atom::Bond
,
IMP::atom::Bonded
get_bottom_z() :
IMP::npctransport::ExcludeZRangeSingletonScore
get_boundary_point() :
IMP::algebra::SpherePatch3D
get_bounding_box() :
IMP::algebra::Cone3D
,
IMP::algebra::Cylinder3D
,
IMP::algebra::Ellipsoid3D
,
IMP::algebra::Line3D
,
IMP::algebra::Plane3D
,
IMP::algebra::Segment3D
,
IMP::algebra::SpherePatch3D
,
IMP::algebra::Torus3D
,
IMP::atom::Hierarchy
get_bounding_box_size() :
IMP::npctransport::SimulationData
get_bounding_sphere() :
IMP::atom::Hierarchy
get_bounding_sphere_radius() :
IMP::npctransport::SimulationData
get_bounding_volume_restraint() :
IMP::npctransport::Scoring
get_buckets() :
IMP::multifit::GeometricHash< T, D >
get_by_type() :
IMP::atom::Hierarchy
get_by_unique_id() :
IMP::Model
get_c() :
IMP::algebra::ParabolicFit2D
get_can_refine() :
IMP::atom::BondEndpointsRefiner
,
IMP::core::ChildrenRefiner
,
IMP::core::FixedRefiner
,
IMP::core::LeavesRefiner
,
IMP::core::TableRefiner
,
IMP::multifit::RigidLeavesRefiner
,
IMP::Refiner
get_can_skip() :
IMP::ScoreState
get_cartesian_coordinates() :
IMP::algebra::SphericalVector3D
get_cc() :
IMP.multifit.cluster.AlignmentClustering
get_ccc() :
IMP::em2d::RegistrationResult
,
IMP.EMageFit.solutions_io.ResultsDB
get_ccs() :
IMP::em2d::CollisionCrossSection
get_center() :
IMP::kmeans::KMeans
get_center_of_mass() :
IMP.bayesianem.restraint.GaussianEMRestraintWrapper
,
IMP.pmi.restraints.em.GaussianEMRestraint
,
IMP.pmi1.restraints.em.GaussianEMRestraint
get_centroid() :
IMP::em::DensityMap
get_chain_id() :
IMP::atom::PDBRecord
,
IMP::core::StructureProvenance
get_chain_restraints() :
IMP::npctransport::FGChain
get_chain_restraints_on() :
IMP::npctransport::Scoring
get_chain_type() :
IMP::atom::Chain
,
IMP.pmi.alphabets.ResidueAlphabet
get_chain_type_key() :
IMP::atom::Chain
get_chains_of_super_rigid_bodies() :
IMP.pmi.topology.TopologyReader
,
IMP.pmi1.topology.TopologyReader
get_changed_key() :
IMP::core::Hierarchy
get_charge() :
IMP::atom::Charged
get_charmm_type() :
IMP::atom::CHARMMAtom
get_chi1() :
IMP::rotamer::RotamerAngleTuple
get_chi2() :
IMP::rotamer::RotamerAngleTuple
get_chi3() :
IMP::rotamer::RotamerAngleTuple
get_chi4() :
IMP::rotamer::RotamerAngleTuple
get_chi_square_experimental() :
IMP::statistics::ChiSquareMetric
get_child() :
IMP::atom::Hierarchy
get_child_index() :
IMP::core::Hierarchy
get_children() :
IMP::atom::Hierarchy
get_close_beads_container() :
IMP::npctransport::Scoring
get_close_pairs() :
IMP::core::BoxSweepClosePairsFinder
,
IMP::core::ClosePairsFinder
,
IMP::core::GridClosePairsFinder
,
IMP::core::NearestNeighborsClosePairsFinder
,
IMP::core::QuadraticClosePairsFinder
,
IMP::core::RigidClosePairsFinder
,
IMP::misc::MetricClosePairsFinder< LowerBound, UpperBound >
get_cluster() :
IMP::statistics::PartitionalClustering
,
IMP::statistics::PartitionalClusteringWithCenter
get_cluster_data() :
IMP.pmi.macros.AnalysisReplicaExchange
,
IMP.pmi1.macros.AnalysisReplicaExchange
get_cluster_elements() :
IMP::em2d::ClusterSet
get_cluster_formed_at_step() :
IMP::em2d::ClusterSet
get_cluster_representative() :
IMP::statistics::PartitionalClustering
,
IMP::statistics::PartitionalClusteringWithCenter
get_clusters_below_cutoff() :
IMP::em2d::ClusterSet
get_coarse_registration() :
IMP::em2d::ProjectionFinder
get_coarse_registration_time() :
IMP::em2d::ProjectionFinder
get_coarse_registrations_for_subject() :
IMP::em2d::ProjectionFinder
get_complete_registration() :
IMP::em2d::ProjectionFinder
get_components() :
IMP::atom::BondsGeometry
,
IMP::atom::HierarchiesGeometry
,
IMP::atom::HierarchyGeometry
,
IMP::atom::SelectionGeometry
,
IMP::core::EdgePairGeometry
,
IMP::core::EdgePairsGeometry
,
IMP::core::RigidBodyDerivativesGeometry
,
IMP::core::RigidBodyFramesGeometry
,
IMP::core::RigidBodyHierarchyGeometry
,
IMP::core::SurfaceGeometry
,
IMP::core::XYZDerivativesGeometry
,
IMP::core::XYZRsGeometry
,
IMP::display::BoundingBoxGeometry
,
IMP::display::CylinderGeometry
,
IMP::display::EllipsoidGeometry
,
IMP::display::FilterGeometry
,
IMP::display::Geometry
,
IMP::display::GeometrySet
,
IMP::display::LabelGeometry
,
IMP::display::PlaneGeometry
,
IMP::display::PointGeometry
,
IMP::display::PolygonGeometry
,
IMP::display::ReferenceFrameGeometry
,
IMP::display::RestraintGeometry
,
IMP::display::RestraintSetGeometry
,
IMP::display::SegmentGeometry
,
IMP::display::SphereGeometry
,
IMP::display::SurfaceMeshGeometry
,
IMP::display::TriangleGeometry
,
IMP::npctransport::SitesGeometry
,
IMP::npctransport::SlabWithCylindricalPoreWireGeometry
,
IMP::npctransport::SlabWithToroidalPoreWireGeometry
,
IMP::npctransport::TypedSitesGeometry
,
IMP.pmi.topology.TopologyReader
,
IMP.pmi1.topology.TopologyReader
get_condition_string() :
IMP.EMageFit.database.Database2
get_cone_3d_geometry() :
IMP::algebra::Cone3D
get_connected_index_pairs() :
IMP::core::ConnectivityRestraint
get_connected_pairs() :
IMP::core::MSConnectivityRestraint
,
IMP::npc::CompositeRestraint
get_container_pairs() :
IMP.pmi.restraints.basic.ResidueProteinProximityRestraint
get_contains() :
IMP::algebra::BoundingBoxD< D >
,
IMP::algebra::Cone3D
,
IMP::algebra::SphereD< D >
,
IMP::algebra::SpherePatch3D
,
IMP::algebra::UnitSimplexBaseD< D >
,
IMP::misc::LogPairScore
get_contains_any_sorted_residue() :
IMP::atom::Fragment
get_contains_atom() :
IMP::atom::CHARMMConnection< D >
get_contains_residue() :
IMP::atom::Fragment
get_contents_hash() :
IMP::Container
get_context() :
IMP.parallel.Manager
get_contribution() :
IMP::isd::AtomicCrossLinkMSRestraint
get_contribution_particle_indexes() :
IMP::isd::CrossLinkMSRestraint
get_contribution_psi_index() :
IMP::isd::CrossLinkMSRestraint
get_contribution_sigma_indexes() :
IMP::isd::CrossLinkMSRestraint
get_contribution_sigmas() :
IMP::isd::AtomicCrossLinkMSRestraint
get_converter() :
IMP.pmi.io.crosslink.CrossLinkDataBaseKeywordsConverter
,
IMP.pmi1.io.crosslink.CrossLinkDataBaseKeywordsConverter
get_coordinate() :
IMP::core::XYZ
get_coordinates() :
IMP::core::RigidBody
,
IMP::core::XYZ
,
IMP::rotamer::ResidueRotamer
get_coordinates_are_optimized() :
IMP::core::RigidBody
,
IMP::core::XYZ
get_corner() :
IMP::algebra::BoundingBoxD< D >
get_count() :
IMP::core::HierarchyCounter
get_cropped() :
IMP::em::DensityMap
get_cross_correlation_coefficient() :
IMP::em2d::PCAFitRestraint
,
IMP::isd::GaussianEMRestraint
get_current_angle_from_cartesian_witnesses() :
IMP::kinematics::BondAngleRevoluteJoint
,
IMP::kinematics::DihedralAngleRevoluteJoint
,
IMP::kinematics::RevoluteJoint
get_current_file_name() :
IMP::display::TextWriter
get_current_time() :
IMP::atom::Simulator
get_custom_scoring_function() :
IMP::npctransport::Scoring
get_cylinder_3d_geometry() :
IMP::algebra::Cylinder3D
get_cylindrical_pore_key() :
IMP::npctransport::SlabWithCylindricalPore
get_data() :
IMP::algebra::VectorBaseD< D >
,
IMP::em2d::Image
,
IMP::Model
,
IMP::statistics::ChiSquareMetric
get_data_point() :
IMP::kmeans::KMeans
get_data_type() :
IMP::em::DensityHeader
get_decorator_name() :
IMP::example::ExampleDecorator
get_default_backbone_k() :
IMP::npctransport::Scoring
get_default_radius_key() :
IMP::misc::CustomXYZR
get_default_traits() :
IMP::core::Hierarchy
get_delta_q() :
IMP::saxs::Profile
get_denominator() :
IMP::core::WeightedSumOfExponential
get_density() :
IMP::core::ClusterProvenance
,
IMP::em::DensityMap
,
IMP::em::Voxel
,
IMP::isd::OneDimensionalDistribution
,
IMP::isd::OneDimensionalSufficientDistribution
,
IMP.pmi.analysis.GetModelDensity
,
IMP.pmi1.analysis.GetModelDensity
,
IMP.sampcon.precision_rmsd.GetModelDensity
get_density_as_hierarchy() :
IMP.bayesianem.restraint.GaussianEMRestraintWrapper
get_dependencies_updated() :
IMP::Model
get_depth() :
IMP::core::Surface
get_derivative() :
IMP::core::XYZ
get_derivative_matrix() :
IMP::isd::BivariateFunction
,
IMP::isd::Covariance1DFunction
,
IMP::isd::GeneralizedGuinierPorodFunction
,
IMP::isd::Linear1DFunction
,
IMP::isd::UnivariateFunction
get_derivative_vector() :
IMP::isd::GeneralizedGuinierPorodFunction
,
IMP::isd::Linear1DFunction
,
IMP::isd::UnivariateFunction
get_derivatives() :
IMP::core::XYZ
get_derivatives_numpy() :
IMP::Model
get_diffusion_coefficient() :
IMP::atom::Diffusion
,
IMP::npctransport::ChainStatisticsOptimizerState
get_diffusion_coefficient_key() :
IMP::atom::Diffusion
get_dihedral_parameters() :
IMP::atom::CHARMMParameters
get_dim_index_by_location() :
IMP::em::DensityMap
get_dimension() :
IMP::algebra::UnitSimplexBaseD< D >
,
IMP::algebra::UnitSimplexD< D >
,
IMP::algebra::UnitSimplexD<-1 >
get_direction() :
IMP::algebra::Cone3D
,
IMP::algebra::Line3D
,
IMP::algebra::Segment3D
,
IMP::core::Direction
,
IMP::core::DirectionMover
get_direction_derivative() :
IMP::core::Direction
get_direction_derivatives() :
IMP::core::Direction
get_direction_is_optimized() :
IMP::core::Direction
get_direction_key() :
IMP::core::Direction
get_displacement_direction() :
IMP::npctransport::SlabWithCylindricalPorePairScore
get_displacement_magnitude() :
IMP::npctransport::SlabWithCylindricalPorePairScore
get_distance_at_minimum() :
IMP::core::SurfaceTetheredChain
,
IMP::misc::FreelyJointedChain
get_distance_at_step() :
IMP::em2d::ClusterSet
get_distance_from_envelope() :
IMP::em::MapDistanceTransform
get_distance_to() :
IMP::core::Surface
get_distance_to_center() :
IMP::core::Surface
get_docking_order() :
IMP.EMageFit.buildxlinks.DockOrder
get_dof() :
IMP::kinematics::DOFsSampler
get_dofs() :
IMP::kinematics::DOFsSampler
get_dummy_form_factor() :
IMP::saxs::FormFactorTable
get_dummy_form_factors() :
IMP::saxs::FormFactorTable
get_dummy_water_form_factor() :
IMP::saxs::FormFactorTable
get_Dxi() :
IMP::isd::PenalizedComplexityPrior
get_dynamic_info() :
IMP::bayesianem::GaussianEMRestraint
,
IMP::em2d::PCAFitRestraint
,
IMP::isd::GaussianEMRestraint
,
IMP::isd::UniformPrior
,
IMP::Restraint
get_element() :
IMP::atom::Atom
,
IMP::atom::ElementTable
,
IMP::atom::PDBRecord
get_ellipsoid_3d_geometry() :
IMP::algebra::Ellipsoid3D
get_embedding() :
IMP::domino::NestedRigidBodyStates
,
IMP::domino::ParticleStates
,
IMP::domino::RigidBodyStates
,
IMP::domino::XYZStates
get_end() :
IMP::spb::HelixDecorator
get_end_index() :
IMP::algebra::BoundedGridRangeD< D >
get_ending_radius() :
IMP::em2d::PolarResamplingParameters
get_epsilon() :
IMP::atom::ForceFieldParameters
get_equilibrium_rest_length_factor() :
IMP::npctransport::RelaxingSpring
get_equilibrium_rest_length_factor_key() :
IMP::npctransport::RelaxingSpring
get_exchange_array() :
IMP::mpi::ReplicaExchange
get_excluded_volume_k() :
IMP::npctransport::Scoring
get_extended_index() :
IMP::algebra::DefaultEmbeddingD< D >
,
IMP::algebra::GridD< D, StorageT, Value, EmbeddingT >
,
IMP::algebra::LogEmbeddingD< D >
get_fAngle1() :
IMP::em::ImageHeader
get_fFlag() :
IMP::em::ImageHeader
get_fg_bead_types() :
IMP::npctransport::SimulationData
get_fg_chain_roots() :
IMP::npctransport::SimulationData
get_fg_chain_types() :
IMP::npctransport::SimulationData
get_fg_chains() :
IMP::npctransport::Scoring
,
IMP::npctransport::SimulationData
get_fields() :
IMP.pmi.output.ProcessOutput
,
IMP.pmi1.output.ProcessOutput
get_file_dataset() :
IMP.pmi1.representation.Representation
get_filename() :
IMP::core::ScriptProvenance
,
IMP::core::StructureProvenance
get_filename_key() :
IMP::RestraintInfo
get_filename_value() :
IMP::RestraintInfo
get_filenames_key() :
IMP::RestraintInfo
get_filenames_value() :
IMP::RestraintInfo
get_fine_registration_time() :
IMP::em2d::ProjectionFinder
get_fit_error() :
IMP::algebra::LinearFit2D
,
IMP::algebra::ParabolicFit2D
get_flatten() :
IMP.pmi.tools.Segments
,
IMP.pmi1.tools.Segments
get_flexible_beads() :
IMP.pmi.dof.DegreesOfFreedom
get_float_key() :
IMP::RestraintInfo
get_float_value() :
IMP::RestraintInfo
get_floater_types() :
IMP::npctransport::SimulationData
get_floats_key() :
IMP::RestraintInfo
get_floats_numpy() :
IMP::Model
get_floats_value() :
IMP::RestraintInfo
get_floppy_body_movers() :
IMP.pmi.dof.DegreesOfFreedom
get_force() :
IMP::atom::BrownianDynamics
get_forces() :
IMP::atom::BrownianDynamics
get_form_factor() :
IMP::saxs::FormFactorTable
get_form_factors() :
IMP::saxs::FormFactorTable
get_friction_scale_factor() :
IMP::atom::TAMDParticle
get_friction_scale_factor_key() :
IMP::atom::TAMDParticle
get_friend_index() :
IMP::mpi::ReplicaExchange
get_friend_parameter() :
IMP::mpi::ReplicaExchange
get_full_graph() :
IMP.pmi.restraints.proteomics.ConnectivityNetworkRestraint
,
IMP.pmi1.restraints.proteomics.ConnectivityNetworkRestraint
get_full_pair_filter() :
IMP::atom::CHARMMStereochemistryRestraint
get_function() :
IMP::core::WeightedSum
,
IMP::core::WeightedSumOfExponential
get_function_number() :
IMP::core::WeightedSum
,
IMP::core::WeightedSumOfExponential
get_gamma_value() :
IMP.pmi.restraints.saxs.SAXSISDRestraint
,
IMP.pmi1.restraints.saxs.SAXSISDRestraint
get_gaussian() :
IMP::core::Gaussian
get_global_coordinates() :
IMP::algebra::ReferenceFrame3D
get_global_covariance() :
IMP::core::Gaussian
get_global_reference_frame() :
IMP::algebra::ReferenceFrame3D
get_global_score() :
IMP::em2d::ProjectionFinder
get_good_scoring_models() :
IMP.sampcon.good_scoring_model_selector.GoodScoringModelSelector
get_gradient_of_rotated() :
IMP::algebra::Rotation3D
get_had_good_score() :
IMP::ScoringFunction
get_has_attribute() :
IMP::Model
get_has_bounding_box() :
IMP::npctransport::Scoring
,
IMP::npctransport::SimulationData
get_has_bounding_sphere() :
IMP::npctransport::Scoring
,
IMP::npctransport::SimulationData
get_has_bounding_volume() :
IMP::npctransport::Scoring
,
IMP::npctransport::SimulationData
get_has_data() :
IMP::Model
get_has_dependencies() :
IMP::ModelObject
get_has_index() :
IMP::algebra::BoundedGridRangeD< D >
,
IMP::algebra::SparseGridStorageD< D, VT, Base, Map >
get_has_lower() :
IMP::isd::Nuisance
get_has_particle() :
IMP::Model
get_has_required_score_states() :
IMP::ModelObject
get_has_resolution() :
IMP::em::DensityHeader
get_has_slope() :
IMP::isd::CrossLinkMSRestraint
get_header() :
IMP::em2d::Image
,
IMP::em::DensityMap
get_header_writable() :
IMP::em::DensityMap
get_height() :
IMP::core::Surface
get_hessian() :
IMP::isd::GaussianProcessInterpolationRestraint
get_hierarchies() :
IMP::atom::Selection
,
IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
get_hierarchies_at_given_resolution() :
IMP.pmi1.representation.Representation
get_hierarchy() :
IMP.pmi.topology.Molecule
,
IMP.pmi.topology.State
,
IMP.pmi.topology.System
get_id() :
IMP::atom::Chain
get_id_key() :
IMP::atom::Chain
get_ideal() :
IMP::atom::Angle
,
IMP::atom::Dihedral
get_ideal_helices() :
IMP.pmi.topology.Molecule
get_image_index() :
IMP::em2d::RegistrationResult
get_improper_parameters() :
IMP::atom::CHARMMParameters
get_in_ball() :
IMP::algebra::NearestNeighborD< D >
get_index() :
IMP::algebra::BoundedGridRangeD< D >
,
IMP::algebra::SparseGridStorageD< D, VT, Base, Map >
,
IMP::atom::Residue
,
IMP::Particle
get_index_range() :
IMP::atom::Domain
get_indexes() :
IMP::atom::BondPairContainer
,
IMP::container::AllBipartitePairContainer
,
IMP::container::AllPairContainer
,
IMP::container::CloseBipartitePairContainer
,
IMP::container::ClosePairContainer
,
IMP::container::ConnectingPairContainer
,
IMP::container::ConsecutivePairContainer
,
IMP::container::ExclusiveConsecutivePairContainer
,
IMP::container::PredicatePairsRestraint
,
IMP::container::PredicateQuadsRestraint
,
IMP::container::PredicateSingletonsRestraint
,
IMP::container::PredicateTripletsRestraint
,
IMP::PairContainer
,
IMP::QuadContainer
,
IMP::SingletonContainer
,
IMP::TripletContainer
get_indexes_in_place() :
IMP::container::PairContainerSet
,
IMP::container::QuadContainerSet
,
IMP::container::SingletonContainerSet
,
IMP::container::TripletContainerSet
get_individual_placement_statistics() :
IMP.EMageFit.solutions_io.ResultsDB
get_initial_simulation_time_ns() :
IMP::npctransport::SimulationData
get_inner_joints() :
IMP::kinematics::CompositeJoint
get_inner_point_at() :
IMP::algebra::Cylinder3D
get_inner_state() :
IMP::domino::PermutationStates
get_input_file_name() :
IMP.test.TestCase
get_input_index() :
IMP::atom::Atom
get_inputs() :
IMP::isd::BivariateFunction
,
IMP::isd::Covariance1DFunction
,
IMP::isd::GeneralizedGuinierPorodFunction
,
IMP::isd::Linear1DFunction
,
IMP::isd::UnivariateFunction
,
IMP::ModelObject
,
IMP::ParticleInputs
,
IMP::score_functor::Score
,
IMP::score_functor::ScoreWithCache
get_int_key() :
IMP::RestraintInfo
get_int_value() :
IMP::RestraintInfo
get_interaction_k() :
IMP::npctransport::Scoring
get_interaction_range_for() :
IMP::npctransport::Scoring
get_interaction_type() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_interactions() :
IMP::ModelObject
get_internal_bonds() :
IMP::atom::Hierarchy
get_internal_coordinates() :
IMP::core::RigidBodyMember
get_internal_derivatives() :
IMP::core::NonRigidMember
get_internal_rotational_derivatives() :
IMP::core::NonRigidMember
get_internal_transformation() :
IMP::core::RigidBodyMember
get_interp() :
IMP.isd.TuneRex.CvEstimator
get_ints_key() :
IMP::RestraintInfo
get_ints_numpy() :
IMP::Model
get_ints_value() :
IMP::RestraintInfo
get_inv_rsigsq() :
IMP::em::KernelParameters
get_inverse() :
IMP::algebra::Rotation2D
,
IMP::algebra::Rotation3D
,
IMP::algebra::Transformation2D
get_is_activated() :
IMP::npctransport::Statistics
get_is_aggregate() :
IMP::Restraint
get_is_atom() :
IMP::atom::PDBRecord
get_is_by_ref_supported() :
IMP::Refiner
get_is_decomposable() :
IMP::Container
get_is_evaluate_if_below() :
IMP::ScoreAccumulator
get_is_evaluate_if_good() :
IMP::ScoreAccumulator
get_is_exclude_floaters_from_slab_initially() :
IMP::npctransport::SimulationData
get_is_fg_bead() :
IMP::npctransport::SimulationData
get_is_fg_chain() :
IMP::npctransport::SimulationData
get_is_heterogen() :
IMP::atom::Hierarchy
get_is_last_entry_from_top() :
IMP::npctransport::Transporting
get_is_last_entry_from_top_key() :
IMP::npctransport::Transporting
get_is_length_variable() :
IMP::isd::CrossLinkMSRestraint
get_is_ok() :
IMP::domino::SubsetFilter
,
IMP::em2d::DistanceFilter
get_is_pore_radius_dynamic() :
IMP::npctransport::SimulationData
get_is_selected() :
IMP::atom::AllPDBSelector
,
IMP::atom::AndPDBSelector
,
IMP::atom::ATOMPDBSelector
,
IMP::atom::AtomTypePDBSelector
,
IMP::atom::BackbonePDBSelector
,
IMP::atom::CAlphaPDBSelector
,
IMP::atom::CBetaPDBSelector
,
IMP::atom::ChainPDBSelector
,
IMP::atom::CPDBSelector
,
IMP::atom::HydrogenPDBSelector
,
IMP::atom::NonAlternativePDBSelector
,
IMP::atom::NonHydrogenPDBSelector
,
IMP::atom::NonWaterNonHydrogenPDBSelector
,
IMP::atom::NonWaterPDBSelector
,
IMP::atom::NotPDBSelector
,
IMP::atom::NPDBSelector
,
IMP::atom::OrPDBSelector
,
IMP::atom::PDBSelector
,
IMP::atom::PPDBSelector
,
IMP::atom::ResidueTypePDBSelector
,
IMP::atom::WaterPDBSelector
,
IMP::atom::XorPDBSelector
get_is_setup() :
IMP::atom::Angle
,
IMP::atom::Atom
,
IMP::atom::Charged
,
IMP::atom::CHARMMAtom
,
IMP::atom::Diffusion
,
IMP::atom::Hierarchy
,
IMP::atom::LennardJones
,
IMP::atom::RigidBodyDiffusion
,
IMP::atom::SecondaryStructureResidue
,
IMP::atom::TAMDParticle
,
IMP::core::Direction
,
IMP::core::DirectionAngle
,
IMP::core::Hierarchy
,
IMP::core::NonRigidMember
,
IMP::core::RigidBody
,
IMP::core::RigidBodyMember
,
IMP::core::RigidMember
,
IMP::core::Surface
,
IMP::core::XYZR
,
IMP::em2d::ProjectionParameters
,
IMP::example::ExampleDecorator
,
IMP::kinematics::KinematicNode
,
IMP::misc::CustomXYZR
,
IMP::npctransport::RelaxingSpring
,
IMP::npctransport::SlabWithCylindricalPore
,
IMP::npctransport::SlabWithPore
,
IMP::npctransport::SlabWithToroidalPore
,
IMP::npctransport::Transporting
get_is_simulation_particle() :
IMP::atom::BrownianDynamics
,
IMP::atom::MolecularDynamics
,
IMP::atom::Simulator
,
IMP::isd::MolecularDynamics
,
IMP::spb::MolecularDynamicsWithWte
get_is_slab_with_cylindrical_pore() :
IMP::npctransport::SimulationData
get_is_slab_with_toroidal_pore() :
IMP::npctransport::SimulationData
get_is_srk() :
IMP::atom::BrownianDynamics
get_is_trivially_zero() :
IMP::score_functor::Score
get_is_trivially_zero_with_cache() :
IMP::score_functor::ScoreWithCache
get_is_valid() :
IMP::algebra::Rotation3D
,
IMP::algebra::Transformation3D
,
IMP::atom::Hierarchy
,
IMP::Decorator
get_is_xyz_hist_stats() :
IMP::npctransport::SimulationData
get_jacobian_of_rotated() :
IMP::algebra::Rotation3D
get_joints() :
IMP::kinematics::ProteinKinematics
get_Jxi() :
IMP::isd::PenalizedComplexityPrior
get_k() :
IMP::core::Harmonic
,
IMP::npctransport::ExcludeZRangeSingletonScore
,
IMP::npctransport::LinearSoftSpherePairScore
,
IMP::npctransport::ZBiasSingletonScore
get_k1() :
IMP::npctransport::HarmonicSpringSingletonScore
get_k2() :
IMP::npctransport::HarmonicSpringSingletonScore
get_k_attraction() :
IMP::npctransport::LinearInteractionPairScore
get_k_from_standard_deviation() :
IMP::core::Harmonic
get_k_repulsion() :
IMP::npctransport::LinearInteractionPairScore
get_key_exists() :
IMP::Key< ID >
get_keys() :
IMP::em2d::ProjectionParameters
get_kinematic_forest() :
IMP::kinematics::ProteinKinematics
get_kinetic_energy() :
IMP::atom::MolecularDynamics
,
IMP::isd::MolecularDynamics
,
IMP::spb::MolecularDynamicsWithWte
get_kinetic_temperature() :
IMP::atom::MolecularDynamics
,
IMP::spb::MolecularDynamicsWithWte
get_last_accepted_energy() :
IMP::core::MonteCarlo
get_last_last_score() :
IMP::Restraint
get_last_score() :
IMP::Optimizer
,
IMP::Restraint
,
IMP::RestraintSet
,
IMP::ScoringFunction
get_last_time_step() :
IMP::atom::Simulator
get_last_tracked_z() :
IMP::npctransport::Transporting
get_last_tracked_z_key() :
IMP::npctransport::Transporting
get_leaves() :
IMP::atom::Hierarchy
get_left_join_command() :
IMP.EMageFit.solutions_io.ResultsDB
get_length() :
IMP::atom::Bond
,
IMP::isd::CrossLinkMSRestraint
,
IMP::kinematics::PrismaticJoint
get_lim() :
IMP::em::KernelParameters
get_line_3d_geometry() :
IMP::algebra::Line3D
get_link_length() :
IMP::core::SurfaceTetheredChain
,
IMP::misc::FreelyJointedChain
get_link_number() :
IMP::core::SurfaceTetheredChain
,
IMP::misc::FreelyJointedChain
get_linkage_matrix() :
IMP::em2d::ClusterSet
get_linkage_matrix_in_matlab_format() :
IMP::em2d::ClusterSet
get_list() :
IMP.pmi.io.crosslink.ResiduePairListParser
,
IMP.pmi1.io.crosslink.ResiduePairListParser
get_local_coordinates() :
IMP::algebra::ReferenceFrame3D
get_local_covariance() :
IMP::core::Gaussian
get_local_diffusion_coefficients() :
IMP::npctransport::ChainStatisticsOptimizerState
get_local_reference_frame() :
IMP::algebra::ReferenceFrame3D
get_location() :
IMP::core::SoftwareProvenance
get_location_by_voxel() :
IMP::em::DensityMap
get_location_in_dim_by_voxel() :
IMP::em::DensityMap
get_locations_string() :
IMP::em::DensityMap
get_log_generalized_variance() :
IMP::isd::MultivariateFNormalSufficient
get_logdet_hessian() :
IMP::isd::GaussianProcessInterpolationRestraint
get_magnitude() :
IMP.test.TestCase
get_mass() :
IMP::atom::ElementTable
get_mass_key() :
IMP::atom::Mass
get_max_distance() :
IMP::saxs::Distribution< ValueT >
get_max_q() :
IMP::saxs::Profile
get_max_step() :
IMP::atom::BrownianDynamics
get_max_value() :
IMP::em::DensityMap
get_maximum() :
IMP::ScoreAccumulator
get_maximum_extended_index() :
IMP::algebra::BoundedGridRangeD< D >
get_maximum_number_of_minutes() :
IMP::npctransport::SimulationData
get_maximum_range() :
IMP::score_functor::AddScores< BaseDistanceScore0, BaseDistanceScore1 >
,
IMP::score_functor::Score
,
IMP::score_functor::ScoreWithCache
get_maximum_rotation() :
IMP::core::DirectionMover
,
IMP::core::SurfaceMover
get_maximum_time_step() :
IMP::atom::Simulator
get_maximum_translation() :
IMP::core::SurfaceMover
get_maximum_value_in_xy_plane() :
IMP::em::DensityMap
get_maximum_value_in_xz_plane() :
IMP::em::DensityMap
get_maximum_value_in_yz_plane() :
IMP::em::DensityMap
get_mbar() :
IMP.isd.TuneRex.CvEstimator
get_mean() :
IMP::core::Harmonic
get_mean_bond_distance() :
IMP::npctransport::ChainStatisticsOptimizerState
get_mean_end_to_end_distance() :
IMP::npctransport::ChainStatisticsOptimizerState
get_mean_radius_of_gyration() :
IMP::npctransport::ChainStatisticsOptimizerState
get_mean_square_bond_distance() :
IMP::npctransport::ChainStatisticsOptimizerState
get_mean_square_end_to_end_distance() :
IMP::npctransport::ChainStatisticsOptimizerState
get_mean_square_radius_of_gyration() :
IMP::npctransport::ChainStatisticsOptimizerState
get_mean_square_residuals() :
IMP::isd::MultivariateFNormalSufficient
get_member_indexes() :
IMP::core::RigidBody
get_member_particle_indexes() :
IMP::core::RigidBody
get_method() :
IMP::core::FilterProvenance
,
IMP::core::SampleProvenance
get_min_and_max_values() :
IMP::em2d::Image
get_min_q() :
IMP::saxs::Profile
get_min_value() :
IMP::em::DensityMap
get_minimum_extended_index() :
IMP::algebra::BoundedGridRangeD< D >
get_minimum_resampled_value() :
IMP::em::SampledDensityMap
get_minimum_spanning_tree() :
IMP.pmi.restraints.proteomics.ConnectivityNetworkRestraint
,
IMP.pmi1.restraints.proteomics.ConnectivityNetworkRestraint
get_minor_radius_h2v_aspect_ratio_key() :
IMP::npctransport::SlabWithToroidalPore
get_minus_exponent() :
IMP::isd::MultivariateFNormalSufficient
get_minus_log_normalization() :
IMP::isd::GaussianProcessInterpolationRestraint
,
IMP::isd::MultivariateFNormalSufficient
get_model() :
IMP::Decorator
,
IMP::npctransport::ParticleFactory
,
IMP::npctransport::Scoring
,
IMP::npctransport::Statistics
get_model_dens_map() :
IMP::em::FitRestraint
get_model_objects() :
IMP::Model
get_modeling_trajectory() :
IMP.pmi.macros.AnalysisReplicaExchange0
,
IMP.pmi1.macros.AnalysisReplicaExchange0
get_moldict_coorddict() :
IMP.pmi.analysis.RMSD
,
IMP.pmi1.analysis.RMSD
get_molecule() :
IMP.pmi.topology.State
get_molecules() :
IMP.pmi.macros.BuildSystem
,
IMP.pmi.topology.State
get_moment() :
IMP::algebra::Line3D
get_movable_particles() :
IMP::core::MonteCarlo
get_movers() :
IMP.pmi.dof.DegreesOfFreedom
,
IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
get_multiplicity() :
IMP::atom::Dihedral
get_my_index() :
IMP::mpi::ReplicaExchange
get_my_parameter() :
IMP::mpi::ReplicaExchange
get_n_entries_bottom() :
IMP::npctransport::Transporting
get_n_entries_bottom_key() :
IMP::npctransport::Transporting
get_n_entries_top() :
IMP::npctransport::Transporting
get_n_entries_top_key() :
IMP::npctransport::Transporting
get_n_transports_down() :
IMP::npctransport::ParticleTransportStatisticsOptimizerState
get_n_transports_up() :
IMP::npctransport::ParticleTransportStatisticsOptimizerState
get_name() :
IMP::atom::ElementTable
,
IMP::em2d::Image
,
IMP::em2d::RegistrationResult
,
IMP.EMageFit.buildxlinks.Xlink
,
IMP.pmi.topology.Molecule
get_native_rank() :
IMP.EMageFit.solutions_io.ResultsDB
get_native_solution() :
IMP.EMageFit.solutions_io.ResultsDB
get_ndims_x() :
IMP::isd::GeneralizedGuinierPorodFunction
,
IMP::isd::Linear1DFunction
,
IMP::isd::UnivariateFunction
get_ndims_x1() :
IMP::isd::BivariateFunction
,
IMP::isd::Covariance1DFunction
get_ndims_y() :
IMP::isd::BivariateFunction
,
IMP::isd::Covariance1DFunction
,
IMP::isd::GeneralizedGuinierPorodFunction
,
IMP::isd::Linear1DFunction
,
IMP::isd::UnivariateFunction
get_nearest_neighbor() :
IMP::algebra::NearestNeighborD< D >
get_nearest_neighbors() :
IMP::algebra::NearestNeighborD< D >
get_nearest_state() :
IMP::domino::NestedRigidBodyStates
,
IMP::domino::ParticleStates
,
IMP::domino::RigidBodyStates
,
IMP::domino::XYZStates
get_neighbors() :
IMP::core::NeighborsTable
get_next_state() :
IMP::domino::SubsetFilter
get_non_atomic_residues() :
IMP.pmi.topology.Molecule
get_non_optimizable_beads() :
IMP::npctransport::SimulationData
get_non_sets_and_sets() :
IMP::RestraintSet
get_normal() :
IMP::core::Surface
get_normal_derivative() :
IMP::core::Surface
get_normal_derivatives() :
IMP::core::Surface
get_normal_is_optimized() :
IMP::core::Surface
get_normal_x() :
IMP::core::Surface
get_normal_y() :
IMP::core::Surface
get_normal_z() :
IMP::core::Surface
get_nth_largest_cluster() :
IMP.EMageFit.solutions_io.ResultsDB
get_nuisance_movers_parameters() :
IMP.pmi.samplers.MonteCarlo
,
IMP.pmi1.samplers.MonteCarlo
get_nuisances_from_restraint() :
IMP.pmi.dof.DegreesOfFreedom
get_num_restraints() :
IMP.pmi.restraints.stereochemistry.ConnectivityRestraint
,
IMP.pmi1.restraints.stereochemistry.ConnectivityRestraint
get_number_of_accepted_steps() :
IMP::core::MonteCarlo
get_number_of_angles() :
IMP::em2d::PolarResamplingParameters
get_number_of_assignments_for_vertex() :
IMP::domino::DominoSampler
get_number_of_beads() :
IMP::npctransport::FGChain
get_number_of_bonds() :
IMP::atom::HelixRestraint
get_number_of_cases() :
IMP::rotamer::ResidueRotamer
get_number_of_centers() :
IMP::kmeans::KMeans
get_number_of_contributions() :
IMP::isd::AtomicCrossLinkMSRestraint
,
IMP::isd::ResidueProteinProximityRestraint
get_number_of_copies() :
IMP.pmi.topology.State
get_number_of_data_points() :
IMP::kmeans::KMeans
get_number_of_dihedrals() :
IMP::atom::HelixRestraint
get_number_of_downward_steps() :
IMP::core::MonteCarlo
get_number_of_entries() :
IMP::domino::RestraintCache
get_number_of_filename() :
IMP::RestraintInfo
get_number_of_filenames() :
IMP::RestraintInfo
get_number_of_float() :
IMP::RestraintInfo
get_number_of_floats() :
IMP::RestraintInfo
get_number_of_frames() :
IMP::core::CombineProvenance
,
IMP::core::FilterProvenance
,
IMP::core::SampleProvenance
get_number_of_full_rebuilds() :
IMP::container::ClosePairContainer
get_number_of_int() :
IMP::RestraintInfo
get_number_of_ints() :
IMP::RestraintInfo
get_number_of_iterations() :
IMP::core::SampleProvenance
get_number_of_masks() :
IMP::em2d::RigidBodiesImageFitRestraint
get_number_of_members() :
IMP::core::ClusterProvenance
get_number_of_optimized_particles() :
IMP::isd::BivariateFunction
,
IMP::isd::Covariance1DFunction
,
IMP::isd::GeneralizedGuinierPorodFunction
,
IMP::isd::Linear1DFunction
,
IMP::isd::UnivariateFunction
get_number_of_partial_rebuilds() :
IMP::container::ClosePairContainer
get_number_of_particle_indexes() :
IMP::RestraintInfo
get_number_of_particles() :
IMP::isd::BivariateFunction
,
IMP::isd::Covariance1DFunction
,
IMP::isd::GeneralizedGuinierPorodFunction
,
IMP::isd::Linear1DFunction
,
IMP::isd::UnivariateFunction
get_number_of_particles_1() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_number_of_particles_2() :
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_number_of_proposed_steps() :
IMP::core::MonteCarlo
get_number_of_refined() :
IMP::Refiner
get_number_of_replicas() :
IMP::core::SampleProvenance
,
IMP::mpi::ReplicaExchange
get_number_of_rings() :
IMP::em2d::PolarResamplingParameters
get_number_of_runs() :
IMP::core::CombineProvenance
get_number_of_solutions() :
IMP::em::FittingSolutions
get_number_of_states() :
IMP.pmi.topology.System
get_number_of_steps() :
IMP::em2d::ClusterSet
,
IMP::kinematics::DOF
get_number_of_string() :
IMP::RestraintInfo
get_number_of_strings() :
IMP::RestraintInfo
get_number_of_unique_crosslinked_sites() :
IMP.pmi.io.crosslink.CrossLinkDataBase
get_number_of_update_calls() :
IMP::container::ClosePairContainer
get_number_of_updates() :
IMP::OptimizerState
get_number_of_upward_steps() :
IMP::core::MonteCarlo
get_number_of_voxels() :
IMP::algebra::BoundedGridRangeD< D >
,
IMP::em::DensityMap
get_number_of_weights() :
IMP::isd::Weight
get_number_of_weights_key() :
IMP::isd::Weight
get_number_unique() :
IMP::Key< ID >
get_nx() :
IMP::em::DensityHeader
get_ny() :
IMP::em::DensityHeader
get_nz() :
IMP::em::DensityHeader
get_obstacle_particles() :
IMP::npctransport::SimulationData
get_obstacle_types() :
IMP::npctransport::SimulationData
get_old_rot() :
IMP::em::ImageHeader
get_one_letter_code_from_residue_type() :
IMP.pmi.alphabets.ResidueAlphabet
get_opposite() :
IMP::algebra::Line3D
,
IMP::algebra::Plane3D
get_optimizable_beads() :
IMP::npctransport::SimulationData
get_order() :
IMP::atom::Bond
get_ordered_joints() :
IMP::kinematics::KinematicForest
,
IMP::kinematics::ProteinKinematics
get_orientation() :
IMP::em2d::GridStates
get_origin() :
IMP::em::DensityHeader
get_output() :
IMP.pmi.analysis.RMSD
,
IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi1.analysis.RMSD
,
IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi1.restraints.RestraintBase
get_outputs() :
IMP::ModelObject
,
IMP::ParticleOutputs
get_owner() :
IMP::npctransport::ParticleTransportStatisticsOptimizerState
get_padded_atom_name() :
IMP::atom::PDBRecord
get_pair_filter() :
IMP::atom::CHARMMStereochemistryRestraint
,
IMP::atom::OrientedSoapPairScore
get_pair_score() :
IMP::core::ConnectivityRestraint
,
IMP::core::MSConnectivityRestraint
get_parameters_optimized() :
IMP::em2d::ProjectionParameters
get_parent() :
IMP::atom::Hierarchy
,
IMP::core::Hierarchy
get_particle() :
IMP::atom::Angle
,
IMP::atom::Dihedral
,
IMP::core::DirectionAngle
,
IMP::Decorator
,
IMP::Model
get_particle_assignments() :
IMP::domino::AssignmentContainer
,
IMP::domino::CappedAssignmentContainer
,
IMP::domino::HeapAssignmentContainer
,
IMP::domino::ListAssignmentContainer
,
IMP::domino::PackedAssignmentContainer
,
IMP::domino::RangeViewAssignmentContainer
,
IMP::domino::ReadAssignmentContainer
,
IMP::domino::ReadHDF5AssignmentContainer
,
IMP::domino::SampleAssignmentContainer
,
IMP::domino::WriteAssignmentContainer
,
IMP::domino::WriteHDF5AssignmentContainer
get_particle_index() :
IMP::core::DirectionAngle
,
IMP::Decorator
get_particle_indexes() :
IMP::Model
get_particle_indexes_key() :
IMP::RestraintInfo
get_particle_indexes_value() :
IMP::RestraintInfo
get_particle_is_optimized() :
IMP::isd::BivariateFunction
,
IMP::isd::Covariance1DFunction
,
IMP::isd::GeneralizedGuinierPorodFunction
,
IMP::isd::Linear1DFunction
,
IMP::isd::UnivariateFunction
get_particle_key() :
IMP::core::DirectionAngle
get_particle_name() :
IMP::Model
get_particle_pairs() :
IMP::misc::LogPairScore
,
IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi.restraints.stereochemistry.ConnectivityRestraint
,
IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi1.restraints.stereochemistry.ConnectivityRestraint
get_particles_at_all_resolutions() :
IMP.pmi.topology.Molecule
get_particles_from_selection_tuples() :
IMP.pmi1.representation.Representation
get_particles_size() :
IMP::Model
get_particles_to_sample() :
IMP.pmi.restraints.crosslinking.AtomicCrossLinkMSRestraint
,
IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi1.restraints.crosslinking.AtomicCrossLinkMSRestraint
,
IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi1.restraints.RestraintBase
get_pdb() :
IMP.isd.shared_functions.sfo_common
get_pdb_names() :
IMP.pmi.output.Output
get_period() :
IMP::OptimizerState
get_phi() :
IMP::kinematics::ProteinKinematics
get_placement_fields() :
IMP.EMageFit.solutions_io.ResultsDB
get_placement_score_from_coordinates() :
IMP.multifit.cluster.AlignmentClustering
get_placement_statistics() :
IMP.EMageFit.solutions_io.ResultsDB
get_plane() :
IMP::core::Surface
get_plane_3d_geometry() :
IMP::algebra::Plane3D
get_point() :
IMP::algebra::Segment3D
,
IMP::algebra::Triangle3D
,
IMP::example::ExampleTemplateClassD< D >
get_point_on_line() :
IMP::algebra::Line3D
get_pore_radius() :
IMP::npctransport::SimulationData
,
IMP::npctransport::SlabWithPore
get_pore_radius_k() :
IMP::npctransport::SimulationData
get_pore_radius_key() :
IMP::npctransport::SlabWithPore
get_position() :
IMP::em2d::GridStates
get_posterior_mean() :
IMP::isd::GaussianProcessInterpolation
get_precision() :
IMP::core::ClusterProvenance
,
IMP.pmi.analysis.Precision
,
IMP.pmi1.analysis.Precision
get_predicate_pair_score() :
IMP::npctransport::Scoring
get_predicates_pair_restraint() :
IMP::npctransport::Scoring
get_preprocessing_time() :
IMP::em2d::ProjectionFinder
get_previous() :
IMP::core::Provenance
get_prob_coil() :
IMP::atom::SecondaryStructureResidue
get_prob_helix() :
IMP::atom::SecondaryStructureResidue
get_prob_strand() :
IMP::atom::SecondaryStructureResidue
get_probability() :
IMP::bayesianem::GaussianEMRestraint
,
IMP::isd::GaussianEMRestraint
,
IMP::isd::GaussianProcessInterpolationRestraint
,
IMP::isd::StudentTRestraint
,
IMP::isd::TALOSRestraint
,
IMP::rotamer::ResidueRotamer
,
IMP::rotamer::RotamerAngleTuple
get_probability_distribution_function() :
IMP::statistics::HistogramD< D, Grid >
get_profile() :
IMP::saxs::ProfileFitter< ScoringFunctionT >
get_projected() :
IMP::algebra::Plane3D
get_projected_area() :
IMP::em2d::CollisionCrossSection
get_projection() :
IMP::em2d::ProjectionStates
get_projection_index() :
IMP::em2d::RegistrationResult
get_prot_name_from_particle() :
IMP.pmi.output.Output
,
IMP.pmi1.output.Output
get_psi() :
IMP::isd::AtomicCrossLinkMSRestraint
,
IMP::kinematics::ProteinKinematics
get_quaternion() :
IMP::algebra::Rotation3D
get_quaternion_1() :
IMP::em2d::ProjectionParameters
get_quaternion_2() :
IMP::em2d::ProjectionParameters
get_quaternion_3() :
IMP::em2d::ProjectionParameters
get_quaternion_4() :
IMP::em2d::ProjectionParameters
get_radius() :
IMP::algebra::Cone3D
,
IMP::atom::ForceFieldParameters
,
IMP::em2d::PolarResamplingParameters
,
IMP::misc::CustomXYZR
,
IMP::npctransport::ParticleFactory
,
IMP::saxs::FormFactorTable
get_radius_key() :
IMP::core::XYZR
get_radius_of_gyration() :
IMP::multifit::RadiusOfGyrationRestraint
get_radius_step() :
IMP::em2d::PolarResamplingParameters
get_range() :
IMP::npctransport::SimulationData
get_range_attraction() :
IMP::npctransport::LinearInteractionPairScore
get_range_indexes() :
IMP::atom::BondPairContainer
,
IMP::container::AllBipartitePairContainer
,
IMP::container::AllPairContainer
,
IMP::container::CloseBipartitePairContainer
,
IMP::container::ClosePairContainer
,
IMP::container::ConnectingPairContainer
,
IMP::container::ConsecutivePairContainer
,
IMP::container::ExclusiveConsecutivePairContainer
,
IMP::PairContainer
,
IMP::QuadContainer
,
IMP::SingletonContainer
,
IMP::TripletContainer
get_reciprocal_product() :
IMP::algebra::Line3D
get_reduced_coordinates() :
IMP::core::RigidBodyTunneler
get_reference_frame() :
IMP::core::RigidBody
,
IMP::core::Surface
get_reference_particle_index() :
IMP::atom::TAMDParticle
get_reference_particle_index_key() :
IMP::atom::TAMDParticle
get_refined() :
IMP::atom::BondEndpointsRefiner
,
IMP::core::ChildrenRefiner
,
IMP::core::FixedRefiner
,
IMP::core::LeavesRefiner
,
IMP::core::TableRefiner
,
IMP::multifit::RigidLeavesRefiner
,
IMP::Refiner
get_refined_indexes() :
IMP::core::FixedRefiner
,
IMP::Refiner
get_refined_indexes_by_ref() :
IMP::core::FixedRefiner
,
IMP::Refiner
get_reflect_probability() :
IMP::core::DirectionMover
,
IMP::core::SurfaceMover
get_registration_results() :
IMP::em2d::Em2DRestraint
,
IMP::em2d::ProjectionFinder
get_representation() :
IMP::atom::Representation
,
IMP.pmi1.macros.BuildModel
get_representations() :
IMP::atom::Representation
get_represented() :
IMP.pmi.topology.Molecule
get_required_score_states() :
IMP::ModelObject
get_resampled() :
IMP::em::DensityMap
get_resampling_map() :
IMP::em2d::PolarResamplingParameters
get_resampling_maps() :
IMP::em2d::PolarResamplingParameters
get_residue() :
IMP::atom::Hierarchy
get_residue_coordinates() :
IMP.EMageFit.buildxlinks.InitialDockingFromXlinks
get_residue_name() :
IMP::atom::PDBRecord
get_residue_offset() :
IMP::core::StructureProvenance
get_residue_particle() :
IMP.EMageFit.buildxlinks.InitialDockingFromXlinks
get_residue_type_from_one_letter_code() :
IMP.pmi.alphabets.ResidueAlphabet
get_residues() :
IMP.pmi.topology.Molecule
get_resolution() :
IMP::em::DensityHeader
get_resolutions() :
IMP::atom::Representation
get_rest_length() :
IMP::npctransport::RelaxingSpring
get_rest_length_diffusion_coefficient() :
IMP::npctransport::RelaxingSpring
get_rest_length_diffusion_coefficient_key() :
IMP::npctransport::RelaxingSpring
get_rest_length_factor() :
IMP::npctransport::FGChain
get_rest_length_key() :
IMP::npctransport::RelaxingSpring
get_restraint() :
IMP.pmi1.restraints.RestraintBase
get_restraint_for_rmf() :
IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi1.restraints.RestraintBase
get_restraint_set() :
IMP::multifit::ProteomicsEMAlignmentAtomic
,
IMP.pmi1.restraints.RestraintBase
get_restraint_sets() :
IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
get_restraint_value_for_assignment() :
IMP.EMageFit.domino_model.DominoModel
get_restraints() :
IMP::domino::RestraintCache
,
IMP.pmi.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
,
IMP.pmi1.restraints.crosslinking.CrossLinkingMassSpectrometryRestraint
get_restraints_for_native() :
IMP.EMageFit.domino_model.DominoModel
get_restraints_names_used() :
IMP.EMageFit.domino_model.DominoModel
get_results_unordered() :
IMP.parallel.Context
get_reversed() :
IMP::em::ImageHeader
get_rigid_bodies() :
IMP::kinematics::ProteinKinematics
,
IMP.pmi.dof.DegreesOfFreedom
,
IMP.pmi.topology.TopologyReader
,
IMP.pmi1.topology.TopologyReader
get_rkdist() :
IMP::em::KernelParameters
get_rkdistsq() :
IMP::em::KernelParameters
get_rmf_sos_writer() :
IMP::npctransport::SimulationData
get_rmsd_wrt_reference_structure_with_alignment() :
IMP.pmi.analysis.Precision
,
IMP.pmi1.analysis.Precision
get_rmsf() :
IMP.pmi.analysis.Precision
,
IMP.pmi1.analysis.Precision
get_rnormfac() :
IMP::em::KernelParameters
get_root() :
IMP::atom::Hierarchy
get_root_of_type() :
IMP::npctransport::SimulationData
get_rotamer() :
IMP::rotamer::RotamerCalculator
get_rotamers() :
IMP::rotamer::RotamerLibrary
get_rotamers_fast() :
IMP::rotamer::RotamerLibrary
get_rotated() :
IMP::algebra::Rotation2D
,
IMP::algebra::Rotation3D
get_rotated_adjoint() :
IMP::algebra::Rotation3D
get_rotated_one_coordinate() :
IMP::algebra::Rotation3D
get_rotation() :
IMP::algebra::Transformation2D
,
IMP::algebra::Transformation3D
,
IMP::core::RigidBody
,
IMP::em2d::RegistrationResult
get_rotation_about_joint_in_parent_coordinates() :
IMP::kinematics::RevoluteJoint
get_rotation_keys() :
IMP::core::RigidBody
get_rotational_derivatives() :
IMP::core::RigidBody
get_rotational_diffusion_coefficient() :
IMP::atom::RigidBodyDiffusion
get_rotational_diffusion_coefficient_key() :
IMP::atom::RigidBodyDiffusion
get_rsig() :
IMP::em::KernelParameters
get_rsigsq() :
IMP::em::KernelParameters
get_sample() :
IMP::atom::BrownianDynamics
,
IMP::kinematics::DOFsSampler
get_sample_assignments() :
IMP::domino::DiscreteSampler
get_sample_assignments_for_vertex() :
IMP::domino::DominoSampler
get_score() :
IMP::domino::RestraintCache
,
IMP::em2d::RegistrationResult
,
IMP::em2d::ScoreFunction
,
IMP::em::FittingSolutions
,
IMP::Restraint
,
IMP::score_functor::Score
get_score_and_derivative() :
IMP::score_functor::Score
get_score_and_derivative_with_cache() :
IMP::score_functor::ScoreWithCache
get_score_functor() :
IMP::score_functor::DistancePairScore< DistanceScoreT >
,
IMP::score_functor::DistancePairScoreWithCache< DistanceScoreT >
get_score_threshold() :
IMP::core::MonteCarlo
get_score_with_cache() :
IMP::score_functor::ScoreWithCache
get_scoring() :
IMP::npctransport::SimulationData
get_scoring_function() :
IMP.EMageFit.domino_model.DominoModel
,
IMP::npctransport::Scoring
,
IMP::Optimizer
,
IMP::Sampler
get_scoring_function_restraints() :
IMP::npctransport::Scoring
get_sd() :
IMP::npctransport::Scoring
,
IMP::npctransport::Statistics
get_second_derivative_matrix() :
IMP::isd::BivariateFunction
,
IMP::isd::Covariance1DFunction
get_second_derivative_vector() :
IMP::isd::GeneralizedGuinierPorodFunction
,
IMP::isd::Linear1DFunction
,
IMP::isd::UnivariateFunction
get_secondary_structure_is_set() :
IMP::multifit::AnchorsData
get_segment_3d_geometry() :
IMP::algebra::Segment3D
get_segment_starting_at() :
IMP::algebra::Line3D
get_selected_particle_indexes() :
IMP::atom::Selection
get_selected_particles() :
IMP::atom::Selection
get_sequence() :
IMP::atom::Chain
get_sequence_key() :
IMP::atom::Chain
get_sequence_offset() :
IMP::atom::Chain
get_sequence_offset_key() :
IMP::atom::Chain
get_setup_keys() :
IMP.pmi.io.crosslink.CrossLinkDataBaseKeywordsConverter
,
IMP.pmi1.io.crosslink.CrossLinkDataBaseKeywordsConverter
get_Sigma_condition_number() :
IMP::isd::MultivariateFNormalSufficient
get_Sigma_eigenvalues() :
IMP::isd::MultivariateFNormalSufficient
get_simulation_data() :
IMP::npctransport::ParticleFactory
get_simulation_particle_indexes() :
IMP::atom::Simulator
get_simulation_particles() :
IMP::atom::Simulator
get_site_centers() :
IMP::npctransport::SimulationData
get_site_display_radius() :
IMP::npctransport::SimulationData
get_site_interactions_statistics() :
IMP::npctransport::Scoring
get_sites() :
IMP::npctransport::SimulationData
get_sites_k() :
IMP::npctransport::SitesPairScore
get_sites_range() :
IMP::npctransport::SitesPairScore
get_size() :
IMP::rotamer::ResidueRotamer
get_slab_particle() :
IMP::npctransport::SimulationData
get_slab_restraint() :
IMP::npctransport::Scoring
get_slice() :
IMP::domino::RestraintCache
get_slope() :
IMP::bayesianem::GaussianEMRestraint
,
IMP::isd::GaussianEMRestraint
get_software_name() :
IMP::core::SoftwareProvenance
get_solutions() :
IMP.EMageFit.solutions_io.ResultsDB
get_solutions_from_list() :
IMP.EMageFit.solutions_io.ResultsDB
get_solutions_results_table() :
IMP.EMageFit.solutions_io.ResultsDB
get_solvent_accessibility() :
IMP::saxs::SolventAccessibleSurface
get_source_chain_id() :
IMP::atom::StructureSource
get_source_id() :
IMP::atom::StructureSource
get_source_protein1() :
IMP::isd::CrossLinkMSRestraint
get_source_protein2() :
IMP::isd::CrossLinkMSRestraint
get_source_residue1() :
IMP::isd::CrossLinkMSRestraint
get_source_residue2() :
IMP::isd::CrossLinkMSRestraint
get_spacing() :
IMP::em::DensityHeader
,
IMP::em::DensityMap
get_sphere() :
IMP::core::XYZR
,
IMP::misc::CustomXYZR
get_sphere_derivatives_numpy() :
IMP::Model
get_sphere_patch_3d_geometry() :
IMP::algebra::SpherePatch3D
get_spheres_numpy() :
IMP::Model
get_sq2pi3() :
IMP::em::KernelParameters
get_square_root_distances() :
IMP::saxs::RadialDistributionFunction
get_squared_distance_to_centers() :
IMP::kmeans::KMeans
get_standard_deviation() :
IMP::statistics::ChiSquareMetric
get_starting_radius() :
IMP::em2d::PolarResamplingParameters
get_state() :
IMP.pmi.topology.Molecule
get_states() :
IMP.pmi.topology.System
get_static_info() :
IMP::bayesianem::GaussianEMRestraint
,
IMP::em2d::PCAFitRestraint
,
IMP::isd::CrossLinkMSRestraint
,
IMP::isd::GaussianEMRestraint
,
IMP::isd::UniformPrior
,
IMP::npc::MembraneExclusionRestraint
,
IMP::npc::MembraneSurfaceLocationConditionalRestraint
,
IMP::npc::MembraneSurfaceLocationRestraint
,
IMP::npc::XYRadialPositionLowerRestraint
,
IMP::npc::XYRadialPositionRestraint
,
IMP::npc::XYRadialPositionUpperRestraint
,
IMP::npc::YAxialPositionLowerRestraint
,
IMP::npc::YAxialPositionRestraint
,
IMP::npc::YAxialPositionUpperRestraint
,
IMP::npc::ZAxialPositionLowerRestraint
,
IMP::npc::ZAxialPositionRestraint
,
IMP::npc::ZAxialPositionUpperRestraint
,
IMP::pmi::CrossLinkRestraintSet
,
IMP::Restraint
,
IMP::saxs::Restraint
get_statistics() :
IMP::npctransport::SimulationData
get_statistics_fraction() :
IMP::npctransport::SimulationData
get_step_size() :
IMP::kinematics::DOF
get_stiffness() :
IMP::atom::Angle
,
IMP::atom::Bond
,
IMP::atom::Dihedral
get_stream() :
IMP::display::TextWriter
get_strength() :
IMP::domino::EqualitySubsetFilterTable
,
IMP::domino::EquivalenceAndExclusionSubsetFilterTable
,
IMP::domino::EquivalenceSubsetFilterTable
,
IMP::domino::ExclusionSubsetFilterTable
,
IMP::domino::ListSubsetFilterTable
,
IMP::domino::MinimumRestraintScoreSubsetFilterTable
,
IMP::domino::PairListSubsetFilterTable
,
IMP::domino::ProbabilisticSubsetFilterTable
,
IMP::domino::RestraintScoreSubsetFilterTable
,
IMP::domino::SubsetFilterTable
,
IMP::em2d::DistanceFilterTable
,
IMP::example::ExampleSubsetFilterTable
get_string() :
IMP::Key< ID >
get_string_key() :
IMP::RestraintInfo
get_string_value() :
IMP::RestraintInfo
get_strings_key() :
IMP::RestraintInfo
get_strings_value() :
IMP::RestraintInfo
get_subset() :
IMP::domino::ParticleStatesTable
get_subset_filter() :
IMP::domino::EqualitySubsetFilterTable
,
IMP::domino::EquivalenceAndExclusionSubsetFilterTable
,
IMP::domino::EquivalenceSubsetFilterTable
,
IMP::domino::ExclusionSubsetFilterTable
,
IMP::domino::ListSubsetFilterTable
,
IMP::domino::MinimumRestraintScoreSubsetFilterTable
,
IMP::domino::PairListSubsetFilterTable
,
IMP::domino::ProbabilisticSubsetFilterTable
,
IMP::domino::RestraintScoreSubsetFilterTable
,
IMP::domino::SubsetFilterTable
,
IMP::em2d::DistanceFilterTable
,
IMP::example::ExampleSubsetFilterTable
get_sufficient_statistics() :
IMP::isd::vonMisesSufficient
get_sumFX() :
IMP::isd::FStudentT
get_super_rigid_bodies() :
IMP.pmi.topology.TopologyReader
,
IMP.pmi1.topology.TopologyReader
get_surface() :
IMP::core::SurfaceMover
get_surface_area() :
IMP::algebra::Cone3D
,
IMP::algebra::Cylinder3D
,
IMP::algebra::Ellipsoid3D
,
IMP::algebra::Torus3D
get_surface_point_at() :
IMP::algebra::Cylinder3D
get_symm_axis_alignments_from_model_to_density() :
IMP::cnmultifit::AlignSymmetric
get_table() :
IMP.EMageFit.database.Database2
get_table_column_names() :
IMP.EMageFit.database.Database2
get_table_types() :
IMP.EMageFit.database.Database2
get_temperature() :
IMP::atom::Simulator
get_temperature_scale_factor() :
IMP::atom::TAMDParticle
get_temperature_scale_factor_key() :
IMP::atom::TAMDParticle
get_thickness() :
IMP::npctransport::SlabWithPore
get_thickness_key() :
IMP::npctransport::SlabWithPore
get_threshold() :
IMP::core::FilterProvenance
get_timessig() :
IMP::em::KernelParameters
get_tip() :
IMP::algebra::Cone3D
get_tmp_file_name() :
IMP.test.TestCase
get_top() :
IMP::em::DensityHeader
get_top_z() :
IMP::npctransport::ExcludeZRangeSingletonScore
get_toroidal_pore_key() :
IMP::npctransport::SlabWithToroidalPore
get_torque() :
IMP::core::RigidBody
get_torus_3d_geometry() :
IMP::algebra::Torus3D
get_torus_distance() :
IMP::algebra::Torus3D
get_total_count() :
IMP::statistics::HistogramD< D, Grid >
get_total_n_transports() :
IMP::npctransport::ParticleTransportStatisticsOptimizerState
get_traits() :
IMP::atom::Hierarchy
get_transformation() :
IMP::em2d::PCAFitRestraint
,
IMP::em::FittingSolutions
get_transformation_child_to_parent() :
IMP::kinematics::Joint
get_transformation_child_to_parent_no_checks() :
IMP::kinematics::Joint
get_transformation_from() :
IMP::algebra::ReferenceFrame3D
get_transformation_to() :
IMP::algebra::ReferenceFrame3D
get_transformed() :
IMP::algebra::Transformation2D
,
IMP::algebra::Transformation3D
,
IMP::em::DensityMap
get_transformed_adjoint() :
IMP::algebra::Transformation3D
get_transformed_into() :
IMP::em::DensityMap
get_translation() :
IMP::algebra::Transformation2D
,
IMP::algebra::Transformation3D
get_translation_x() :
IMP::em2d::ProjectionParameters
get_translation_y() :
IMP::em2d::ProjectionParameters
get_transport_time_points_in_ns() :
IMP::npctransport::ParticleTransportStatisticsOptimizerState
get_trigger_last_updated() :
IMP::Model
get_trimmed_atom_name() :
IMP::atom::PDBRecord
get_tunnel_radius() :
IMP::npctransport::SimulationData
get_tunnel_radius_k() :
IMP::npctransport::SimulationData
get_type() :
IMP::atom::Bond
get_type_changed_key() :
IMP::atom::Residue
get_type_name() :
IMP::em2d::Image
,
IMP::npctransport::BipartitePairsStatisticsOptimizerState
get_unary_function() :
IMP::core::GenericAttributeSingletonScore< UF >
get_uniprot_accession() :
IMP::atom::Chain
get_uniprot_accession_key() :
IMP::atom::Chain
get_unique_id() :
IMP::Model
get_unit_cell() :
IMP::algebra::DefaultEmbeddingD< D >
,
IMP::algebra::LogEmbeddingD< D >
get_unit_simplex() :
IMP::isd::Weight
get_vacuum_form_factor() :
IMP::saxs::FormFactorTable
get_vacuum_form_factors() :
IMP::saxs::FormFactorTable
get_vacuum_water_form_factor() :
IMP::saxs::FormFactorTable
get_value() :
IMP::core::OrderedTypePairPredicate
,
IMP::core::OrderedTypeQuadPredicate
,
IMP::core::OrderedTypeSingletonPredicate
,
IMP::core::OrderedTypeTripletPredicate
,
IMP::em::DensityMap
get_value_index() :
IMP::atom::BondedPairFilter
,
IMP::atom::SameResiduePairFilter
,
IMP::atom::SoapPairFilter
,
IMP::atom::StereochemistryPairFilter
,
IMP::container::ConsecutivePairFilter
,
IMP::container::ExclusiveConsecutivePairFilter
,
IMP::container::InContainerPairFilter
,
IMP::container::InContainerQuadFilter
,
IMP::container::InContainerSingletonFilter
,
IMP::container::InContainerTripletFilter
,
IMP::core::AllSamePairPredicate
,
IMP::core::AllSameQuadPredicate
,
IMP::core::AllSameSingletonPredicate
,
IMP::core::AllSameTripletPredicate
,
IMP::core::AttributeSingletonPredicate
,
IMP::core::CoinFlipPairPredicate
,
IMP::core::CoinFlipQuadPredicate
,
IMP::core::CoinFlipSingletonPredicate
,
IMP::core::CoinFlipTripletPredicate
,
IMP::core::ConstantPairPredicate
,
IMP::core::ConstantQuadPredicate
,
IMP::core::ConstantSingletonPredicate
,
IMP::core::ConstantTripletPredicate
,
IMP::core::InBoundingBox3DSingletonPredicate
,
IMP::core::IsCollisionPairPredicate
,
IMP::core::OrderedTypePairPredicate
,
IMP::core::OrderedTypeQuadPredicate
,
IMP::core::OrderedTypeSingletonPredicate
,
IMP::core::OrderedTypeTripletPredicate
,
IMP::core::UnorderedTypePairPredicate
,
IMP::core::UnorderedTypeQuadPredicate
,
IMP::core::UnorderedTypeSingletonPredicate
,
IMP::core::UnorderedTypeTripletPredicate
,
IMP::misc::CommonEndpointPairFilter
,
IMP::PairPredicate
,
IMP::QuadPredicate
,
IMP::SingletonPredicate
,
IMP::spb::SameParticlePairFilter
,
IMP::spb::SameRigidBodyPairFilter
,
IMP::TripletPredicate
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
get_values() :
IMP.pmi.io.crosslink.CrossLinkDataBase
get_variances() :
IMP::core::Gaussian
get_vector_to() :
IMP::core::XYZ
get_version() :
IMP::core::SoftwareProvenance
get_version_info() :
IMP::algebra::DynamicNearestNeighbor3D
,
IMP::algebra::EuclideanVectorKDMetric
,
IMP::algebra::MaxVectorKDMetric
,
IMP::algebra::NearestNeighborD< D >
,
IMP::atom::AllPDBSelector
,
IMP::atom::AndPDBSelector
,
IMP::atom::AngleSingletonScore
,
IMP::atom::ATOMPDBSelector
,
IMP::atom::AtomTypePDBSelector
,
IMP::atom::BackbonePDBSelector
,
IMP::atom::BerendsenThermostatOptimizerState
,
IMP::atom::BondedPairFilter
,
IMP::atom::BondEndpointsRefiner
,
IMP::atom::BondGeometry
,
IMP::atom::BondPairContainer
,
IMP::atom::BondsGeometry
,
IMP::atom::BondSingletonScore
,
IMP::atom::BrownianDynamics
,
IMP::atom::CAAngleRestraint
,
IMP::atom::CADihedralRestraint
,
IMP::atom::CAlphaPDBSelector
,
IMP::atom::CBetaPDBSelector
,
IMP::atom::ChainPDBSelector
,
IMP::atom::CHARMMIdealResidueTopology
,
IMP::atom::CHARMMParameters
,
IMP::atom::CHARMMPatch
,
IMP::atom::CHARMMResidueTopology
,
IMP::atom::CHARMMResidueTopologyBase
,
IMP::atom::CHARMMSegmentTopology
,
IMP::atom::CHARMMStereochemistryRestraint
,
IMP::atom::CHARMMTopology
,
IMP::atom::CoulombPairScore
,
IMP::atom::CoverBond
,
IMP::atom::CPDBSelector
,
IMP::atom::DihedralSingletonScore
,
IMP::atom::EzRestraint
,
IMP::atom::ForceSwitch
,
IMP::atom::HelixRestraint
,
IMP::atom::HierarchiesGeometry
,
IMP::atom::HierarchyGeometry
,
IMP::atom::HydrogenPDBSelector
,
IMP::atom::ImproperSingletonScore
,
IMP::atom::LangevinThermostatOptimizerState
,
IMP::atom::LennardJonesPairScore
,
IMP::atom::MolecularDynamics
,
IMP::atom::NonAlternativePDBSelector
,
IMP::atom::NonHydrogenPDBSelector
,
IMP::atom::NonWaterNonHydrogenPDBSelector
,
IMP::atom::NonWaterPDBSelector
,
IMP::atom::NotPDBSelector
,
IMP::atom::NPDBSelector
,
IMP::atom::OrPDBSelector
,
IMP::atom::PPDBSelector
,
IMP::atom::RemoveRigidMotionOptimizerState
,
IMP::atom::RemoveTranslationOptimizerState
,
IMP::atom::ResidueTypePDBSelector
,
IMP::atom::SameResiduePairFilter
,
IMP::atom::SelectionGeometry
,
IMP::atom::SoapPairFilter
,
IMP::atom::StereochemistryPairFilter
,
IMP::atom::VelocityScalingOptimizerState
,
IMP::atom::WaterPDBSelector
,
IMP::atom::WritePDBOptimizerState
,
IMP::atom::XorPDBSelector
,
IMP::bayesianem::GaussianEMRestraint
,
IMP::Configuration
,
IMP::ConfigurationSet
,
IMP::container::AllBipartitePairContainer
,
IMP::container::AllPairContainer
,
IMP::container::CloseBipartitePairContainer
,
IMP::container::ClosePairContainer
,
IMP::container::ConnectingPairContainer
,
IMP::container::ConsecutivePairContainer
,
IMP::container::ConsecutivePairFilter
,
IMP::container::DistributePairsScoreState
,
IMP::container::DistributeQuadsScoreState
,
IMP::container::DistributeSingletonsScoreState
,
IMP::container::DistributeTripletsScoreState
,
IMP::container::DynamicListPairContainer
,
IMP::container::DynamicListQuadContainer
,
IMP::container::DynamicListSingletonContainer
,
IMP::container::DynamicListTripletContainer
,
IMP::container::EventPairsOptimizerState
,
IMP::container::EventQuadsOptimizerState
,
IMP::container::EventSingletonsOptimizerState
,
IMP::container::EventTripletsOptimizerState
,
IMP::container::ExclusiveConsecutivePairContainer
,
IMP::container::ExclusiveConsecutivePairFilter
,
IMP::container::InContainerPairFilter
,
IMP::container::InContainerQuadFilter
,
IMP::container::InContainerSingletonFilter
,
IMP::container::InContainerTripletFilter
,
IMP::container::ListPairContainer
,
IMP::container::ListQuadContainer
,
IMP::container::ListSingletonContainer
,
IMP::container::ListTripletContainer
,
IMP::container::MinimumPairRestraint
,
IMP::container::MinimumPairScore
,
IMP::container::MinimumQuadRestraint
,
IMP::container::MinimumQuadScore
,
IMP::container::MinimumSingletonRestraint
,
IMP::container::MinimumSingletonScore
,
IMP::container::MinimumTripletRestraint
,
IMP::container::MinimumTripletScore
,
IMP::container::PairContainerSet
,
IMP::container::PairContainerStatistics
,
IMP::container::PairsConstraint
,
IMP::container::PairsOptimizerState
,
IMP::container::PairsRestraint
,
IMP::container::PredicatePairsRestraint
,
IMP::container::PredicateQuadsRestraint
,
IMP::container::PredicateSingletonsRestraint
,
IMP::container::PredicateTripletsRestraint
,
IMP::container::QuadContainerSet
,
IMP::container::QuadContainerStatistics
,
IMP::container::QuadsConstraint
,
IMP::container::QuadsOptimizerState
,
IMP::container::QuadsRestraint
,
IMP::container::SingletonContainerSet
,
IMP::container::SingletonContainerStatistics
,
IMP::container::SingletonsConstraint
,
IMP::container::SingletonsOptimizerState
,
IMP::container::SingletonsRestraint
,
IMP::container::TripletContainerSet
,
IMP::container::TripletContainerStatistics
,
IMP::container::TripletsConstraint
,
IMP::container::TripletsOptimizerState
,
IMP::container::TripletsRestraint
,
IMP::core::AllSamePairPredicate
,
IMP::core::AllSameQuadPredicate
,
IMP::core::AllSameSingletonPredicate
,
IMP::core::AllSameTripletPredicate
,
IMP::core::AngleRestraint
,
IMP::core::AngleTripletScore
,
IMP::core::AttributeSingletonPredicate
,
IMP::core::BallMover
,
IMP::core::BoxSweepClosePairsFinder
,
IMP::core::CentroidOfRefined
,
IMP::core::ChecksScoreState
,
IMP::core::ChildrenRefiner
,
IMP::core::ClosedCubicSpline
,
IMP::core::ClosePairsPairScore
,
IMP::core::CoinFlipPairPredicate
,
IMP::core::CoinFlipQuadPredicate
,
IMP::core::CoinFlipSingletonPredicate
,
IMP::core::CoinFlipTripletPredicate
,
IMP::core::ConjugateGradients
,
IMP::core::ConnectivityRestraint
,
IMP::core::ConstantPairPredicate
,
IMP::core::ConstantQuadPredicate
,
IMP::core::ConstantRestraint
,
IMP::core::ConstantSingletonPredicate
,
IMP::core::ConstantTripletPredicate
,
IMP::core::Cosine
,
IMP::core::CoverRefined
,
IMP::core::DerivativesFromRefined
,
IMP::core::DerivativesToRefined
,
IMP::core::DiameterRestraint
,
IMP::core::DihedralRestraint
,
IMP::core::DirectionMover
,
IMP::core::DistancePairScore
,
IMP::core::EdgePairGeometry
,
IMP::core::EdgePairsGeometry
,
IMP::core::ExcludedVolumeRestraint
,
IMP::core::FixedRefiner
,
IMP::core::GenericAttributeSingletonScore< UF >
,
IMP::core::GenericBoundingBox3DSingletonScore< UF >
,
IMP::core::GenericBoundingSphere3DSingletonScore< UF >
,
IMP::core::GenericDistanceToSingletonScore< UF >
,
IMP::core::GridClosePairsFinder
,
IMP::core::Harmonic
,
IMP::core::HarmonicDistancePairScore
,
IMP::core::HarmonicLowerBound
,
IMP::core::HarmonicSphereDistancePairScore
,
IMP::core::HarmonicSurfaceDepthPairScore
,
IMP::core::HarmonicSurfaceDistancePairScore
,
IMP::core::HarmonicSurfaceHeightPairScore
,
IMP::core::HarmonicUpperBound
,
IMP::core::HarmonicUpperBoundSphereDiameterPairScore
,
IMP::core::HarmonicUpperBoundSphereDistancePairScore
,
IMP::core::HarmonicWell
,
IMP::core::InBoundingBox3DSingletonPredicate
,
IMP::core::IsCollisionPairPredicate
,
IMP::core::KClosePairsPairScore
,
IMP::core::LateralSurfaceConstraint
,
IMP::core::LeavesRefiner
,
IMP::core::Linear
,
IMP::core::LogNormalMover
,
IMP::core::MCCGSampler
,
IMP::core::MinimumRestraint
,
IMP::core::MonteCarlo
,
IMP::core::MonteCarloWithBasinHopping
,
IMP::core::MonteCarloWithLocalOptimization
,
IMP::core::MoveStatisticsScoreState
,
IMP::core::MSConnectivityRestraint
,
IMP::core::MultipleBinormalRestraint
,
IMP::core::NearestNeighborsClosePairsFinder
,
IMP::core::NeighborsTable
,
IMP::core::NormalizedSphereDistancePairScore
,
IMP::core::NormalMover
,
IMP::core::OrderedTypePairPredicate
,
IMP::core::OrderedTypeQuadPredicate
,
IMP::core::OrderedTypeSingletonPredicate
,
IMP::core::OrderedTypeTripletPredicate
,
IMP::core::PairConstraint
,
IMP::core::PairRestraint
,
IMP::core::PredicateSingletonScore< Predicate, Score >
,
IMP::core::QuadConstraint
,
IMP::core::QuadraticClosePairsFinder
,
IMP::core::QuadRestraint
,
IMP::core::RefinedPairsPairScore
,
IMP::core::RigidBodyAnglePairScore
,
IMP::core::RigidBodyDerivativeGeometry
,
IMP::core::RigidBodyDerivativesGeometry
,
IMP::core::RigidBodyFrameGeometry
,
IMP::core::RigidBodyFramesGeometry
,
IMP::core::RigidBodyHierarchyGeometry
,
IMP::core::RigidBodyMover
,
IMP::core::RigidBodyTunneler
,
IMP::core::RigidBodyUmbrella
,
IMP::core::RigidClosePairsFinder
,
IMP::core::SerialMover
,
IMP::core::SingletonConstraint
,
IMP::core::SingletonRestraint
,
IMP::core::SoftSpherePairScore
,
IMP::core::SoftSubSurfacePairScore
,
IMP::core::SoftSuperSurfacePairScore
,
IMP::core::SphereDistancePairScore
,
IMP::core::SphereDistanceToSingletonScore
,
IMP::core::SteepestDescent
,
IMP::core::SubsetMover
,
IMP::core::SurfaceDepthPairScore
,
IMP::core::SurfaceDistancePairScore
,
IMP::core::SurfaceGeometry
,
IMP::core::SurfaceGeometryConstraint
,
IMP::core::SurfaceHeightPairScore
,
IMP::core::SurfaceMover
,
IMP::core::SurfaceSymmetryConstraint
,
IMP::core::SurfaceTetheredChain
,
IMP::core::TableRefiner
,
IMP::core::Transform
,
IMP::core::TransformationAndReflectionSymmetry
,
IMP::core::TransformationSymmetry
,
IMP::core::TransformationSymmetryMover
,
IMP::core::TransformedDistancePairScore
,
IMP::core::TripletConstraint
,
IMP::core::TripletRestraint
,
IMP::core::TruncatedHarmonic< DIRECTION >
,
IMP::core::TypedPairScore
,
IMP::core::UnorderedTypePairPredicate
,
IMP::core::UnorderedTypeQuadPredicate
,
IMP::core::UnorderedTypeSingletonPredicate
,
IMP::core::UnorderedTypeTripletPredicate
,
IMP::core::VolumeRestraint
,
IMP::core::WeightedDerivativesToRefined
,
IMP::core::WeightedSphereDistancePairScore
,
IMP::core::WeightedSum
,
IMP::core::WeightedSumOfExponential
,
IMP::core::WriteRestraintScoresOptimizerState
,
IMP::core::XYZDerivativeGeometry
,
IMP::core::XYZDerivativesGeometry
,
IMP::core::XYZRGeometry
,
IMP::core::XYZRsGeometry
,
IMP::display::BoundingBoxGeometry
,
IMP::display::CylinderGeometry
,
IMP::display::EllipsoidGeometry
,
IMP::display::FilterGeometry
,
IMP::display::GeometrySet
,
IMP::display::LabelGeometry
,
IMP::display::PlaneGeometry
,
IMP::display::PointGeometry
,
IMP::display::PolygonGeometry
,
IMP::display::PymolWriter
,
IMP::display::ReferenceFrameGeometry
,
IMP::display::RestraintGeometry
,
IMP::display::RestraintSetGeometry
,
IMP::display::SegmentGeometry
,
IMP::display::SphereGeometry
,
IMP::display::SurfaceMeshGeometry
,
IMP::display::TriangleGeometry
,
IMP::display::WriteOptimizerState
,
IMP::domino::BranchAndBoundAssignmentsTable
,
IMP::domino::BranchAndBoundSampler
,
IMP::domino::CappedAssignmentContainer
,
IMP::domino::CompoundStates
,
IMP::domino::DependencyScoreState
,
IMP::domino::DominoSampler
,
IMP::domino::EqualitySubsetFilterTable
,
IMP::domino::EquivalenceAndExclusionSubsetFilterTable
,
IMP::domino::EquivalenceSubsetFilterTable
,
IMP::domino::ExclusionSubsetFilterTable
,
IMP::domino::HeapAssignmentContainer
,
IMP::domino::IndexStates
,
IMP::domino::ListAssignmentContainer
,
IMP::domino::ListAssignmentsTable
,
IMP::domino::ListSubsetFilterTable
,
IMP::domino::MinimumRestraintScoreSubsetFilterTable
,
IMP::domino::NestedRigidBodyStates
,
IMP::domino::PackedAssignmentContainer
,
IMP::domino::PairListSubsetFilterTable
,
IMP::domino::ParticleStatesTable
,
IMP::domino::PermutationStates
,
IMP::domino::ProbabilisticSubsetFilterTable
,
IMP::domino::RangeViewAssignmentContainer
,
IMP::domino::ReadAssignmentContainer
,
IMP::domino::ReadHDF5AssignmentContainer
,
IMP::domino::RecursiveAssignmentsTable
,
IMP::domino::RecursiveStates
,
IMP::domino::RestraintCache
,
IMP::domino::RestraintScoreSubsetFilterTable
,
IMP::domino::RigidBodyStates
,
IMP::domino::SampleAssignmentContainer
,
IMP::domino::SimpleAssignmentsTable
,
IMP::domino::WriteAssignmentContainer
,
IMP::domino::WriteHDF5AssignmentContainer
,
IMP::domino::XYZStates
,
IMP::em2d::CollisionCrossSection
,
IMP::em2d::DistanceFilter
,
IMP::em2d::DistanceFilterTable
,
IMP::em2d::DummyRestraint
,
IMP::em2d::Em2DRestraint
,
IMP::em2d::GridStates
,
IMP::em2d::Image
,
IMP::em2d::ImageReaderWriter
,
IMP::em2d::JPGImageReaderWriter
,
IMP::em2d::ParticlesDummyRestraint
,
IMP::em2d::PCAFitRestraint
,
IMP::em2d::ProjectionFinder
,
IMP::em2d::ProjectionParametersScoreState
,
IMP::em2d::ProjectionStates
,
IMP::em2d::RelativePositionMover
,
IMP::em2d::RigidBodiesImageFitRestraint
,
IMP::em2d::ScoreFunction
,
IMP::em2d::SpiderImageReaderWriter
,
IMP::em2d::TIFFImageReaderWriter
,
IMP::em::CoarseCCatIntervals
,
IMP::em::DensityFillingRestraint
,
IMP::em::DensityMap
,
IMP::em::EMReaderWriter
,
IMP::em::EnvelopeFitRestraint
,
IMP::em::EnvelopePenetrationRestraint
,
IMP::em::EnvelopeScore
,
IMP::em::FitRestraint
,
IMP::em::FitRestraintBayesEM3D
,
IMP::em::HighDensityEmbedding
,
IMP::em::MapReaderWriter
,
IMP::em::MRCReaderWriter
,
IMP::em::PCAAligner
,
IMP::em::PCAFitRestraint
,
IMP::em::SpiderMapReaderWriter
,
IMP::em::XplorReaderWriter
,
IMP::example::ExampleComplexRestraint
,
IMP::example::ExampleConstraint
,
IMP::example::ExampleObject
,
IMP::example::ExamplePairScore
,
IMP::example::ExampleRestraint
,
IMP::example::ExampleSingletonModifier
,
IMP::example::ExampleSubsetFilterTable
,
IMP::example::ExampleUnaryFunction
,
IMP::gsl::ConjugateGradients
,
IMP::gsl::QuasiNewton
,
IMP::gsl::Simplex
,
IMP::isd::AmbiguousNOERestraint
,
IMP::isd::AmbiguousRestraint
,
IMP::isd::AtomicCrossLinkMSRestraint
,
IMP::isd::Covariance1DFunction
,
IMP::isd::CrossLinkData
,
IMP::isd::CrossLinkMSRestraint
,
IMP::isd::CysteineCrossLinkData
,
IMP::isd::CysteineCrossLinkRestraint
,
IMP::isd::Distribution
,
IMP::isd::FNormal
,
IMP::isd::FretData
,
IMP::isd::FretRestraint
,
IMP::isd::FStudentT
,
IMP::isd::GammaPrior
,
IMP::isd::GaussianAnchorEMRestraint
,
IMP::isd::GaussianEMRestraint
,
IMP::isd::GaussianProcessInterpolation
,
IMP::isd::GaussianProcessInterpolationRestraint
,
IMP::isd::GaussianRestraint
,
IMP::isd::GeneralizedGuinierPorodFunction
,
IMP::isd::HybridMonteCarlo
,
IMP::isd::ISDRestraint
,
IMP::isd::JeffreysRestraint
,
IMP::isd::Linear1DFunction
,
IMP::isd::LognormalAmbiguousRestraint
,
IMP::isd::LognormalRestraint
,
IMP::isd::LogWrapper
,
IMP::isd::MarginalHBondRestraint
,
IMP::isd::MarginalNOERestraint
,
IMP::isd::MolecularDynamicsMover
,
IMP::isd::MultivariateFNormalSufficient
,
IMP::isd::NOERestraint
,
IMP::isd::NormalSigmaPCRestraint
,
IMP::isd::OneDimensionalDistribution
,
IMP::isd::OneDimensionalSufficientDistribution
,
IMP::isd::PenalizedComplexityPrior
,
IMP::isd::RepulsiveDistancePairScore
,
IMP::isd::ResidueProteinProximityRestraint
,
IMP::isd::StudentTRestraint
,
IMP::isd::TALOSRestraint
,
IMP::isd::UniformPrior
,
IMP::isd::vonMises
,
IMP::isd::vonMisesKappaConjugateRestraint
,
IMP::isd::vonMisesKappaJeffreysRestraint
,
IMP::isd::vonMisesSufficient
,
IMP::isd::WeightMover
,
IMP::isd::WeightRestraint
,
IMP::kinematics::DihedralMover
,
IMP::kinematics::DirectionalDOF
,
IMP::kinematics::DOF
,
IMP::kinematics::DOFsSampler
,
IMP::kinematics::Joint
,
IMP::kinematics::KinematicForest
,
IMP::kinematics::KinematicForestScoreState
,
IMP::kinematics::LocalPlanner
,
IMP::kinematics::ProteinKinematics
,
IMP::kinematics::RevoluteJointMover
,
IMP::kinematics::RRT
,
IMP::kmeans::KMeans
,
IMP::misc::CommonEndpointPairFilter
,
IMP::misc::DecayPairContainerOptimizerState
,
IMP::misc::FreelyJointedChain
,
IMP::misc::LogPairScore
,
IMP::misc::LowestRefinedPairScore
,
IMP::misc::MetricClosePairsFinder< LowerBound, UpperBound >
,
IMP::misc::SoftCylinderPairScore
,
IMP::misc::StateAdaptor
,
IMP::misc::WormLikeChain
,
IMP::Model
,
IMP::mpi::ReplicaExchange
,
IMP::multifit::AssemblyHeader
,
IMP::multifit::ComplementarityRestraint
,
IMP::multifit::ComponentHeader
,
IMP::multifit::DummyRestraint
,
IMP::multifit::Ensemble
,
IMP::multifit::FFTFitting
,
IMP::multifit::FFTFittingOutput
,
IMP::multifit::FittingStates
,
IMP::multifit::ProbabilisticAnchorGraph
,
IMP::multifit::ProteomicsData
,
IMP::multifit::ProteomicsEMAlignmentAtomic
,
IMP::multifit::RadiusOfGyrationRestraint
,
IMP::multifit::RigidLeavesRefiner
,
IMP::multifit::SettingsData
,
IMP::multifit::WeightedExcludedVolumeRestraint
,
IMP::npc::AssemblySymmetryByDihedralRestraint
,
IMP::npc::AssemblySymmetryByDistanceRestraint
,
IMP::npc::CompositeRestraint
,
IMP::npc::MembraneExclusionRestraint
,
IMP::npc::MembraneSurfaceLocationConditionalRestraint
,
IMP::npc::MembraneSurfaceLocationRestraint
,
IMP::npc::MinimumSphereDistancePairScore
,
IMP::npc::PerinuclearVolumeLocationRestraint
,
IMP::npc::PoreSideVolumeLocationRestraint
,
IMP::npc::ProteinChainRestraint
,
IMP::npc::ProteinContactRestraint
,
IMP::npc::ProteinProximityRestraint
,
IMP::npc::XYRadialPositionLowerRestraint
,
IMP::npc::XYRadialPositionRestraint
,
IMP::npc::XYRadialPositionUpperRestraint
,
IMP::npc::YAxialPositionLowerRestraint
,
IMP::npc::YAxialPositionRestraint
,
IMP::npc::YAxialPositionUpperRestraint
,
IMP::npc::ZAxialPositionLowerRestraint
,
IMP::npc::ZAxialPositionRestraint
,
IMP::npc::ZAxialPositionUpperRestraint
,
IMP::npctransport::AnchorToCylidnricalPorePairScore
,
IMP::npctransport::BipartitePairsStatisticsOptimizerState
,
IMP::npctransport::BodyStatisticsOptimizerState
,
IMP::npctransport::ChainStatisticsOptimizerState
,
IMP::npctransport::ExcludeZRangeSingletonScore
,
IMP::npctransport::FGChain
,
IMP::npctransport::FunctorLinearInteractionPairScore
,
IMP::npctransport::FunctorLinearSoftSpherePairScore
,
IMP::npctransport::GlobalStatisticsOptimizerState
,
IMP::npctransport::HarmonicSpringSingletonScore
,
IMP::npctransport::HarmonicWellPairScore
,
IMP::npctransport::LinearInteractionPairScore
,
IMP::npctransport::LinearSoftSpherePairScore
,
IMP::npctransport::LinearWellPairScore
,
IMP::npctransport::ParticleFactory
,
IMP::npctransport::ParticleTransportStatisticsOptimizerState
,
IMP::npctransport::Scoring
,
IMP::npctransport::SimulationData
,
IMP::npctransport::SitesGeometry
,
IMP::npctransport::SitesPairScore
,
IMP::npctransport::SlabWithCylindricalPorePairScore
,
IMP::npctransport::SlabWithCylindricalPoreWireGeometry
,
IMP::npctransport::SlabWithToroidalPorePairScore
,
IMP::npctransport::SlabWithToroidalPoreWireGeometry
,
IMP::npctransport::Statistics
,
IMP::npctransport::TypedSitesGeometry
,
IMP::npctransport::ZBiasSingletonScore
,
IMP::Object
,
IMP::Particle
,
IMP::pmi1::CompositeRestraint
,
IMP::pmi1::InternalCoordinatesConstraint
,
IMP::pmi1::MembraneRestraint
,
IMP::pmi1::SigmoidRestraintSphere
,
IMP::pmi1::TransformMover
,
IMP::pmi::CompositeRestraint
,
IMP::pmi::CrossLinkRestraintSet
,
IMP::pmi::MembraneRestraint
,
IMP::pmi::TransformMover
,
IMP::RestraintInfo
,
IMP::RestraintSet
,
IMP::rmf::HierarchyLoadLink
,
IMP::rmf::HierarchySaveLink
,
IMP::rmf::SaveOptimizerState
,
IMP::rotamer::RotamerCalculator
,
IMP::rotamer::RotamerLibrary
,
IMP::SaveToConfigurationSetOptimizerState
,
IMP::saxs::ChiScore
,
IMP::saxs::ChiScoreLog
,
IMP::saxs::Profile
,
IMP::saxs::RadiusOfGyrationRestraint
,
IMP::saxs::RatioVolatilityScore
,
IMP::saxs::Restraint
,
IMP::saxs::RigidBodiesProfileHandler
,
IMP::score_functor::DistancePairScore< DistanceScoreT >
,
IMP::score_functor::DistancePairScoreWithCache< DistanceScoreT >
,
IMP::score_functor::ScoreUnaryFunction< Score, D >
,
IMP::score_functor::SurfaceDistancePairScore< DistanceScoreT >
,
IMP::spb::AttributeDistancePairScore
,
IMP::spb::BoxedMover
,
IMP::spb::CellMover
,
IMP::spb::ChiSquareMetric
,
IMP::spb::ContactMapMetric
,
IMP::spb::DiameterRgyrRestraint
,
IMP::spb::DistanceRMSDMetric
,
IMP::spb::DistanceTerminiRestraint
,
IMP::spb::EM2DRestraint
,
IMP::spb::Gaussian
,
IMP::spb::KinkPairScore
,
IMP::spb::MonteCarloWithWte
,
IMP::spb::NuisanceRangeModifier
,
IMP::spb::PbcBoxedMover
,
IMP::spb::PbcBoxedRigidBodyMover
,
IMP::spb::RigidBodyNewMover
,
IMP::spb::RMSDMetric
,
IMP::spb::SameParticlePairFilter
,
IMP::spb::SameRigidBodyPairFilter
,
IMP::spb::TiltSingletonScore
,
IMP::spb::TransformationSymmetry
,
IMP::spb::TwoStateGoModelRestraint
,
IMP::spb::UniformBoundedRestraint
,
IMP::statistics::ChiSquareMetric
,
IMP::statistics::ConfigurationSetRMSDMetric
,
IMP::statistics::ConfigurationSetXYZEmbedding
,
IMP::statistics::EuclideanMetric
,
IMP::statistics::ParticleEmbedding
,
IMP::statistics::PartitionalClusteringWithCenter
,
IMP::statistics::RecursivePartitionalClusteringEmbedding
,
IMP::statistics::RecursivePartitionalClusteringMetric
,
IMP::statistics::VectorDEmbedding
,
IMP::symmetry::BallMover
,
IMP::symmetry::RigidBodyMover
get_vertex_assignments() :
IMP::domino::DominoSampler
get_volume() :
IMP::algebra::Cone3D
,
IMP::algebra::Cylinder3D
,
IMP::algebra::Ellipsoid3D
,
IMP::algebra::Torus3D
,
IMP::saxs::FormFactorTable
get_voxel_by_location() :
IMP::em::DensityMap
get_was_good() :
IMP::Restraint
get_water_dummy_form_factors() :
IMP::saxs::FormFactorTable
get_water_form_factor() :
IMP::saxs::FormFactorTable
get_water_form_factors() :
IMP::saxs::FormFactorTable
get_water_vacuum_form_factors() :
IMP::saxs::FormFactorTable
get_weight() :
IMP::core::WeightedSum
,
IMP::core::WeightedSumOfExponential
,
IMP::isd::Weight
,
IMP::statistics::Embedding
,
IMP::statistics::Metric
get_weight_derivative() :
IMP::isd::Weight
get_weight_key() :
IMP::isd::Weight
get_weight_keys() :
IMP::isd::Weight
get_weights() :
IMP::core::WeightedSum
,
IMP::core::WeightedSumOfExponential
,
IMP::isd::Weight
get_weights_are_optimized() :
IMP::isd::Weight
get_weights_derivatives() :
IMP::isd::Weight
get_x() :
IMP::core::XYZ
get_xlinks_for_pair() :
IMP.EMageFit.buildxlinks.XlinksDict
get_xorigin() :
IMP::em::DensityHeader
get_xyz_keys() :
IMP::core::XYZ
get_xyz_stats_crop_factor() :
IMP::npctransport::SimulationData
get_xyz_stats_max_box_size_A() :
IMP::npctransport::SimulationData
get_xyz_stats_voxel_size_A() :
IMP::npctransport::SimulationData
get_y() :
IMP::core::XYZ
get_yorigin() :
IMP::em::DensityHeader
get_z() :
IMP::core::XYZ
get_z_bias_restraints() :
IMP::npctransport::Scoring
get_zorigin() :
IMP::em::DensityHeader
GlobalStatisticsOptimizerState() :
IMP::npctransport::GlobalStatisticsOptimizerState
GridD() :
IMP::algebra::GridD< D, StorageT, Value, EmbeddingT >
GridStates() :
IMP::em2d::GridStates