Here is a list of all documented class members with links to the class documentation for each member:
- a -
- accept()
: IMP::core::MonteCarloMover
- activate_statistics()
: IMP::npctransport::SimulationData
- add()
: IMP::container::DynamicListPairContainer
, IMP::container::DynamicListQuadContainer
, IMP::container::DynamicListSingletonContainer
, IMP::container::DynamicListTripletContainer
, IMP::container::ListPairContainer
, IMP::container::ListQuadContainer
, IMP::container::ListSingletonContainer
, IMP::container::ListTripletContainer
, IMP::em::DensityMap
, IMP.EMageFit.buildxlinks.XlinksDict
, IMP.pmi.tools.Segments
, IMP.pmi1.tools.Segments
, IMP::saxs::Profile
, IMP::saxs::RadialDistributionFunction
, IMP::statistics::HistogramD< D, Grid >
- add_alias()
: IMP::Key< ID >
- add_all_atom_densities()
: IMP.pmi1.representation.Representation
- add_all_restraints()
: IMP::multifit::ProteomicsEMAlignmentAtomic
- add_atom_types()
: IMP::atom::CHARMMTopology
- add_attribute()
: IMP::Model
- add_bonds()
: IMP::atom::CHARMMTopology
, IMP::atom::ForceFieldParameters
- add_branch_and_bound_assignments_table()
: IMP.EMageFit.domino_model.DominoModel
- add_cache_attribute()
: IMP::Model
- add_category()
: IMP.isd.Statistics.Statistics
- add_ccc_table()
: IMP.EMageFit.solutions_io.ResultsDB
- add_chain_restraints()
: IMP::npctransport::Scoring
- add_charges()
: IMP::atom::CHARMMTopology
- add_child()
: IMP::atom::Hierarchy
- add_cluster_record()
: IMP.EMageFit.solutions_io.ResultsDB
- add_clusters_table()
: IMP.EMageFit.solutions_io.ResultsDB
- add_column()
: IMP.EMageFit.database.Database2
- add_columns()
: IMP.EMageFit.database.Database2
- add_component_beads()
: IMP.pmi1.representation.Representation
- add_component_density()
: IMP.pmi1.representation.Representation
- add_component_hierarchy_clone()
: IMP.pmi1.representation.Representation
- add_component_necklace()
: IMP.pmi1.representation.Representation
- add_component_pdb()
: IMP.pmi1.representation.Representation
- add_component_sequence()
: IMP.pmi1.representation.Representation
- add_configuration()
: IMP::statistics::ChiSquareMetric
- add_contribution()
: IMP::isd::AtomicCrossLinkMSRestraint
- add_coordinates()
: IMP::atom::CHARMMTopology
, IMP.isd.Statistics.Statistics
- add_data()
: IMP.isd.Analysis.Analysis
, IMP::Model
- add_data_pt()
: IMP::kmeans::KMeans
- add_dihedrals()
: IMP::atom::CHARMMTopology
- add_downstream_joint()
: IMP::kinematics::CompositeJoint
- add_edge()
: IMP::kinematics::KinematicForest
- add_entry()
: IMP.isd.Statistics.Statistics
- add_entry_point()
: IMP::core::RigidBodyTunneler
- add_errors()
: IMP::saxs::Profile
- add_exclusion_filter_table()
: IMP.EMageFit.domino_model.DominoModel
- add_fg_chain_stats()
: IMP::npctransport::Statistics
- add_filename()
: IMP::RestraintInfo
- add_filenames()
: IMP::RestraintInfo
- add_float()
: IMP::RestraintInfo
- add_floater_stats()
: IMP::npctransport::Statistics
- add_floats()
: IMP::RestraintInfo
- add_full_datum()
: IMP.isd.TALOSReader.TALOSReader
- add_impropers()
: IMP::atom::CHARMMTopology
- add_in_plane_transformation()
: IMP::em2d::RegistrationResult
- add_int()
: IMP::RestraintInfo
- add_interaction()
: IMP::npctransport::Scoring
, IMP::npctransport::SimulationData
- add_interaction_stats()
: IMP::npctransport::Statistics
- add_internal_transformations()
: IMP::em2d::RelativePositionMover
- add_ints()
: IMP::RestraintInfo
- add_mean_datum()
: IMP.isd.TALOSReader.TALOSReader
- add_member()
: IMP::core::RigidBody
- add_metadata()
: IMP.pmi1.representation.Representation
- add_missing_atoms()
: IMP::atom::CHARMMTopology
- add_model()
: IMP.mmcif.util.Writer
- add_native_record()
: IMP.EMageFit.solutions_io.ResultsDB
- add_noise()
: IMP::saxs::Profile
- add_non_rigid_member()
: IMP::core::RigidBody
- add_optimizer_states()
: IMP::npctransport::Statistics
- add_partial_profiles()
: IMP::saxs::Profile
- add_particle()
: IMP::core::TableRefiner
, IMP::Model
- add_particle_indexes()
: IMP::RestraintInfo
- add_placement_scores_table()
: IMP.EMageFit.solutions_io.ResultsDB
- add_predicate()
: IMP::container::DistributePairsScoreState
, IMP::container::DistributeQuadsScoreState
, IMP::container::DistributeSingletonsScoreState
, IMP::container::DistributeTripletsScoreState
- add_protein()
: IMP::multifit::ProteomicsData
- add_protocol_output()
: IMP.pmi.macros.AnalysisReplicaExchange0
, IMP.pmi.topology.System
, IMP.pmi1.macros.AnalysisReplicaExchange0
, IMP.pmi1.representation.Representation
- add_radii()
: IMP::atom::ForceFieldParameters
- add_record()
: IMP.EMageFit.solutions_io.ResultsDB
- add_representation()
: IMP::atom::Representation
, IMP.pmi.topology.Molecule
- add_restrained_anchor_bead()
: IMP::npctransport::Scoring
- add_restraint()
: IMP.EMageFit.domino_model.DominoModel
- add_restraint_score_filter_table()
: IMP.EMageFit.domino_model.DominoModel
- add_restraints()
: IMP::domino::RestraintCache
- add_results_table()
: IMP.EMageFit.solutions_io.ResultsDB
- add_rigid_bodies_in_chain()
: IMP::kinematics::KinematicForest
- add_rmf()
: IMP.mmcif.util.Writer
, IMP.pmi.plotting.topology.TopologyPlot
, IMP.pmi1.plotting.topology.TopologyPlot
- add_score()
: IMP::ScoreAccumulator
- add_sequence()
: IMP::atom::CHARMMTopology
- add_solution()
: IMP::em::FittingSolutions
- add_state()
: IMP.pmi.macros.BuildSystem
- add_string()
: IMP::RestraintInfo
- add_strings()
: IMP::RestraintInfo
- add_structure()
: IMP.pmi.analysis.Precision
, IMP.pmi.topology.Molecule
, IMP.pmi1.analysis.Precision
- add_structures()
: IMP.pmi.analysis.Precision
, IMP.pmi1.analysis.Precision
- add_subunits_density()
: IMP.pmi.analysis.GetModelDensity
, IMP.pmi1.analysis.GetModelDensity
, IMP.sampcon.precision_rmsd.GetModelDensity
- add_target_density_to_hierarchy()
: IMP.bayesianem.restraint.GaussianEMRestraintWrapper
, IMP.pmi.restraints.em.GaussianEMRestraint
, IMP.pmi1.restraints.em.GaussianEMRestraint
- add_task()
: IMP.parallel.Context
- add_term()
: IMP::core::MultipleBinormalRestraint
- add_to_angle_derivative()
: IMP::core::DirectionAngle
- add_to_derivative()
: IMP::core::XYZ
- add_to_derivatives()
: IMP::core::RigidBody
, IMP::core::XYZ
, IMP::isd::BivariateFunction
, IMP::isd::Covariance1DFunction
, IMP::isd::GeneralizedGuinierPorodFunction
, IMP::isd::Linear1DFunction
, IMP::isd::UnivariateFunction
- add_to_direction_derivative()
: IMP::core::Direction
- add_to_direction_derivatives()
: IMP::core::Direction
- add_to_internal_derivatives()
: IMP::core::NonRigidMember
- add_to_internal_rotational_derivatives()
: IMP::core::NonRigidMember
- add_to_map()
: IMP::em::DensityMap
- add_to_model()
: IMP.pmi1.restraints.RestraintBase
- add_to_normal_derivative()
: IMP::core::Surface
- add_to_normal_derivatives()
: IMP::core::Surface
- add_to_particle_derivative()
: IMP::isd::BivariateFunction
, IMP::isd::Covariance1DFunction
, IMP::isd::GeneralizedGuinierPorodFunction
, IMP::isd::Linear1DFunction
, IMP::isd::UnivariateFunction
- add_to_pore_radius_derivative()
: IMP::npctransport::SlabWithPore
- add_to_radius_derivative()
: IMP::core::XYZR
- add_to_rotational_derivatives()
: IMP::core::RigidBody
- add_to_torque()
: IMP::core::RigidBody
- add_to_weight_derivative()
: IMP::isd::Weight
- add_to_weights_derivatives()
: IMP::isd::Weight
- add_type()
: IMP::npc::CompositeRestraint
- add_undecorator()
: IMP::Model
- add_upstream_joint()
: IMP::kinematics::CompositeJoint
- add_voxel()
: IMP::algebra::SparseGridStorageD< D, VT, Base, Map >
- add_weight()
: IMP::isd::Weight
- add_weight_lazy()
: IMP::isd::Weight
- add_well_depths()
: IMP::atom::ForceFieldParameters
- add_worker()
: IMP.parallel.Manager
- add_z_bias_restraint()
: IMP::npctransport::Scoring
- after_evaluate()
: IMP::ScoreState
- aggregate()
: IMP.pmi.macros.AnalysisReplicaExchange
, IMP.pmi1.macros.AnalysisReplicaExchange
- align()
: IMP::em::PCAAligner
- align_rigid_bodies_states()
: IMP.EMageFit.domino_model.DominoModel
- align_sequence()
: IMP.pmi.io.crosslink.CrossLinkDataBase
- AlignSymmetric()
: IMP::cnmultifit::AlignSymmetric
- AllPairContainer()
: IMP::container::AllPairContainer
- AmbiguousNOERestraint()
: IMP::isd::AmbiguousNOERestraint
- AmbiguousRestraint()
: IMP::isd::AmbiguousRestraint
- AnchorToCylidnricalPorePairScore()
: IMP::npctransport::AnchorToCylidnricalPorePairScore
- AngleRestraint()
: IMP::core::AngleRestraint
- AngleSingletonScore()
: IMP::atom::AngleSingletonScore
- AngleTripletScore()
: IMP::core::AngleTripletScore
- angular_D_factor_
: IMP::npctransport::ParticleFactory
- append()
: IMP.isd.utils.Pipe
- append_database()
: IMP.pmi.io.crosslink.CrossLinkDataBase
- apply()
: IMP::atom::CHARMMPatch
, IMP::em2d::ProjectionMask
, IMP::kinematics::DOFsSampler
, IMP::kinematics::FibrilSampler
, IMP::kinematics::UniformBackboneSampler
, IMP::PairContainer
, IMP::QuadContainer
, IMP::SingletonContainer
, IMP::TripletContainer
- apply_default_patches()
: IMP::atom::CHARMMSegmentTopology
, IMP::atom::CHARMMTopology
- apply_generic()
: IMP::container::ConsecutivePairContainer
, IMP::container::ExclusiveConsecutivePairContainer
, IMP::container::PairContainerSet
, IMP::container::QuadContainerSet
, IMP::container::SingletonContainerSet
, IMP::container::TripletContainerSet
, IMP::PairContainer
, IMP::QuadContainer
, IMP::SingletonContainer
, IMP::TripletContainer
- apply_generic_moved()
: IMP::PairContainer
, IMP::QuadContainer
, IMP::SingletonContainer
, IMP::TripletContainer
- apply_index()
: IMP::atom::CoverBond
, IMP::core::CentroidOfRefined
, IMP::core::CoverRefined
, IMP::core::DerivativesFromRefined
, IMP::core::DerivativesToRefined
, IMP::core::Transform
, IMP::core::TransformationAndReflectionSymmetry
, IMP::core::TransformationSymmetry
, IMP::core::WeightedDerivativesToRefined
, IMP::example::ExampleSingletonModifier
, IMP::PairModifier
, IMP::pmi1::InternalCoordinatesConstraint
, IMP::QuadModifier
, IMP::SingletonModifier
, IMP::spb::NuisanceRangeModifier
, IMP::spb::TransformationSymmetry
, IMP::TripletModifier
- apply_indexes()
: IMP::atom::CoverBond
, IMP::core::CentroidOfRefined
, IMP::core::CoverRefined
, IMP::core::DerivativesFromRefined
, IMP::core::DerivativesToRefined
, IMP::core::Transform
, IMP::core::TransformationAndReflectionSymmetry
, IMP::core::TransformationSymmetry
, IMP::core::WeightedDerivativesToRefined
, IMP::example::ExampleSingletonModifier
, IMP::PairModifier
, IMP::pmi1::InternalCoordinatesConstraint
, IMP::QuadModifier
, IMP::SingletonModifier
, IMP::spb::NuisanceRangeModifier
, IMP::spb::TransformationSymmetry
, IMP::TripletModifier
- apply_indexes_moved()
: IMP::PairModifier
, IMP::QuadModifier
, IMP::SingletonModifier
, IMP::TripletModifier
- apply_last_sample()
: IMP::kinematics::DOFsSampler
- apply_molecular_assignments()
: IMP.pmi.macros.AnalysisReplicaExchange
, IMP.pmi1.macros.AnalysisReplicaExchange
- apply_moved()
: IMP::PairContainer
, IMP::QuadContainer
, IMP::SingletonContainer
, IMP::TripletContainer
- apply_to_current_contents()
: IMP::SparseSymmetricPairMemoizer< Generator, Checker >
- apply_transform_safely()
: IMP::kinematics::KinematicForest
- assert_number()
: IMP.test.DirectorObjectChecker
, IMP.test.RefCountChecker
- assertApplicationExitedCleanly()
: IMP.test.ApplicationTestCase
- assertClassNames()
: IMP.test.TestCase
- assertFunctionNames()
: IMP.test.TestCase
- assertNotImplemented()
: IMP.test.TestCase
- assertNumPyArrayEqual()
: IMP.test.TestCase
- assertRaisesInternalException()
: IMP.test.TestCase
- assertRaisesUsageException()
: IMP.test.TestCase
- assertSequenceAlmostEqual()
: IMP.test.TestCase
- assertShow()
: IMP.test.TestCase
- assertValueObjects()
: IMP.test.TestCase
- assertXYZDerivativesInTolerance()
: IMP.test.TestCase
- assign_velocities()
: IMP::atom::MolecularDynamics
, IMP::isd::MolecularDynamics
, IMP::spb::MolecularDynamicsWithWte
- Astart
: IMP::em::SpiderHeader
- at()
: IMP::algebra::ExtendedGridIndexD< D >
- AtomicCrossLinkMSRestraint()
: IMP::isd::AtomicCrossLinkMSRestraint
- AttributeDistancePairScore()
: IMP::spb::AttributeDistancePairScore