- a -

• accept() : IMP::core::MonteCarloMover
• activate_statistics() : IMP::npctransport::SimulationData
• add() : IMP::bff::DecayConvolution , IMP::bff::DecayLinearization , IMP::bff::DecayModifier , IMP::bff::DecayPattern , IMP::bff::DecayPileup , IMP::bff::DecayScale , 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::saxs::Profile , IMP::saxs::RadialDistributionFunction , IMP::statistics::HistogramD< D, Grid >
• add_alias() : IMP::Key< ID >
• 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_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 , IMP.spatiotemporal.graphNode.graphNode
• 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_lifetime() : IMP::bff::DecayLifetimeHandler
• add_mean_datum() : IMP.isd.TALOSReader.TALOSReader
• add_member() : IMP::core::RigidBody
• 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
• 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
• add_score() : IMP::ScoreAccumulator , IMP.spatiotemporal.graphNode.graphNode
• 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
• add_structures() : IMP.pmi.analysis.Precision
• add_subunits_density() : IMP.pmi.analysis.GetModelDensity , IMP.sampcon.precision_rmsd.GetModelDensity
• add_target_density_to_hierarchy() : IMP.bayesianem.restraint.GaussianEMRestraintWrapper , IMP.pmi.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_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::npc::SlabWithPore , 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_uniprot_reference() : IMP.pmi.mmcif.Entity
• 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
• 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
• 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::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::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
• apply_moved() : IMP::PairContainer , IMP::QuadContainer , IMP::SingletonContainer , IMP::TripletContainer
• apply_simple_moving_average() : IMP::bff::DecayCurve
• 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
• assertCompileFails() : 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
• at() : IMP::algebra::ExtendedGridIndexD< D >
• AtomicCrossLinkMSRestraint() : IMP::isd::AtomicCrossLinkMSRestraint
• AttributeDistancePairScore() : IMP::spb::AttributeDistancePairScore
• AVNetworkRestraint() : IMP::bff::AVNetworkRestraint