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IMP Reference Guide
2.20.2
The Integrative Modeling Platform
IMP Manual
Reference Guide
Tutorial Index
Modules
Classes
Examples
Class List
Class Index
Class Hierarchy
Class Members
All
Functions
Variables
Enumerations
Related Functions
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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
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
at() :
IMP::algebra::ExtendedGridIndexD< D >
AtomicCrossLinkMSRestraint() :
IMP::isd::AtomicCrossLinkMSRestraint
AttributeDistancePairScore() :
IMP::spb::AttributeDistancePairScore