Factory Index

Table of Contents

• IMP (kernel)
• IMP.algebra
• IMP.atom
• IMP.container
• IMP.core
• IMP.display
• IMP.domino
• IMP.em
• IMP.em2d
• IMP.example
• IMP.isd
• IMP.kinematics
• IMP.misc
• IMP.multifit
• IMP.npctransport
• IMP.pmi
• IMP.pmi1
• IMP.rmf
• IMP.rotamer
• IMP.saxs
• IMP.spb
• IMP.statistics

Overview

Functions that create objects of a given type:

See also Argument Index, Class Examples, Function Examples

IMP (kernel)

Class	Factories
IMP::AdvancedFlag	IMP::AdvancedFlag::operator=()
IMP::Array	IMP::isd::AtomicCrossLinkMSRestraint::get_contribution(), IMP::isd::AtomicCrossLinkMSRestraint::get_contribution_sigmas(), IMP::isd::CrossLinkMSRestraint::get_contribution_particle_indexes(), IMP::isd::CrossLinkMSRestraint::get_contribution_sigma_indexes(), IMP::npctransport::make_unordered_particle_index_pair(), IMP::npctransport::make_unordered_particle_index_pair()
IMP::ConfigurationSet	IMP::Sampler::create_sample(), IMP::Sampler::do_sample(), IMP::core::MCCGSampler::do_sample(), IMP::core::MCCGSampler::get_rejected_configurations(), IMP::domino::DiscreteSampler::do_sample(), IMP::kinematics::RRT::do_sample()
IMP::Constraint	IMP::atom::CenterOfMass::get_constraint(), IMP::core::Centroid::get_constraint(), IMP::core::Cover::get_constraint()
IMP::DerivativeAccumulator	IMP::DerivativeAccumulator::operator=(), IMP::ScoreAccumulator::get_derivative_accumulator()
IMP::EventException	IMP::EventException::operator=()
IMP::Exception	IMP::Exception::operator=()
IMP::Flag	IMP::Flag::operator=()
IMP::IOException	IMP::IOException::operator=()
IMP::IndexException	IMP::IndexException::operator=()
IMP::Key	IMP::Key::operator+(), IMP::Key::operator++(), IMP::Key::operator--(), IMP::Key::add_alias(), IMP::misc::CustomXYZR::get_decorator_traits(), IMP::misc::CustomXYZR::get_default_decorator_traits()
IMP::Model	IMP::ConfigurationSet::get_model(), IMP::Decorator::get_model(), IMP::Model::get_by_unique_id(), IMP::ModelObject::get_model(), IMP::ParticleAdaptor::get_model(), IMP::Sampler::get_model(), IMP::domino::Subset::get_model(), IMP::multifit::ProteomicsEMAlignmentAtomic::get_model(), IMP::npctransport::ParticleFactory::get_model(), IMP::npctransport::Scoring::get_model(), IMP::npctransport::Scoring::get_model(), IMP::npctransport::SimulationData::get_model(), IMP::npctransport::SimulationData::get_model(), IMP::npctransport::Statistics::get_model(), IMP::npctransport::Statistics::get_model()
IMP::ModelException	IMP::ModelException::operator=()
IMP::Object	IMP::Model::get_data(), IMP::RestraintSet::load_cereal(), IMP::atom::DihedralSingletonScore::load_cereal(), IMP::atom::WritePDBOptimizerState::load_cereal(), IMP::container::ClosePairContainer::load_cereal(), IMP::container::ListPairContainer::load_cereal(), IMP::container::ListQuadContainer::load_cereal(), IMP::container::ListSingletonContainer::load_cereal(), IMP::container::ListTripletContainer::load_cereal(), IMP::container::PairsConstraint::load_cereal(), IMP::container::PairsRestraint::load_cereal(), IMP::container::PredicatePairsRestraint::load_cereal(), IMP::container::PredicateQuadsRestraint::load_cereal(), IMP::container::PredicateSingletonsRestraint::load_cereal(), IMP::container::PredicateTripletsRestraint::load_cereal(), IMP::container::QuadsConstraint::load_cereal(), IMP::container::QuadsRestraint::load_cereal(), IMP::container::SingletonsConstraint::load_cereal(), IMP::container::SingletonsRestraint::load_cereal(), IMP::container::TripletsConstraint::load_cereal(), IMP::container::TripletsRestraint::load_cereal(), IMP::core::AllSamePairPredicate::load_cereal(), IMP::core::AllSameQuadPredicate::load_cereal(), IMP::core::AllSameSingletonPredicate::load_cereal(), IMP::core::AllSameTripletPredicate::load_cereal(), IMP::core::AngleRestraint::load_cereal(), IMP::core::AngleTripletScore::load_cereal(), IMP::core::BallMover::load_cereal(), IMP::core::ChecksScoreState::load_cereal(), IMP::core::ConstantPairPredicate::load_cereal(), IMP::core::ConstantQuadPredicate::load_cereal(), IMP::core::ConstantRestraint::load_cereal(), IMP::core::ConstantSingletonPredicate::load_cereal(), IMP::core::ConstantTripletPredicate::load_cereal(), IMP::core::Cosine::load_cereal(), IMP::core::DistanceRestraint::load_cereal(), IMP::core::GenericDistanceToSingletonScore::load_cereal(), IMP::core::GridClosePairsFinder::load_cereal(), IMP::core::Harmonic::load_cereal(), IMP::core::HarmonicLowerBound::load_cereal(), IMP::core::HarmonicUpperBound::load_cereal(), IMP::core::Linear::load_cereal(), IMP::core::PairConstraint::load_cereal(), IMP::core::PairRestraint::load_cereal(), IMP::core::QuadConstraint::load_cereal(), IMP::core::QuadRestraint::load_cereal(), IMP::core::RestraintsScoringFunction::load_cereal(), IMP::core::RigidBodyMover::load_cereal(), IMP::core::RigidClosePairsFinder::load_cereal(), IMP::core::SerialMover::load_cereal(), IMP::core::SingletonConstraint::load_cereal(), IMP::core::SingletonRestraint::load_cereal(), IMP::core::SubsetMover::load_cereal(), IMP::core::Transform::load_cereal(), IMP::core::TripletConstraint::load_cereal(), IMP::core::TripletRestraint::load_cereal(), IMP::core::UnorderedTypePairPredicate::load_cereal(), IMP::core::UnorderedTypeQuadPredicate::load_cereal(), IMP::core::UnorderedTypeSingletonPredicate::load_cereal(), IMP::core::UnorderedTypeTripletPredicate::load_cereal(), IMP::example::ExampleConstraint::load_cereal(), IMP::example::ExamplePairScore::load_cereal(), IMP::example::ExampleRestraint::load_cereal(), IMP::example::ExampleSingletonModifier::load_cereal(), IMP::example::ExampleUnaryFunction::load_cereal(), IMP::isd::AmbiguousNOERestraint::load_cereal(), IMP::isd::AmbiguousRestraint::load_cereal(), IMP::isd::AtomicCrossLinkMSRestraint::load_cereal(), IMP::isd::CrossLinkMSRestraint::load_cereal(), IMP::isd::CysteineCrossLinkRestraint::load_cereal(), IMP::isd::FretRestraint::load_cereal(), IMP::isd::GaussianEMRestraint::load_cereal(), IMP::isd::JeffreysRestraint::load_cereal(), IMP::isd::LogWrapper::load_cereal(), IMP::isd::UniformPrior::load_cereal(), IMP::npc::AssemblySymmetryByDihedralRestraint::load_cereal(), IMP::npc::AssemblySymmetryByDistanceRestraint::load_cereal(), IMP::npc::MembraneExclusionRestraint::load_cereal(), IMP::npc::MembraneSurfaceLocationConditionalRestraint::load_cereal(), IMP::npc::MembraneSurfaceLocationRestraint::load_cereal(), IMP::npc::MinimumSphereDistancePairScore::load_cereal(), IMP::npc::PerinuclearVolumeLocationRestraint::load_cereal(), IMP::npc::PoreSideVolumeLocationRestraint::load_cereal(), IMP::npc::ProteinChainRestraint::load_cereal(), IMP::npc::ProteinContactRestraint::load_cereal(), IMP::npc::ProteinProximityRestraint::load_cereal(), IMP::npc::XYRadialPositionLowerRestraint::load_cereal(), IMP::npc::XYRadialPositionRestraint::load_cereal(), IMP::npc::XYRadialPositionUpperRestraint::load_cereal(), IMP::npc::YAxialPositionLowerRestraint::load_cereal(), IMP::npc::YAxialPositionRestraint::load_cereal(), IMP::npc::YAxialPositionUpperRestraint::load_cereal(), IMP::npc::ZAxialPositionLowerRestraint::load_cereal(), IMP::npc::ZAxialPositionRestraint::load_cereal(), IMP::npc::ZAxialPositionUpperRestraint::load_cereal(), IMP::npctransport::Scoring::create_backbone_restraint(), IMP::pmi::CrossLinkRestraintSet::load_cereal(), IMP::pmi::TransformMover::load_cereal(), IMP::saxs::Profile::load_cereal(), IMP::saxs::Restraint::load_cereal()
IMP::Optimizer	IMP::OptimizerState::get_optimizer(), IMP::core::MonteCarloWithLocalOptimization::get_local_optimizer()
IMP::OptimizerState	IMP::Optimizer::get_optimizer_state(), IMP::core::MCCGSampler::get_optimizer_state()
IMP::PairContainer	IMP::container::PairContainerSet::get_pair_container(), IMP::display::PairsGeometry::get_container(), IMP::misc::DecayPairContainerOptimizerState::get_output_container(), IMP::npctransport::Scoring::create_close_beads_container(), IMP::npctransport::Scoring::create_close_beads_container(), IMP::npctransport::Scoring::get_close_beads_container()
IMP::PairPredicate	IMP::container::CloseBipartitePairContainer::get_pair_filter(), IMP::container::ClosePairContainer::get_pair_filter(), IMP::core::ClosePairsFinder::get_pair_filter(), IMP::core::ExcludedVolumeRestraint::get_pair_filter()
IMP::PairScore	IMP::container::PredicatePairsRestraint::get_score_for_predicate(), IMP::core::ConnectivityRestraint::get_pair_score(), IMP::core::MSConnectivityRestraint::get_pair_score(), IMP::core::TypedPairScore::get_pair_score(), IMP::npctransport::Scoring::get_predicate_pair_score(), IMP::npctransport::Scoring::get_predicate_pair_score()
IMP::Particle	IMP::Decorator::get_particle(), IMP::Decorator::operator->(), IMP::Model::get_particle(), IMP::Refiner::get_refined(), IMP::atom::Angle::get_particle(), IMP::atom::Angle::get_particle(), IMP::atom::Dihedral::get_particle(), IMP::atom::Dihedral::get_particle(), IMP::atom::SecondaryStructureResidue::get_particle(), IMP::atom::Simulator::get_particle(), IMP::core::DirectionAngle::get_particle(), IMP::core::DirectionAngle::get_particle(), IMP::core::Reference::get_reference_particle(), IMP::display::SingletonGeometry::get_particle(), IMP::em::DensityFillingRestraint::get_particle(), IMP::em::EnvelopePenetrationRestraint::get_particle(), IMP::em::FitRestraint::get_particle(), IMP::em::PCAFitRestraint::get_particle(), IMP::kinematics::KinematicForest::get_parent(), IMP::multifit::RadiusOfGyrationRestraint::get_particle(), IMP::multifit::WeightedExcludedVolumeRestraint::get_particle(), IMP::npctransport::BodyStatisticsOptimizerState::get_particle(), IMP::npctransport::FGChain::get_bead(), IMP::npctransport::ParticleFactory::create(), IMP::npctransport::ParticleTransportStatisticsOptimizerState::get_particle(), IMP::npctransport::RelaxingSpring::get_bonded_particle_0(), IMP::npctransport::RelaxingSpring::get_bonded_particle_1(), IMP::npctransport::SimulationData::get_slab_particle(), IMP::rmf::HierarchyLoadLink::do_create(), IMP::spb::add_ISD_particles()
IMP::QuadContainer	IMP::container::QuadContainerSet::get_quad_container()
IMP::QuadScore	IMP::container::PredicateQuadsRestraint::get_score_for_predicate()
IMP::Restraint	IMP::Model::get_dependent_restraints(), IMP::Restraint::create_current_decomposition(), IMP::Restraint::create_decomposition(), IMP::RestraintSet::get_restraint(), IMP::RestraintsAdaptor::get(), IMP::core::MinimumRestraint::get_restraint(), IMP::display::RestraintGeometry::get_restraint(), IMP::npctransport::Scoring::create_backbone_restraint(), IMP::npctransport::Scoring::create_bounding_volume_restraint(), IMP::npctransport::Scoring::create_slab_restraint(), IMP::npctransport::Scoring::create_z_bias_restraint(), IMP::npctransport::Scoring::get_bounding_volume_restraint(), IMP::npctransport::Scoring::get_pore_radius_restraint(), IMP::npctransport::Scoring::get_slab_restraint(), IMP::atom::create_connectivity_restraint(), IMP::atom::create_connectivity_restraint(), IMP::atom::create_distance_restraint(), IMP::atom::create_excluded_volume_restraint(), IMP::atom::create_excluded_volume_restraint(), IMP::atom::create_internal_connectivity_restraint(), IMP::atom::create_internal_connectivity_restraint(), IMP::example::create_chain_restraint(), IMP::example::create_excluded_volume(), IMP::multifit::create_weighted_excluded_volume_restraint()
IMP::RestraintInfo	IMP::Restraint::get_dynamic_info(), IMP::Restraint::get_static_info(), IMP::bayesianem::GaussianEMRestraint::get_dynamic_info(), IMP::bayesianem::GaussianEMRestraint::get_static_info(), IMP::em2d::PCAFitRestraint::get_dynamic_info(), IMP::em2d::PCAFitRestraint::get_static_info(), IMP::isd::CrossLinkMSRestraint::get_static_info(), IMP::isd::GaussianEMRestraint::get_dynamic_info(), IMP::isd::GaussianEMRestraint::get_static_info(), IMP::isd::UniformPrior::get_dynamic_info(), IMP::isd::UniformPrior::get_static_info(), IMP::npc::MembraneExclusionRestraint::get_static_info(), IMP::npc::MembraneSurfaceLocationConditionalRestraint::get_static_info(), IMP::npc::MembraneSurfaceLocationRestraint::get_static_info(), IMP::npc::XYRadialPositionLowerRestraint::get_static_info(), IMP::npc::XYRadialPositionRestraint::get_static_info(), IMP::npc::XYRadialPositionUpperRestraint::get_static_info(), IMP::npc::YAxialPositionLowerRestraint::get_static_info(), IMP::npc::YAxialPositionRestraint::get_static_info(), IMP::npc::YAxialPositionUpperRestraint::get_static_info(), IMP::npc::ZAxialPositionLowerRestraint::get_static_info(), IMP::npc::ZAxialPositionRestraint::get_static_info(), IMP::npc::ZAxialPositionUpperRestraint::get_static_info(), IMP::pmi::CrossLinkRestraintSet::get_static_info(), IMP::saxs::Restraint::get_static_info()
IMP::RestraintSet	IMP::display::RestraintSetGeometry::get_restraint_set(), IMP::multifit::ProteomicsEMAlignmentAtomic::get_restraint_set(), IMP::pmi::create_elastic_network(), IMP::pmi1::create_elastic_network(), IMP::spb::spb_assemble_restraints()
IMP::ScoreAccumulator	IMP::ScoreAccumulator::operator=(), IMP::ScoringFunction::get_score_accumulator(), IMP::ScoringFunction::get_score_accumulator_if_below(), IMP::ScoringFunction::get_score_accumulator_if_good()
IMP::ScoreState	IMP::Model::get_score_state()
IMP::ScoringFunction	IMP::Optimizer::get_scoring_function(), IMP::Restraint::create_scoring_function(), IMP::Restraint::create_internal_scoring_function(), IMP::Sampler::get_scoring_function(), IMP::ScoringFunctionAdaptor::get(), IMP::ScoringFunctionAdaptor::get(), IMP::ScoringFunctionAdaptor::get(), IMP::ScoringFunctionAdaptor::get(), IMP::npctransport::Scoring::get_custom_scoring_function(), IMP::npctransport::Scoring::get_custom_scoring_function(), IMP::npctransport::Scoring::get_scoring_function()
IMP::Showable	IMP::Showable::operator=()
IMP::SingletonContainer	IMP::container::SingletonContainerSet::get_singleton_container(), IMP::display::SingletonsGeometry::get_container()
IMP::SingletonScore	IMP::container::PredicateSingletonsRestraint::get_score_for_predicate()
IMP::TextOutput	IMP::create_temporary_file(), IMP::get_log_target()
IMP::TripletContainer	IMP::container::TripletContainerSet::get_triplet_container()
IMP::TripletScore	IMP::container::PredicateTripletsRestraint::get_score_for_predicate()
IMP::TypeException	IMP::TypeException::operator=()
IMP::UnaryFunction	IMP::atom::BondSingletonScore::get_unary_function(), IMP::core::WeightedSum::get_function(), IMP::core::WeightedSumOfExponential::get_function()
IMP::UsageException	IMP::UsageException::operator=()
IMP::Value	IMP::algebra::GridD::at(), IMP::algebra::GridD::at(), IMP::algebra::GridD::operator[](), IMP::algebra::GridD::operator[]()
IMP::ValueException	IMP::ValueException::operator=()
IMP::Vector	IMP::ConstVector::ConstVector(), IMP::Container::get_all_possible_indexes(), IMP::Key::get_all_strings(), IMP::LRUCache::get_keys(), IMP::Model::get_dependent_particles(), IMP::Model::get_particle_indexes(), IMP::ModelObject::get_interactions(), IMP::ModelObject::do_get_interactions(), IMP::Refiner::get_refined(), IMP::Refiner::get_refined_indexes(), IMP::Refiner::get_refined_indexes_by_ref(), IMP::RestraintInfo::get_particle_indexes_value(), IMP::SingletonContainer::get_contents(), IMP::SingletonContainer::get_indexes(), IMP::SingletonContainer::get_range_indexes(), IMP::algebra::BoundedGridRangeD::get_all_indexes(), IMP::algebra::BoundedGridRangeD::get_indexes(), IMP::algebra::BoundedGridRangeD::get_extended_indexes(), IMP::algebra::DenseGridStorageD::get_all_voxels(), IMP::algebra::PrincipalComponentAnalysisD::get_principal_components(), IMP::algebra::SparseGridStorageD::get_indexes(), IMP::algebra::UnboundedGridRangeD::get_extended_indexes(), IMP::atom::BondEndpointsRefiner::get_refined(), IMP::atom::BondPairContainer::get_all_possible_indexes(), IMP::atom::Bonded::get_bond_indexes(), IMP::atom::CHARMMConnection::get_atoms(), IMP::atom::CHARMMParameters::create_angles(), IMP::atom::CHARMMParameters::create_dihedrals(), IMP::atom::CHARMMTopology::add_bonds(), IMP::atom::CHARMMTopology::add_dihedrals(), IMP::atom::CHARMMTopology::add_impropers(), IMP::atom::Hierarchy::get_children(), IMP::atom::Hierarchy::get_by_type(), IMP::atom::Hierarchy::get_internal_bonds(), IMP::atom::Hierarchy::get_leaves(), IMP::atom::Hierarchy::get_leaves(), IMP::atom::Representation::get_representations(), IMP::atom::Selection::get_hierarchies(), IMP::atom::Selection::get_selected_particle_indexes(), IMP::atom::Selection::get_selected_particles(), IMP::atom::Simulator::get_particles(), IMP::atom::Simulator::get_simulation_particle_indexes(), IMP::atom::Simulator::get_simulation_particles(), IMP::bayesianem::GaussianEMRestraint::get_indexes(), IMP::container::AllBipartitePairContainer::get_all_possible_indexes(), IMP::container::AllPairContainer::get_all_possible_indexes(), IMP::container::CloseBipartitePairContainer::get_all_possible_indexes(), IMP::container::ClosePairContainer::get_all_possible_indexes(), IMP::container::ConnectingPairContainer::get_all_possible_indexes(), IMP::container::ConsecutivePairContainer::get_all_possible_indexes(), IMP::container::ExclusiveConsecutivePairContainer::get_all_possible_indexes(), IMP::container::PairContainerSet::get_all_possible_indexes(), IMP::container::PredicateSingletonsRestraint::get_indexes(), IMP::container::QuadContainerSet::get_all_possible_indexes(), IMP::container::SingletonContainerSet::get_all_possible_indexes(), IMP::container::TripletContainerSet::get_all_possible_indexes(), IMP::core::ChildrenRefiner::get_refined(), IMP::core::FixedRefiner::get_refined(), IMP::core::FixedRefiner::get_refined_indexes(), IMP::core::FixedRefiner::get_refined_indexes_by_ref(), IMP::core::Hierarchy::get_children_indexes(), IMP::core::IncrementalScoringFunction::get_movable_indexes(), IMP::core::LeavesRefiner::get_refined(), IMP::core::MonteCarlo::get_movable_particles(), IMP::core::NeighborsTable::get_neighbors(), IMP::core::RigidBody::get_body_member_particle_indexes(), IMP::core::RigidBody::get_member_indexes(), IMP::core::RigidBody::get_member_particle_indexes(), IMP::core::RigidBody::get_rigid_members(), IMP::core::TableRefiner::get_refined(), IMP::domino::DisjointSetsSubsetFilterTable::get_set(), IMP::domino::ParticleStatesTable::get_particles(), IMP::domino::Subset::get_sorted(), IMP::em::DensityFillingRestraint::get_particles(), IMP::em::EnvelopePenetrationRestraint::get_particles(), IMP::em::FitRestraint::get_particles(), IMP::em::PCAFitRestraint::get_particles(), IMP::em::SampledDensityMap::get_sampled_particles(), IMP::em::SampledDensityMap::get_xyzr_particles(), IMP::isd::GaussianAnchorEMRestraint::get_density_particles(), IMP::kinematics::KinematicForest::get_children(), IMP::kinematics::ProteinKinematics::get_rigid_bodies(), IMP::kinematics::ProteinKinematics::quick_hack_converter(), IMP::multi_state::MultiStateModel::get_states(), IMP::multifit::AnchorsData::get_secondary_structure_particles(), IMP::multifit::Ensemble::get_molecules(), IMP::multifit::Ensemble::get_rigid_bodies(), IMP::multifit::GeometricHash::neighbors_data(), IMP::multifit::ProteomicsEMAlignmentAtomic::get_molecules(), IMP::multifit::ProteomicsEMAlignmentAtomic::get_rigid_bodies(), IMP::multifit::RadiusOfGyrationRestraint::get_particles(), IMP::multifit::RigidLeavesRefiner::get_refined(), IMP::multifit::WeightedExcludedVolumeRestraint::get_particles(), IMP::npctransport::FGChain::get_beads(), IMP::npctransport::SimulationData::get_beads(), IMP::npctransport::SimulationData::get_beads_byref(), IMP::npctransport::SimulationData::get_fg_chain_roots(), IMP::npctransport::SimulationData::get_fg_chains(), IMP::npctransport::SimulationData::get_non_optimizable_beads(), IMP::npctransport::SimulationData::get_obstacle_particles(), IMP::npctransport::SimulationData::get_optimizable_beads(), IMP::rmf::SimpleLoadLink::create(), IMP::rmf::SimpleLoadLink::create(), IMP::saxs::FormFactorTable::get_dummy_form_factors(), IMP::saxs::FormFactorTable::get_form_factors(), IMP::saxs::FormFactorTable::get_vacuum_form_factors(), IMP::saxs::FormFactorTable::get_water_dummy_form_factors(), IMP::saxs::FormFactorTable::get_water_form_factors(), IMP::saxs::FormFactorTable::get_water_vacuum_form_factors(), IMP::saxs::ProfileClustering::get_clusters(), IMP::saxs::SolventAccessibleSurface::get_solvent_accessibility(), IMP::saxs::WeightedFitParameters::get_weights(), IMP::spb::CellMover::get_particles(), IMP::spb::PbcBoxedRigidBodyMover::get_particles(), IMP::symmetry::RigidBodyMover::get_particles(), IMP::get_input_particles(), IMP::get_output_particles(), IMP::write_particles_to_buffer(), IMP::get_dependent_particles(), IMP::get_indexes(), IMP::get_particles(), IMP::atom::read_multimodel_pdb(), IMP::atom::read_psipred(), IMP::atom::read_psipred(), IMP::atom::get_charmm_untyped_atoms(), IMP::atom::get_chi_dihedral_atom_types(), IMP::atom::get_chi_dihedral_atoms(), IMP::atom::get_leaves(), IMP::atom::get_omega_dihedral_atoms(), IMP::atom::get_phi_dihedral_atoms(), IMP::atom::get_psi_dihedral_atoms(), IMP::atom::read_multimodel_mmcif(), IMP::atom::read_multimodel_pdb_or_mmcif(), IMP::atom::setup_coarse_secondary_structure_residues(), IMP::core::create_rigid_bodies(), IMP::core::create_xyzr_particles(), IMP::domino::get_order(), IMP::em::density2particles(), IMP::npctransport::create_hierarchies_with_sites(), IMP::npctransport::get_non_optimizable_particles(), IMP::npctransport::get_optimizable_particles(), IMP::npctransport::get_particle_indexes(), IMP::rmf::create_hierarchies(), IMP::rmf::create_particles(), IMP::spb::create_coiled_coil(), IMP::spb::create_representation()
IMP::VersionInfo	IMP::Configuration::get_version_info(), IMP::ConfigurationSet::get_version_info(), IMP::Model::get_version_info(), IMP::Object::get_version_info(), IMP::Particle::get_version_info(), IMP::RestraintInfo::get_version_info(), IMP::RestraintSet::get_version_info(), IMP::SaveToConfigurationSetOptimizerState::get_version_info(), IMP::algebra::DynamicNearestNeighbor3D::get_version_info(), IMP::algebra::EuclideanVectorKDMetric::get_version_info(), IMP::algebra::MaxVectorKDMetric::get_version_info(), IMP::algebra::NearestNeighborD::get_version_info(), IMP::atom::ATOMPDBSelector::get_version_info(), IMP::atom::AllPDBSelector::get_version_info(), IMP::atom::AndPDBSelector::get_version_info(), IMP::atom::AngleSingletonScore::get_version_info(), IMP::atom::AtomTypePDBSelector::get_version_info(), IMP::atom::BackbonePDBSelector::get_version_info(), IMP::atom::BerendsenThermostatOptimizerState::get_version_info(), IMP::atom::BondEndpointsRefiner::get_version_info(), IMP::atom::BondGeometry::get_version_info(), IMP::atom::BondPairContainer::get_version_info(), IMP::atom::BondSingletonScore::get_version_info(), IMP::atom::BondedPairFilter::get_version_info(), IMP::atom::BondsGeometry::get_version_info(), IMP::atom::BrownianDynamics::get_version_info(), IMP::atom::CAAngleRestraint::get_version_info(), IMP::atom::CADihedralRestraint::get_version_info(), IMP::atom::CAlphaPDBSelector::get_version_info(), IMP::atom::CBetaPDBSelector::get_version_info(), IMP::atom::CHARMMIdealResidueTopology::get_version_info(), IMP::atom::CHARMMParameters::get_version_info(), IMP::atom::CHARMMPatch::get_version_info(), IMP::atom::CHARMMResidueTopology::get_version_info(), IMP::atom::CHARMMResidueTopologyBase::get_version_info(), IMP::atom::CHARMMSegmentTopology::get_version_info(), IMP::atom::CHARMMStereochemistryRestraint::get_version_info(), IMP::atom::CHARMMTopology::get_version_info(), IMP::atom::CPDBSelector::get_version_info(), IMP::atom::ChainPDBSelector::get_version_info(), IMP::atom::CoulombPairScore::get_version_info(), IMP::atom::CoverBond::get_version_info(), IMP::atom::DihedralSingletonScore::get_version_info(), IMP::atom::EzRestraint::get_version_info(), IMP::atom::ForceSwitch::get_version_info(), IMP::atom::HelixRestraint::get_version_info(), IMP::atom::HierarchiesGeometry::get_version_info(), IMP::atom::HierarchyGeometry::get_version_info(), IMP::atom::HydrogenPDBSelector::get_version_info(), IMP::atom::ImproperSingletonScore::get_version_info(), IMP::atom::LangevinThermostatOptimizerState::get_version_info(), IMP::atom::LennardJonesPairScore::get_version_info(), IMP::atom::MolecularDynamics::get_version_info(), IMP::atom::NPDBSelector::get_version_info(), IMP::atom::NonAlternativePDBSelector::get_version_info(), IMP::atom::NonHydrogenPDBSelector::get_version_info(), IMP::atom::NonWaterNonHydrogenPDBSelector::get_version_info(), IMP::atom::NonWaterPDBSelector::get_version_info(), IMP::atom::NotPDBSelector::get_version_info(), IMP::atom::OrPDBSelector::get_version_info(), IMP::atom::PPDBSelector::get_version_info(), IMP::atom::RemoveRigidMotionOptimizerState::get_version_info(), IMP::atom::RemoveTranslationOptimizerState::get_version_info(), IMP::atom::ResidueTypePDBSelector::get_version_info(), IMP::atom::SameResiduePairFilter::get_version_info(), IMP::atom::SelectionGeometry::get_version_info(), IMP::atom::SoapPairFilter::get_version_info(), IMP::atom::StereochemistryPairFilter::get_version_info(), IMP::atom::VelocityScalingOptimizerState::get_version_info(), IMP::atom::WaterPDBSelector::get_version_info(), IMP::atom::WritePDBOptimizerState::get_version_info(), IMP::atom::XorPDBSelector::get_version_info(), IMP::bayesianem::GaussianEMRestraint::get_version_info(), IMP::container::AllBipartitePairContainer::get_version_info(), IMP::container::AllPairContainer::get_version_info(), IMP::container::CloseBipartitePairContainer::get_version_info(), 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IMP::npctransport::HarmonicSpringSingletonScore::get_version_info(), IMP::npctransport::HarmonicWellPairScore::get_version_info(), IMP::npctransport::LinearInteractionPairScore::get_version_info(), IMP::npctransport::LinearSoftSpherePairScore::get_version_info(), IMP::npctransport::LinearWellPairScore::get_version_info(), IMP::npctransport::ParticleFactory::get_version_info(), IMP::npctransport::ParticleTransportStatisticsOptimizerState::get_version_info(), IMP::npctransport::Scoring::get_version_info(), IMP::npctransport::SimulationData::get_version_info(), IMP::npctransport::SitesGeometry::get_version_info(), IMP::npctransport::SitesPairScore::get_version_info(), IMP::npctransport::SlabWithCylindricalPorePairScore::get_version_info(), IMP::npctransport::SlabWithCylindricalPoreWireGeometry::get_version_info(), IMP::npctransport::SlabWithToroidalPorePairScore::get_version_info(), IMP::npctransport::SlabWithToroidalPoreWireGeometry::get_version_info(), IMP::npctransport::Statistics::get_version_info(), IMP::npctransport::TypedSitesGeometry::get_version_info(), IMP::npctransport::ZBiasSingletonScore::get_version_info(), IMP::pmi1::CompositeRestraint::get_version_info(), IMP::pmi1::InternalCoordinatesConstraint::get_version_info(), IMP::pmi1::MembraneRestraint::get_version_info(), IMP::pmi1::SigmoidRestraintSphere::get_version_info(), IMP::pmi1::TransformMover::get_version_info(), IMP::pmi::CompositeRestraint::get_version_info(), IMP::pmi::CrossLinkRestraintSet::get_version_info(), IMP::pmi::MembraneRestraint::get_version_info(), IMP::pmi::TransformMover::get_version_info(), IMP::rmf::HierarchyLoadLink::get_version_info(), IMP::rmf::HierarchySaveLink::get_version_info(), IMP::rmf::SaveOptimizerState::get_version_info(), IMP::rotamer::RotamerCalculator::get_version_info(), IMP::rotamer::RotamerLibrary::get_version_info(), IMP::saxs::ChiScore::get_version_info(), IMP::saxs::ChiScoreLog::get_version_info(), IMP::saxs::Profile::get_version_info(), IMP::saxs::RadiusOfGyrationRestraint::get_version_info(), IMP::saxs::RatioVolatilityScore::get_version_info(), IMP::saxs::Restraint::get_version_info(), IMP::saxs::RigidBodiesProfileHandler::get_version_info(), IMP::score_functor::DistancePairScore::get_version_info(), IMP::score_functor::DistancePairScoreWithCache::get_version_info(), IMP::score_functor::ScoreUnaryFunction::get_version_info(), IMP::score_functor::SurfaceDistancePairScore::get_version_info(), IMP::spb::AttributeDistancePairScore::get_version_info(), IMP::spb::BoxedMover::get_version_info(), IMP::spb::CellMover::get_version_info(), IMP::spb::ChiSquareMetric::get_version_info(), IMP::spb::ContactMapMetric::get_version_info(), IMP::spb::DiameterRgyrRestraint::get_version_info(), IMP::spb::DistanceRMSDMetric::get_version_info(), IMP::spb::DistanceTerminiRestraint::get_version_info(), IMP::spb::EM2DRestraint::get_version_info(), IMP::spb::Gaussian::get_version_info(), IMP::spb::KinkPairScore::get_version_info(), IMP::spb::MonteCarloWithWte::get_version_info(), IMP::spb::NuisanceRangeModifier::get_version_info(), IMP::spb::PbcBoxedMover::get_version_info(), IMP::spb::PbcBoxedRigidBodyMover::get_version_info(), IMP::spb::RMSDMetric::get_version_info(), IMP::spb::RigidBodyNewMover::get_version_info(), IMP::spb::SameParticlePairFilter::get_version_info(), IMP::spb::SameRigidBodyPairFilter::get_version_info(), IMP::spb::TiltSingletonScore::get_version_info(), IMP::spb::TransformationSymmetry::get_version_info(), IMP::spb::TwoStateGoModelRestraint::get_version_info(), IMP::spb::UniformBoundedRestraint::get_version_info(), IMP::statistics::ChiSquareMetric::get_version_info(), IMP::statistics::ConfigurationSetRMSDMetric::get_version_info(), IMP::statistics::ConfigurationSetXYZEmbedding::get_version_info(), IMP::statistics::EuclideanMetric::get_version_info(), IMP::statistics::ParticleEmbedding::get_version_info(), IMP::statistics::PartitionalClusteringWithCenter::get_version_info(), IMP::statistics::RecursivePartitionalClusteringEmbedding::get_version_info(), IMP::statistics::RecursivePartitionalClusteringMetric::get_version_info(), IMP::statistics::VectorDEmbedding::get_version_info(), IMP::symmetry::BallMover::get_version_info(), IMP::symmetry::RigidBodyMover::get_version_info()

IMP.algebra

Class	Factories
IMP::algebra::BoundingBoxD	IMP::algebra::BoundingBoxD::operator+=(), IMP::algebra::BoundingBoxD::operator+=(), IMP::algebra::BoundingBoxD::operator+=(), IMP::algebra::Cone3D::get_bounding_box(), IMP::algebra::Cylinder3D::get_bounding_box(), IMP::algebra::DefaultEmbeddingD::get_bounding_box(), IMP::algebra::DefaultEmbeddingD::get_bounding_box(), IMP::algebra::Ellipsoid3D::get_bounding_box(), IMP::algebra::GridD::get_bounding_box(), IMP::algebra::Line3D::get_bounding_box(), IMP::algebra::LogEmbeddingD::get_bounding_box(), IMP::algebra::LogEmbeddingD::get_bounding_box(), IMP::algebra::Plane3D::get_bounding_box(), IMP::algebra::Segment3D::get_bounding_box(), IMP::algebra::SpherePatch3D::get_bounding_box(), IMP::algebra::Torus3D::get_bounding_box(), IMP::atom::Hierarchy::get_bounding_box(), IMP::display::BoundingBoxGeometry::get_geometry(), IMP::em::SampledDensityMap::calculate_particles_bounding_box(), IMP::statistics::HistogramD::get_bounding_box(), IMP::algebra::get_cube_kd(), IMP::algebra::get_transformed(), IMP::algebra::get_unit_bounding_box_kd(), IMP::core::get_bounding_box(), IMP::em::get_bounding_box(), IMP::em::get_bounding_box()
IMP::algebra::Cone3D	IMP::algebra::Cone3D::get_cone_3d_geometry()
IMP::algebra::Cylinder3D	IMP::algebra::Cylinder3D::get_cylinder_3d_geometry(), IMP::core::SurfaceGeometry::get_cylinder(), IMP::display::CylinderGeometry::get_geometry(), IMP::npctransport::SimulationData::get_cylinder()
IMP::algebra::DenseGridStorageD	IMP::algebra::DenseGridStorageD::operator=(), IMP::em::get_grid()
IMP::algebra::Ellipsoid3D	IMP::algebra::Ellipsoid3D::get_ellipsoid_3d_geometry(), IMP::display::EllipsoidGeometry::get_geometry()
IMP::algebra::ExtendedGridIndexD	IMP::algebra::BoundedGridRangeD::get_extended_indexes(), IMP::algebra::BoundedGridRangeD::get_end_index(), IMP::algebra::BoundedGridRangeD::get_maximum_extended_index(), IMP::algebra::BoundedGridRangeD::get_minimum_extended_index(), IMP::algebra::DefaultEmbeddingD::get_extended_index(), IMP::algebra::ExtendedGridIndexD::get_offset(), IMP::algebra::ExtendedGridIndexD::get_uniform_offset(), IMP::algebra::GridD::get_nearest_extended_index(), IMP::algebra::GridD::get_extended_index(), IMP::algebra::LogEmbeddingD::get_extended_index(), IMP::algebra::UnboundedGridRangeD::get_extended_indexes()
IMP::algebra::FixedXYZ	IMP::algebra::get_fixed_xyz_from_rotation()
IMP::algebra::Gaussian3D	IMP::core::Gaussian::get_gaussian(), IMP::algebra::get_gaussian_from_covariance()
IMP::algebra::GridD	IMP::em::get_grid()
IMP::algebra::GridIndexD	IMP::algebra::BoundedGridRangeD::get_all_indexes(), IMP::algebra::BoundedGridRangeD::get_indexes(), IMP::algebra::BoundedGridRangeD::get_index(), IMP::algebra::DefaultEmbeddingD::get_index(), IMP::algebra::GridD::get_nearest_index(), IMP::algebra::GridD::add_voxel(), IMP::algebra::LogEmbeddingD::get_index(), IMP::algebra::SparseGridStorageD::get_indexes(), IMP::algebra::SparseGridStorageD::add_voxel(), IMP::algebra::SparseGridStorageD::get_index()
IMP::algebra::Line3D	IMP::algebra::Line3D::get_opposite(), IMP::algebra::Line3D::get_line_3d_geometry(), IMP::algebra::get_transformed()
IMP::algebra::Plane3D	IMP::algebra::Cone3D::get_base_plane(), IMP::algebra::Plane3D::get_opposite(), IMP::algebra::Plane3D::get_plane_3d_geometry(), IMP::algebra::SpherePatch3D::get_plane(), IMP::core::Surface::get_plane()
IMP::algebra::ReferenceFrame3D	IMP::algebra::Ellipsoid3D::get_reference_frame(), IMP::algebra::Gaussian3D::get_reference_frame(), IMP::algebra::ReferenceFrame3D::get_global_reference_frame(), IMP::algebra::ReferenceFrame3D::get_local_reference_frame(), IMP::algebra::ReferenceFrame3D::operator=(), IMP::core::RigidBody::get_reference_frame(), IMP::core::Surface::get_reference_frame(), IMP::display::ReferenceFrameGeometry::get_geometry(), IMP::domino::RigidBodyStates::get_reference_frame(), IMP::kinematics::KinematicForest::get_reference_frame_safe(), IMP::algebra::get_transformed(), IMP::core::get_initial_reference_frame(), IMP::core::get_initial_reference_frame()
IMP::algebra::Rotation2D	IMP::algebra::Rotation2D::get_inverse(), IMP::algebra::Transformation2D::get_rotation(), IMP::algebra::compose(), IMP::algebra::get_identity_rotation_2d(), IMP::algebra::get_random_rotation_2d(), IMP::algebra::get_rotation_to_x_axis()
IMP::algebra::Rotation3D	IMP::algebra::Rotation3D::get_inverse(), IMP::algebra::Rotation3D::operator*(), IMP::algebra::Rotation3D::operator/(), IMP::algebra::Rotation3D::operator/=(), IMP::algebra::Rotation3D::operator=(), IMP::algebra::Transformation3D::get_rotation(), IMP::atom::BrownianDynamicsTAMD::compute_rotation_0(), IMP::core::RigidBody::get_rotation(), IMP::em2d::GridStates::get_orientation(), IMP::em2d::ProjectionParameters::get_rotation(), IMP::em2d::RegistrationResult::get_rotation(), IMP::em::PCAAligner::get_rotation_matrix(), IMP::algebra::get_rotation_from_fixed_xyz(), IMP::algebra::get_rotation_from_fixed_zxz(), IMP::algebra::get_rotation_from_fixed_zyz(), IMP::algebra::compose(), IMP::algebra::get_identity_rotation_3d(), IMP::algebra::get_interpolated(), IMP::algebra::get_random_rotation_3d(), IMP::algebra::get_random_rotation_3d(), IMP::algebra::get_rotation_about_axis(), IMP::algebra::get_rotation_about_normalized_axis(), IMP::algebra::get_rotation_from_matrix(), IMP::algebra::get_rotation_from_matrix(), IMP::algebra::get_rotation_from_vector4d(), IMP::algebra::get_rotation_from_x_y_axes(), IMP::algebra::get_rotation_taking_first_to_second(), IMP::bayesianem::get_rotation_matrix()
IMP::algebra::Segment3D	IMP::algebra::Cylinder3D::get_segment(), IMP::algebra::Line3D::get_segment_starting_at(), IMP::algebra::Segment3D::get_segment_3d_geometry(), IMP::core::RigidBodyTorque::extract_geometry(), IMP::core::RigidBodyTorque::get_geometry(), IMP::core::SurfaceGeometry::get_segment(), IMP::display::SegmentGeometry::get_geometry(), IMP::algebra::get_shortest_segment(), IMP::algebra::get_shortest_segment(), IMP::algebra::get_projected(), IMP::algebra::get_segment_connecting_first_to_second()
IMP::algebra::SphereD	IMP::algebra::get_unit_sphere_kd()
IMP::algebra::SpherePatch3D	IMP::algebra::SpherePatch3D::get_sphere_patch_3d_geometry()
IMP::algebra::Torus3D	IMP::algebra::Torus3D::get_torus_3d_geometry()
IMP::algebra::Transformation2D	IMP::algebra::Transformation2D::get_inverse(), IMP::algebra::Transformation2D::operator*(), IMP::algebra::Transformation2D::operator*=(), IMP::algebra::Transformation2D::operator/(), IMP::algebra::Transformation2D::operator/=(), IMP::algebra::Transformation2D::operator=(), IMP::algebra::compose(), IMP::algebra::get_identity_transformation_2d(), IMP::algebra::get_rotation_about_point(), IMP::algebra::get_transformation_aligning_pair()
IMP::algebra::Transformation3D	IMP::algebra::ReferenceFrame3D::get_inverse(), IMP::algebra::ReferenceFrame3D::get_transformation_from(), IMP::algebra::ReferenceFrame3D::get_transformation_to(), IMP::algebra::Transformation3D::get_inverse(), IMP::algebra::Transformation3D::operator*(), IMP::algebra::Transformation3D::operator*=(), IMP::algebra::Transformation3D::operator/(), IMP::algebra::Transformation3D::operator/=(), IMP::algebra::Transformation3D::operator=(), IMP::core::RigidBodyMember::get_internal_transformation(), IMP::core::SurfaceSymmetryConstraint::get_transformation(), IMP::core::TransformationSymmetry::get_internal_transformation(), IMP::core::TransformationSymmetry::get_transformation(), IMP::core::TransformationSymmetryMover::get_random_rotation_about_point(), IMP::domino::NestedRigidBodyStates::get_transformation(), IMP::em2d::PCAFitRestraint::get_transformation(), IMP::em::EnvelopeFitRestraint::get_transformation(), IMP::em::FittingSolutions::get_transformation(), IMP::kinematics::Joint::get_transformation_child_to_parent(), IMP::kinematics::Joint::get_transformation_child_to_parent_no_checks(), IMP::kinematics::RevoluteJoint::get_rotation_about_joint_in_parent_coordinates(), IMP::multifit::FittingSolutionRecord::get_dock_transformation(), IMP::multifit::FittingSolutionRecord::get_fit_transformation(), IMP::pmi1::TransformMover::get_last_transformation(), IMP::pmi::TransformMover::get_last_transformation(), IMP::spb::DistanceRMSDMetric::get_transformation(), IMP::spb::PbcBoxedMover::get_transformation(), IMP::spb::PbcBoxedRigidBodyMover::get_transformation(), IMP::spb::TransformationSymmetry::get_transformation(), IMP::algebra::get_transformation_aligning_first_to_second(), IMP::algebra::compose(), IMP::algebra::get_identity_transformation_3d(), IMP::algebra::get_random_local_transformation(), IMP::algebra::get_rotation_about_point(), IMP::algebra::get_transformation_3d(), IMP::algebra::get_transformation_from_first_to_second(), IMP::algebra::get_transformation_from_first_triangle_to_second(), IMP::atom::get_transformation_aligning_first_to_second(), IMP::bayesianem::get_transformation_aligning_first_to_second(), IMP::cnmultifit::calc_transformation_around_axis(), IMP::core::get_transformation_aligning_first_to_second()
IMP::algebra::Triangle3D	IMP::display::TriangleGeometry::get_geometry(), IMP::algebra::get_largest_triangle(), IMP::algebra::get_triangle_3d()
IMP::algebra::UnitSimplexD_3-1_01_4	IMP::isd::Weight::get_unit_simplex()
IMP::algebra::VectorD	IMP::algebra::BoundingBoxD::get_corner(), IMP::algebra::DefaultEmbeddingD::get_center(), IMP::algebra::DefaultEmbeddingD::get_center(), IMP::algebra::DefaultEmbeddingD::get_origin(), IMP::algebra::DefaultEmbeddingD::get_unit_cell(), IMP::algebra::LogEmbeddingD::get_center(), IMP::algebra::LogEmbeddingD::get_center(), IMP::algebra::LogEmbeddingD::get_origin(), IMP::algebra::LogEmbeddingD::get_unit_cell(), IMP::algebra::PrincipalComponentAnalysisD::get_centroid(), IMP::algebra::PrincipalComponentAnalysisD::get_principal_component(), IMP::algebra::PrincipalComponentAnalysisD::get_principal_components(), IMP::algebra::PrincipalComponentAnalysisD::get_principal_values(), IMP::algebra::SphereD::get_center(), IMP::algebra::UnitSimplexBaseD::get_barycenter(), IMP::algebra::VectorD::get_unit_vector(), IMP::algebra::VectorD::operator*(), IMP::algebra::VectorD::operator*=(), IMP::algebra::VectorD::operator+(), IMP::algebra::VectorD::operator+=(), IMP::algebra::VectorD::operator-(), IMP::algebra::VectorD::operator-(), IMP::algebra::VectorD::operator-=(), IMP::algebra::VectorD::operator/(), IMP::algebra::VectorD::operator/=(), IMP::core::RigidBody::get_rotational_derivatives(), IMP::example::ExampleTemplateClassD::get_point(), IMP::multifit::GeometricHash::from_bucket(), IMP::statistics::HistogramD::get_mean(), IMP::statistics::HistogramD::get_standard_deviation(), IMP::algebra::get_random_vector_in(), IMP::algebra::get_random_vector_on_unit_sphere(), IMP::algebra::get_basis_vector_kd(), IMP::algebra::get_ones_vector_kd(), IMP::algebra::get_zero_vector_kd()

IMP.atom

Class	Factories
IMP::atom::Angle	IMP::atom::Angle::setup_particle(), IMP::atom::Angle::setup_particle()
IMP::atom::Atom	IMP::atom::Atom::setup_particle(), IMP::atom::Atom::setup_particle(), IMP::atom::Atom::setup_particle(), IMP::atom::Atom::setup_particle(), IMP::atom::CHARMMBondEndpoint::get_atom(), IMP::atom::get_atom(), IMP::kinematics::find_atom(), IMP::kinematics::get_ca_atom()
IMP::atom::AtomType	IMP::atom::Atom::get_atom_type(), IMP::atom::get_atom_type(), IMP::atom::add_atom_type()
IMP::atom::Bond	IMP::atom::BondGraph::get_bond(), IMP::atom::Bonded::get_bond(), IMP::atom::create_bond(), IMP::atom::create_bond(), IMP::atom::create_custom_bond(), IMP::atom::get_bond(), IMP::kinematics::create_bond()
IMP::atom::Bonded	IMP::atom::Bond::get_bonded(), IMP::atom::Bonded::get_bonded(), IMP::atom::Bonded::setup_particle(), IMP::atom::Bonded::setup_particle()
IMP::atom::BrownianDynamics	IMP::npctransport::SimulationData::get_bd()
IMP::atom::CHARMMAtom	IMP::atom::CHARMMAtom::setup_particle(), IMP::atom::CHARMMAtom::setup_particle()
IMP::atom::CHARMMAtomTopology	IMP::atom::CHARMMResidueTopologyBase::get_atom(), IMP::atom::CHARMMResidueTopologyBase::get_atom(), IMP::atom::CHARMMResidueTopologyBase::get_atom()
IMP::atom::CHARMMBondEndpoint	IMP::atom::CHARMMConnection::get_endpoint()
IMP::atom::CHARMMConnection	IMP::atom::CHARMMResidueTopologyBase::get_angle(), IMP::atom::CHARMMResidueTopologyBase::get_bond(), IMP::atom::CHARMMResidueTopologyBase::get_dihedral(), IMP::atom::CHARMMResidueTopologyBase::get_improper()
IMP::atom::CHARMMIdealResidueTopology	IMP::atom::CHARMMParameters::get_residue_topology()
IMP::atom::CHARMMInternalCoordinate	IMP::atom::CHARMMResidueTopologyBase::get_internal_coordinate()
IMP::atom::CHARMMParameters	IMP::atom::CHARMMTopology::get_parameters(), IMP::atom::get_all_atom_CHARMM_parameters(), IMP::atom::get_heavy_atom_CHARMM_parameters()
IMP::atom::CHARMMPatch	IMP::atom::CHARMMParameters::get_patch()
IMP::atom::CHARMMResidueTopology	IMP::atom::CHARMMSegmentTopology::get_residue()
IMP::atom::CHARMMSegmentTopology	IMP::atom::CHARMMTopology::get_segment()
IMP::atom::CHARMMTopology	IMP::atom::CHARMMParameters::create_topology()
IMP::atom::CenterOfMass	IMP::atom::CenterOfMass::setup_particle(), IMP::atom::CenterOfMass::setup_particle(), IMP::atom::CenterOfMass::setup_particle(), IMP::atom::CenterOfMass::setup_particle()
IMP::atom::Chain	IMP::atom::Chain::setup_particle(), IMP::atom::Chain::setup_particle(), IMP::atom::Chain::setup_particle(), IMP::atom::Chain::setup_particle(), IMP::atom::Chain::setup_particle(), IMP::atom::Chain::setup_particle(), IMP::atom::get_chain()
IMP::atom::ChainType	IMP::atom::Chain::get_chain_type()
IMP::atom::Charged	IMP::atom::Charged::setup_particle(), IMP::atom::Charged::setup_particle(), IMP::atom::Charged::setup_particle(), IMP::atom::Charged::setup_particle()
IMP::atom::Copy	IMP::atom::Copy::setup_particle(), IMP::atom::Copy::setup_particle()
IMP::atom::Diffusion	IMP::atom::Diffusion::setup_particle(), IMP::atom::Diffusion::setup_particle(), IMP::atom::Diffusion::setup_particle(), IMP::atom::Diffusion::setup_particle(), IMP::atom::Diffusion::setup_particle(), IMP::atom::Diffusion::setup_particle()
IMP::atom::Dihedral	IMP::atom::Dihedral::setup_particle(), IMP::atom::Dihedral::setup_particle()
IMP::atom::Domain	IMP::atom::Domain::setup_particle(), IMP::atom::Domain::setup_particle(), IMP::atom::Domain::setup_particle(), IMP::atom::Domain::setup_particle()
IMP::atom::ElementTable	IMP::atom::get_element_table()
IMP::atom::Fragment	IMP::atom::Fragment::setup_particle(), IMP::atom::Fragment::setup_particle(), IMP::atom::Fragment::setup_particle(), IMP::atom::Fragment::setup_particle(), IMP::atom::Fragment::setup_particle(), IMP::atom::Fragment::setup_particle()
IMP::atom::Hierarchy	IMP::atom::CHARMMTopology::create_hierarchy(), IMP::atom::Hierarchy::get_child(), IMP::atom::Hierarchy::get_parent(), IMP::atom::Hierarchy::setup_particle(), IMP::atom::Hierarchy::create_clone(), IMP::atom::Hierarchy::create_clone_one(), IMP::atom::Hierarchy::create_fragment(), IMP::atom::Hierarchy::get_residue(), IMP::atom::Hierarchy::get_root(), IMP::atom::Representation::get_representation(), IMP::npctransport::FGChain::get_root(), IMP::npctransport::SimulationData::get_root(), IMP::npctransport::SimulationData::get_root_of_type(), IMP::atom::create_simplified_along_backbone(), IMP::atom::create_simplified_along_backbone(), IMP::atom::read_mol2(), IMP::atom::read_pdb(), IMP::atom::create_protein(), IMP::atom::create_protein(), IMP::atom::create_simplified_assembly_from_volume(), IMP::atom::create_simplified_from_volume(), IMP::atom::get_next_residue(), IMP::atom::get_previous_residue(), IMP::atom::read_mmcif(), IMP::atom::read_pdb_or_mmcif(), IMP::multifit::create_coarse_molecule_from_density()
IMP::atom::LennardJones	IMP::atom::LennardJones::setup_particle(), IMP::atom::LennardJones::setup_particle(), IMP::atom::LennardJones::setup_particle(), IMP::atom::LennardJones::setup_particle()
IMP::atom::Mass	IMP::atom::Mass::setup_particle(), IMP::atom::Mass::setup_particle(), IMP::atom::Mass::setup_particle(), IMP::atom::Mass::setup_particle()
IMP::atom::Molecule	IMP::atom::Molecule::setup_particle(), IMP::atom::Molecule::setup_particle(), IMP::atom::Molecule::setup_particle(), IMP::atom::Molecule::setup_particle(), IMP::spb::create_GFP(), IMP::spb::create_merged_protein(), IMP::spb::create_protein(), IMP::spb::create_protein()
IMP::atom::PDBSelector	IMP::atom::get_default_pdb_selector()
IMP::atom::Representation	IMP::atom::Representation::setup_particle(), IMP::atom::Representation::setup_particle(), IMP::atom::Representation::setup_particle(), IMP::atom::Representation::setup_particle(), IMP::atom::Representation::setup_particle(), IMP::atom::Representation::setup_particle(), IMP::atom::get_representation()
IMP::atom::Residue	IMP::atom::Residue::setup_particle(), IMP::atom::Residue::setup_particle(), IMP::atom::Residue::setup_particle(), IMP::atom::Residue::setup_particle(), IMP::atom::Residue::setup_particle(), IMP::atom::Residue::setup_particle(), IMP::atom::Residue::setup_particle(), IMP::atom::Residue::setup_particle(), IMP::atom::get_residue(), IMP::kinematics::find_residue()
IMP::atom::ResidueType	IMP::atom::CHARMMParameters::parse_residue_line(), IMP::atom::Residue::get_residue_type(), IMP::atom::get_residue_type(), IMP::atom::get_residue_type()
IMP::atom::RigidBodyDiffusion	IMP::atom::RigidBodyDiffusion::setup_particle(), IMP::atom::RigidBodyDiffusion::setup_particle()
IMP::atom::SecondaryStructureResidue	IMP::atom::SecondaryStructureResidue::setup_particle(), IMP::atom::SecondaryStructureResidue::setup_particle(), IMP::atom::SecondaryStructureResidue::setup_particle(), IMP::atom::setup_coarse_secondary_structure_residue()
IMP::atom::Selection	IMP::atom::Selection::create_clone()
IMP::atom::Simulator	IMP::npctransport::ParticleTransportStatisticsOptimizerState::get_owner()
IMP::atom::SoapPairFilter	IMP::atom::OrientedSoapPairScore::get_pair_filter()
IMP::atom::State	IMP::atom::State::setup_particle(), IMP::atom::State::setup_particle(), IMP::atom::State::setup_particle(), IMP::atom::State::setup_particle()
IMP::atom::StereochemistryPairFilter	IMP::atom::CHARMMStereochemistryRestraint::get_full_pair_filter(), IMP::atom::CHARMMStereochemistryRestraint::get_pair_filter()
IMP::atom::StructureSource	IMP::atom::StructureSource::setup_particle(), IMP::atom::StructureSource::setup_particle()
IMP::atom::TAMDCentroid	IMP::atom::TAMDCentroid::setup_particle(), IMP::atom::TAMDCentroid::setup_particle(), IMP::atom::TAMDCentroid::setup_particle(), IMP::atom::TAMDCentroid::setup_particle()
IMP::atom::TAMDParticle	IMP::atom::TAMDParticle::setup_particle(), IMP::atom::TAMDParticle::setup_particle(), IMP::atom::TAMDParticle::setup_particle(), IMP::atom::TAMDParticle::setup_particle()

IMP.container

Class	Factories
IMP::container::DynamicListPairContainer	IMP::container::DistributePairsScoreState::add_predicate()
IMP::container::DynamicListQuadContainer	IMP::container::DistributeQuadsScoreState::add_predicate()
IMP::container::DynamicListSingletonContainer	IMP::container::DistributeSingletonsScoreState::add_predicate()
IMP::container::DynamicListTripletContainer	IMP::container::DistributeTripletsScoreState::add_predicate()
IMP::container::MinimumPairRestraint	IMP::spb::do_bipartite_mindist(), IMP::spb::do_bipartite_mindist(), IMP::spb::y2h_restraint(), IMP::spb::y2h_restraint(), IMP::spb::y2h_restraint(), IMP::spb::y2h_restraint()
IMP::container::PairContainerSet	IMP::container::PairContainerSet::get_set()
IMP::container::PredicatePairsRestraint	IMP::npctransport::Scoring::create_predicates_pair_restraint(), IMP::npctransport::Scoring::get_predicates_pair_restraint()
IMP::container::QuadContainerSet	IMP::container::QuadContainerSet::get_set()
IMP::container::SingletonContainerSet	IMP::container::SingletonContainerSet::get_set()
IMP::container::TripletContainerSet	IMP::container::TripletContainerSet::get_set()

IMP.core

Class	Factories
IMP::core::Centroid	IMP::core::Centroid::setup_particle(), IMP::core::Centroid::setup_particle(), IMP::core::Centroid::setup_particle(), IMP::core::Centroid::setup_particle()
IMP::core::ClusterProvenance	IMP::core::ClusterProvenance::setup_particle(), IMP::core::ClusterProvenance::setup_particle(), IMP::core::ClusterProvenance::setup_particle(), IMP::core::ClusterProvenance::setup_particle(), IMP::core::ClusterProvenance::setup_particle(), IMP::core::ClusterProvenance::setup_particle(), IMP::core::ClusterProvenance::setup_particle(), IMP::core::ClusterProvenance::setup_particle()
IMP::core::CombineProvenance	IMP::core::CombineProvenance::setup_particle(), IMP::core::CombineProvenance::setup_particle(), IMP::core::CombineProvenance::setup_particle(), IMP::core::CombineProvenance::setup_particle()
IMP::core::Cover	IMP::core::Cover::setup_particle(), IMP::core::Cover::setup_particle(), IMP::core::Cover::setup_particle(), IMP::core::Cover::setup_particle()
IMP::core::DataObject	IMP::multifit::ComplementarityRestraint::get_grid_object()
IMP::core::Direction	IMP::core::Direction::setup_particle(), IMP::core::Direction::setup_particle(), IMP::core::DirectionMover::get_direction()
IMP::core::DirectionAngle	IMP::core::DirectionAngle::setup_particle(), IMP::core::DirectionAngle::setup_particle(), IMP::core::DirectionAngle::setup_particle(), IMP::core::DirectionAngle::setup_particle()
IMP::core::DistancePairScore	IMP::spb::get_pair_score()
IMP::core::FilterProvenance	IMP::core::FilterProvenance::setup_particle(), IMP::core::FilterProvenance::setup_particle(), IMP::core::FilterProvenance::setup_particle(), IMP::core::FilterProvenance::setup_particle()
IMP::core::Gaussian	IMP::core::Gaussian::setup_particle(), IMP::core::Gaussian::setup_particle(), IMP::core::Gaussian::setup_particle(), IMP::core::Gaussian::setup_particle()
IMP::core::Hierarchy	IMP::core::Hierarchy::get_child(), IMP::core::Hierarchy::get_parent(), IMP::core::Hierarchy::setup_particle(), IMP::core::Hierarchy::setup_particle(), IMP::core::Hierarchy::setup_particle(), IMP::core::Hierarchy::setup_particle(), IMP::core::Hierarchy::setup_particle(), IMP::core::Hierarchy::setup_particle(), IMP::core::get_root()
IMP::core::HierarchyTraits	IMP::atom::Hierarchy::get_traits(), IMP::core::Hierarchy::get_decorator_traits(), IMP::core::Hierarchy::get_traits(), IMP::core::Hierarchy::get_default_decorator_traits(), IMP::core::Hierarchy::get_default_traits()
IMP::core::IncrementalScoringFunction	IMP::core::MonteCarlo::get_incremental_scoring_function()
IMP::core::MonteCarlo	IMP::spb::setup_SPBMonteCarlo()
IMP::core::MonteCarloMover	IMP::core::MonteCarlo::get_mover()
IMP::core::NonRigidMember	IMP::core::NonRigidMember::operator=()
IMP::core::OrderedTypePairPredicate	IMP::npctransport::Scoring::get_ordered_type_pair_predicate(), IMP::npctransport::Scoring::get_ordered_type_pair_predicate()
IMP::core::Provenance	IMP::core::Provenance::setup_particle(), IMP::core::Provenance::setup_particle(), IMP::core::Provenance::get_previous(), IMP::core::Provenanced::get_provenance(), IMP::rmf::HierarchyLoadLink::create_one_provenance(), IMP::core::create_clone()
IMP::core::Provenanced	IMP::core::Provenanced::setup_particle(), IMP::core::Provenanced::setup_particle()
IMP::core::Reference	IMP::core::Reference::setup_particle(), IMP::core::Reference::setup_particle()
IMP::core::RigidBody	IMP::core::RigidBody::operator=(), IMP::core::RigidBody::setup_particle(), IMP::core::RigidBody::setup_particle(), IMP::core::RigidBody::setup_particle(), IMP::core::RigidBody::setup_particle(), IMP::core::RigidBodyMember::get_rigid_body(), IMP::kinematics::Joint::get_child_node(), IMP::kinematics::Joint::get_parent_node(), IMP::spb::CellMover::get_rigid_bodies(), IMP::spb::PbcBoxedRigidBodyMover::get_rigid_bodies(), IMP::symmetry::RigidBodyMover::get_rigid_bodies(), IMP::atom::create_compatible_rigid_body(), IMP::atom::create_rigid_body(), IMP::atom::create_rigid_body(), IMP::spb::get_rigid_bodies()
IMP::core::RigidBodyMember	IMP::core::RigidBodyMember::operator=()
IMP::core::RigidMember	IMP::core::RigidMember::operator=()
IMP::core::SampleProvenance	IMP::core::SampleProvenance::setup_particle(), IMP::core::SampleProvenance::setup_particle(), IMP::core::SampleProvenance::setup_particle(), IMP::core::SampleProvenance::setup_particle(), IMP::core::SampleProvenance::setup_particle(), IMP::core::SampleProvenance::setup_particle()
IMP::core::ScriptProvenance	IMP::core::ScriptProvenance::setup_particle(), IMP::core::ScriptProvenance::setup_particle(), IMP::core::ScriptProvenance::setup_particle(), IMP::core::ScriptProvenance::setup_particle()
IMP::core::SoftwareProvenance	IMP::core::SoftwareProvenance::setup_particle(), IMP::core::SoftwareProvenance::setup_particle(), IMP::core::SoftwareProvenance::setup_particle(), IMP::core::SoftwareProvenance::setup_particle()
IMP::core::SphereDistancePairScore	IMP::spb::get_sphere_pair_score(), IMP::spb::get_sphere_pair_score()
IMP::core::StructureProvenance	IMP::core::StructureProvenance::setup_particle(), IMP::core::StructureProvenance::setup_particle(), IMP::core::StructureProvenance::setup_particle(), IMP::core::StructureProvenance::setup_particle(), IMP::core::StructureProvenance::setup_particle(), IMP::core::StructureProvenance::setup_particle()
IMP::core::Surface	IMP::core::Surface::setup_particle(), IMP::core::Surface::setup_particle(), IMP::core::Surface::setup_particle(), IMP::core::Surface::setup_particle(), IMP::core::Surface::setup_particle(), IMP::core::Surface::setup_particle(), IMP::core::Surface::setup_particle(), IMP::core::Surface::setup_particle(), IMP::core::SurfaceGeometry::get_geometry(), IMP::core::SurfaceGeometryConstraint::get_surface(), IMP::core::SurfaceMover::get_surface()
IMP::core::SurfaceGeometry	IMP::core::SurfaceGeometryConstraint::get_geometry(), IMP::core::create_geometry(), IMP::core::get_constrained_surface_geometry()
IMP::core::Typed	IMP::core::Typed::setup_particle(), IMP::core::Typed::setup_particle()
IMP::core::XYZ	IMP::core::XYZ::setup_particle(), IMP::core::XYZ::setup_particle(), IMP::core::XYZ::setup_particle(), IMP::core::XYZ::setup_particle(), IMP::kinematics::DihedralAngleRevoluteJoint::get_a(), IMP::kinematics::DihedralAngleRevoluteJoint::get_b(), IMP::kinematics::DihedralAngleRevoluteJoint::get_c(), IMP::kinematics::DihedralAngleRevoluteJoint::get_d()
IMP::core::XYZR	IMP::core::XYZR::setup_particle(), IMP::core::XYZR::setup_particle(), IMP::core::XYZR::setup_particle(), IMP::core::XYZR::setup_particle(), IMP::core::XYZR::setup_particle(), IMP::core::XYZR::setup_particle(), IMP::atom::create_cover()

IMP.display

Class	Factories
IMP::display::BoundingBoxGeometry	IMP::display::create_geometry()
IMP::display::Color	IMP::display::Color::operator=(), IMP::display::Colored::get_color(), IMP::display::Geometry::get_color(), IMP::display::PairGeometry::get_color(), IMP::display::SingletonGeometry::get_color(), IMP::display::get_jet_color(), IMP::display::get_hot_color(), IMP::display::get_rgb_color(), IMP::display::get_gray_color(), IMP::display::get_gnuplot_color(), IMP::display::get_display_color(), IMP::display::get_interpolated_rgb()
IMP::display::Colored	IMP::display::Colored::setup_particle(), IMP::display::Colored::setup_particle()
IMP::display::CylinderGeometry	IMP::display::create_geometry()
IMP::display::EllipsoidGeometry	IMP::display::create_geometry()
IMP::display::Geometry	IMP::display::WriteOptimizerState::get_geometry(), IMP::npctransport::SimulationData::get_static_geometry()
IMP::display::PointGeometry	IMP::display::create_geometry()
IMP::display::PolygonGeometry	IMP::display::create_geometry()
IMP::display::ReferenceFrameGeometry	IMP::display::create_geometry()
IMP::display::SegmentGeometry	IMP::display::create_geometry()
IMP::display::SphereGeometry	IMP::display::create_geometry()
IMP::display::TriangleGeometry	IMP::display::create_geometry()
IMP::display::Writer	IMP::display::WriterAdaptor::get_writer(), IMP::display::WriterAdaptor::operator->(), IMP::display::create_writer()

IMP.domino

Class	Factories
IMP::domino::Assignment	IMP::domino::AssignmentContainer::get_assignment(), IMP::domino::CappedAssignmentContainer::get_assignment(), IMP::domino::HeapAssignmentContainer::get_assignment(), IMP::domino::ListAssignmentContainer::get_assignment(), IMP::domino::Order::get_subset_ordered(), IMP::domino::PackedAssignmentContainer::get_assignment(), IMP::domino::RangeViewAssignmentContainer::get_assignment(), IMP::domino::ReadAssignmentContainer::get_assignment(), IMP::domino::ReadHDF5AssignmentContainer::get_assignment(), IMP::domino::SampleAssignmentContainer::get_assignment(), IMP::domino::Slice::get_sliced(), IMP::domino::WriteAssignmentContainer::get_assignment(), IMP::domino::WriteHDF5AssignmentContainer::get_assignment(), IMP::domino::get_nearest_assignment()
IMP::domino::AssignmentsTable	IMP::domino::DiscreteSampler::get_assignments_table_to_use()
IMP::domino::ParticleStates	IMP::domino::ParticleStatesTable::get_particle_states()
IMP::domino::ParticleStatesTable	IMP::domino::DiscreteSampler::get_particle_states_table(), IMP::multifit::ProteomicsEMAlignmentAtomic::set_particle_states_table()
IMP::domino::Slice	IMP::domino::RestraintCache::get_slice(), IMP::domino::get_slice()
IMP::domino::Subset	IMP::domino::ParticleStatesTable::get_subset(), IMP::domino::RestraintCache::get_subset(), IMP::domino::Slice::get_sliced(), IMP::domino::get_difference(), IMP::domino::get_intersection(), IMP::domino::get_union()
IMP::domino::SubsetFilter	IMP::domino::EqualitySubsetFilterTable::get_subset_filter(), IMP::domino::EquivalenceAndExclusionSubsetFilterTable::get_subset_filter(), IMP::domino::EquivalenceSubsetFilterTable::get_subset_filter(), IMP::domino::ExclusionSubsetFilterTable::get_subset_filter(), IMP::domino::ListSubsetFilterTable::get_subset_filter(), IMP::domino::MinimumRestraintScoreSubsetFilterTable::get_subset_filter(), IMP::domino::PairListSubsetFilterTable::get_subset_filter(), IMP::domino::ProbabilisticSubsetFilterTable::get_subset_filter(), IMP::domino::RestraintScoreSubsetFilterTable::get_subset_filter(), IMP::domino::SubsetFilterTable::get_subset_filter(), IMP::em2d::DistanceFilterTable::get_subset_filter(), IMP::example::ExampleSubsetFilterTable::get_subset_filter()
IMP::domino::SubsetFilterTable	IMP::domino::DiscreteSampler::get_subset_filter_table()

IMP.em

Class	Factories
IMP::em::DensityHeader	IMP::em::DensityMap::get_header(), IMP::em::DensityMap::get_header_writable(), IMP::em::create_density_header()
IMP::em::DensityMap	IMP::em::DensityMap::get_cropped(), IMP::em::DensityMap::get_cropped(), IMP::em::DensityMap::get_cropped(), IMP::em::DensityMap::pad_margin(), IMP::em::DensityMap::create_density_map(), IMP::em::DensityMap::create_density_map(), IMP::em::DensityMap::get_binarized_interior(), IMP::em::DensityMap::get_resampled(), IMP::em::DensityMap::get_transformed(), IMP::em::DensityMap::get_transformed(), IMP::em::DensityMap::read_map(), IMP::em::DensityMap::read_map(), IMP::multifit::FFTFitting::crop_margin(), IMP::bayesianem::get_masked_map(), IMP::bayesianem::get_sub_map(), IMP::cnmultifit::build_cn_dens_assembly(), IMP::em::bayesem3d_get_density_from_particle(), IMP::em::binarize(), IMP::em::create_density_map(), IMP::em::create_density_map(), IMP::em::create_density_map(), IMP::em::get_max_map(), IMP::em::get_segment(), IMP::em::get_segment(), IMP::em::get_segment_by_masking(), IMP::em::get_threshold_map(), IMP::em::interpolate_map(), IMP::em::mask_and_norm(), IMP::em::multiply(), IMP::multifit::create_hit_map(), IMP::multifit::grid2map(), IMP::multifit::remove_background()
IMP::em::FittingSolutions	IMP::cnmultifit::fit_cn_assembly(), IMP::cnmultifit::fit_cn_assembly(), IMP::cnmultifit::symmetry_local_fitting(), IMP::em::compute_fitting_scores(), IMP::em::compute_fitting_scores(), IMP::em::local_rigid_fitting(), IMP::em::local_rigid_fitting_around_point(), IMP::em::local_rigid_fitting_around_points(), IMP::em::local_rigid_fitting_grid_search(), IMP::multifit::convert_multifit_to_em_format(), IMP::multifit::pca_based_rigid_fitting(), IMP::multifit::pca_based_rigid_fitting()
IMP::em::ImageHeader	IMP::em2d::Image::get_header()
IMP::em::KernelParameters	IMP::em::SampledDensityMap::get_kernel_params()
IMP::em::SampledDensityMap	IMP::em::FitRestraint::get_model_dens_map(), IMP::em::particles2binarized_density(), IMP::em::particles2density()
IMP::em::SurfaceShellDensityMap	IMP::em::particles2surface()
IMP::em::Voxel	IMP::em::Voxel::setup_particle(), IMP::em::Voxel::setup_particle()

IMP.em2d

Class	Factories
IMP::em2d::Image	IMP::em2d::ProjectionStates::get_projection()
IMP::em2d::ProjectionParameters	IMP::em2d::ProjectionParameters::setup_particle(), IMP::em2d::ProjectionParameters::setup_particle()

IMP.example

Class	Factories
IMP::example::ExampleDecorator	IMP::example::ExampleDecorator::setup_particle(), IMP::example::ExampleDecorator::setup_particle()

IMP.isd

Class	Factories
IMP::isd::FretRestraint	IMP::spb::fret_restraint(), IMP::spb::fret_restraint(), IMP::spb::fret_restraint()
IMP::isd::MolecularDynamics	IMP::isd::HybridMonteCarlo::get_md(), IMP::isd::MolecularDynamicsMover::get_md()
IMP::isd::Nuisance	IMP::isd::Nuisance::setup_particle(), IMP::isd::Nuisance::setup_particle(), IMP::isd::Nuisance::setup_particle(), IMP::isd::Nuisance::setup_particle()
IMP::isd::Scale	IMP::isd::NormalSigmaPCRestraint::get_sigma(), IMP::isd::Scale::setup_particle(), IMP::isd::Scale::setup_particle(), IMP::isd::Scale::setup_particle(), IMP::isd::Scale::setup_particle()
IMP::isd::Switching	IMP::isd::Switching::setup_particle(), IMP::isd::Switching::setup_particle(), IMP::isd::Switching::setup_particle(), IMP::isd::Switching::setup_particle()
IMP::isd::Weight	IMP::isd::Weight::setup_particle(), IMP::isd::Weight::setup_particle(), IMP::isd::Weight::setup_particle(), IMP::isd::Weight::setup_particle(), IMP::isd::Weight::setup_particle(), IMP::isd::Weight::setup_particle()

IMP.kinematics

Class	Factories
IMP::kinematics::DOF	IMP::kinematics::DOFsSampler::get_dof()
IMP::kinematics::DOFValues	IMP::kinematics::DOFsSampler::get_sample(), IMP::kinematics::DOFsSampler::do_get_sample(), IMP::kinematics::DirectionalDOF::get_dofs_values(), IMP::kinematics::FibrilSampler::do_get_sample(), IMP::kinematics::LocalPlanner::plan(), IMP::kinematics::PathLocalPlanner::plan(), IMP::kinematics::RRT::RRTNode::get_DOFValues(), IMP::kinematics::UniformBackboneSampler::do_get_sample()
IMP::kinematics::DihedralAngleRevoluteJoint	IMP::kinematics::ProteinKinematics::get_chi1_joint(), IMP::kinematics::ProteinKinematics::get_chi2_joint(), IMP::kinematics::ProteinKinematics::get_chi3_joint(), IMP::kinematics::ProteinKinematics::get_chi4_joint(), IMP::kinematics::ProteinKinematics::get_chi5_joint(), IMP::kinematics::ProteinKinematics::get_joint(), IMP::kinematics::ProteinKinematics::get_other_joint(), IMP::kinematics::ProteinKinematics::get_phi_joint(), IMP::kinematics::ProteinKinematics::get_psi_joint()
IMP::kinematics::Joint	IMP::kinematics::KinematicForest::add_edge(), IMP::kinematics::KinematicNode::get_in_joint()
IMP::kinematics::KinematicForest	IMP::kinematics::Joint::get_owner_kf(), IMP::kinematics::KinematicNode::get_owner(), IMP::kinematics::ProteinKinematics::get_kinematic_forest()
IMP::kinematics::KinematicNode	IMP::kinematics::KinematicNode::setup_particle(), IMP::kinematics::KinematicNode::setup_particle(), IMP::kinematics::KinematicNode::setup_particle(), IMP::kinematics::KinematicNode::setup_particle(), IMP::kinematics::KinematicNode::setup_particle(), IMP::kinematics::KinematicNode::setup_particle()
IMP::kinematics::RRT::RRTNode	IMP::kinematics::RRT::get_q_near(), IMP::kinematics::RRT::RRTNode::get_edges()

IMP.misc

Class	Factories
IMP::misc::CustomXYZR	IMP::misc::CustomXYZR::setup_particle(), IMP::misc::CustomXYZR::setup_particle(), IMP::misc::CustomXYZR::setup_particle(), IMP::misc::CustomXYZR::setup_particle(), IMP::misc::CustomXYZR::setup_particle(), IMP::misc::CustomXYZR::setup_particle()

IMP.multifit

Class	Factories
IMP::multifit::AnchorsData	IMP::multifit::ProteinsAnchorsSamplingSpace::get_anchors(), IMP::multifit::molecule2anchors(), IMP::multifit::read_anchors_data()
IMP::multifit::AssemblyHeader	IMP::multifit::SettingsData::get_assembly_header()
IMP::multifit::ComponentHeader	IMP::multifit::SettingsData::get_component_header()
IMP::multifit::Ensemble	IMP::multifit::load_ensemble()
IMP::multifit::FFTFittingOutput	IMP::multifit::FFTFitting::do_global_fitting(), IMP::multifit::FFTFitting::do_local_fitting()
IMP::multifit::ProteinsAnchorsSamplingSpace	IMP::multifit::get_part_of_sampling_space(), IMP::multifit::read_protein_anchors_mapping()
IMP::multifit::ProteomicsData	IMP::multifit::ProteinsAnchorsSamplingSpace::get_proteomics_data(), IMP::multifit::get_partial_proteomics_data(), IMP::multifit::read_proteomics_data()
IMP::multifit::SettingsData	IMP::multifit::get_partial_assembly_setting_data(), IMP::multifit::read_settings()

IMP.npctransport

Class	Factories
IMP::npctransport::FGChain	IMP::npctransport::create_fg_chain(), IMP::npctransport::get_fg_chain(), IMP::npctransport::get_fg_chain()
IMP::npctransport::RelaxingSpring	IMP::npctransport::RelaxingSpring::setup_particle(), IMP::npctransport::RelaxingSpring::setup_particle()
IMP::npctransport::Scoring	IMP::npctransport::SimulationData::get_scoring(), IMP::npctransport::SimulationData::get_scoring()
IMP::npctransport::SimulationData	IMP::npctransport::ParticleFactory::get_simulation_data(), IMP::npctransport::Scoring::get_sd(), IMP::npctransport::Scoring::get_sd(), IMP::npctransport::Statistics::get_sd(), IMP::npctransport::Statistics::get_sd(), IMP::npctransport::startup()
IMP::npctransport::SlabWithCylindricalPore	IMP::npctransport::SlabWithCylindricalPore::setup_particle(), IMP::npctransport::SlabWithCylindricalPore::setup_particle()
IMP::npctransport::SlabWithPore	IMP::npctransport::SlabWithPore::setup_particle(), IMP::npctransport::SlabWithPore::setup_particle()
IMP::npctransport::SlabWithToroidalPore	IMP::npctransport::SlabWithToroidalPore::setup_particle(), IMP::npctransport::SlabWithToroidalPore::setup_particle(), IMP::npctransport::SlabWithToroidalPore::setup_particle(), IMP::npctransport::SlabWithToroidalPore::setup_particle()
IMP::npctransport::Statistics	IMP::npctransport::SimulationData::get_statistics(), IMP::npctransport::SimulationData::get_statistics()
IMP::npctransport::Transporting	IMP::npctransport::Transporting::setup_particle(), IMP::npctransport::Transporting::setup_particle()

IMP.pmi

Class	Factories
IMP::pmi::Resolution	IMP::pmi::Resolution::setup_particle(), IMP::pmi::Resolution::setup_particle()
IMP::pmi::Symmetric	IMP::pmi::Symmetric::setup_particle(), IMP::pmi::Symmetric::setup_particle()
IMP::pmi::Uncertainty	IMP::pmi::Uncertainty::setup_particle(), IMP::pmi::Uncertainty::setup_particle()

IMP.pmi1

Class	Factories
IMP::pmi1::Resolution	IMP::pmi1::Resolution::setup_particle(), IMP::pmi1::Resolution::setup_particle()
IMP::pmi1::Symmetric	IMP::pmi1::Symmetric::setup_particle(), IMP::pmi1::Symmetric::setup_particle()
IMP::pmi1::Uncertainty	IMP::pmi1::Uncertainty::setup_particle(), IMP::pmi1::Uncertainty::setup_particle()

IMP.rmf

Class	Factories
IMP::rmf::SaveOptimizerState	IMP::npctransport::SimulationData::get_rmf_sos_writer()

IMP.rotamer

Class	Factories
IMP::rotamer::ResidueRotamer	IMP::rotamer::RotamerCalculator::get_rotamer()

IMP.saxs

Class	Factories
IMP::saxs::DeltaDistributionFunction	IMP::saxs::DerivativeCalculator::precompute_derivative_helpers()
IMP::saxs::FitParameters	IMP::saxs::ProfileFitter::fit_profile(), IMP::saxs::ProfileFitter::search_fit_parameters()
IMP::saxs::FormFactorTable	IMP::saxs::get_default_form_factor_table()
IMP::saxs::Profile	IMP::saxs::ProfileFitter::get_profile(), IMP::saxs::compute_profile()
IMP::saxs::WeightedFitParameters	IMP::multi_state::MultiStateModelScore::get_fit_parameters(), IMP::multi_state::MultiStateModelScore::get_fit_parameters(), IMP::multi_state::SAXSMultiCombinationScore::get_fit_parameters(), IMP::multi_state::SAXSMultiCombinationScore::get_fit_parameters(), IMP::multi_state::SAXSMultiStateModelScore::get_fit_parameters(), IMP::multi_state::SAXSMultiStateModelScore::get_fit_parameters(), IMP::saxs::WeightedProfileFitter::fit_profile(), IMP::saxs::WeightedProfileFitter::search_fit_parameters()

IMP.spb

Class	Factories
IMP::spb::EM2DRestraint	IMP::spb::em2d_restraint(), IMP::spb::em2d_restraint()
IMP::spb::HelixDecorator	IMP::spb::HelixDecorator::setup_particle()

IMP.statistics

Class	Factories
IMP::statistics::HistogramD	IMP::statistics::HistogramD::get_frequencies(), IMP::statistics::HistogramD::get_probability_distribution_function()
IMP::statistics::PartitionalClustering	IMP::statistics::RecursivePartitionalClusteringEmbedding::create_full_clustering(), IMP::statistics::RecursivePartitionalClusteringMetric::create_full_clustering(), IMP::spb::create_gromos_clustering(), IMP::statistics::create_centrality_clustering(), IMP::statistics::create_centrality_clustering(), IMP::statistics::create_connectivity_clustering(), IMP::statistics::create_diameter_clustering(), IMP::statistics::create_gromos_clustering()
IMP::statistics::PartitionalClusteringWithCenter	IMP::statistics::create_bin_based_clustering(), IMP::statistics::create_connectivity_clustering(), IMP::statistics::create_lloyds_kmeans()