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::algebra::EuclideanVectorKDMetric::load_cereal(), IMP::algebra::MaxVectorKDMetric::load_cereal(), IMP::atom::DihedralSingletonScore::load_cereal(), IMP::atom::WritePDBOptimizerState::load_cereal(), IMP::container::CloseBipartitePairContainer::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::DirectionMover::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::LogNormalMover::load_cereal(), IMP::core::NormalMover::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::SurfaceMover::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::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(), IMP::container::ClosePairContainer::get_version_info(), IMP::container::ConnectingPairContainer::get_version_info(), IMP::container::ConsecutivePairContainer::get_version_info(), IMP::container::ConsecutivePairFilter::get_version_info(), IMP::container::DistributePairsScoreState::get_version_info(), IMP::container::DistributeQuadsScoreState::get_version_info(), IMP::container::DistributeSingletonsScoreState::get_version_info(), IMP::container::DistributeTripletsScoreState::get_version_info(), IMP::container::DynamicListPairContainer::get_version_info(), IMP::container::DynamicListQuadContainer::get_version_info(), IMP::container::DynamicListSingletonContainer::get_version_info(), IMP::container::DynamicListTripletContainer::get_version_info(), IMP::container::EventPairsOptimizerState::get_version_info(), IMP::container::EventQuadsOptimizerState::get_version_info(), IMP::container::EventSingletonsOptimizerState::get_version_info(), 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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() |