Factory Index

Table of Contents

• Overview
• IMP.algebra
• IMP.atom
• IMP.base
• IMP.container
• IMP.core
• IMP.display
• IMP.domino
• IMP.em
• IMP.em2d
• IMP.example
• IMP.isd
• IMP.kernel
• IMP.kinematics
• IMP.misc
• IMP.multifit
• IMP.restrainer
• IMP.rotamer
• IMP.saxs
• IMP.statistics

Overview

Functions that create objects of a given type:

See also Argument Index, Class Examples, Function Examples

IMP.algebra

Class	Factories
IMP::algebra::BoundingBoxD	IMP::algebra::BoundingBoxD::operator+=(), IMP::algebra::BoundingBoxD::operator+=(), IMP::algebra::BoundingBoxD::operator+=(), IMP::algebra::DefaultEmbeddingD::get_bounding_box(), IMP::algebra::DefaultEmbeddingD::get_bounding_box(), IMP::algebra::GridD::get_bounding_box(), IMP::algebra::LogEmbeddingD::get_bounding_box(), IMP::algebra::LogEmbeddingD::get_bounding_box(), IMP::display::BoundingBoxGeometry::get_geometry(), IMP::em::SampledDensityMap::calculate_particles_bounding_box(), IMP::statistics::HistogramD::get_bounding_box(), IMP::algebra::get_bounding_box(), IMP::algebra::get_bounding_box(), IMP::algebra::get_bounding_box(), IMP::algebra::get_bounding_box(), IMP::algebra::get_bounding_box(), IMP::algebra::get_bounding_box(), IMP::algebra::get_cube_kd(), IMP::algebra::get_transformed(), IMP::algebra::get_unit_bounding_box_kd(), IMP::atom::get_bounding_box(), IMP::core::get_bounding_box(), IMP::em::get_bounding_box(), IMP::em::get_bounding_box(), IMP::kernel::get_bounding_box_d_geometry()
IMP::algebra::Cone3D	IMP::algebra::get_cone_3d_geometry()
IMP::algebra::Cylinder3D	IMP::display::CylinderGeometry::get_geometry(), IMP::algebra::get_cylinder_3d_geometry()
IMP::algebra::DenseGridStorageD	IMP::algebra::DenseGridStorageD::operator=(), IMP::em::get_grid()
IMP::algebra::Ellipsoid3D	IMP::display::EllipsoidGeometry::get_geometry(), IMP::algebra::get_ellipsoid_3d_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::SparseGridStorageD::get_maximum_extended_index(), IMP::algebra::SparseGridStorageD::get_minimum_extended_index(), IMP::algebra::UnboundedGridRangeD::get_extended_indexes()
IMP::algebra::FixedXYZ	IMP::algebra::get_fixed_xyz_from_rotation()
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_all_indexes(), IMP::algebra::SparseGridStorageD::get_indexes(), IMP::algebra::SparseGridStorageD::add_voxel(), IMP::algebra::SparseGridStorageD::get_index()
IMP::algebra::Plane3D	IMP::algebra::Cone3D::get_base_plane(), IMP::algebra::Plane3D::get_opposite(), IMP::algebra::SpherePatch3D::get_plane(), IMP::algebra::get_plane_3d_geometry()
IMP::algebra::ReferenceFrame3D	IMP::algebra::ReferenceFrame3D::get_global_reference_frame(), IMP::algebra::ReferenceFrame3D::get_local_reference_frame(), IMP::core::RigidBody::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::Ellipsoid3D::get_rotation(), IMP::algebra::Rotation3D::get_inverse(), IMP::algebra::Rotation3D::operator*(), IMP::algebra::Rotation3D::operator/(), IMP::algebra::Rotation3D::operator/=(), IMP::algebra::Transformation3D::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_vector4d(), IMP::algebra::get_rotation_from_x_y_axes(), IMP::algebra::get_rotation_taking_first_to_second()
IMP::algebra::Segment3D	IMP::algebra::Cylinder3D::get_segment(), IMP::core::RigidBodyTorque::extract_geometry(), IMP::core::RigidBodyTorque::get_geometry(), IMP::display::SegmentGeometry::get_geometry(), IMP::algebra::get_shortest_segment(), IMP::algebra::get_shortest_segment(), IMP::algebra::get_segment_3d_geometry()
IMP::algebra::SphereD	IMP::algebra::get_unit_sphere_kd()
IMP::algebra::SpherePatch3D	IMP::algebra::get_sphere_patch_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::compose(), IMP::algebra::get_identity_transformation_2d(), IMP::algebra::get_rotation_about_point(), IMP::algebra::get_transformation_aligning_pair()
IMP::algebra::Transformation3D	IMP::algebra::Ellipsoid3D::get_transformation(), 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::core::RigidBodyMember::get_internal_transformation(), IMP::domino::NestedRigidBodyStates::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::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::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::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::VectorD::get_unit_vector(), 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_basis_vector_kd()

IMP.atom

Class	Factories
IMP::atom::Angle	IMP::atom::Angle::decorate_particle(), IMP::atom::Angle::setup_particle(), IMP::atom::Angle::setup_particle()
IMP::atom::Atom	IMP::atom::Atom::decorate_particle(), 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::Hierarchy::get_as_atom(), IMP::atom::get_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::Bond::decorate_particle(), 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::atom::Bonded	IMP::atom::Bond::get_bonded(), IMP::atom::Bonded::get_bonded(), IMP::atom::Bonded::decorate_particle(), IMP::atom::Bonded::setup_particle(), IMP::atom::Bonded::setup_particle()
IMP::atom::CHARMMAtom	IMP::atom::CHARMMAtom::decorate_particle(), 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::Chain	IMP::atom::Chain::decorate_particle(), IMP::atom::Chain::setup_particle(), IMP::atom::Chain::setup_particle(), IMP::atom::Chain::setup_particle(), IMP::atom::Chain::setup_particle(), IMP::atom::Hierarchy::get_as_chain(), IMP::atom::get_chain()
IMP::atom::Charged	IMP::atom::Charged::decorate_particle(), 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::decorate_particle(), IMP::atom::Copy::setup_particle(), IMP::atom::Copy::setup_particle()
IMP::atom::Diffusion	IMP::atom::Diffusion::decorate_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::Diffusion::setup_particle()
IMP::atom::Dihedral	IMP::atom::Dihedral::decorate_particle(), IMP::atom::Dihedral::setup_particle(), IMP::atom::Dihedral::setup_particle()
IMP::atom::Domain	IMP::atom::Domain::decorate_particle(), IMP::atom::Domain::setup_particle(), IMP::atom::Domain::setup_particle(), IMP::atom::Domain::setup_particle(), IMP::atom::Domain::setup_particle(), IMP::atom::Domain::setup_particle(), IMP::atom::Domain::setup_particle(), IMP::atom::Hierarchy::get_as_domain()
IMP::atom::ElementTable	IMP::atom::get_element_table()
IMP::atom::Fragment	IMP::atom::Fragment::decorate_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::Fragment::setup_particle(), IMP::atom::Hierarchy::get_as_fragment()
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::create_simplified_along_backbone(), IMP::atom::create_simplified_along_backbone(), IMP::atom::read_mol2(), IMP::atom::read_pdb(), IMP::atom::create_clone(), IMP::atom::create_clone_one(), IMP::atom::create_fragment(), IMP::atom::create_protein(), IMP::atom::create_protein(), IMP::atom::get_next_residue(), IMP::atom::get_previous_residue(), IMP::atom::get_residue(), IMP::atom::get_root(), IMP::multifit::create_coarse_molecule_from_density(), IMP::multifit::create_coarse_molecule_from_molecule()
IMP::atom::LennardJones	IMP::atom::LennardJones::decorate_particle(), 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::Hierarchy::get_as_mass(), IMP::atom::Mass::decorate_particle(), IMP::atom::Mass::setup_particle(), IMP::atom::Mass::setup_particle()
IMP::atom::Molecule	IMP::atom::Hierarchy::get_as_molecule(), IMP::atom::Molecule::decorate_particle(), IMP::atom::Molecule::setup_particle(), IMP::atom::Molecule::setup_particle(), IMP::atom::Molecule::setup_particle(), IMP::atom::Molecule::setup_particle()
IMP::atom::PDBSelector	IMP::atom::get_default_pdb_selector()
IMP::atom::Residue	IMP::atom::Hierarchy::get_as_residue(), IMP::atom::Residue::decorate_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::Residue::setup_particle(), IMP::atom::get_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::decorate_particle(), IMP::atom::RigidBodyDiffusion::setup_particle(), IMP::atom::RigidBodyDiffusion::setup_particle()
IMP::atom::SecondaryStructureResidue	IMP::atom::SecondaryStructureResidue::decorate_particle(), IMP::atom::SecondaryStructureResidue::setup_particle(), IMP::atom::SecondaryStructureResidue::setup_particle(), IMP::atom::SecondaryStructureResidue::setup_particle(), IMP::atom::setup_coarse_secondary_structure_residue()
IMP::atom::StereochemistryPairFilter	IMP::atom::CHARMMStereochemistryRestraint::get_pair_filter()

IMP.base

Class	Factories
IMP::base::Object	IMP::kernel::Model::get_data()
IMP::base::TextOutput	IMP::base::create_temporary_file(), IMP::base::get_log_target()
IMP::base::Vector	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_all_indexes(), 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::Bonded::get_bonds(), 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::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::base::ConstVector::ConstVector(), IMP::base::LRUCache::get_keys(), 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::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::IncrementalScoringFunction::get_movable_indexes(), IMP::core::IncrementalScoringFunction::get_movable_particles(), IMP::core::LeavesRefiner::get_refined(), IMP::core::MonteCarlo::get_movable_particles(), IMP::core::Mover::get_output_particles(), IMP::core::Mover::propose_move(), IMP::core::MoverBase::get_output_particles(), IMP::core::MoverBase::propose_move(), IMP::core::NeighborsTable::get_neighbors(), IMP::core::RigidBody::get_body_member_particle_indexes(), IMP::core::RigidBody::get_member_particle_indexes(), IMP::core::RigidBody::get_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::BivariateFunction::get_input_particles(), IMP::isd::Covariance1DFunction::get_input_particles(), IMP::isd::GaussianProcessInterpolation::get_input_particles(), IMP::isd::GeneralizedGuinierPorodFunction::get_input_particles(), IMP::isd::Linear1DFunction::get_input_particles(), IMP::isd::UnivariateFunction::get_input_particles(), IMP::kernel::Container::get_all_possible_indexes(), IMP::kernel::Container::get_all_possible_particles(), IMP::kernel::Key::get_all_strings(), IMP::kernel::Model::get_particle_indexes(), IMP::kernel::Model::get_particles(), IMP::kernel::ModelObject::get_interactions(), IMP::kernel::ModelObject::do_get_interactions(), IMP::kernel::ParticleInputs::get_input_particles(), IMP::kernel::ParticleOutputs::get_output_particles(), IMP::kernel::Refiner::get_refined(), IMP::kernel::Refiner::get_refined_indexes(), IMP::kernel::Restraint::get_input_particles(), IMP::kernel::ScoreState::get_input_particles(), IMP::kernel::ScoreState::get_output_particles(), IMP::kernel::SingletonContainer::get_indexes(), IMP::kernel::SingletonContainer::get_particles(), IMP::kernel::SingletonContainer::get_range_indexes(), IMP::kinematics::KinematicForest::get_children(), IMP::kinematics::ProteinKinematics::get_rigid_bodies(), 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::WeightedExcludedVolumeRestraint::get_particles(), IMP::rmf::SimpleLoadLink::create(), IMP::rmf::SimpleLoadLink::create(), IMP::symmetry::RigidBodyMover::get_particles(), IMP::atom::read_multimodel_pdb(), IMP::atom::read_psipred(), IMP::atom::read_psipred(), IMP::atom::get_by_type(), IMP::atom::get_charmm_untyped_atoms(), IMP::atom::get_internal_bonds(), IMP::atom::get_leaves(), IMP::atom::get_leaves(), IMP::atom::get_leaves(), IMP::atom::get_phi_dihedral_atoms(), IMP::atom::get_psi_dihedral_atoms(), 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::kernel::get_input_particles(), IMP::kernel::get_output_particles(), IMP::kernel::write_particles_to_buffer(), IMP::kernel::get_dependent_particles(), IMP::kernel::get_indexes(), IMP::kernel::get_particles(), IMP::kernel::get_required_particles(), IMP::multifit::create_coarse_molecules_from_molecules(), IMP::restrainer::set_rigid_bodies(), IMP::rmf::create_hierarchies(), IMP::rmf::create_particles()
IMP::base::VersionInfo	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::AllMol2Selector::get_version_info(), IMP::atom::AllPDBSelector::get_version_info(), IMP::atom::AndPDBSelector::get_version_info(), IMP::atom::AngleSingletonScore::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::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::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::NonHydrogenMol2Selector::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::SameResiduePairFilter::get_version_info(), IMP::atom::SelectionGeometry::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::base::Object::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(), IMP::container::EventTripletsOptimizerState::get_version_info(), IMP::container::ExclusiveConsecutivePairContainer::get_version_info(), IMP::container::ExclusiveConsecutivePairFilter::get_version_info(), IMP::container::InContainerPairFilter::get_version_info(), IMP::container::InContainerQuadFilter::get_version_info(), IMP::container::InContainerSingletonFilter::get_version_info(), IMP::container::InContainerTripletFilter::get_version_info(), IMP::container::ListPairContainer::get_version_info(), IMP::container::ListQuadContainer::get_version_info(), IMP::container::ListSingletonContainer::get_version_info(), IMP::container::ListTripletContainer::get_version_info(), IMP::container::MinimumPairRestraint::get_version_info(), IMP::container::MinimumPairScore::get_version_info(), IMP::container::MinimumQuadRestraint::get_version_info(), IMP::container::MinimumQuadScore::get_version_info(), IMP::container::MinimumSingletonRestraint::get_version_info(), IMP::container::MinimumSingletonScore::get_version_info(), IMP::container::MinimumTripletRestraint::get_version_info(), IMP::container::MinimumTripletScore::get_version_info(), IMP::container::PairContainerSet::get_version_info(), IMP::container::PairContainerStatistics::get_version_info(), IMP::container::PairsConstraint::get_version_info(), IMP::container::PairsOptimizerState::get_version_info(), IMP::container::PredicatePairsRestraint::get_version_info(), IMP::container::PredicateQuadsRestraint::get_version_info(), IMP::container::PredicateSingletonsRestraint::get_version_info(), IMP::container::PredicateTripletsRestraint::get_version_info(), IMP::container::QuadContainerSet::get_version_info(), IMP::container::QuadContainerStatistics::get_version_info(), IMP::container::QuadsConstraint::get_version_info(), IMP::container::QuadsOptimizerState::get_version_info(), IMP::container::SingletonContainerSet::get_version_info(), IMP::container::SingletonContainerStatistics::get_version_info(), IMP::container::SingletonsConstraint::get_version_info(), IMP::container::SingletonsOptimizerState::get_version_info(), IMP::container::TripletContainerSet::get_version_info(), IMP::container::TripletContainerStatistics::get_version_info(), IMP::container::TripletsConstraint::get_version_info(), IMP::container::TripletsOptimizerState::get_version_info(), IMP::core::AllSamePairPredicate::get_version_info(), IMP::core::AllSameQuadPredicate::get_version_info(), IMP::core::AllSameSingletonPredicate::get_version_info(), IMP::core::AllSameTripletPredicate::get_version_info(), IMP::core::AngleRestraint::get_version_info(), IMP::core::AngleTripletScore::get_version_info(), IMP::core::AttributeSingletonPredicate::get_version_info(), IMP::core::BallMover::get_version_info(), IMP::core::BoxSweepClosePairsFinder::get_version_info(), IMP::core::CentroidOfRefined::get_version_info(), IMP::core::ChecksScoreState::get_version_info(), IMP::core::ChildrenRefiner::get_version_info(), IMP::core::ClosePairsPairScore::get_version_info(), IMP::core::ClosedCubicSpline::get_version_info(), IMP::core::CoinFlipPairPredicate::get_version_info(), IMP::core::CoinFlipQuadPredicate::get_version_info(), IMP::core::CoinFlipSingletonPredicate::get_version_info(), IMP::core::CoinFlipTripletPredicate::get_version_info(), IMP::core::ConjugateGradients::get_version_info(), IMP::core::ConnectivityRestraint::get_version_info(), IMP::core::ConstantPairPredicate::get_version_info(), IMP::core::ConstantQuadPredicate::get_version_info(), IMP::core::ConstantRestraint::get_version_info(), IMP::core::ConstantSingletonPredicate::get_version_info(), IMP::core::ConstantTripletPredicate::get_version_info(), IMP::core::Cosine::get_version_info(), IMP::core::CoverRefined::get_version_info(), IMP::core::DerivativesFromRefined::get_version_info(), IMP::core::DerivativesToRefined::get_version_info(), IMP::core::DiameterRestraint::get_version_info(), IMP::core::DihedralRestraint::get_version_info(), IMP::core::DistancePairScore::get_version_info(), IMP::core::EdgePairGeometry::get_version_info(), IMP::core::EdgePairsGeometry::get_version_info(), IMP::core::ExcludedVolumeRestraint::get_version_info(), IMP::core::FixedRefiner::get_version_info(), IMP::core::GenericAttributeSingletonScore::get_version_info(), IMP::core::GenericBoundingBox3DSingletonScore::get_version_info(), IMP::core::GenericDistanceToSingletonScore::get_version_info(), IMP::core::GridClosePairsFinder::get_version_info(), IMP::core::Harmonic::get_version_info(), IMP::core::HarmonicDistancePairScore::get_version_info(), IMP::core::HarmonicLowerBound::get_version_info(), IMP::core::HarmonicSphereDistancePairScore::get_version_info(), IMP::core::HarmonicUpperBound::get_version_info(), IMP::core::HarmonicUpperBoundSphereDiameterPairScore::get_version_info(), IMP::core::HarmonicUpperBoundSphereDistancePairScore::get_version_info(), IMP::core::HarmonicWell::get_version_info(), IMP::core::InBoundingBox3DSingletonPredicate::get_version_info(), IMP::core::IncrementalScoringFunction::get_version_info(), IMP::core::IsCollisionPairPredicate::get_version_info(), IMP::core::KClosePairsPairScore::get_version_info(), IMP::core::LeavesRefiner::get_version_info(), IMP::core::Linear::get_version_info(), IMP::core::MCCGSampler::get_version_info(), IMP::core::MSConnectivityRestraint::get_version_info(), IMP::core::MinimumRestraint::get_version_info(), IMP::core::MonteCarlo::get_version_info(), IMP::core::MonteCarloWithBasinHopping::get_version_info(), IMP::core::MonteCarloWithLocalOptimization::get_version_info(), IMP::core::MoveStatisticsScoreState::get_version_info(), IMP::core::NearestNeighborsClosePairsFinder::get_version_info(), IMP::core::NeighborsTable::get_version_info(), IMP::core::NormalMover::get_version_info(), IMP::core::NormalizedSphereDistancePairScore::get_version_info(), IMP::core::OrderedTypePairPredicate::get_version_info(), IMP::core::OrderedTypeQuadPredicate::get_version_info(), IMP::core::OrderedTypeSingletonPredicate::get_version_info(), IMP::core::OrderedTypeTripletPredicate::get_version_info(), IMP::core::PairConstraint::get_version_info(), IMP::core::PairRestraint::get_version_info(), IMP::core::PredicateSingletonScore::get_version_info(), IMP::core::QuadConstraint::get_version_info(), IMP::core::QuadRestraint::get_version_info(), IMP::core::QuadraticClosePairsFinder::get_version_info(), IMP::core::RefinedPairsPairScore::get_version_info(), IMP::core::RigidBodyDerivativeGeometry::get_version_info(), IMP::core::RigidBodyDerivativesGeometry::get_version_info(), IMP::core::RigidBodyFrameGeometry::get_version_info(), IMP::core::RigidBodyFramesGeometry::get_version_info(), IMP::core::RigidBodyHierarchyGeometry::get_version_info(), IMP::core::RigidBodyMover::get_version_info(), IMP::core::RigidClosePairsFinder::get_version_info(), IMP::core::SerialMover::get_version_info(), IMP::core::SingletonConstraint::get_version_info(), IMP::core::SingletonRestraint::get_version_info(), IMP::core::SoftSpherePairScore::get_version_info(), IMP::core::SphereDistancePairScore::get_version_info(), IMP::core::SphereDistanceToSingletonScore::get_version_info(), IMP::core::SteepestDescent::get_version_info(), IMP::core::TableRefiner::get_version_info(), IMP::core::Transform::get_version_info(), IMP::core::TransformationAndReflectionSymmetry::get_version_info(), IMP::core::TransformationSymmetry::get_version_info(), IMP::core::TransformedDistancePairScore::get_version_info(), IMP::core::TripletConstraint::get_version_info(), IMP::core::TripletRestraint::get_version_info(), IMP::core::TruncatedHarmonic::get_version_info(), IMP::core::TypedPairScore::get_version_info(), IMP::core::UnorderedTypePairPredicate::get_version_info(), IMP::core::UnorderedTypeQuadPredicate::get_version_info(), IMP::core::UnorderedTypeSingletonPredicate::get_version_info(), IMP::core::UnorderedTypeTripletPredicate::get_version_info(), IMP::core::VolumeRestraint::get_version_info(), IMP::core::WeightedSphereDistancePairScore::get_version_info(), IMP::core::WriteRestraintScoresOptimizerState::get_version_info(), IMP::core::XYZDerivativeGeometry::get_version_info(), IMP::core::XYZDerivativesGeometry::get_version_info(), IMP::core::XYZRGeometry::get_version_info(), IMP::core::XYZRsGeometry::get_version_info(), IMP::display::BildWriter::get_version_info(), IMP::display::BoundingBoxGeometry::get_version_info(), IMP::display::CMMWriter::get_version_info(), IMP::display::ChimeraWriter::get_version_info(), IMP::display::CylinderGeometry::get_version_info(), IMP::display::EllipsoidGeometry::get_version_info(), IMP::display::FilterGeometry::get_version_info(), IMP::display::GeometrySet::get_version_info(), IMP::display::LabelGeometry::get_version_info(), IMP::display::PlaneGeometry::get_version_info(), IMP::display::PointGeometry::get_version_info(), IMP::display::PolygonGeometry::get_version_info(), IMP::display::PymolWriter::get_version_info(), IMP::display::ReferenceFrameGeometry::get_version_info(), IMP::display::RestraintGeometry::get_version_info(), IMP::display::RestraintSetGeometry::get_version_info(), IMP::display::SegmentGeometry::get_version_info(), IMP::display::SphereGeometry::get_version_info(), IMP::display::SurfaceMeshGeometry::get_version_info(), IMP::display::TriangleGeometry::get_version_info(), IMP::display::WriteOptimizerState::get_version_info(), IMP::domino::BranchAndBoundAssignmentsTable::get_version_info(), IMP::domino::BranchAndBoundSampler::get_version_info(), IMP::domino::CappedAssignmentContainer::get_version_info(), IMP::domino::CompoundStates::get_version_info(), IMP::domino::DependencyScoreState::get_version_info(), IMP::domino::DominoSampler::get_version_info(), IMP::domino::EqualitySubsetFilterTable::get_version_info(), IMP::domino::EquivalenceAndExclusionSubsetFilterTable::get_version_info(), IMP::domino::EquivalenceSubsetFilterTable::get_version_info(), IMP::domino::ExclusionSubsetFilterTable::get_version_info(), IMP::domino::HeapAssignmentContainer::get_version_info(), IMP::domino::IndexStates::get_version_info(), IMP::domino::ListAssignmentContainer::get_version_info(), IMP::domino::ListAssignmentsTable::get_version_info(), IMP::domino::ListSubsetFilterTable::get_version_info(), IMP::domino::MinimumRestraintScoreSubsetFilterTable::get_version_info(), IMP::domino::NestedRigidBodyStates::get_version_info(), IMP::domino::PackedAssignmentContainer::get_version_info(), IMP::domino::PairListSubsetFilterTable::get_version_info(), IMP::domino::ParticleStatesTable::get_version_info(), IMP::domino::PermutationStates::get_version_info(), IMP::domino::ProbabilisticSubsetFilterTable::get_version_info(), IMP::domino::RangeViewAssignmentContainer::get_version_info(), IMP::domino::ReadAssignmentContainer::get_version_info(), IMP::domino::ReadHDF5AssignmentContainer::get_version_info(), IMP::domino::RecursiveAssignmentsTable::get_version_info(), IMP::domino::RecursiveStates::get_version_info(), IMP::domino::RestraintCache::get_version_info(), IMP::domino::RestraintScoreSubsetFilterTable::get_version_info(), IMP::domino::RigidBodyStates::get_version_info(), IMP::domino::SampleAssignmentContainer::get_version_info(), IMP::domino::SimpleAssignmentsTable::get_version_info(), IMP::domino::WriteAssignmentContainer::get_version_info(), IMP::domino::WriteHDF5AssignmentContainer::get_version_info(), IMP::domino::XYZStates::get_version_info(), IMP::em2d::CollisionCrossSection::get_version_info(), IMP::em2d::DistanceFilter::get_version_info(), IMP::em2d::DistanceFilterTable::get_version_info(), IMP::em2d::DummyRestraint::get_version_info(), IMP::em2d::Em2DRestraint::get_version_info(), IMP::em2d::Fine2DRegistrationRestraint::get_version_info(), IMP::em2d::GridStates::get_version_info(), IMP::em2d::Image::get_version_info(), IMP::em2d::ImageReaderWriter::get_version_info(), IMP::em2d::JPGImageReaderWriter::get_version_info(), IMP::em2d::ParticlesDummyRestraint::get_version_info(), IMP::em2d::ProjectionFinder::get_version_info(), IMP::em2d::ProjectionParametersScoreState::get_version_info(), IMP::em2d::ProjectionStates::get_version_info(), IMP::em2d::RelativePositionMover::get_version_info(), IMP::em2d::RigidBodiesImageFitRestraint::get_version_info(), IMP::em2d::ScoreFunction::get_version_info(), IMP::em2d::SpiderImageReaderWriter::get_version_info(), IMP::em2d::TIFFImageReaderWriter::get_version_info(), IMP::em::CoarseCC::get_version_info(), IMP::em::CoarseCCatIntervals::get_version_info(), IMP::em::DensityFillingRestraint::get_version_info(), IMP::em::DensityMap::get_version_info(), IMP::em::EMReaderWriter::get_version_info(), IMP::em::EnvelopeFitRestraint::get_version_info(), IMP::em::EnvelopePenetrationRestraint::get_version_info(), IMP::em::EnvelopeScore::get_version_info(), IMP::em::FitRestraint::get_version_info(), IMP::em::HighDensityEmbedding::get_version_info(), IMP::em::MRCReaderWriter::get_version_info(), IMP::em::MapReaderWriter::get_version_info(), IMP::em::PCAAligner::get_version_info(), IMP::em::PCAFitRestraint::get_version_info(), IMP::em::SpiderMapReaderWriter::get_version_info(), IMP::em::XplorReaderWriter::get_version_info(), IMP::example::ExampleComplexRestraint::get_version_info(), IMP::example::ExampleConstraint::get_version_info(), IMP::example::ExampleObject::get_version_info(), IMP::example::ExamplePairScore::get_version_info(), IMP::example::ExampleRestraint::get_version_info(), IMP::example::ExampleSingletonModifier::get_version_info(), IMP::example::ExampleSubsetFilterTable::get_version_info(), IMP::example::ExampleUnaryFunction::get_version_info(), IMP::gsl::ConjugateGradients::get_version_info(), IMP::gsl::QuasiNewton::get_version_info(), IMP::gsl::Simplex::get_version_info(), IMP::isd::AmbiguousNOERestraint::get_version_info(), IMP::isd::AmbiguousRestraint::get_version_info(), IMP::isd::Covariance1DFunction::get_version_info(), IMP::isd::CrossLinkData::get_version_info(), IMP::isd::CysteineCrossLinkData::get_version_info(), IMP::isd::CysteineCrossLinkRestraint::get_version_info(), IMP::isd::FNormal::get_version_info(), IMP::isd::FretData::get_version_info(), IMP::isd::FretRestraint::get_version_info(), IMP::isd::GaussianProcessInterpolation::get_version_info(), IMP::isd::GaussianProcessInterpolationRestraint::get_version_info(), IMP::isd::GaussianRestraint::get_version_info(), IMP::isd::GeneralizedGuinierPorodFunction::get_version_info(), IMP::isd::HybridMonteCarlo::get_version_info(), IMP::isd::JeffreysRestraint::get_version_info(), IMP::isd::Linear1DFunction::get_version_info(), IMP::isd::LognormalRestraint::get_version_info(), IMP::isd::MarginalHBondRestraint::get_version_info(), IMP::isd::MarginalNOERestraint::get_version_info(), IMP::isd::MolecularDynamicsMover::get_version_info(), IMP::isd::MultivariateFNormalSufficient::get_version_info(), IMP::isd::NOERestraint::get_version_info(), IMP::isd::RepulsiveDistancePairScore::get_version_info(), IMP::isd::TALOSRestraint::get_version_info(), IMP::isd::WeightMover::get_version_info(), IMP::isd::WeightRestraint::get_version_info(), IMP::isd::vonMises::get_version_info(), IMP::isd::vonMisesKappaConjugateRestraint::get_version_info(), IMP::isd::vonMisesKappaJeffreysRestraint::get_version_info(), IMP::isd::vonMisesSufficient::get_version_info(), IMP::kernel::Configuration::get_version_info(), IMP::kernel::ConfigurationSet::get_version_info(), IMP::kernel::Model::get_version_info(), IMP::kernel::Particle::get_version_info(), IMP::kernel::RestraintSet::get_version_info(), IMP::kernel::SaveToConfigurationSetOptimizerState::get_version_info(), IMP::kinematics::DOF::get_version_info(), IMP::kinematics::DOFsSampler::get_version_info(), IMP::kinematics::Joint::get_version_info(), IMP::kinematics::KinematicForest::get_version_info(), IMP::kinematics::KinematicForestScoreState::get_version_info(), IMP::kinematics::LocalPlanner::get_version_info(), IMP::kinematics::RRT::get_version_info(), IMP::kmeans::KMeans::get_version_info(), IMP::misc::CommonEndpointPairFilter::get_version_info(), IMP::misc::DecayPairContainerOptimizerState::get_version_info(), IMP::misc::LogPairScore::get_version_info(), IMP::misc::LowestRefinedPairScore::get_version_info(), IMP::misc::MetricClosePairsFinder::get_version_info(), IMP::misc::SoftCylinderPairScore::get_version_info(), IMP::misc::StateAdaptor::get_version_info(), IMP::misc::WormLikeChain::get_version_info(), IMP::modeller::MultipleBinormalRestraint::get_version_info(), IMP::mpi::ReplicaExchange::get_version_info(), IMP::multifit::AssemblyHeader::get_version_info(), IMP::multifit::ComplementarityRestraint::get_version_info(), IMP::multifit::ComponentHeader::get_version_info(), IMP::multifit::DensityDataPoints::get_version_info(), IMP::multifit::DummyRestraint::get_version_info(), IMP::multifit::Ensemble::get_version_info(), IMP::multifit::FFTFitting::get_version_info(), IMP::multifit::FFTFittingOutput::get_version_info(), IMP::multifit::FittingStates::get_version_info(), IMP::multifit::ProbabilisticAnchorGraph::get_version_info(), IMP::multifit::ProteomicsData::get_version_info(), IMP::multifit::ProteomicsEMAlignmentAtomic::get_version_info(), IMP::multifit::RadiusOfGyrationRestraint::get_version_info(), IMP::multifit::SettingsData::get_version_info(), IMP::multifit::WeightedExcludedVolumeRestraint::get_version_info(), IMP::restrainer::SimpleConnectivity::get_version_info(), IMP::restrainer::SimpleDiameter::get_version_info(), IMP::restrainer::SimpleDistance::get_version_info(), IMP::restrainer::SimpleEMFit::get_version_info(), IMP::restrainer::SimpleExcludedVolume::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::Profile::get_version_info(), IMP::saxs::RadiusOfGyrationRestraint::get_version_info(), IMP::saxs::Restraint::get_version_info(), IMP::score_functor::DistancePairScore::get_version_info(), IMP::score_functor::ScoreUnaryFunction::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::base::map	IMP::misc::MetricClosePairsFinder::get_index()

IMP.container

Class	Factories
IMP::container::ClosePairContainer	IMP::example::create_excluded_volume()
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::PairContainerSet	IMP::container::PairContainerSet::get_set()
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::decorate_particle(), IMP::core::Centroid::setup_particle(), IMP::core::Centroid::setup_particle(), IMP::core::Centroid::setup_particle(), IMP::core::Centroid::setup_particle()
IMP::core::ConnectivityRestraint	IMP::restrainer::SimpleConnectivity::get_restraint()
IMP::core::Cover	IMP::core::Cover::decorate_particle(), 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::DiameterRestraint	IMP::restrainer::SimpleDiameter::get_restraint()
IMP::core::DistanceRestraint	IMP::restrainer::SimpleDistance::get_restraint()
IMP::core::ExcludedVolumeRestraint	IMP::restrainer::SimpleExcludedVolume::get_restraint()
IMP::core::HarmonicUpperBound	IMP::restrainer::SimpleConnectivity::get_harmonic_upper_bound(), IMP::restrainer::SimpleDiameter::get_harmonic_upper_bound(), IMP::restrainer::SimpleDistance::get_harmonic_upper_bound()
IMP::core::Hierarchy	IMP::core::Hierarchy::get_child(), IMP::core::Hierarchy::get_parent(), IMP::core::Hierarchy::decorate_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::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::MonteCarloMover	IMP::core::MonteCarlo::get_mover(), IMP::example::create_serial_mover()
IMP::core::NonRigidMember	IMP::core::NonRigidMember::decorate_particle()
IMP::core::Reference	IMP::core::Reference::decorate_particle(), IMP::core::Reference::setup_particle(), IMP::core::Reference::setup_particle()
IMP::core::RigidBody	IMP::core::RigidBody::decorate_particle(), 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::symmetry::RigidBodyMover::get_rigid_bodies(), IMP::atom::create_compatible_rigid_body(), IMP::atom::create_rigid_body(), IMP::atom::create_rigid_body()
IMP::core::RigidBodyMember	IMP::core::RigidBodyMember::decorate_particle()
IMP::core::RigidMember	IMP::core::RigidMember::decorate_particle()
IMP::core::SphereDistancePairScore	IMP::restrainer::SimpleConnectivity::get_sphere_distance_pair_score()
IMP::core::Typed	IMP::core::Typed::decorate_particle(), IMP::core::Typed::setup_particle(), IMP::core::Typed::setup_particle()
IMP::core::XYZ	IMP::atom::Hierarchy::get_as_xyz(), IMP::core::XYZ::decorate_particle(), IMP::core::XYZ::setup_particle(), IMP::core::XYZ::setup_particle(), IMP::core::XYZ::setup_particle(), IMP::core::XYZ::setup_particle()
IMP::core::XYZR	IMP::atom::Hierarchy::get_as_xyzr(), IMP::core::XYZR::decorate_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::core::XYZR::setup_particle(), IMP::atom::create_cover()

IMP.display

Class	Factories
IMP::display::BoundingBoxGeometry	IMP::display::create_geometry()
IMP::display::Color	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_grey_color(), IMP::display::get_gnuplot_color(), IMP::display::get_display_color(), IMP::display::get_interpolated_rgb()
IMP::display::Colored	IMP::display::Colored::decorate_particle(), 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::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::pad_margin(), IMP::multifit::FFTFitting::crop_margin(), IMP::cnmultifit::build_cn_dens_assembly(), IMP::em::binarize(), IMP::em::create_density_map(), IMP::em::create_density_map(), IMP::em::create_density_map(), IMP::em::create_density_map(), IMP::em::get_binarized_interior(), IMP::em::get_max_map(), IMP::em::get_resampled(), IMP::em::get_segment(), IMP::em::get_segment(), IMP::em::get_segment_by_masking(), IMP::em::get_threshold_map(), IMP::em::get_transformed(), IMP::em::get_transformed(), IMP::em::interpolate_map(), IMP::em::mask_and_norm(), IMP::em::multiply(), IMP::em::read_map(), IMP::em::read_map(), IMP::multifit::create_hit_map(), IMP::multifit::grid2map(), IMP::multifit::remove_background(), IMP::restrainer::load_em_density_map()
IMP::em::FitRestraint	IMP::restrainer::SimpleEMFit::get_restraint()
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::RadiusDependentKernelParameters	IMP::em::KernelParameters::get_params(), IMP::em::KernelParameters::set_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::decorate_particle(), 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::decorate_particle(), IMP::em2d::ProjectionParameters::setup_particle(), IMP::em2d::ProjectionParameters::setup_particle()
IMP::em2d::RegistrationResult	IMP::em2d::Fine2DRegistrationRestraint::get_final_registration()

IMP.example

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

IMP.isd

Class	Factories
IMP::isd::MolecularDynamics	IMP::isd::HybridMonteCarlo::get_md(), IMP::isd::MolecularDynamicsMover::get_md()
IMP::isd::Nuisance	IMP::isd::Nuisance::decorate_particle(), 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::Scale::decorate_particle(), 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::decorate_particle(), 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::decorate_particle(), IMP::isd::Weight::setup_particle(), IMP::isd::Weight::setup_particle()

IMP.kernel

Class	Factories
IMP::kernel::ConfigurationSet	IMP::kernel::Sampler::create_sample(), IMP::kernel::Sampler::get_sample(), IMP::kernel::Sampler::do_sample()
IMP::kernel::DerivativeAccumulator	IMP::kernel::ScoreAccumulator::get_derivative_accumulator()
IMP::kernel::Key	IMP::kernel::Key::operator+(), IMP::kernel::Key::operator++(), IMP::kernel::Key::operator--(), IMP::kernel::Key::add_alias(), IMP::misc::CustomXYZR::get_decorator_traits(), IMP::misc::CustomXYZR::get_default_decorator_traits()
IMP::kernel::Model	IMP::domino::Subset::get_model(), IMP::kernel::ConfigurationSet::get_model(), IMP::kernel::Decorator::get_model(), IMP::kernel::ModelObject::get_model(), IMP::kernel::ParticleAdaptor::get_model(), IMP::kernel::Sampler::get_model(), IMP::multifit::ProteomicsEMAlignmentAtomic::get_model()
IMP::kernel::Optimizer	IMP::kernel::OptimizerState::get_optimizer()
IMP::kernel::OptimizerState	IMP::kernel::Optimizer::get_optimizer_state()
IMP::kernel::Particle	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::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::kernel::Decorator::get_particle(), IMP::kernel::Model::get_particle(), IMP::kernel::Refiner::get_refined(), IMP::kernel::SingletonContainer::get_particle(), IMP::kinematics::KinematicForest::get_parent(), IMP::multifit::RadiusOfGyrationRestraint::get_particle(), IMP::multifit::WeightedExcludedVolumeRestraint::get_particle(), IMP::rmf::HierarchyLoadLink::do_create()
IMP::kernel::Restraint	IMP::core::MinimumRestraint::get_restraint(), IMP::display::RestraintGeometry::get_restraint(), IMP::kernel::Model::get_restraint(), IMP::kernel::Restraint::create_current_decomposition(), IMP::kernel::Restraint::create_decomposition(), IMP::kernel::RestraintSet::get_restraint(), IMP::kernel::RestraintsAdaptor::get(), IMP::kernel::RestraintsAdaptor::get(), 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::kernel::RestraintSet	IMP::display::RestraintSetGeometry::get_restraint_set(), IMP::kernel::Model::get_root_restraint_set()
IMP::kernel::ScoreAccumulator	IMP::kernel::ScoringFunction::get_score_accumulator(), IMP::kernel::ScoringFunction::get_score_accumulator_if_below(), IMP::kernel::ScoringFunction::get_score_accumulator_if_good()
IMP::kernel::ScoreState	IMP::kernel::Model::get_score_state()
IMP::kernel::ScoringFunction	IMP::kernel::Optimizer::get_scoring_function(), IMP::kernel::Restraint::create_scoring_function(), IMP::kernel::Restraint::create_internal_scoring_function(), IMP::kernel::Sampler::get_scoring_function(), IMP::kernel::ScoringFunctionAdaptor::get(), IMP::kernel::ScoringFunctionAdaptor::get(), IMP::kernel::ScoringFunctionAdaptor::get(), IMP::kernel::ScoringFunctionAdaptor::get(), IMP::kernel::ScoringFunctionAdaptor::get()

IMP.kinematics

Class	Factories
IMP::kinematics::DOF	IMP::kinematics::DOFsSampler::get_dof()
IMP::kinematics::DihedralAngleRevoluteJoint	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::decorate_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::KinematicNode::setup_particle()

IMP.misc

Class	Factories
IMP::misc::CustomXYZR	IMP::misc::CustomXYZR::decorate_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::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.restrainer

Class	Factories
IMP::restrainer::SimpleConnectivity	IMP::restrainer::create_simple_connectivity_on_molecules(), IMP::restrainer::create_simple_connectivity_on_rigid_bodies()
IMP::restrainer::SimpleDiameter	IMP::restrainer::create_simple_diameter()
IMP::restrainer::SimpleDistance	IMP::restrainer::create_simple_distance()
IMP::restrainer::SimpleEMFit	IMP::restrainer::create_simple_em_fit(), IMP::restrainer::create_simple_em_fit()
IMP::restrainer::SimpleExcludedVolume	IMP::restrainer::create_simple_excluded_volume_on_molecules(), IMP::restrainer::create_simple_excluded_volume_on_rigid_bodies()

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::FormFactorTable	IMP::saxs::default_form_factor_table()

IMP.statistics

Class	Factories
IMP::statistics::Histogram	IMP::cnmultifit::my_get_density_histogram(), IMP::multifit::get_density_histogram()
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::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()