Argument Index

Table of Contents

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

Overview

Functions that take objects of a given type as arguments:

See also Factory Index, Argument Index, Class Examples, Function Examples

IMP.algebra

Class	Users
IMP::algebra::BoundingBoxD	IMP::algebra::BoundingBoxD::get_contains(), IMP::algebra::BoundingBoxD::operator+(), IMP::algebra::BoundingBoxD::operator+=(), IMP::algebra::DefaultEmbeddingD::initialize_from_box(), IMP::algebra::GridD::voxels_begin(), IMP::algebra::GridD::voxels_end(), IMP::algebra::GridD::voxels_begin(), IMP::algebra::GridD::voxels_end(), IMP::algebra::GridD::indexes_begin(), IMP::algebra::GridD::indexes_end(), IMP::algebra::GridD::extended_indexes_begin(), IMP::algebra::GridD::extended_indexes_end(), IMP::algebra::GridD::get_indexes(), IMP::algebra::GridD::get_extended_indexes(), IMP::algebra::GridD::GridD(), IMP::algebra::GridD::GridD(), IMP::algebra::GridD::GridD(), IMP::algebra::GridD::set_bounding_box(), IMP::algebra::LogEmbeddingD::initialize_from_box(), IMP::algebra::LogEmbeddingD::LogEmbeddingD(), IMP::core::GenericBoundingBox3DSingletonScore::GenericBoundingBox3DSingletonScore(), IMP::core::MCCGSampler::set_bounding_box(), IMP::display::BoundingBoxGeometry::BoundingBoxGeometry(), IMP::display::BoundingBoxGeometry::BoundingBoxGeometry(), IMP::display::BoundingBoxGeometry::BoundingBoxGeometry(), IMP::display::BoundingBoxGeometry::BoundingBoxGeometry(), IMP::display::BoundingBoxGeometry::set_geometry(), IMP::example::ExampleSingletonModifier::ExampleSingletonModifier(), IMP::statistics::HistogramD::HistogramD(), IMP::algebra::get_random_vector_in(), IMP::algebra::get_random_vector_on(), IMP::algebra::get_grid_interior_cover_by_spacing(), IMP::algebra::get_edges(), IMP::algebra::get_interiors_intersect(), IMP::algebra::get_intersection(), IMP::algebra::get_maximum_length(), IMP::algebra::get_transformed(), IMP::algebra::get_union(), IMP::algebra::get_vertices(), IMP::algebra::get_volume(), IMP::core::create_bounding_box_3d_singleton_score(), IMP::display::create_geometry(), IMP::em::create_density_header()
IMP::algebra::Cone3D	IMP::algebra::Cone3D::get_bounding_box(), IMP::algebra::Cone3D::get_cone_3d_geometry(), IMP::algebra::Cone3D::get_surface_area(), IMP::algebra::Cone3D::get_volume(), IMP::algebra::Cone3D::set_cone_3d_geometry(), IMP::algebra::get_uniform_surface_cover()
IMP::algebra::Cylinder3D	IMP::algebra::Cylinder3D::get_bounding_box(), IMP::algebra::Cylinder3D::get_cylinder_3d_geometry(), IMP::algebra::Cylinder3D::get_surface_area(), IMP::algebra::Cylinder3D::get_volume(), IMP::algebra::Cylinder3D::set_cylinder_3d_geometry(), IMP::display::CylinderGeometry::CylinderGeometry(), IMP::display::CylinderGeometry::CylinderGeometry(), IMP::display::CylinderGeometry::CylinderGeometry(), IMP::display::CylinderGeometry::CylinderGeometry(), IMP::display::CylinderGeometry::set_geometry(), IMP::algebra::get_random_vector_in(), IMP::algebra::get_uniform_surface_cover(), IMP::algebra::get_grid_surface_cover(), IMP::display::create_geometry()
IMP::algebra::DenseGridStorageD	IMP::algebra::DenseGridStorageD::copy_from(), IMP::algebra::DenseGridStorageD::DenseGridStorageD(), IMP::algebra::DenseGridStorageD::operator=(), IMP::em::create_density_map()
IMP::algebra::Ellipsoid3D	IMP::algebra::Ellipsoid3D::get_bounding_box(), IMP::algebra::Ellipsoid3D::get_ellipsoid_3d_geometry(), IMP::algebra::Ellipsoid3D::get_surface_area(), IMP::algebra::Ellipsoid3D::get_volume(), IMP::algebra::Ellipsoid3D::set_ellipsoid_3d_geometry(), IMP::display::EllipsoidGeometry::EllipsoidGeometry(), IMP::display::EllipsoidGeometry::EllipsoidGeometry(), IMP::display::EllipsoidGeometry::EllipsoidGeometry(), IMP::display::EllipsoidGeometry::EllipsoidGeometry(), IMP::display::EllipsoidGeometry::set_geometry(), IMP::display::create_geometry()
IMP::algebra::ExtendedGridIndexD	IMP::algebra::BoundedGridRangeD::indexes_begin(), IMP::algebra::BoundedGridRangeD::indexes_end(), IMP::algebra::BoundedGridRangeD::extended_indexes_begin(), IMP::algebra::BoundedGridRangeD::extended_indexes_end(), IMP::algebra::BoundedGridRangeD::get_indexes(), IMP::algebra::BoundedGridRangeD::get_extended_indexes(), IMP::algebra::BoundedGridRangeD::get_has_index(), IMP::algebra::BoundedGridRangeD::get_index(), IMP::algebra::DefaultEmbeddingD::get_center(), IMP::algebra::DefaultEmbeddingD::get_bounding_box(), IMP::algebra::ExtendedGridIndexD::compare(), IMP::algebra::ExtendedGridIndexD::IMP_COMPARISONS(), IMP::algebra::ExtendedGridIndexD::IMP_HASHABLE_INLINE(), IMP::algebra::LogEmbeddingD::get_center(), IMP::algebra::LogEmbeddingD::get_bounding_box(), IMP::algebra::SparseGridStorageD::indexes_begin(), IMP::algebra::SparseGridStorageD::indexes_end(), IMP::algebra::SparseGridStorageD::get_indexes(), IMP::algebra::SparseGridStorageD::add_voxel(), IMP::algebra::SparseGridStorageD::get_has_index(), IMP::algebra::SparseGridStorageD::get_index(), IMP::algebra::UnboundedGridRangeD::extended_indexes_begin(), IMP::algebra::UnboundedGridRangeD::extended_indexes_end(), IMP::algebra::UnboundedGridRangeD::get_extended_indexes(), IMP::algebra::UnboundedGridRangeD::get_has_index()
IMP::algebra::Gaussian3D	IMP::core::Gaussian::do_setup_particle(), IMP::core::Gaussian::setup_particle(), IMP::core::Gaussian::setup_particle(), IMP::algebra::get_covariance()
IMP::algebra::GridD	IMP::display::IsosurfaceGeometry::IsosurfaceGeometry(), IMP::algebra::get_bounding_box(), IMP::algebra::get_linearly_interpolated(), IMP::algebra::get_trilinearly_interpolated(), IMP::em::create_density_map(), IMP::em::create_density_map()
IMP::algebra::GridIndexD	IMP::algebra::DefaultEmbeddingD::get_center(), IMP::algebra::DefaultEmbeddingD::get_bounding_box(), IMP::algebra::DenseGridStorageD::at(), IMP::algebra::DenseGridStorageD::at(), IMP::algebra::DenseGridStorageD::operator[](), IMP::algebra::DenseGridStorageD::operator[](), IMP::algebra::GridD::get_extended_index(), IMP::algebra::GridIndexD::compare(), IMP::algebra::GridIndexD::IMP_COMPARISONS(), IMP::algebra::GridIndexD::IMP_HASHABLE_INLINE(), IMP::algebra::LogEmbeddingD::get_center(), IMP::algebra::LogEmbeddingD::get_bounding_box(), IMP::algebra::SparseGridStorageD::at(), IMP::algebra::SparseGridStorageD::at(), IMP::algebra::SparseGridStorageD::operator[](), IMP::algebra::SparseGridStorageD::operator[](), IMP::algebra::SparseGridStorageD::remove_voxel()
IMP::algebra::Plane3D	IMP::algebra::Plane3D::get_area(), IMP::algebra::Plane3D::get_bounding_box(), IMP::algebra::Plane3D::get_plane_3d_geometry(), IMP::algebra::Plane3D::set_plane_3d_geometry(), IMP::algebra::Reflection3D::Reflection3D(), IMP::algebra::SpherePatch3D::SpherePatch3D(), IMP::display::FilterGeometry::FilterGeometry(), IMP::display::PlaneGeometry::PlaneGeometry(), IMP::algebra::get_distance(), IMP::algebra::get_reflected()
IMP::algebra::PrincipalComponentAnalysisD	IMP::algebra::PrincipalComponentAnalysisD::compare(), IMP::algebra::get_alignments_from_first_to_second(), IMP::multifit::write_markers()
IMP::algebra::ReferenceFrame3D	IMP::algebra::Ellipsoid3D::Ellipsoid3D(), IMP::algebra::Gaussian3D::Gaussian3D(), IMP::algebra::ReferenceFrame3D::get_global_reference_frame(), IMP::algebra::ReferenceFrame3D::get_local_reference_frame(), IMP::core::RigidBody::add_member_internal(), IMP::core::RigidBody::do_setup_particle(), IMP::core::RigidBody::set_reference_frame(), IMP::core::RigidBody::set_reference_frame_lazy(), IMP::core::RigidBody::setup_particle(), IMP::core::RigidBody::setup_particle(), IMP::display::ReferenceFrameGeometry::ReferenceFrameGeometry(), IMP::display::ReferenceFrameGeometry::ReferenceFrameGeometry(), IMP::display::ReferenceFrameGeometry::ReferenceFrameGeometry(), IMP::display::ReferenceFrameGeometry::ReferenceFrameGeometry(), IMP::display::ReferenceFrameGeometry::set_geometry(), IMP::kinematics::KinematicForest::set_reference_frame_safe(), IMP::algebra::get_transformation_from_first_to_second(), IMP::algebra::get_transformed(), IMP::display::create_geometry()
IMP::algebra::Reflection3D	IMP::core::TransformationAndReflectionSymmetry::TransformationAndReflectionSymmetry()
IMP::algebra::Rotation2D	IMP::algebra::Transformation2D::Transformation2D(), IMP::algebra::compose(), IMP::algebra::get_rotation_about_point()
IMP::algebra::Rotation3D	IMP::algebra::Ellipsoid3D::Ellipsoid3D(), IMP::algebra::Rotation3D::operator*(), IMP::algebra::Rotation3D::operator/(), IMP::algebra::Rotation3D::operator/=(), IMP::algebra::Transformation3D::Transformation3D(), IMP::em2d::ProjectionParameters::set_rotation(), IMP::em2d::RegistrationResult::RegistrationResult(), IMP::em2d::RegistrationResult::set_rotation(), IMP::algebra::get_fixed_xyz_from_rotation(), IMP::algebra::compose(), IMP::algebra::get_axis_and_angle(), IMP::algebra::get_distance(), IMP::algebra::get_interpolated(), IMP::algebra::get_random_rotation_3d(), IMP::algebra::get_rotation_about_point(), IMP::em2d::do_project_particles(), IMP::em2d::do_project_vectors(), IMP::em2d::do_project_vectors(), IMP::em2d::get_unique_index()
IMP::algebra::Segment3D	IMP::algebra::Cone3D::Cone3D(), IMP::algebra::Cylinder3D::Cylinder3D(), IMP::algebra::Segment3D::get_bounding_box(), IMP::algebra::Segment3D::get_segment_3d_geometry(), IMP::display::SegmentGeometry::SegmentGeometry(), IMP::display::SegmentGeometry::SegmentGeometry(), IMP::display::SegmentGeometry::SegmentGeometry(), IMP::display::SegmentGeometry::SegmentGeometry(), IMP::display::SegmentGeometry::set_geometry(), IMP::algebra::get_shortest_segment(), IMP::algebra::get_shortest_segment(), IMP::algebra::get_distance(), IMP::algebra::get_distance(), IMP::algebra::get_relative_projection_on_segment(), IMP::algebra::set_segment_3d_geometry(), IMP::display::create_geometry()
IMP::algebra::SphereD	IMP::algebra::SphereD::get_contains(), IMP::algebra::get_random_vector_in(), IMP::algebra::get_random_vector_in(), IMP::algebra::get_random_vector_on(), IMP::algebra::get_uniform_surface_cover(), IMP::algebra::get_uniform_upper_hemisphere_cover(), IMP::algebra::get_distance(), IMP::algebra::get_interiors_intersect(), IMP::algebra::get_power_distance(), IMP::algebra::get_vector_geometry()
IMP::algebra::SpherePatch3D	IMP::algebra::SpherePatch3D::get_area(), IMP::algebra::SpherePatch3D::get_bounding_box(), IMP::algebra::SpherePatch3D::get_sphere_patch_3d_geometry(), IMP::algebra::SpherePatch3D::set_sphere_patch_3d_geometry(), IMP::algebra::get_uniform_surface_cover()
IMP::algebra::Transformation2D	IMP::algebra::Transformation2D::operator*(), IMP::algebra::Transformation2D::operator*=(), IMP::algebra::Transformation2D::operator/(), IMP::algebra::Transformation2D::operator/=(), IMP::em2d::RegistrationResult::add_in_plane_transformation(), IMP::algebra::compose(), IMP::algebra::get_transformation_3d(), IMP::em2d::get_transformed()
IMP::algebra::Transformation3D	IMP::algebra::ReferenceFrame3D::ReferenceFrame3D(), IMP::algebra::Transformation3D::operator*(), IMP::algebra::Transformation3D::operator*=(), IMP::algebra::Transformation3D::operator/(), IMP::algebra::Transformation3D::operator/=(), IMP::core::RigidBodyMember::set_internal_transformation(), IMP::core::Transform::Transform(), IMP::core::TransformationAndReflectionSymmetry::TransformationAndReflectionSymmetry(), IMP::core::TransformationSymmetry::TransformationSymmetry(), IMP::core::TransformedDistancePairScore::TransformedDistancePairScore(), IMP::core::TransformedDistancePairScore::set_transformation(), IMP::em::EnvelopeScore::is_penetrating(), IMP::em::EnvelopeScore::score(), IMP::em::FittingSolutions::add_solution(), IMP::em::FittingSolutions::multiply(), IMP::kinematics::Joint::set_transformation_child_to_parent_no_checks(), IMP::kinematics::TransformationJoint::set_transformation_child_to_parent(), IMP::multifit::FittingSolutionRecord::set_dock_transformation(), IMP::multifit::FittingSolutionRecord::set_fit_transformation(), IMP::algebra::compose(), IMP::algebra::get_rmsd_transforming_first(), IMP::algebra::get_transformed(), IMP::algebra::get_transformed(), IMP::algebra::get_weighted_rmsd_transforming_first(), IMP::atom::get_rmsd(), IMP::atom::get_rmsd(), IMP::atom::get_rmsd(), IMP::atom::get_rmsd(), IMP::atom::get_rmsd_transforming_first(), IMP::atom::get_rmsd_transforming_first(), IMP::atom::transform(), IMP::cnmultifit::build_cn_dens_assembly(), IMP::cnmultifit::transform_cn_assembly(), IMP::core::transform(), IMP::core::transform(), IMP::em::get_number_of_particles_outside_of_the_density(), IMP::em::get_percentage_of_voxels_covered_by_particles(), IMP::em::get_transformed(), IMP::em::get_transformed(), IMP::em::get_transformed_into(), IMP::em::get_transformed_into2()
IMP::algebra::Triangle3D	IMP::display::TriangleGeometry::TriangleGeometry(), IMP::display::TriangleGeometry::TriangleGeometry(), IMP::display::TriangleGeometry::TriangleGeometry(), IMP::display::TriangleGeometry::TriangleGeometry(), IMP::display::TriangleGeometry::set_geometry(), IMP::algebra::get_transformation_from_first_triangle_to_second(), IMP::display::create_geometry()
IMP::algebra::VectorBaseD	IMP::algebra::VectorBaseD::check_compatible_vector(), IMP::algebra::VectorBaseD::get_scalar_product()
IMP::algebra::VectorD	IMP::algebra::BoundingBoxD::BoundingBoxD(), IMP::algebra::BoundingBoxD::BoundingBoxD(), IMP::algebra::BoundingBoxD::BoundingBoxD(), IMP::algebra::BoundingBoxD::get_contains(), IMP::algebra::BoundingBoxD::operator+=(), IMP::algebra::DefaultEmbeddingD::get_elementwise_product(), IMP::algebra::DefaultEmbeddingD::DefaultEmbeddingD(), IMP::algebra::DefaultEmbeddingD::get_extended_index(), IMP::algebra::DefaultEmbeddingD::get_index(), IMP::algebra::DefaultEmbeddingD::set_origin(), IMP::algebra::DefaultEmbeddingD::set_unit_cell(), IMP::algebra::GridD::get_nearest_index(), IMP::algebra::GridD::get_nearest_extended_index(), IMP::algebra::GridD::GridD(), IMP::algebra::GridD::GridD(), IMP::algebra::GridD::GridD(), IMP::algebra::GridD::add_voxel(), IMP::algebra::GridD::at(), IMP::algebra::GridD::at(), IMP::algebra::GridD::operator[](), IMP::algebra::GridD::operator[](), IMP::algebra::LogEmbeddingD::LogEmbeddingD(), IMP::algebra::LogEmbeddingD::LogEmbeddingD(), IMP::algebra::LogEmbeddingD::LogEmbeddingD(), IMP::algebra::LogEmbeddingD::get_extended_index(), IMP::algebra::LogEmbeddingD::get_index(), IMP::algebra::LogEmbeddingD::set_origin(), IMP::algebra::LogEmbeddingD::set_unit_cell(), IMP::algebra::LogEmbeddingD::set_unit_cell(), IMP::algebra::NearestNeighborD::NearestNeighborD(), IMP::algebra::NearestNeighborD::get_in_ball(), IMP::algebra::NearestNeighborD::get_nearest_neighbor(), IMP::algebra::NearestNeighborD::get_nearest_neighbors(), IMP::algebra::PrincipalComponentAnalysisD::PrincipalComponentAnalysisD(), IMP::algebra::PrincipalComponentAnalysisD::set_centroid(), IMP::algebra::Rotation3D::Rotation3D(), IMP::algebra::SphereD::SphereD(), IMP::algebra::SphereD::get_contains(), IMP::algebra::VectorD::VectorD(), IMP::algebra::VectorD::operator*(), IMP::algebra::VectorD::operator+(), IMP::algebra::VectorD::operator+=(), IMP::algebra::VectorD::operator-(), IMP::algebra::VectorD::operator-=(), IMP::example::ExampleTemplateClassD::ExampleTemplateClassD(), IMP::multifit::GeometricHash::GeometricHash(), IMP::multifit::GeometricHash::add(), IMP::multifit::GeometricHash::bucket(), IMP::multifit::GeometricHash::neighbors(), IMP::multifit::GeometricHash::neighbors(), IMP::multifit::GeometricHash::neighbors(), IMP::multifit::GeometricHash::neighbors(), IMP::multifit::GeometricHash::neighbors_data(), IMP::multifit::GeometricHash::cube_inside_sphere_rec(), IMP::multifit::GeometricHash::to_bucket(), IMP::multifit::GeometricHash::inf_distance(), IMP::statistics::HistogramD::add(), IMP::statistics::HistogramD::get_standard_deviation(), IMP::algebra::get_l2_norm(), IMP::algebra::get_l1_norm(), IMP::algebra::get_linf_norm(), IMP::algebra::compare(), IMP::algebra::get_distance(), IMP::algebra::get_elementwise_product(), IMP::algebra::get_elementwise_product(), IMP::algebra::get_linearly_interpolated(), IMP::algebra::get_principal_components(), IMP::algebra::get_rotation_from_vector4d(), IMP::algebra::get_squared_distance(), IMP::algebra::operator*()

IMP.atom

Class	Users
IMP::atom::Atom	IMP::atom::Atom::do_setup_particle(), IMP::atom::Atom::setup_particle(), IMP::atom::Atom::setup_particle(), IMP::atom::CHARMMParameters::get_force_field_atom_type(), IMP::atom::ForceFieldParameters::get_epsilon(), IMP::atom::ForceFieldParameters::get_radius(), IMP::atom::ForceFieldParameters::get_force_field_atom_type(), IMP::score_functor::OrientedSoap::score_doublets(), IMP::atom::get_residue()
IMP::atom::AtomType	IMP::atom::Atom::do_setup_particle(), IMP::atom::Atom::set_atom_type(), IMP::atom::Atom::setup_particle(), IMP::atom::Atom::setup_particle(), IMP::atom::CHARMMResidueTopologyBase::get_atom(), IMP::atom::ForceFieldParameters::Bond::Bond(), IMP::atom::Selection::Selection(), IMP::atom::Selection::set_atom_type(), IMP::rotamer::ResidueRotamer::get_atom_exists(), IMP::rotamer::ResidueRotamer::get_coordinates(), IMP::rotamer::ResidueRotamer::get_number_of_cases(), IMP::rotamer::ResidueRotamer::add_coordinates(), IMP::rotamer::ResidueRotamer::get_coordinates(), IMP::saxs::FormFactorTable::get_carbon_atom_type(), IMP::saxs::FormFactorTable::get_nitrogen_atom_type(), IMP::saxs::FormFactorTable::get_oxygen_atom_type(), IMP::saxs::FormFactorTable::get_sulfur_atom_type(), IMP::atom::get_atom(), IMP::atom::get_element_for_atom_type()
IMP::atom::Bond	IMP::atom::BondGeometry::BondGeometry(), IMP::atom::create_bond(), IMP::atom::destroy_bond()
IMP::atom::Bonded	IMP::atom::create_bond(), IMP::atom::create_bond(), IMP::atom::create_custom_bond(), IMP::atom::get_bond()
IMP::atom::BrownianDynamics	IMP::atom::get_maximum_time_step_estimate()
IMP::atom::CHARMMAtomTopology	IMP::atom::CHARMMAtomTopology::CHARMMAtomTopology(), IMP::atom::CHARMMResidueTopologyBase::add_atom()
IMP::atom::CHARMMBondEndpoint	IMP::atom::CHARMMConnection::CHARMMConnection(), IMP::atom::CHARMMInternalCoordinate::CHARMMInternalCoordinate()
IMP::atom::CHARMMConnection	IMP::atom::CHARMMResidueTopologyBase::add_angle(), IMP::atom::CHARMMResidueTopologyBase::add_bond(), IMP::atom::CHARMMResidueTopologyBase::add_dihedral(), IMP::atom::CHARMMResidueTopologyBase::add_improper()
IMP::atom::CHARMMIdealResidueTopology	IMP::atom::CHARMMParameters::add_residue_topology(), IMP::atom::CHARMMResidueTopology::CHARMMResidueTopology()
IMP::atom::CHARMMInternalCoordinate	IMP::atom::CHARMMResidueTopologyBase::add_internal_coordinate()
IMP::atom::CHARMMParameters	IMP::atom::CHARMMSegmentTopology::apply_default_patches(), IMP::atom::CHARMMTopology::CHARMMTopology()
IMP::atom::CHARMMPatch	IMP::atom::CHARMMParameters::add_patch()
IMP::atom::CHARMMResidueTopology	IMP::atom::CHARMMBondEndpoint::CHARMMBondEndpoint(), IMP::atom::CHARMMBondEndpoint::get_atom(), IMP::atom::CHARMMConnection::get_atoms(), IMP::atom::CHARMMPatch::apply(), IMP::atom::CHARMMPatch::apply(), IMP::atom::CHARMMSegmentTopology::remove_residue(), IMP::atom::CHARMMSegmentTopology::add_residue()
IMP::atom::CHARMMResidueTopologyBase	IMP::atom::CHARMMParameters::parse_atom_line(), IMP::atom::CHARMMParameters::parse_bond_line()
IMP::atom::CHARMMSegmentTopology	IMP::atom::CHARMMTopology::remove_segment(), IMP::atom::CHARMMTopology::add_segment()
IMP::atom::CHARMMTopology	IMP::atom::CHARMMStereochemistryRestraint::CHARMMStereochemistryRestraint(), IMP::atom::CHARMMStereochemistryRestraint::CHARMMStereochemistryRestraint()
IMP::atom::Chain	IMP::atom::Chain::do_setup_particle(), IMP::atom::Chain::setup_particle(), IMP::atom::Chain::setup_particle(), IMP::atom::create_simplified_along_backbone()
IMP::atom::Domain	IMP::atom::Domain::do_setup_particle(), IMP::atom::Domain::setup_particle(), IMP::atom::Domain::setup_particle()
IMP::atom::ForceFieldParameters	IMP::atom::add_bonds(), IMP::atom::add_radii()
IMP::atom::Fragment	IMP::atom::Fragment::do_setup_particle(), IMP::atom::Fragment::setup_particle(), IMP::atom::Fragment::setup_particle()
IMP::atom::Hierarchy	IMP::atom::BondGraph::BondGraph(), IMP::atom::CHARMMBondEndpoint::get_atom(), IMP::atom::CHARMMConnection::get_atoms(), IMP::atom::CHARMMParameters::create_topology(), IMP::atom::CHARMMStereochemistryRestraint::CHARMMStereochemistryRestraint(), IMP::atom::CHARMMStereochemistryRestraint::CHARMMStereochemistryRestraint(), IMP::atom::CHARMMTopology::map_residue_topology_to_hierarchy(), IMP::atom::CHARMMTopology::add_atom_types(), IMP::atom::CHARMMTopology::add_bonds(), IMP::atom::CHARMMTopology::add_charges(), IMP::atom::CHARMMTopology::add_coordinates(), IMP::atom::CHARMMTopology::add_dihedrals(), IMP::atom::CHARMMTopology::add_impropers(), IMP::atom::CHARMMTopology::add_missing_atoms(), IMP::atom::CHARMMTopology::setup_hierarchy(), IMP::atom::ForceFieldParameters::add_bonds(), IMP::atom::ForceFieldParameters::add_radii(), IMP::atom::ForceFieldParameters::add_well_depths(), IMP::atom::Hierarchy::add_child(), IMP::atom::ProteinLigandRestraint::initialize(), IMP::atom::ProteinLigandRestraint::ProteinLigandRestraint(), IMP::atom::ProteinLigandRestraint::ProteinLigandRestraint(), IMP::atom::Selection::Selection(), IMP::atom::Selection::Selection(), IMP::kinematics::KinematicForest::KinematicForest(), IMP::kinematics::ProteinKinematics::ProteinKinematics(), IMP::kinematics::ProteinKinematics::ProteinKinematics(), IMP::multifit::Ensemble::add_component_and_fits(), IMP::multifit::FFTFitting::do_global_fitting(), IMP::multifit::FFTFitting::do_local_fitting(), IMP::multifit::FFTFitting::prepare_probe(), IMP::multifit::MergeTreeBuilder::increase_edge(), IMP::rotamer::RotamerCalculator::transform(), IMP::atom::add_dope_score_data(), IMP::atom::create_simplified_along_backbone(), IMP::atom::get_residue_indexes(), IMP::atom::get_residue_type(), IMP::atom::get_chain_id_char(), IMP::atom::get_atom_type(), IMP::atom::get_domain_name(), IMP::atom::write_mol2(), IMP::atom::read_pdb(), IMP::atom::add_protein_ligand_score_data(), IMP::atom::show_molecular_hierarchy(), IMP::atom::add_bonds(), IMP::atom::add_radii(), IMP::atom::create_clone(), IMP::atom::create_clone_one(), IMP::atom::create_compatible_rigid_body(), IMP::atom::create_rigid_body(), IMP::atom::create_simplified_assembly_from_volume(), IMP::atom::create_simplified_from_volume(), IMP::atom::destroy(), IMP::atom::get_bounding_box(), IMP::atom::get_bounding_sphere(), IMP::atom::get_by_type(), IMP::atom::get_chain(), IMP::atom::get_chain_id(), IMP::atom::get_charmm_untyped_atoms(), IMP::atom::get_copy_index(), IMP::atom::get_hierarchy_tree(), IMP::atom::get_internal_bonds(), IMP::atom::get_is_heterogen(), IMP::atom::get_leaves(), IMP::atom::get_molecule_name(), IMP::atom::get_residue(), IMP::atom::get_resolution(), IMP::atom::get_root(), IMP::atom::get_state_index(), IMP::atom::remove_charmm_untyped_atoms(), IMP::atom::setup_as_approximation(), IMP::atom::show(), IMP::atom::transform(), IMP::multifit::create_coarse_molecule_from_molecule(), IMP::multifit::fft_based_rigid_fitting(), IMP::multifit::get_close_to_point(), IMP::multifit::get_points_close_to_molecule(), IMP::multifit::get_points_far_from_molecule(), IMP::multifit::molecule2anchors(), IMP::rmf::add_hierarchy()
IMP::atom::LennardJones	IMP::atom::LennardJonesPairScore::get_factors()
IMP::atom::Mol2Selector	IMP::atom::read_mol2()
IMP::atom::Molecule	IMP::atom::Molecule::do_setup_particle(), IMP::atom::Molecule::setup_particle(), IMP::atom::Molecule::setup_particle()
IMP::atom::PDBSelector	IMP::atom::AndPDBSelector::AndPDBSelector(), IMP::atom::NotPDBSelector::NotPDBSelector(), IMP::atom::OrPDBSelector::OrPDBSelector(), IMP::atom::read_pdb(), IMP::atom::read_multimodel_pdb()
IMP::atom::Residue	IMP::atom::ForceFieldParameters::add_bonds(), IMP::atom::ForceFieldParameters::add_bonds(), IMP::atom::Residue::do_setup_particle(), IMP::atom::Residue::setup_particle(), IMP::atom::Residue::setup_particle(), IMP::kinematics::ProteinKinematics::get_phi(), IMP::kinematics::ProteinKinematics::get_psi(), IMP::kinematics::ProteinKinematics::set_phi(), IMP::kinematics::ProteinKinematics::set_psi(), IMP::kinematics::ProteinKinematics::add_dihedral_joint(), IMP::kinematics::ProteinKinematics::add_dihedral_joints(), IMP::kinematics::ProteinKinematics::get_phi_joint(), IMP::kinematics::ProteinKinematics::get_psi_joint(), IMP::rotamer::ResidueRotamer::set_coordinates(), IMP::rotamer::RotamerCalculator::get_rotamer(), IMP::atom::get_atom(), IMP::atom::get_next_residue(), IMP::atom::get_phi_dihedral_atoms(), IMP::atom::get_previous_residue(), IMP::atom::get_psi_dihedral_atoms()
IMP::atom::ResidueType	IMP::atom::CHARMMIdealResidueTopology::CHARMMIdealResidueTopology(), IMP::atom::CHARMMParameters::get_residue_topology(), IMP::atom::CHARMMParameters::parse_atom_line(), IMP::atom::CHARMMParameters::parse_bond_line(), IMP::atom::CHARMMResidueTopology::CHARMMResidueTopology(), IMP::atom::Residue::do_setup_particle(), IMP::atom::Residue::set_residue_type(), 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::Selection::Selection(), IMP::atom::Selection::set_residue_type(), IMP::rotamer::ResidueRotamer::ResidueRotamer(), IMP::rotamer::RotamerLibrary::get_rotamers(), IMP::rotamer::RotamerLibrary::get_rotamers_fast(), IMP::saxs::FormFactorTable::get_carbon_atom_type(), IMP::saxs::FormFactorTable::get_dummy_form_factor(), IMP::saxs::FormFactorTable::get_form_factor(), IMP::saxs::FormFactorTable::get_nitrogen_atom_type(), IMP::saxs::FormFactorTable::get_oxygen_atom_type(), IMP::saxs::FormFactorTable::get_sulfur_atom_type(), IMP::saxs::FormFactorTable::get_vacuum_form_factor(), IMP::atom::get_volume_from_residue_type(), IMP::atom::get_mass(), IMP::atom::get_one_letter_code()
IMP::atom::SecondaryStructureResidue	IMP::atom::get_secondary_structure_match_score()
IMP::atom::Selection	IMP::atom::Selection::set_difference(), IMP::atom::Selection::set_intersection(), IMP::atom::Selection::set_symmetric_difference(), IMP::atom::Selection::set_union(), IMP::atom::SelectionGeometry::SelectionGeometry(), IMP::atom::write_pdb(), IMP::atom::write_pdb_of_c_alphas(), IMP::atom::create_cover(), IMP::atom::create_distance_restraint(), IMP::atom::create_internal_connectivity_restraint(), IMP::atom::create_internal_connectivity_restraint(), IMP::atom::get_leaves(), IMP::atom::get_mass(), IMP::atom::get_radius_of_gyration(), IMP::atom::get_rmsd(), IMP::atom::get_rmsd(), IMP::atom::get_rmsd_transforming_first(), IMP::atom::get_surface_area(), IMP::atom::get_volume()
IMP::atom::Simulator	IMP::rmf::SaveOptimizerState::set_simulator()
IMP::atom::SmoothingFunction	IMP::atom::CoulombPairScore::CoulombPairScore(), IMP::atom::LennardJonesPairScore::LennardJonesPairScore()

IMP.base

Class	Users
IMP::base::Array	IMP::atom::BondedPairFilter::get_value_index(), IMP::atom::CoulombPairScore::evaluate_index(), IMP::atom::LennardJonesPairScore::evaluate_index(), IMP::atom::SameResiduePairFilter::get_value_index(), IMP::atom::SoapPairFilter::get_value_index(), IMP::atom::StereochemistryPairFilter::get_value_index(), IMP::base::Array::compare(), IMP::container::ConsecutivePairContainer::get_contains(), IMP::container::ConsecutivePairFilter::get_value_index(), IMP::container::ExclusiveConsecutivePairContainer::get_contains(), IMP::container::ExclusiveConsecutivePairFilter::get_value_index(), IMP::container::InContainerPairFilter::get_value_index(), IMP::container::InContainerQuadFilter::get_value_index(), IMP::container::InContainerTripletFilter::get_value_index(), IMP::container::MinimumPairScore::do_create_current_decomposition(), IMP::container::MinimumPairScore::evaluate_index(), IMP::container::MinimumQuadScore::do_create_current_decomposition(), IMP::container::MinimumQuadScore::evaluate_index(), IMP::container::MinimumTripletScore::do_create_current_decomposition(), IMP::container::MinimumTripletScore::evaluate_index(), IMP::core::AllSamePairPredicate::get_value_index(), IMP::core::AllSameQuadPredicate::get_value_index(), IMP::core::AllSameTripletPredicate::get_value_index(), IMP::core::AngleTripletScore::evaluate_index(), IMP::core::ClosePairsPairScore::get_close_pairs(), IMP::core::ClosePairsPairScore::create_current_decomposition(), IMP::core::ClosePairsPairScore::evaluate_if_good_index(), IMP::core::ClosePairsPairScore::evaluate_index(), IMP::core::CoinFlipPairPredicate::get_value_index(), IMP::core::CoinFlipQuadPredicate::get_value_index(), IMP::core::CoinFlipTripletPredicate::get_value_index(), IMP::core::ConstantPairPredicate::get_value_index(), IMP::core::ConstantQuadPredicate::get_value_index(), IMP::core::ConstantTripletPredicate::get_value_index(), IMP::core::DistancePairScore::evaluate_index(), IMP::core::HarmonicDistancePairScore::evaluate_index(), IMP::core::HarmonicSphereDistancePairScore::evaluate_index(), IMP::core::HarmonicUpperBoundSphereDiameterPairScore::evaluate_index(), IMP::core::HarmonicUpperBoundSphereDistancePairScore::evaluate_index(), IMP::core::IsCollisionPairPredicate::get_value_index(), IMP::core::KClosePairsPairScore::get_close_pairs(), IMP::core::KClosePairsPairScore::create_current_decomposition(), IMP::core::KClosePairsPairScore::evaluate_if_good_index(), IMP::core::KClosePairsPairScore::evaluate_index(), IMP::core::NormalizedSphereDistancePairScore::evaluate_index(), IMP::core::OrderedTypePairPredicate::get_value_index(), IMP::core::OrderedTypeQuadPredicate::get_value_index(), IMP::core::OrderedTypeTripletPredicate::get_value_index(), IMP::core::PairConstraint::PairConstraint(), IMP::core::PairRestraint::PairRestraint(), IMP::core::QuadConstraint::QuadConstraint(), IMP::core::QuadRestraint::QuadRestraint(), IMP::core::RefinedPairsPairScore::evaluate_index(), IMP::core::SoftSpherePairScore::evaluate_index(), IMP::core::SphereDistancePairScore::evaluate_index(), IMP::core::TransformedDistancePairScore::evaluate_index(), IMP::core::TripletConstraint::TripletConstraint(), IMP::core::TripletRestraint::TripletRestraint(), IMP::core::TypedPairScore::evaluate_index(), IMP::core::UnorderedTypePairPredicate::get_value_index(), IMP::core::UnorderedTypeQuadPredicate::get_value_index(), IMP::core::UnorderedTypeTripletPredicate::get_value_index(), IMP::core::WeightedSphereDistancePairScore::evaluate_index(), IMP::example::ExamplePairScore::evaluate_index(), IMP::isd::CrossLinkMSRestraint::add_contribution(), IMP::isd::RepulsiveDistancePairScore::evaluate_index(), IMP::kernel::PairModifier::apply_index(), IMP::kernel::PairPredicate::get_value_index(), IMP::kernel::PairPredicate::operator()(), IMP::kernel::PairScore::create_current_decomposition(), IMP::kernel::PairScore::evaluate_if_good_index(), IMP::kernel::PairScore::evaluate_index(), IMP::kernel::PairScore::do_create_current_decomposition(), IMP::kernel::QuadModifier::apply_index(), IMP::kernel::QuadPredicate::get_value_index(), IMP::kernel::QuadPredicate::operator()(), IMP::kernel::QuadScore::create_current_decomposition(), IMP::kernel::QuadScore::evaluate_if_good_index(), IMP::kernel::QuadScore::evaluate_index(), IMP::kernel::QuadScore::do_create_current_decomposition(), IMP::kernel::TripletModifier::apply_index(), IMP::kernel::TripletPredicate::get_value_index(), IMP::kernel::TripletPredicate::operator()(), IMP::kernel::TripletScore::create_current_decomposition(), IMP::kernel::TripletScore::evaluate_if_good_index(), IMP::kernel::TripletScore::evaluate_index(), IMP::kernel::TripletScore::do_create_current_decomposition(), IMP::misc::CommonEndpointPairFilter::get_value_index(), IMP::misc::LogPairScore::evaluate_index(), IMP::misc::LowestRefinedPairScore::evaluate_index(), IMP::misc::SoftCylinderPairScore::evaluate_index(), IMP::score_functor::AddScores::get_is_trivially_zero(), IMP::score_functor::AddScores::get_maximum_range(), IMP::score_functor::AddScores::get_score(), IMP::score_functor::AddScores::get_score_and_derivative(), IMP::score_functor::DistancePairScore::evaluate_index(), IMP::score_functor::Harmonic::get_score(), IMP::score_functor::Harmonic::get_score_and_derivative(), IMP::score_functor::HarmonicLowerBound::get_is_trivially_zero(), IMP::score_functor::HarmonicLowerBound::get_maximum_range(), IMP::score_functor::HarmonicLowerBound::get_score(), IMP::score_functor::HarmonicLowerBound::get_score_and_derivative(), IMP::score_functor::HarmonicUpperBound::get_score(), IMP::score_functor::HarmonicUpperBound::get_score_and_derivative(), IMP::score_functor::LinearLowerBound::get_is_trivially_zero(), IMP::score_functor::LinearLowerBound::get_maximum_range(), IMP::score_functor::LinearLowerBound::get_score(), IMP::score_functor::LinearLowerBound::get_score_and_derivative(), IMP::score_functor::OpenCubicSpline::get_is_trivially_zero(), IMP::score_functor::OpenCubicSpline::get_maximum_range(), IMP::score_functor::OpenCubicSpline::get_score(), IMP::score_functor::OpenCubicSpline::get_score_and_derivative(), IMP::score_functor::OrientedSoap::get_is_trivially_zero(), IMP::score_functor::OrientedSoap::get_maximum_range(), IMP::score_functor::OrientedSoap::get_score(), IMP::score_functor::OrientedSoap::get_score_and_derivative(), IMP::score_functor::Shift::get_is_trivially_zero(), IMP::score_functor::Shift::get_maximum_range(), IMP::score_functor::Shift::get_score(), IMP::score_functor::Shift::get_score_and_derivative(), IMP::score_functor::SphereDistance::get_rsum(), IMP::score_functor::SphereDistance::get_is_trivially_zero(), IMP::score_functor::SphereDistance::get_maximum_range(), IMP::score_functor::SphereDistance::get_score(), IMP::score_functor::SphereDistance::get_score_and_derivative(), IMP::score_functor::Statistical::get_score_and_derivative(), IMP::score_functor::UnaryFunctionEvaluate::get_score(), IMP::score_functor::UnaryFunctionEvaluate::get_score_and_derivative(), IMP::score_functor::WeightScore::get_score(), IMP::score_functor::WeightScore::get_score_and_derivative()
IMP::base::ConstVector	IMP::base::ConstVector::compare(), IMP::base::swap()
IMP::base::Index	IMP::base::Index::IMP_COMPARISONS_1(), IMP::base::Index::IMP_HASHABLE_INLINE(), IMP::base::IndexVector::at(), IMP::base::IndexVector::at(), IMP::base::IndexVector::operator[](), IMP::base::IndexVector::operator[](), IMP::base::get_as_unsigned_int(), IMP::base::resize_to_fit()
IMP::base::Object	IMP::base::CreateLogContext::CreateLogContext(), IMP::base::CreateLogContext::CreateLogContext(), IMP::base::CreateLogContext::set(), IMP::base::Object::add_live_object(), IMP::base::Object::remove_live_object(), IMP::base::Object::compare(), IMP::base::SetCheckState::do_set(), IMP::base::SetCheckState::SetCheckState(), IMP::base::SetCheckState::set(), IMP::base::SetLogState::do_set(), IMP::base::SetLogState::SetLogState(), IMP::base::SetLogState::set(), IMP::base::Timer::Timer(), IMP::base::Timer::Timer(), IMP::kernel::Decorator::compare(), IMP::kernel::Model::add_data(), IMP::base::object_cast(), IMP::rmf::get_node_from_association(), IMP::rmf::get_node_from_association(), IMP::rmf::get_has_associated_node(), IMP::rmf::set_association()
IMP::base::TextInput	IMP::atom::CHARMMParameters::read_parameter_file(), IMP::atom::CHARMMParameters::read_topology_file(), IMP::atom::CHARMMParameters::CHARMMParameters(), IMP::atom::DopePairScore::DopePairScore(), IMP::atom::ProteinLigandAtomPairScore::ProteinLigandAtomPairScore(), IMP::atom::ProteinLigandRestraint::ProteinLigandRestraint(), IMP::core::StatisticalPairScore::StatisticalPairScore(), IMP::core::StatisticalPairScore::StatisticalPairScore(), IMP::score_functor::Dope::Dope(), IMP::score_functor::SingletonStatistical::SingletonStatistical(), IMP::score_functor::Soap::Soap(), IMP::score_functor::Statistical::Statistical(), IMP::score_functor::Statistical::Statistical(), IMP::algebra::read_pts(), IMP::algebra::read_spheres(), IMP::atom::read_mol2(), IMP::atom::read_pdb(), IMP::atom::read_pdb(), IMP::atom::read_multimodel_pdb(), IMP::atom::read_psipred(), IMP::atom::read_psipred()
IMP::base::TextOutput	IMP::base::SetLogTarget::SetLogTarget(), IMP::base::SetLogTarget::set(), IMP::core::WriteRestraintScoresOptimizerState::WriteRestraintScoresOptimizerState(), IMP::display::ChimeraWriter::ChimeraWriter(), IMP::display::PymolWriter::PymolWriter(), IMP::display::TextWriter::TextWriter(), IMP::algebra::write_pts(), IMP::algebra::write_spheres(), IMP::atom::write_mol2(), IMP::atom::write_pdb(), IMP::atom::write_pdb_of_c_alphas(), IMP::atom::write_multimodel_pdb(), IMP::atom::show_as_graphviz(), IMP::base::set_log_target(), IMP::base::show_timings(), IMP::core::show_rigid_body_hierarchy(), IMP::domino::show_as_graphviz(), IMP::kernel::show_as_graphviz(), IMP::multifit::write_connolly_surface()
IMP::base::Vector	IMP::algebra::BoundingBoxD::BoundingBoxD(), IMP::algebra::NearestNeighborD::NearestNeighborD(), IMP::algebra::PrincipalComponentAnalysisD::PrincipalComponentAnalysisD(), IMP::atom::AngleSingletonScore::do_get_inputs(), IMP::atom::AngleSingletonScore::evaluate_if_good_indexes(), IMP::atom::AngleSingletonScore::evaluate_indexes(), IMP::atom::BerendsenThermostatOptimizerState::BerendsenThermostatOptimizerState(), IMP::atom::BerendsenThermostatOptimizerState::set_particles(), IMP::atom::BondEndpointsRefiner::do_get_inputs(), IMP::atom::BondSingletonScore::do_get_inputs(), IMP::atom::BondSingletonScore::evaluate_if_good_indexes(), IMP::atom::BondSingletonScore::evaluate_indexes(), IMP::atom::BondedPairFilter::do_get_inputs(), IMP::atom::BrownianDynamics::advance_chunk(), IMP::atom::BrownianDynamics::do_step(), IMP::atom::BrownianDynamics::setup(), IMP::atom::CHARMMConnection::CHARMMConnection(), IMP::atom::CHARMMInternalCoordinate::CHARMMInternalCoordinate(), IMP::atom::CHARMMParameters::add_angle(), IMP::atom::CHARMMParameters::add_dihedral(), IMP::atom::CHARMMParameters::parse_dihedrals_parameters_line(), IMP::atom::CHARMMParameters::create_angles(), IMP::atom::CHARMMParameters::create_dihedrals(), IMP::atom::CoulombPairScore::do_get_inputs(), IMP::atom::CoverBond::apply_indexes(), IMP::atom::CoverBond::do_get_inputs(), IMP::atom::CoverBond::do_get_outputs(), IMP::atom::DihedralSingletonScore::do_get_inputs(), IMP::atom::DihedralSingletonScore::evaluate_if_good_indexes(), IMP::atom::DihedralSingletonScore::evaluate_indexes(), IMP::atom::EzRestraint::EzRestraint(), IMP::atom::ImproperSingletonScore::do_get_inputs(), IMP::atom::ImproperSingletonScore::evaluate_if_good_indexes(), IMP::atom::ImproperSingletonScore::evaluate_indexes(), IMP::atom::LangevinThermostatOptimizerState::set_particles(), IMP::atom::LennardJonesPairScore::do_get_inputs(), IMP::atom::MolecularDynamics::do_step(), IMP::atom::MolecularDynamics::setup(), IMP::atom::MolecularDynamics::propagate_coordinates(), IMP::atom::MolecularDynamics::propagate_velocities(), IMP::atom::MolecularDynamics::setup_degrees_of_freedom(), IMP::atom::RemoveRigidMotionOptimizerState::set_particles(), IMP::atom::RemoveTranslationOptimizerState::set_particles(), IMP::atom::SameResiduePairFilter::do_get_inputs(), IMP::atom::Selection::set_hierarchies(), IMP::atom::Selection::Selection(), IMP::atom::Selection::Selection(), IMP::atom::Selection::Selection(), IMP::atom::Selection::Selection(), IMP::atom::Simulator::remove_particles(), IMP::atom::Simulator::set_particles(), IMP::atom::Simulator::set_particles_order(), IMP::atom::Simulator::add_particles(), IMP::atom::Simulator::do_step(), IMP::atom::Simulator::setup(), IMP::atom::SoapPairFilter::do_get_inputs(), IMP::atom::StereochemistryPairFilter::do_get_inputs(), IMP::atom::StereochemistryPairFilter::set_angles(), IMP::atom::StereochemistryPairFilter::set_bonds(), IMP::atom::StereochemistryPairFilter::set_dihedrals(), IMP::atom::VelocityScalingOptimizerState::set_particles(), IMP::atom::WritePDBOptimizerState::WritePDBOptimizerState(), IMP::base::ConstVector::ConstVector(), IMP::base::SparseSymmetricPairMemoizer::SparseSymmetricPairMemoizer(), IMP::cnmultifit::AlignSymmetric::get_symm_axis_alignments_from_model_to_density(), IMP::cnmultifit::AlignSymmetric::score_alignment(), IMP::cnmultifit::CnSymmAxisDetector::CnSymmAxisDetector(), IMP::cnmultifit::MolCnSymmAxisDetector::MolCnSymmAxisDetector(), IMP::container::ConsecutivePairContainer::ConsecutivePairContainer(), IMP::container::ConsecutivePairFilter::do_get_inputs(), IMP::container::DynamicListSingletonContainer::add_particles(), IMP::container::DynamicListSingletonContainer::set_particles(), IMP::container::ExclusiveConsecutivePairContainer::ExclusiveConsecutivePairContainer(), IMP::container::ExclusiveConsecutivePairFilter::do_get_inputs(), IMP::container::InContainerPairFilter::do_get_inputs(), IMP::container::InContainerQuadFilter::do_get_inputs(), IMP::container::InContainerSingletonFilter::do_get_inputs(), IMP::container::InContainerSingletonFilter::get_value(), IMP::container::InContainerSingletonFilter::get_value_index(), IMP::container::InContainerTripletFilter::do_get_inputs(), IMP::container::ListSingletonContainer::ListSingletonContainer(), IMP::container::ListSingletonContainer::ListSingletonContainer(), IMP::container::ListSingletonContainer::set_particles(), IMP::container::ListSingletonContainer::set_particles(), IMP::container::MinimumPairScore::do_get_inputs(), IMP::container::MinimumQuadScore::do_get_inputs(), IMP::container::MinimumSingletonScore::do_get_inputs(), IMP::container::MinimumSingletonScore::evaluate_if_good_indexes(), IMP::container::MinimumSingletonScore::evaluate_indexes(), IMP::container::MinimumTripletScore::do_get_inputs(), IMP::core::AllSamePairPredicate::do_get_inputs(), IMP::core::AllSameQuadPredicate::do_get_inputs(), IMP::core::AllSameSingletonPredicate::do_get_inputs(), IMP::core::AllSameSingletonPredicate::get_value(), IMP::core::AllSameSingletonPredicate::get_value_index(), IMP::core::AllSameTripletPredicate::do_get_inputs(), IMP::core::AngleTripletScore::do_get_inputs(), IMP::core::AttributeSingletonPredicate::do_get_inputs(), IMP::core::AttributeSingletonPredicate::get_value(), IMP::core::AttributeSingletonPredicate::get_value_index(), IMP::core::BallMover::initialize(), IMP::core::BoxSweepClosePairsFinder::do_get_inputs(), IMP::core::BoxSweepClosePairsFinder::get_close_pairs(), IMP::core::BoxSweepClosePairsFinder::get_close_pairs(), IMP::core::CentroidOfRefined::apply_indexes(), IMP::core::CentroidOfRefined::do_get_inputs(), IMP::core::CentroidOfRefined::do_get_outputs(), IMP::core::ChildrenRefiner::do_get_inputs(), IMP::core::ClosePairsFinder::get_close_pairs(), IMP::core::ClosePairsFinder::get_close_pairs(), IMP::core::ClosePairsFinder::get_close_pairs(), IMP::core::ClosePairsFinder::get_close_pairs(), IMP::core::ClosePairsPairScore::do_get_inputs(), IMP::core::CoinFlipPairPredicate::do_get_inputs(), IMP::core::CoinFlipQuadPredicate::do_get_inputs(), IMP::core::CoinFlipSingletonPredicate::do_get_inputs(), IMP::core::CoinFlipSingletonPredicate::get_value(), IMP::core::CoinFlipSingletonPredicate::get_value_index(), IMP::core::CoinFlipTripletPredicate::do_get_inputs(), IMP::core::ConjugateGradients::get_score(), IMP::core::ConjugateGradients::line_search(), IMP::core::ConstantPairPredicate::do_get_inputs(), IMP::core::ConstantQuadPredicate::do_get_inputs(), IMP::core::ConstantSingletonPredicate::do_get_inputs(), IMP::core::ConstantSingletonPredicate::get_value(), IMP::core::ConstantSingletonPredicate::get_value_index(), IMP::core::ConstantTripletPredicate::do_get_inputs(), IMP::core::CoverRefined::apply_indexes(), IMP::core::CoverRefined::do_get_inputs(), IMP::core::CoverRefined::do_get_outputs(), IMP::core::DerivativesFromRefined::apply_indexes(), IMP::core::DerivativesFromRefined::do_get_inputs(), IMP::core::DerivativesFromRefined::do_get_outputs(), IMP::core::DerivativesToRefined::apply_indexes(), IMP::core::DerivativesToRefined::do_get_inputs(), IMP::core::DerivativesToRefined::do_get_outputs(), IMP::core::DistancePairScore::do_get_inputs(), IMP::core::FixedRefiner::FixedRefiner(), IMP::core::FixedRefiner::FixedRefiner(), IMP::core::FixedRefiner::do_get_inputs(), IMP::core::GenericAttributeSingletonScore::do_get_inputs(), IMP::core::GenericAttributeSingletonScore::evaluate_if_good_indexes(), IMP::core::GenericAttributeSingletonScore::evaluate_indexes(), IMP::core::GenericBoundingBox3DSingletonScore::do_get_inputs(), IMP::core::GenericBoundingBox3DSingletonScore::evaluate_if_good_indexes(), IMP::core::GenericBoundingBox3DSingletonScore::evaluate_indexes(), IMP::core::GenericDistanceToSingletonScore::do_get_inputs(), IMP::core::GenericDistanceToSingletonScore::evaluate_if_good_indexes(), IMP::core::GenericDistanceToSingletonScore::evaluate_indexes(), IMP::core::GridClosePairsFinder::do_get_inputs(), IMP::core::GridClosePairsFinder::get_close_pairs(), IMP::core::GridClosePairsFinder::get_close_pairs(), IMP::core::HarmonicDistancePairScore::do_get_inputs(), IMP::core::HarmonicSphereDistancePairScore::do_get_inputs(), IMP::core::HarmonicUpperBoundSphereDiameterPairScore::do_get_inputs(), IMP::core::HarmonicUpperBoundSphereDistancePairScore::do_get_inputs(), IMP::core::Hierarchy::do_setup_particle(), IMP::core::Hierarchy::do_setup_particle(), IMP::core::Hierarchy::setup_particle(), IMP::core::Hierarchy::setup_particle(), IMP::core::Hierarchy::setup_particle(), IMP::core::Hierarchy::setup_particle(), IMP::core::InBoundingBox3DSingletonPredicate::do_get_inputs(), IMP::core::InBoundingBox3DSingletonPredicate::get_value(), IMP::core::InBoundingBox3DSingletonPredicate::get_value_index(), IMP::core::IncrementalScoringFunction::IncrementalScoringFunction(), IMP::core::IncrementalScoringFunction::add_close_pair_score(), IMP::core::IncrementalScoringFunction::add_close_pair_score(), IMP::core::IncrementalScoringFunction::set_moved_particles(), IMP::core::IsCollisionPairPredicate::do_get_inputs(), IMP::core::KClosePairsPairScore::do_get_inputs(), IMP::core::LeavesRefiner::do_get_inputs(), IMP::core::MSConnectivityRestraint::add_type(), IMP::core::MonteCarlo::do_evaluate(), IMP::core::MoveStatisticsScoreState::MoveStatisticsScoreState(), IMP::core::NearestNeighborsClosePairsFinder::do_get_inputs(), IMP::core::NearestNeighborsClosePairsFinder::get_close_pairs(), IMP::core::NearestNeighborsClosePairsFinder::get_close_pairs(), IMP::core::NormalMover::initialize(), IMP::core::NormalizedSphereDistancePairScore::do_get_inputs(), IMP::core::OrderedTypePairPredicate::do_get_inputs(), IMP::core::OrderedTypeQuadPredicate::do_get_inputs(), IMP::core::OrderedTypeSingletonPredicate::do_get_inputs(), IMP::core::OrderedTypeSingletonPredicate::get_value(), IMP::core::OrderedTypeSingletonPredicate::get_value_index(), IMP::core::OrderedTypeTripletPredicate::do_get_inputs(), IMP::core::PredicateSingletonScore::do_get_inputs(), IMP::core::PredicateSingletonScore::evaluate_if_good_indexes(), IMP::core::PredicateSingletonScore::evaluate_indexes(), IMP::core::QuadraticClosePairsFinder::do_get_inputs(), IMP::core::QuadraticClosePairsFinder::get_close_pairs(), IMP::core::QuadraticClosePairsFinder::get_close_pairs(), IMP::core::RefinedPairsPairScore::do_get_inputs(), IMP::core::RigidBody::set_reference_frame_from_members(), IMP::core::RigidBodyHierarchyGeometry::RigidBodyHierarchyGeometry(), IMP::core::RigidBodyTunneler::RigidBodyTunneler(), IMP::core::RigidClosePairsFinder::do_get_inputs(), IMP::core::RigidClosePairsFinder::get_close_pairs(), IMP::core::RigidClosePairsFinder::get_close_pairs(), IMP::core::RigidClosePairsFinder::get_close_pairs(), IMP::core::SoftSpherePairScore::do_get_inputs(), IMP::core::SphereDistancePairScore::do_get_inputs(), IMP::core::SphereDistanceToSingletonScore::do_get_inputs(), IMP::core::SphereDistanceToSingletonScore::evaluate_if_good_indexes(), IMP::core::SphereDistanceToSingletonScore::evaluate_indexes(), IMP::core::TableRefiner::add_particle(), IMP::core::TableRefiner::do_get_inputs(), IMP::core::TableRefiner::set_particle(), IMP::core::Transform::apply_indexes(), IMP::core::Transform::do_get_inputs(), IMP::core::Transform::do_get_outputs(), IMP::core::TransformationAndReflectionSymmetry::apply_indexes(), IMP::core::TransformationAndReflectionSymmetry::do_get_inputs(), IMP::core::TransformationAndReflectionSymmetry::do_get_outputs(), IMP::core::TransformationSymmetry::apply_indexes(), IMP::core::TransformationSymmetry::do_get_inputs(), IMP::core::TransformationSymmetry::do_get_outputs(), IMP::core::TransformedDistancePairScore::do_get_inputs(), IMP::core::TypedPairScore::do_get_inputs(), IMP::core::UnorderedTypePairPredicate::do_get_inputs(), IMP::core::UnorderedTypeQuadPredicate::do_get_inputs(), IMP::core::UnorderedTypeSingletonPredicate::do_get_inputs(), IMP::core::UnorderedTypeSingletonPredicate::get_value(), IMP::core::UnorderedTypeSingletonPredicate::get_value_index(), IMP::core::UnorderedTypeTripletPredicate::do_get_inputs(), IMP::core::WeightedDerivativesToRefined::apply_indexes(), IMP::core::WeightedDerivativesToRefined::do_get_inputs(), IMP::core::WeightedDerivativesToRefined::do_get_outputs(), IMP::core::WeightedSphereDistancePairScore::do_get_inputs(), IMP::domino::DependencyScoreState::set_input_particles(), IMP::domino::DependencyScoreState::set_output_particles(), IMP::domino::DisjointSetsSubsetFilterTable::add_set(), IMP::domino::Order::Order(), IMP::domino::PairListSubsetFilterTable::fill(), IMP::domino::ParticlesAdaptor::ParticlesAdaptor(), IMP::domino::ReadAssignmentContainer::ReadAssignmentContainer(), IMP::domino::ReadHDF5AssignmentContainer::ReadHDF5AssignmentContainer(), IMP::domino::RestraintCache::load_cache(), IMP::domino::RestraintCache::save_cache(), IMP::domino::Subset::get_sorted(), IMP::domino::Subset::Subset(), IMP::domino::WriteAssignmentContainer::WriteAssignmentContainer(), IMP::domino::WriteHDF5AssignmentContainer::WriteHDF5AssignmentContainer(), IMP::domino::WriteHDF5AssignmentContainer::WriteHDF5AssignmentContainer(), IMP::em2d::CollisionCrossSection::set_model_particles(), IMP::em2d::Fine2DRegistrationRestraint::setup(), IMP::em2d::MasksManager::create_masks(), IMP::em2d::PCAFitRestraint::PCAFitRestraint(), IMP::em2d::ProjectionFinder::set_model_particles(), IMP::em2d::RigidBodiesImageFitRestraint::RigidBodiesImageFitRestraint(), IMP::em::DensityFillingRestraint::DensityFillingRestraint(), IMP::em::DensityFillingRestraint::add_particles(), IMP::em::DensityFillingRestraint::remove_particles(), IMP::em::DensityFillingRestraint::set_particles(), IMP::em::DensityFillingRestraint::set_particles_order(), IMP::em::EnvelopeFitRestraint::EnvelopeFitRestraint(), IMP::em::EnvelopePenetrationRestraint::EnvelopePenetrationRestraint(), IMP::em::EnvelopePenetrationRestraint::add_particles(), IMP::em::EnvelopePenetrationRestraint::remove_particles(), IMP::em::EnvelopePenetrationRestraint::set_particles(), IMP::em::EnvelopePenetrationRestraint::set_particles_order(), IMP::em::FitRestraint::FitRestraint(), IMP::em::FitRestraint::add_particles(), IMP::em::FitRestraint::remove_particles(), IMP::em::FitRestraint::set_particles(), IMP::em::FitRestraint::set_particles_order(), IMP::em::FitRestraint::store_particles(), IMP::em::PCAFitRestraint::PCAFitRestraint(), IMP::em::PCAFitRestraint::add_particles(), IMP::em::PCAFitRestraint::remove_particles(), IMP::em::PCAFitRestraint::set_particles(), IMP::em::PCAFitRestraint::set_particles_order(), IMP::em::PCAFitRestraint::store_particles(), IMP::em::SampledDensityMap::SampledDensityMap(), IMP::em::SampledDensityMap::project(), IMP::em::SampledDensityMap::set_particles(), IMP::em::SampledDensityMap::calculate_particles_bounding_box(), IMP::em::SurfaceShellDensityMap::SurfaceShellDensityMap(), IMP::example::ExamplePairScore::do_get_inputs(), IMP::example::ExampleSingletonModifier::apply_indexes(), IMP::example::ExampleSingletonModifier::do_get_inputs(), IMP::example::ExampleSingletonModifier::do_get_outputs(), IMP::example::ExampleSubsetFilterTable::ExampleSubsetFilterTable(), IMP::isd::CysteineCrossLinkRestraint::add_contribution(), IMP::isd::CysteineCrossLinkRestraint::get_CB_coordinates(), IMP::isd::FretRestraint::FretRestraint(), IMP::isd::HybridMonteCarlo::do_evaluate(), IMP::isd::MolecularDynamics::propagate_coordinates(), IMP::isd::MolecularDynamics::propagate_velocities(), IMP::isd::MolecularDynamics::setup_degrees_of_freedom(), IMP::isd::RepulsiveDistancePairScore::do_get_inputs(), IMP::isd::TALOSRestraint::TALOSRestraint(), IMP::isd::TALOSRestraint::TALOSRestraint(), IMP::kernel::ParticleIndexesAdaptor::ParticleIndexesAdaptor(), IMP::kernel::ParticleIndexesAdaptor::ParticleIndexesAdaptor(), IMP::kernel::ParticleIndexesAdaptor::ParticleIndexesAdaptor(), IMP::kernel::ParticleInputs::get_inputs(), IMP::kernel::ParticleInputs::do_get_inputs(), IMP::kernel::ParticleOutputs::get_outputs(), IMP::kernel::ParticleOutputs::do_get_outputs(), IMP::kernel::SingletonContainerAdaptor::SingletonContainerAdaptor(), IMP::kernel::SingletonModifier::apply_indexes(), IMP::kernel::SingletonPredicate::get_value(), IMP::kernel::SingletonPredicate::get_value_index(), IMP::kernel::SingletonScore::evaluate_if_good_indexes(), IMP::kernel::SingletonScore::evaluate_indexes(), IMP::kinematics::KinematicForest::add_rigid_bodies_in_chain(), IMP::kinematics::KinematicForestScoreState::KinematicForestScoreState(), IMP::kinematics::ProteinKinematics::ProteinKinematics(), IMP::kinematics::ProteinKinematics::add_dihedral_joint(), IMP::kinematics::ProteinKinematics::add_dihedral_joints(), IMP::kinematics::ProteinKinematics::add_dihedral_joints(), IMP::kinematics::ProteinKinematics::init(), IMP::kinematics::ProteinKinematics::mark_rotatable_angles(), IMP::misc::CommonEndpointPairFilter::do_get_inputs(), IMP::misc::LogPairScore::do_get_inputs(), IMP::misc::LowestRefinedPairScore::do_get_inputs(), IMP::misc::MetricClosePairsFinder::get_close_pairs_internal(), IMP::misc::MetricClosePairsFinder::get_close_pairs_internal(), IMP::misc::MetricClosePairsFinder::get_index(), IMP::misc::MetricClosePairsFinder::do_get_inputs(), IMP::misc::MetricClosePairsFinder::get_close_pairs(), IMP::misc::MetricClosePairsFinder::get_close_pairs(), IMP::misc::SoftCylinderPairScore::do_get_inputs(), IMP::multifit::AnchorsData::set_secondary_structure_probabilities(), IMP::multifit::ComplementarityRestraint::ComplementarityRestraint(), IMP::multifit::ComplementarityRestraint::get_grid(), IMP::multifit::ComplementarityRestraint::get_grid_object(), IMP::multifit::Ensemble::get_rmsd(), IMP::multifit::GeometricHash::neighbors(), IMP::multifit::MergeTreeBuilder::MergeTreeBuilder(), IMP::multifit::RadiusOfGyrationRestraint::RadiusOfGyrationRestraint(), IMP::multifit::RadiusOfGyrationRestraint::add_particles(), IMP::multifit::RadiusOfGyrationRestraint::remove_particles(), IMP::multifit::RadiusOfGyrationRestraint::set_particles(), IMP::multifit::RadiusOfGyrationRestraint::set_particles_order(), IMP::multifit::WeightedExcludedVolumeRestraint::WeightedExcludedVolumeRestraint(), IMP::multifit::WeightedExcludedVolumeRestraint::add_particles(), IMP::multifit::WeightedExcludedVolumeRestraint::remove_particles(), IMP::multifit::WeightedExcludedVolumeRestraint::set_particles(), IMP::multifit::WeightedExcludedVolumeRestraint::set_particles_order(), IMP::rmf::HierarchyLoadLink::add_link_recursive(), IMP::rmf::HierarchyLoadLink::create_recursive(), IMP::rmf::HierarchySaveLink::add_recursive(), IMP::rmf::SimpleLoadLink::link(), IMP::rmf::SimpleSaveLink::add(), IMP::saxs::DeltaDistributionFunction::DeltaDistributionFunction(), IMP::saxs::DerivativeCalculator::compute_chisquare_derivative(), IMP::saxs::DerivativeCalculator::compute_chisquare_derivative(), IMP::saxs::DerivativeCalculator::precompute_derivative_helpers(), IMP::saxs::Profile::calculate_I0(), IMP::saxs::Profile::calculate_profile(), IMP::saxs::Profile::calculate_profile(), IMP::saxs::Profile::calculate_profile_constant_form_factor(), IMP::saxs::Profile::calculate_profile_partial(), IMP::saxs::Profile::calculate_profile_partial(), IMP::saxs::Profile::calculate_profile_reciprocal_partial(), IMP::saxs::Profile::calculate_profile_symmetric(), IMP::saxs::Profile::calculate_profile_real(), IMP::saxs::Profile::calculate_profile_real(), IMP::saxs::Profile::calculate_profile_reciprocal(), IMP::saxs::Profile::calculate_profile_reciprocal(), IMP::saxs::RadiusOfGyrationRestraint::RadiusOfGyrationRestraint(), IMP::saxs::Restraint::Restraint(), IMP::saxs::RigidBodiesProfileHandler::RigidBodiesProfileHandler(), IMP::saxs::SolventAccessibleSurface::get_solvent_accessibility(), IMP::saxs::SolventAccessibleSurface::create_sphere_dots(), IMP::score_functor::AddScores::get_inputs(), IMP::score_functor::DistancePairScore::do_get_inputs(), IMP::score_functor::OrientedSoap::get_inputs(), IMP::statistics::ParticleEmbedding::ParticleEmbedding(), IMP::symmetry::BallMover::BallMover(), IMP::symmetry::RigidBodyMover::RigidBodyMover(), IMP::symmetry::RigidBodyMover::get_particles(), IMP::symmetry::RigidBodyMover::get_rigid_bodies(), IMP::algebra::get_principal_components(), IMP::atom::write_multimodel_pdb(), IMP::atom::read_psipred(), IMP::atom::create_excluded_volume_restraint(), IMP::atom::create_fragment(), IMP::atom::create_rigid_body(), IMP::atom::get_component_placement_score(), IMP::atom::get_leaves(), IMP::atom::get_pairwise_rmsd_score(), IMP::atom::get_placement_score(), IMP::atom::get_radius_of_gyration(), IMP::atom::get_rmsd(), IMP::atom::get_rmsd(), IMP::atom::get_rmsd_transforming_first(), IMP::atom::setup_as_approximation(), IMP::atom::setup_coarse_secondary_structure_residue(), IMP::atom::setup_coarse_secondary_structure_residues(), IMP::cnmultifit::cn_symm_score(), IMP::cnmultifit::fit_cn_assembly(), IMP::cnmultifit::generate_cn_transformations(), IMP::cnmultifit::generate_translations_along_symm_axis(), IMP::cnmultifit::get_cn_rmsd(), IMP::cnmultifit::symmetry_local_fitting(), IMP::cnmultifit::transform_cn_assembly(), IMP::container::get_slack_estimate(), IMP::core::assign_blame(), IMP::core::create_blame_geometries(), IMP::core::get_bounding_box(), IMP::core::get_centroid(), IMP::core::get_enclosing_sphere(), IMP::core::get_initial_reference_frame(), IMP::core::get_initial_reference_frame(), IMP::core::set_enclosing_radius(), IMP::core::set_enclosing_sphere(), IMP::domino::get_interaction_graph(), IMP::domino::write_merge_tree(), IMP::domino::read_merge_tree(), IMP::domino::get_index(), IMP::domino::get_partial_index(), IMP::domino::get_possible_interactions(), IMP::em::add_to_map(), IMP::em::compute_fitting_score(), IMP::em::compute_fitting_scores(), IMP::em::get_number_of_particles_outside_of_the_density(), IMP::em::get_numbers_of_particles_outside_of_the_density(), IMP::em::get_percentage_of_voxels_covered_by_particles(), IMP::em::local_rigid_fitting_grid_search(), IMP::em::particles2binarized_density(), IMP::em::particles2density(), IMP::em::particles2surface(), IMP::em2d::create_evenly_distributed_projections(), IMP::em2d::do_project_particles(), IMP::em2d::get_enclosing_image_size(), IMP::em2d::get_projection(), IMP::em2d::get_projections(), IMP::em2d::get_projections(), IMP::example::create_chain_restraint(), IMP::example::create_excluded_volume(), IMP::example::create_serial_mover(), IMP::example::get_number_of_incidences(), IMP::example::optimize_assembly(), IMP::example::optimize_balls(), IMP::kernel::write_particles_to_buffer(), IMP::kernel::read_particles_from_buffer(), IMP::kernel::get_indexes(), IMP::kernel::get_particles(), IMP::multifit::create_coarse_molecules_from_molecules(), IMP::multifit::get_actual_radius_of_gyration(), IMP::multifit::get_anchor_indices_matching_secondary_structure(), IMP::multifit::pca_based_rigid_fitting(), IMP::multifit::write_connolly_surface(), IMP::rmf::add_hierarchies(), IMP::rmf::add_hierarchies(), IMP::rmf::link_hierarchies(), IMP::rmf::add_particles(), IMP::rmf::add_particles(), IMP::rmf::link_particles(), IMP::saxs::compute_max_distance(), IMP::saxs::compute_max_distance(), IMP::saxs::compute_profile(), IMP::saxs::get_coordinates(), IMP::saxs::get_form_factors(), IMP::saxs::radius_of_gyration()

IMP.cnmultifit

Class	Users
IMP::cnmultifit::AlignSymmetric	IMP::cnmultifit::fit_cn_assembly()
IMP::cnmultifit::CnSymmAxisDetector	IMP::cnmultifit::fit_cn_assembly()
IMP::cnmultifit::MolCnSymmAxisDetector	IMP::cnmultifit::fit_cn_assembly()

IMP.container

Class	Users
IMP::container::ClosePairContainer	IMP::container::get_slack_estimate()
IMP::container::ConsecutivePairContainer	IMP::container::ConsecutivePairFilter::ConsecutivePairFilter()

IMP.core

Class	Users
IMP::core::ClosePairsFinder	IMP::container::ClosePairContainer::ClosePairContainer(), IMP::core::RigidClosePairsFinder::RigidClosePairsFinder()
IMP::core::DataObject	IMP::core::DataObject::IMP_OBJECT_METHODS()
IMP::core::Hierarchy	IMP::atom::Hierarchy::Hierarchy(), IMP::atom::HierarchyGeometry::HierarchyGeometry(), IMP::core::Hierarchy::add_child(), IMP::core::Hierarchy::add_child_at(), IMP::core::Hierarchy::remove_child(), IMP::core::HierarchyVisitor::operator()(), IMP::core::ModifierVisitor::operator()(), IMP::core::get_all_descendants(), IMP::core::get_internal(), IMP::core::get_leaves(), IMP::core::get_root(), IMP::core::show(), IMP::multifit::add_surface_index()
IMP::core::HierarchyTraits	IMP::core::ChildrenRefiner::ChildrenRefiner(), IMP::core::Hierarchy::do_setup_particle(), IMP::core::Hierarchy::do_setup_particle(), IMP::core::Hierarchy::do_setup_particle(), IMP::core::Hierarchy::Hierarchy(), IMP::core::Hierarchy::Hierarchy(), IMP::core::Hierarchy::get_is_setup(), IMP::core::Hierarchy::get_is_setup(), 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::HierarchyTraits::operator==(), IMP::core::LeavesRefiner::LeavesRefiner()
IMP::core::IncrementalScoringFunction	IMP::core::MonteCarlo::set_incremental_scoring_function()
IMP::core::IsCollisionPairPredicate	IMP::core::IsCollisionPairPredicate::IMP_PAIR_PREDICATE_METHODS()
IMP::core::MonteCarlo	IMP::core::MCCGSampler::set_up_movers()
IMP::core::MonteCarloMover	IMP::core::MonteCarlo::remove_mover(), IMP::core::MonteCarlo::add_mover()
IMP::core::RigidBody	IMP::core::RigidBody::teardown_particle(), IMP::core::RigidBodyDerivativeGeometry::RigidBodyDerivativeGeometry(), IMP::core::RigidBodyFrameGeometry::RigidBodyFrameGeometry(), IMP::core::RigidBodyHierarchyGeometry::RigidBodyHierarchyGeometry(), IMP::em2d::RelativePositionMover::RelativePositionMover(), IMP::em2d::RelativePositionMover::add_internal_transformations(), IMP::em2d::RigidBodiesImageFitRestraint::get_number_of_masks(), IMP::em2d::RigidBodiesImageFitRestraint::set_orientations(), IMP::em2d::RigidBodiesImageFitRestraint::get_rigid_body_index(), IMP::kinematics::BondAngleRevoluteJoint::BondAngleRevoluteJoint(), IMP::kinematics::CompositeJoint::CompositeJoint(), IMP::kinematics::DihedralAngleRevoluteJoint::DihedralAngleRevoluteJoint(), IMP::kinematics::Joint::Joint(), IMP::kinematics::KinematicForest::add_edge(), IMP::kinematics::KinematicForest::get_coordinates_safe(), IMP::kinematics::KinematicForest::get_is_member(), IMP::kinematics::KinematicForest::get_reference_frame_safe(), IMP::kinematics::KinematicForest::set_coordinates_safe(), IMP::kinematics::KinematicForest::set_reference_frame_safe(), IMP::kinematics::PrismaticJoint::PrismaticJoint(), IMP::kinematics::PrismaticJoint::PrismaticJoint(), IMP::kinematics::RevoluteJoint::RevoluteJoint(), IMP::kinematics::TransformationJoint::TransformationJoint(), IMP::multifit::ComplementarityRestraint::get_grid_object(), IMP::symmetry::RigidBodyMover::RigidBodyMover(), IMP::core::show_rigid_body_hierarchy(), IMP::core::transform(), IMP::em::compute_fitting_scores(), IMP::multifit::create_hit_map(), IMP::multifit::create_weighted_excluded_volume_restraint(), IMP::multifit::pca_based_rigid_fitting()
IMP::core::RigidMember	IMP::core::RigidBody::get_coordinates(), IMP::core::get_root_rigid_body()
IMP::core::SoftSpherePairScore	IMP::core::ExcludedVolumeRestraint::ExcludedVolumeRestraint()
IMP::core::XYZ	IMP::atom::Angle::do_setup_particle(), IMP::atom::Angle::setup_particle(), IMP::atom::Angle::setup_particle(), IMP::atom::Dihedral::do_setup_particle(), IMP::atom::Dihedral::setup_particle(), IMP::atom::Dihedral::setup_particle(), IMP::core::AngleRestraint::AngleRestraint(), IMP::core::XYZ::get_vector_to(), IMP::core::XYZDerivativeGeometry::XYZDerivativeGeometry(), IMP::kinematics::BondAngleRevoluteJoint::BondAngleRevoluteJoint(), IMP::kinematics::BondAngleRevoluteJoint::get_perpendicular_vector(), IMP::kinematics::DihedralAngleRevoluteJoint::DihedralAngleRevoluteJoint(), IMP::kinematics::PrismaticJoint::PrismaticJoint(), IMP::core::get_dihedral(), IMP::core::get_distance(), IMP::core::get_vector_geometry(), IMP::core::set_vector_geometry(), IMP::core::transform()
IMP::core::XYZR	IMP::core::XYZRGeometry::XYZRGeometry(), IMP::core::get_distance(), IMP::core::set_enclosing_radius(), IMP::core::set_enclosing_sphere()

IMP.display

Class	Users
IMP::display::BoundingBoxGeometry	IMP::display::GeometryProcessor::handle_bounding_box()
IMP::display::Color	IMP::display::BoundingBoxGeometry::BoundingBoxGeometry(), IMP::display::BoundingBoxGeometry::BoundingBoxGeometry(), IMP::display::ChimeraWriter::handle_cylinder(), IMP::display::ChimeraWriter::handle_ellipsoid(), IMP::display::ChimeraWriter::handle_point(), IMP::display::ChimeraWriter::handle_polygon(), IMP::display::ChimeraWriter::handle_segment(), IMP::display::ChimeraWriter::handle_sphere(), IMP::display::ChimeraWriter::handle_triangle(), IMP::display::Color::compare(), IMP::display::Colored::do_setup_particle(), IMP::display::Colored::set_color(), IMP::display::Colored::setup_particle(), IMP::display::Colored::setup_particle(), IMP::display::CylinderGeometry::CylinderGeometry(), IMP::display::CylinderGeometry::CylinderGeometry(), IMP::display::EllipsoidGeometry::EllipsoidGeometry(), IMP::display::EllipsoidGeometry::EllipsoidGeometry(), IMP::display::FilterGeometry::handle_cylinder(), IMP::display::FilterGeometry::handle_point(), IMP::display::FilterGeometry::handle_segment(), IMP::display::FilterGeometry::handle_sphere(), IMP::display::Geometry::Geometry(), IMP::display::Geometry::set_color(), IMP::display::GeometryProcessor::handle_anything(), IMP::display::GeometryProcessor::handle_bounding_box(), IMP::display::GeometryProcessor::handle_cylinder(), IMP::display::GeometryProcessor::handle_ellipsoid(), IMP::display::GeometryProcessor::handle_label(), IMP::display::GeometryProcessor::handle_point(), IMP::display::GeometryProcessor::handle_polygon(), IMP::display::GeometryProcessor::handle_segment(), IMP::display::GeometryProcessor::handle_sphere(), IMP::display::GeometryProcessor::handle_surface_mesh(), IMP::display::GeometryProcessor::handle_triangle(), IMP::display::GeometryProcessor::handle_geometry_internal(), IMP::display::GeometrySet::GeometrySet(), IMP::display::GeometrySet::GeometrySet(), IMP::display::PairsGeometry::PairsGeometry(), IMP::display::PointGeometry::PointGeometry(), IMP::display::PointGeometry::PointGeometry(), IMP::display::PolygonGeometry::PolygonGeometry(), IMP::display::PolygonGeometry::PolygonGeometry(), IMP::display::PymolWriter::handle_cylinder(), IMP::display::PymolWriter::handle_label(), IMP::display::PymolWriter::handle_point(), IMP::display::PymolWriter::handle_polygon(), IMP::display::PymolWriter::handle_segment(), IMP::display::PymolWriter::handle_sphere(), IMP::display::PymolWriter::handle_surface(), IMP::display::PymolWriter::handle_triangle(), IMP::display::ReferenceFrameGeometry::ReferenceFrameGeometry(), IMP::display::ReferenceFrameGeometry::ReferenceFrameGeometry(), IMP::display::SegmentGeometry::SegmentGeometry(), IMP::display::SegmentGeometry::SegmentGeometry(), IMP::display::SingletonsGeometry::SingletonsGeometry(), IMP::display::SphereGeometry::SphereGeometry(), IMP::display::SphereGeometry::SphereGeometry(), IMP::display::TriangleGeometry::TriangleGeometry(), IMP::display::TriangleGeometry::TriangleGeometry(), IMP::display::get_interpolated_rgb()
IMP::display::CylinderGeometry	IMP::display::ChimeraWriter::handle_cylinder(), IMP::display::FilterGeometry::handle_cylinder(), IMP::display::GeometryProcessor::handle_cylinder(), IMP::display::PymolWriter::handle_cylinder()
IMP::display::EllipsoidGeometry	IMP::display::ChimeraWriter::handle_ellipsoid(), IMP::display::GeometryProcessor::handle_ellipsoid()
IMP::display::Geometry	IMP::display::FilterGeometry::add_geometry(), IMP::display::GeometryProcessor::handle_anything(), IMP::display::GeometryProcessor::handle_geometry(), IMP::display::GeometryProcessor::handle_geometry_internal(), IMP::display::WriteOptimizerState::add_geometry(), IMP::display::WriteOptimizerState::remove_geometry(), IMP::display::Writer::add_geometry()
IMP::display::LabelGeometry	IMP::display::GeometryProcessor::handle_label(), IMP::display::PymolWriter::handle_label()
IMP::display::PointGeometry	IMP::display::ChimeraWriter::handle_point(), IMP::display::FilterGeometry::handle_point(), IMP::display::GeometryProcessor::handle_point(), IMP::display::PymolWriter::handle_point()
IMP::display::PolygonGeometry	IMP::display::ChimeraWriter::handle_polygon(), IMP::display::GeometryProcessor::handle_polygon(), IMP::display::PymolWriter::handle_polygon()
IMP::display::SegmentGeometry	IMP::display::ChimeraWriter::handle_segment(), IMP::display::FilterGeometry::handle_segment(), IMP::display::GeometryProcessor::handle_segment(), IMP::display::PymolWriter::handle_segment()
IMP::display::SphereGeometry	IMP::display::ChimeraWriter::handle_sphere(), IMP::display::FilterGeometry::handle_sphere(), IMP::display::GeometryProcessor::handle_sphere(), IMP::display::PymolWriter::handle_sphere()
IMP::display::SurfaceMeshGeometry	IMP::display::GeometryProcessor::handle_surface_mesh(), IMP::display::PymolWriter::handle_surface()
IMP::display::TriangleGeometry	IMP::display::ChimeraWriter::handle_triangle(), IMP::display::GeometryProcessor::handle_triangle(), IMP::display::PymolWriter::handle_triangle()
IMP::display::Writer	IMP::display::WriterAdaptor::WriterAdaptor()
IMP::display::WriterAdaptor	IMP::display::WriteOptimizerState::WriteOptimizerState(), IMP::display::WriteOptimizerState::write()

IMP.domino

Class	Users
IMP::domino::Assignment	IMP::domino::AssignmentContainer::add_assignment(), IMP::domino::CappedAssignmentContainer::add_assignment(), IMP::domino::HeapAssignmentContainer::add_assignment(), IMP::domino::ListAssignmentContainer::add_assignment(), IMP::domino::Order::get_list_ordered(), IMP::domino::PackedAssignmentContainer::add_assignment(), IMP::domino::RangeViewAssignmentContainer::add_assignment(), IMP::domino::ReadAssignmentContainer::add_assignment(), IMP::domino::ReadHDF5AssignmentContainer::add_assignment(), IMP::domino::RestraintCache::get_score(), IMP::domino::RestraintCache::get_score(), IMP::domino::RestraintCache::load_last_score(), IMP::domino::SampleAssignmentContainer::add_assignment(), IMP::domino::Slice::get_sliced(), IMP::domino::SubsetFilter::get_is_ok(), IMP::domino::SubsetFilter::get_next_state(), IMP::domino::WriteAssignmentContainer::add_assignment(), IMP::domino::WriteHDF5AssignmentContainer::add_assignment(), IMP::em2d::DistanceFilter::get_is_ok(), IMP::domino::load_particle_states(), IMP::domino::get_distance_if_smaller_than(), IMP::domino::get_embedding(), IMP::domino::swap()
IMP::domino::AssignmentContainer	IMP::domino::AssignmentsTable::load_assignments(), IMP::domino::BranchAndBoundAssignmentsTable::load_assignments(), IMP::domino::CappedAssignmentContainer::CappedAssignmentContainer(), IMP::domino::DominoSampler::load_vertex_assignments(), IMP::domino::DominoSampler::load_vertex_assignments(), IMP::domino::ListAssignmentsTable::load_assignments(), IMP::domino::ListAssignmentsTable::set_assignments(), IMP::domino::RangeViewAssignmentContainer::RangeViewAssignmentContainer(), IMP::domino::RecursiveAssignmentsTable::load_assignments(), IMP::domino::SimpleAssignmentsTable::load_assignments(), IMP::domino::load_leaf_assignments(), IMP::domino::load_merged_assignments(), IMP::domino::load_merged_assignments_random_order()
IMP::domino::AssignmentsTable	IMP::domino::DiscreteSampler::set_assignments_table(), IMP::domino::load_leaf_assignments()
IMP::domino::Order	IMP::domino::swap()
IMP::domino::ParticleStates	IMP::domino::CompoundStates::CompoundStates(), IMP::domino::DiscreteSampler::set_particle_states(), IMP::domino::ParticleStatesTable::set_particle_states(), IMP::domino::PermutationStates::PermutationStates()
IMP::domino::ParticleStatesTable	IMP::domino::BranchAndBoundAssignmentsTable::BranchAndBoundAssignmentsTable(), IMP::domino::BranchAndBoundSampler::BranchAndBoundSampler(), IMP::domino::DiscreteSampler::set_particle_states_table(), IMP::domino::DiscreteSampler::get_subset_filter_tables_to_use(), IMP::domino::DiscreteSampler::DiscreteSampler(), IMP::domino::DisjointSetsSubsetFilterTable::DisjointSetsSubsetFilterTable(), IMP::domino::DominoSampler::DominoSampler(), IMP::domino::EqualitySubsetFilterTable::EqualitySubsetFilterTable(), IMP::domino::EquivalenceAndExclusionSubsetFilterTable::EquivalenceAndExclusionSubsetFilterTable(), IMP::domino::EquivalenceSubsetFilterTable::EquivalenceSubsetFilterTable(), IMP::domino::ExclusionSubsetFilterTable::ExclusionSubsetFilterTable(), IMP::domino::ListSubsetFilterTable::ListSubsetFilterTable(), IMP::domino::ParticlesAdaptor::ParticlesAdaptor(), IMP::domino::RecursiveAssignmentsTable::RecursiveAssignmentsTable(), IMP::domino::RecursiveStates::RecursiveStates(), IMP::domino::RestraintCache::RestraintCache(), IMP::domino::RestraintScoreSubsetFilterTable::RestraintScoreSubsetFilterTable(), IMP::domino::SimpleAssignmentsTable::SimpleAssignmentsTable(), IMP::em2d::DistanceFilter::DistanceFilter(), IMP::em2d::DistanceFilterTable::DistanceFilterTable(), IMP::domino::get_interaction_graph(), IMP::domino::get_merge_tree(), IMP::domino::load_particle_states(), IMP::domino::get_restraints(), IMP::domino::get_distance_if_smaller_than(), IMP::domino::get_embedding(), IMP::domino::get_nearest_assignment(), IMP::domino::get_possible_interactions(), IMP::domino::get_restraint_graph(), IMP::domino::get_state_clusters()
IMP::domino::RestraintCache	IMP::domino::HeapAssignmentContainer::HeapAssignmentContainer(), IMP::domino::MinimumRestraintScoreSubsetFilterTable::MinimumRestraintScoreSubsetFilterTable(), IMP::domino::RestraintScoreSubsetFilterTable::RestraintScoreSubsetFilterTable()
IMP::domino::Slice	IMP::domino::swap()
IMP::domino::Subset	IMP::domino::AssignmentsTable::load_assignments(), IMP::domino::BranchAndBoundAssignmentsTable::load_assignments(), IMP::domino::BranchAndBoundSampler::do_get_sample_assignments(), IMP::domino::DiscreteSampler::do_get_sample_assignments(), IMP::domino::DiscreteSampler::get_sample_assignments(), IMP::domino::DominoSampler::do_get_sample_assignments(), IMP::domino::EqualitySubsetFilterTable::get_strength(), IMP::domino::EqualitySubsetFilterTable::get_subset_filter(), IMP::domino::EquivalenceAndExclusionSubsetFilterTable::get_strength(), IMP::domino::EquivalenceAndExclusionSubsetFilterTable::get_subset_filter(), IMP::domino::EquivalenceSubsetFilterTable::get_strength(), IMP::domino::EquivalenceSubsetFilterTable::get_subset_filter(), IMP::domino::ExclusionSubsetFilterTable::get_strength(), IMP::domino::ExclusionSubsetFilterTable::get_subset_filter(), IMP::domino::HeapAssignmentContainer::HeapAssignmentContainer(), IMP::domino::ListAssignmentsTable::load_assignments(), IMP::domino::ListAssignmentsTable::set_assignments(), IMP::domino::ListSubsetFilterTable::get_strength(), IMP::domino::ListSubsetFilterTable::get_subset_filter(), IMP::domino::MinimumRestraintScoreSubsetFilterTable::get_restraints(), IMP::domino::MinimumRestraintScoreSubsetFilterTable::get_strength(), IMP::domino::MinimumRestraintScoreSubsetFilterTable::get_subset_filter(), IMP::domino::Order::Order(), IMP::domino::PairListSubsetFilterTable::fill(), IMP::domino::PairListSubsetFilterTable::get_strength(), IMP::domino::PairListSubsetFilterTable::get_subset_filter(), IMP::domino::ProbabilisticSubsetFilterTable::get_strength(), IMP::domino::ProbabilisticSubsetFilterTable::get_subset_filter(), IMP::domino::ReadAssignmentContainer::ReadAssignmentContainer(), IMP::domino::ReadHDF5AssignmentContainer::ReadHDF5AssignmentContainer(), IMP::domino::RecursiveAssignmentsTable::load_assignments(), IMP::domino::RecursiveStates::RecursiveStates(), IMP::domino::RestraintCache::add_restraint_internal(), IMP::domino::RestraintCache::add_restraint_set_child_internal(), IMP::domino::RestraintCache::add_restraint_set_internal(), IMP::domino::RestraintCache::get_restraints(), IMP::domino::RestraintCache::get_score(), IMP::domino::RestraintCache::get_slice(), IMP::domino::RestraintCache::load_last_score(), IMP::domino::RestraintScoreSubsetFilterTable::get_strength(), IMP::domino::RestraintScoreSubsetFilterTable::get_subset_filter(), IMP::domino::SimpleAssignmentsTable::load_assignments(), IMP::domino::Slice::get_slice(), IMP::domino::Slice::Slice(), IMP::domino::Slice::get_sliced(), IMP::domino::Subset::get_contains(), IMP::domino::SubsetFilterTable::get_strength(), IMP::domino::SubsetFilterTable::get_subset_filter(), IMP::domino::WriteAssignmentContainer::WriteAssignmentContainer(), IMP::domino::WriteHDF5AssignmentContainer::WriteHDF5AssignmentContainer(), IMP::domino::WriteHDF5AssignmentContainer::WriteHDF5AssignmentContainer(), IMP::em2d::DistanceFilter::DistanceFilter(), IMP::em2d::DistanceFilterTable::DistanceFilterTable(), IMP::em2d::DistanceFilterTable::get_strength(), IMP::em2d::DistanceFilterTable::get_subset_filter(), IMP::example::ExampleSubsetFilterTable::get_indexes(), IMP::example::ExampleSubsetFilterTable::get_strength(), IMP::example::ExampleSubsetFilterTable::get_subset_filter(), IMP::domino::get_is_merge_tree(), IMP::domino::load_particle_states(), IMP::domino::get_restraints(), IMP::domino::get_difference(), IMP::domino::get_distance_if_smaller_than(), IMP::domino::get_embedding(), IMP::domino::get_index(), IMP::domino::get_intersection(), IMP::domino::get_nearest_assignment(), IMP::domino::get_order(), IMP::domino::get_partial_index(), IMP::domino::get_slice(), IMP::domino::get_state_clusters(), IMP::domino::get_union(), IMP::domino::load_leaf_assignments(), IMP::domino::load_merged_assignments(), IMP::domino::load_merged_assignments_random_order(), IMP::domino::swap()
IMP::domino::SubsetFilterTable	IMP::domino::DiscreteSampler::remove_subset_filter_table(), IMP::domino::DiscreteSampler::add_subset_filter_table()

IMP.em

Class	Users
IMP::em::DensityHeader	IMP::em::DensityMap::DensityMap(), IMP::em::DistanceMask::DistanceMask(), IMP::em::EMReaderWriter::read(), IMP::em::EMReaderWriter::write(), IMP::em::MRCReaderWriter::read(), IMP::em::MRCReaderWriter::write(), IMP::em::MapReaderWriter::read(), IMP::em::MapReaderWriter::write(), IMP::em::RadiusDependentDistanceMask::RadiusDependentDistanceMask(), IMP::em::SampledDensityMap::SampledDensityMap(), IMP::em::SpiderMapReaderWriter::read(), IMP::em::SpiderMapReaderWriter::write(), IMP::em::SurfaceShellDensityMap::SurfaceShellDensityMap(), IMP::em::XplorReaderWriter::read(), IMP::em::XplorReaderWriter::write(), IMP::cnmultifit::build_cn_dens_assembly(), IMP::em::DensityHeader_to_ImageHeader(), IMP::em::ImageHeader_to_DensityHeader()
IMP::em::DensityMap	IMP::cnmultifit::AlignSymmetric::AlignSymmetric(), IMP::cnmultifit::CnSymmAxisDetector::CnSymmAxisDetector(), IMP::em::CoarseCC::calc_score(), IMP::em::CoarseCC::cross_correlation_coefficient(), IMP::em::CoarseCC::local_cross_correlation_coefficient(), IMP::em::CoarseCCatIntervals::evaluate(), IMP::em::CoarseConvolution::convolution(), IMP::em::DensityFillingRestraint::DensityFillingRestraint(), IMP::em::DensityMap::add(), IMP::em::DensityMap::copy_map(), IMP::em::DensityMap::pick_max(), IMP::em::DensityMap::same_dimensions(), IMP::em::DensityMap::same_origin(), IMP::em::DensityMap::same_voxel_size(), IMP::em::EnvelopeFitRestraint::EnvelopeFitRestraint(), IMP::em::EnvelopePenetrationRestraint::EnvelopePenetrationRestraint(), IMP::em::FitRestraint::FitRestraint(), IMP::em::HighDensityEmbedding::HighDensityEmbedding(), IMP::em::MapDistanceTransform::MapDistanceTransform(), IMP::em::PCAAligner::PCAAligner(), IMP::em::PCAFitRestraint::PCAFitRestraint(), IMP::multifit::DensityDataPoints::DensityDataPoints(), IMP::multifit::DensityDataPoints::set_density(), IMP::multifit::FFTFitting::do_global_fitting(), IMP::multifit::FFTFitting::do_local_fitting(), IMP::multifit::FFTFitting::copy_density_data(), IMP::multifit::FFTFitting::crop_margin(), IMP::multifit::FFTFitting::prepare_lowres_map(), IMP::multifit::FFTFitting::prepare_poslist(), IMP::multifit::FFTFitting::prepare_poslist_flipped(), IMP::multifit::ProteomicsEMAlignmentAtomic::set_density_map(), IMP::cnmultifit::build_cn_dens_assembly(), IMP::cnmultifit::fit_cn_assembly(), IMP::cnmultifit::fit_cn_assembly(), IMP::cnmultifit::symmetry_local_fitting(), IMP::em::add_to_map(), IMP::em::approximate_molecular_mass(), IMP::em::binarize(), IMP::em::compute_fitting_score(), IMP::em::compute_fitting_scores(), IMP::em::compute_fitting_scores(), IMP::em::convolute(), IMP::em::create_density_map(), IMP::em::density2particles(), IMP::em::density2vectors(), IMP::em::get_binarized_interior(), IMP::em::get_bounding_box(), IMP::em::get_bounding_box(), IMP::em::get_density(), IMP::em::get_grid(), IMP::em::get_interiors_intersect(), IMP::em::get_molecular_mass_at_threshold(), IMP::em::get_number_of_particles_outside_of_the_density(), IMP::em::get_numbers_of_particles_outside_of_the_density(), IMP::em::get_percentage_of_voxels_covered_by_particles(), IMP::em::get_resampled(), IMP::em::get_segment(), IMP::em::get_segment(), IMP::em::get_segment_by_masking(), IMP::em::get_sum(), IMP::em::get_threshold_for_approximate_mass(), IMP::em::get_threshold_for_approximate_volume(), IMP::em::get_threshold_map(), IMP::em::get_transformed(), IMP::em::get_transformed(), IMP::em::get_transformed_into(), IMP::em::get_transformed_into2(), IMP::em::get_volume_at_threshold(), IMP::em::interpolate_map(), 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::em::mask_and_norm(), IMP::em::multiply(), IMP::em::write_map(), IMP::em::write_map(), IMP::multifit::create_coarse_molecule_from_density(), IMP::multifit::create_hit_map(), IMP::multifit::fft_based_rigid_fitting(), IMP::multifit::get_anchors_for_density(), IMP::multifit::get_connected_components(), IMP::multifit::get_segment_maximum(), IMP::multifit::get_segmentation(), IMP::multifit::pca_based_rigid_fitting(), IMP::multifit::pca_based_rigid_fitting(), IMP::multifit::remove_background(), IMP::multifit::write_segment_as_mrc(), IMP::multifit::write_segments_as_mrc()
IMP::em::FittingSolutions	IMP::multifit::convert_em_to_multifit_format()
IMP::em::ImageHeader	IMP::em2d::ImageReaderWriter::read(), IMP::em2d::ImageReaderWriter::read_from_floats(), IMP::em2d::ImageReaderWriter::read_from_ints(), IMP::em2d::ImageReaderWriter::write(), IMP::em2d::ImageReaderWriter::write_to_floats(), IMP::em2d::ImageReaderWriter::write_to_ints(), IMP::em2d::JPGImageReaderWriter::read(), IMP::em2d::JPGImageReaderWriter::read_from_floats(), IMP::em2d::JPGImageReaderWriter::read_from_ints(), IMP::em2d::JPGImageReaderWriter::write(), IMP::em2d::JPGImageReaderWriter::write_to_floats(), IMP::em2d::JPGImageReaderWriter::write_to_ints(), IMP::em2d::RegistrationResult::read_from_image(), IMP::em2d::RegistrationResult::set_in_image(), IMP::em2d::SpiderImageReaderWriter::read(), IMP::em2d::SpiderImageReaderWriter::read_from_floats(), IMP::em2d::SpiderImageReaderWriter::read_from_ints(), IMP::em2d::SpiderImageReaderWriter::write(), IMP::em2d::SpiderImageReaderWriter::write_to_floats(), IMP::em2d::SpiderImageReaderWriter::write_to_ints(), IMP::em2d::TIFFImageReaderWriter::read(), IMP::em2d::TIFFImageReaderWriter::read_from_floats(), IMP::em2d::TIFFImageReaderWriter::read_from_ints(), IMP::em2d::TIFFImageReaderWriter::write(), IMP::em2d::TIFFImageReaderWriter::write_to_floats(), IMP::em2d::TIFFImageReaderWriter::write_to_ints(), IMP::em::DensityHeader_to_ImageHeader(), IMP::em::ImageHeader_to_DensityHeader()
IMP::em::KernelParameters	IMP::em2d::ProjectionMask::ProjectionMask(), IMP::em2d::ProjectionMask::create()
IMP::em::MapDistanceTransform	IMP::em::EnvelopeScore::EnvelopeScore()
IMP::em::MapReaderWriter	IMP::em::read_map(), IMP::em::write_map()
IMP::em::RadiusDependentKernelParameters	IMP::em2d::ProjectionMask::ProjectionMask(), IMP::em2d::ProjectionMask::create()
IMP::em::SampledDensityMap	IMP::em::CoarseCC::calc_score(), IMP::em::CoarseCCatIntervals::evaluate()
IMP::em::SurfaceShellDensityMap	IMP::em::calculate_intersection_score()

IMP.em2d

Class	Users
IMP::em2d::ClusterSet	IMP::em2d::AverageDistanceLinkage::operator()(), IMP::em2d::CompleteLinkage::operator()(), IMP::em2d::SingleLinkage::operator()()
IMP::em2d::Em2DRestraintParameters	IMP::em2d::Em2DRestraint::setup(), IMP::em2d::ProjectionFinder::setup()
IMP::em2d::Image	IMP::em2d::ChiSquaredScore::get_private_score(), IMP::em2d::ChiSquaredScore::set_variance_imag_private(), IMP::em2d::EM2DScore::get_private_score(), IMP::em2d::Fine2DRegistrationRestraint::set_subject_image(), IMP::em2d::Image::set_size(), IMP::em2d::MeanAbsoluteDifference::get_private_score(), IMP::em2d::RigidBodiesImageFitRestraint::RigidBodiesImageFitRestraint(), IMP::em2d::ScoreFunction::get_score(), IMP::em2d::ScoreFunction::set_variance_image(), IMP::em2d::ScoreFunction::get_private_score(), IMP::em2d::ScoreFunction::set_variance_image_private(), IMP::em2d::add_noise(), IMP::em2d::apply_diffusion_filter(), IMP::em2d::apply_mean_outside_mask(), IMP::em2d::apply_variance_filter(), IMP::em2d::crop(), IMP::em2d::do_combined_fill_holes_and_threshold(), IMP::em2d::do_extend_borders(), IMP::em2d::do_fill_holes(), IMP::em2d::do_normalize(), IMP::em2d::do_remove_small_objects(), IMP::em2d::do_resample_polar(), IMP::em2d::do_segmentation(), IMP::em2d::do_subtract_images(), IMP::em2d::get_autocorrelation2d(), IMP::em2d::get_correlation2d(), IMP::em2d::get_cross_correlation_coefficient(), IMP::em2d::get_histogram(), IMP::em2d::get_projection()
IMP::em2d::ImageReaderWriter	IMP::em2d::Image::Image(), IMP::em2d::Image::read(), IMP::em2d::Image::write(), IMP::em2d::ProjectingOptions::ProjectingOptions(), IMP::em2d::read_images(), IMP::em2d::save_images()
IMP::em2d::PolarResamplingParameters	IMP::em2d::do_resample_polar(), IMP::em2d::do_resample_polar()
IMP::em2d::ProjectingOptions	IMP::em2d::create_evenly_distributed_projections(), IMP::em2d::do_project_particles(), IMP::em2d::get_projection(), IMP::em2d::get_projections(), IMP::em2d::get_projections()
IMP::em2d::ProjectingParameters	IMP::em2d::Fine2DRegistrationRestraint::setup(), IMP::em2d::RigidBodiesImageFitRestraint::set_projecting_parameters()
IMP::em2d::RegistrationResult	IMP::em2d::get_projection(), IMP::em2d::get_rotation_error(), IMP::em2d::get_shift_error()
IMP::em2d::ScoreFunction	IMP::em2d::Em2DRestraint::setup(), IMP::em2d::Fine2DRegistrationRestraint::setup(), IMP::em2d::ProjectionFinder::setup(), IMP::em2d::RigidBodiesImageFitRestraint::RigidBodiesImageFitRestraint()
IMP::em2d::SegmentationParameters	IMP::em2d::do_segmentation(), IMP::em2d::do_segmentation()

IMP.isd

Class	Users
IMP::isd::BivariateFunction	IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation()
IMP::isd::CrossLinkData	IMP::isd::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint(), IMP::isd::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint()
IMP::isd::CysteineCrossLinkData	IMP::isd::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint()
IMP::isd::FretData	IMP::isd::FretRestraint::FretRestraint()
IMP::isd::GaussianProcessInterpolation	IMP::isd::GaussianProcessInterpolationRestraint::GaussianProcessInterpolationRestraint()
IMP::isd::LogWrapper	IMP::isd::LogWrapper::on_remove()
IMP::isd::UnivariateFunction	IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation()

IMP.kernel

Class	Users
IMP::kernel::Configuration	IMP::kernel::Configuration::Configuration()
IMP::kernel::ConfigurationSet	IMP::kernel::SaveToConfigurationSetOptimizerState::SaveToConfigurationSetOptimizerState()
IMP::kernel::Container	IMP::kernel::create_restraint()
IMP::kernel::Decorator	IMP::kernel::ParticleAdaptor::ParticleAdaptor(), IMP::kernel::ParticleIndexAdaptor::ParticleIndexAdaptor(), IMP::kernel::get_vector_geometry(), IMP::kernel::set_vector_geometry()
IMP::kernel::DerivativeAccumulator	IMP::atom::CHARMMStereochemistryRestraint::unprotected_evaluate(), IMP::container::PairsRestraint::unprotected_evaluate(), IMP::container::QuadsRestraint::unprotected_evaluate(), IMP::container::SingletonsRestraint::unprotected_evaluate(), IMP::container::TripletsRestraint::unprotected_evaluate(), IMP::core::ConstantRestraint::unprotected_evaluate(), IMP::core::DiameterRestraint::unprotected_evaluate(), IMP::core::DihedralRestraint::unprotected_evaluate(), IMP::core::MSConnectivityRestraint::unprotected_evaluate(), IMP::core::VolumeRestraint::unprotected_evaluate(), IMP::em2d::DummyRestraint::unprotected_evaluate(), IMP::em2d::Em2DRestraint::unprotected_evaluate(), IMP::em2d::Fine2DRegistrationRestraint::unprotected_evaluate(), IMP::em2d::ParticlesDummyRestraint::unprotected_evaluate(), IMP::em2d::RigidBodiesImageFitRestraint::unprotected_evaluate(), IMP::em::DensityFillingRestraint::unprotected_evaluate(), IMP::em::EnvelopePenetrationRestraint::unprotected_evaluate(), IMP::em::FitRestraint::unprotected_evaluate(), IMP::em::PCAFitRestraint::unprotected_evaluate(), IMP::example::ExampleComplexRestraint::unprotected_evaluate(), IMP::isd::AmbiguousNOERestraint::unprotected_evaluate(), IMP::isd::AmbiguousRestraint::unprotected_evaluate(), IMP::isd::CrossLinkMSRestraint::unprotected_evaluate(), IMP::isd::CysteineCrossLinkRestraint::unprotected_evaluate(), IMP::isd::FretRestraint::unprotected_evaluate(), IMP::isd::GaussianRestraint::unprotected_evaluate(), IMP::isd::JeffreysRestraint::unprotected_evaluate(), IMP::isd::LogWrapper::unprotected_evaluate(), IMP::isd::LognormalRestraint::unprotected_evaluate(), IMP::isd::MarginalHBondRestraint::unprotected_evaluate(), IMP::isd::MarginalNOERestraint::unprotected_evaluate(), IMP::isd::NOERestraint::unprotected_evaluate(), IMP::isd::TALOSRestraint::unprotected_evaluate(), IMP::isd::UniformPrior::unprotected_evaluate(), IMP::isd::WeightRestraint::unprotected_evaluate(), IMP::isd::vonMisesKappaConjugateRestraint::unprotected_evaluate(), IMP::isd::vonMisesKappaJeffreysRestraint::unprotected_evaluate(), IMP::kernel::Constraint::do_after_evaluate(), IMP::kernel::Constraint::do_update_derivatives(), IMP::kernel::DerivativeAccumulator::DerivativeAccumulator(), IMP::kernel::PairScore::evaluate(), IMP::kernel::PairScore::evaluate_if_good_index(), IMP::kernel::PairScore::evaluate_if_good_indexes(), IMP::kernel::PairScore::evaluate_index(), IMP::kernel::PairScore::evaluate_indexes(), IMP::kernel::QuadScore::evaluate(), IMP::kernel::QuadScore::evaluate_if_good_index(), IMP::kernel::QuadScore::evaluate_if_good_indexes(), IMP::kernel::QuadScore::evaluate_index(), IMP::kernel::QuadScore::evaluate_indexes(), IMP::kernel::RestraintSet::unprotected_evaluate(), IMP::kernel::ScoreState::after_evaluate(), IMP::kernel::ScoreState::do_after_evaluate(), IMP::kernel::SingletonScore::evaluate(), IMP::kernel::SingletonScore::evaluate_if_good_index(), IMP::kernel::SingletonScore::evaluate_if_good_indexes(), IMP::kernel::SingletonScore::evaluate_index(), IMP::kernel::SingletonScore::evaluate_indexes(), IMP::kernel::TripletScore::evaluate(), IMP::kernel::TripletScore::evaluate_if_good_index(), IMP::kernel::TripletScore::evaluate_if_good_indexes(), IMP::kernel::TripletScore::evaluate_index(), IMP::kernel::TripletScore::evaluate_indexes(), IMP::modeller::MultipleBinormalRestraint::unprotected_evaluate(), IMP::multifit::ComplementarityRestraint::unprotected_evaluate(), IMP::multifit::DummyRestraint::unprotected_evaluate(), IMP::multifit::RadiusOfGyrationRestraint::unprotected_evaluate(), IMP::multifit::WeightedExcludedVolumeRestraint::unprotected_evaluate(), IMP::pmi::CompositeRestraint::unprotected_evaluate(), IMP::pmi::SigmoidRestraintSphere::unprotected_evaluate(), IMP::saxs::RadiusOfGyrationRestraint::unprotected_evaluate(), IMP::saxs::Restraint::unprotected_evaluate()
IMP::kernel::Key	IMP::kernel::Key::add_alias(), IMP::kernel::ScopedAddCacheAttribute::ScopedAddCacheAttribute(), IMP::kernel::ScopedAddCacheAttribute::set(), IMP::kernel::ScopedSetAttribute::ScopedSetAttribute(), IMP::kernel::ScopedSetAttribute::set(), 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::kernel::Model	IMP::atom::Angle::do_setup_particle(), IMP::atom::Angle::Angle(), IMP::atom::Angle::get_is_setup(), IMP::atom::Angle::setup_particle(), IMP::atom::AngleSingletonScore::do_get_inputs(), IMP::atom::AngleSingletonScore::evaluate_if_good_indexes(), IMP::atom::AngleSingletonScore::evaluate_index(), IMP::atom::AngleSingletonScore::evaluate_indexes(), IMP::atom::Atom::do_setup_particle(), IMP::atom::Atom::do_setup_particle(), IMP::atom::Atom::Atom(), IMP::atom::Atom::get_is_setup(), IMP::atom::Atom::setup_particle(), IMP::atom::Atom::setup_particle(), IMP::atom::Bond::Bond(), IMP::atom::Bond::get_is_setup(), IMP::atom::BondEndpointsRefiner::do_get_inputs(), IMP::atom::BondSingletonScore::do_get_inputs(), IMP::atom::BondSingletonScore::evaluate_if_good_indexes(), IMP::atom::BondSingletonScore::evaluate_index(), IMP::atom::BondSingletonScore::evaluate_indexes(), IMP::atom::Bonded::do_setup_particle(), IMP::atom::Bonded::Bonded(), IMP::atom::Bonded::get_is_setup(), IMP::atom::Bonded::setup_particle(), IMP::atom::BondedPairFilter::do_get_inputs(), IMP::atom::BondedPairFilter::get_value_index(), IMP::atom::BondedPairFilter::get_value_index(), IMP::atom::BrownianDynamics::BrownianDynamics(), IMP::atom::CHARMMAtom::do_setup_particle(), IMP::atom::CHARMMAtom::CHARMMAtom(), IMP::atom::CHARMMAtom::get_is_setup(), IMP::atom::CHARMMAtom::setup_particle(), IMP::atom::CHARMMTopology::create_hierarchy(), IMP::atom::CenterOfMass::do_setup_particle(), IMP::atom::CenterOfMass::do_setup_particle(), IMP::atom::CenterOfMass::CenterOfMass(), IMP::atom::CenterOfMass::get_is_setup(), IMP::atom::CenterOfMass::setup_particle(), IMP::atom::CenterOfMass::setup_particle(), IMP::atom::Chain::do_setup_particle(), IMP::atom::Chain::do_setup_particle(), IMP::atom::Chain::do_setup_particle(), IMP::atom::Chain::Chain(), IMP::atom::Chain::get_is_setup(), IMP::atom::Chain::setup_particle(), IMP::atom::Chain::setup_particle(), IMP::atom::Chain::setup_particle(), IMP::atom::Charged::do_setup_particle(), IMP::atom::Charged::do_setup_particle(), IMP::atom::Charged::Charged(), IMP::atom::Charged::get_is_setup(), IMP::atom::Charged::setup_particle(), IMP::atom::Charged::setup_particle(), IMP::atom::Copy::do_setup_particle(), IMP::atom::Copy::get_is_setup(), IMP::atom::Copy::setup_particle(), IMP::atom::Copy::Copy(), IMP::atom::CoulombPairScore::do_get_inputs(), IMP::atom::CoulombPairScore::evaluate_if_good_indexes(), IMP::atom::CoulombPairScore::evaluate_index(), IMP::atom::CoulombPairScore::evaluate_indexes(), IMP::atom::CoverBond::apply_index(), IMP::atom::CoverBond::apply_indexes(), IMP::atom::CoverBond::do_get_inputs(), IMP::atom::CoverBond::do_get_outputs(), IMP::atom::Diffusion::do_setup_particle(), IMP::atom::Diffusion::do_setup_particle(), IMP::atom::Diffusion::do_setup_particle(), IMP::atom::Diffusion::Diffusion(), IMP::atom::Diffusion::get_is_setup(), IMP::atom::Diffusion::setup_particle(), IMP::atom::Diffusion::setup_particle(), IMP::atom::Diffusion::setup_particle(), IMP::atom::Dihedral::do_setup_particle(), IMP::atom::Dihedral::Dihedral(), IMP::atom::Dihedral::get_is_setup(), IMP::atom::Dihedral::setup_particle(), IMP::atom::DihedralSingletonScore::do_get_inputs(), IMP::atom::DihedralSingletonScore::evaluate_if_good_indexes(), IMP::atom::DihedralSingletonScore::evaluate_index(), IMP::atom::DihedralSingletonScore::evaluate_indexes(), IMP::atom::Domain::do_setup_particle(), IMP::atom::Domain::do_setup_particle(), IMP::atom::Domain::get_is_setup(), IMP::atom::Domain::setup_particle(), IMP::atom::Domain::setup_particle(), IMP::atom::Domain::Domain(), IMP::atom::Fragment::do_setup_particle(), IMP::atom::Fragment::do_setup_particle(), IMP::atom::Fragment::set_residue_indexes(), IMP::atom::Fragment::set_residue_indexes(), IMP::atom::Fragment::get_is_setup(), IMP::atom::Fragment::setup_particle(), IMP::atom::Fragment::setup_particle(), IMP::atom::Fragment::setup_particle(), IMP::atom::Fragment::Fragment(), IMP::atom::Hierarchy::Hierarchy(), IMP::atom::Hierarchy::get_is_setup(), IMP::atom::Hierarchy::setup_particle(), IMP::atom::ImproperSingletonScore::do_get_inputs(), IMP::atom::ImproperSingletonScore::evaluate_if_good_indexes(), IMP::atom::ImproperSingletonScore::evaluate_index(), IMP::atom::ImproperSingletonScore::evaluate_indexes(), IMP::atom::LennardJones::do_setup_particle(), IMP::atom::LennardJones::LennardJones(), IMP::atom::LennardJones::get_is_setup(), IMP::atom::LennardJones::setup_particle(), IMP::atom::LennardJones::setup_particle(), IMP::atom::LennardJonesPairScore::do_get_inputs(), IMP::atom::LennardJonesPairScore::evaluate_if_good_indexes(), IMP::atom::LennardJonesPairScore::evaluate_index(), IMP::atom::LennardJonesPairScore::evaluate_indexes(), IMP::atom::Mass::do_setup_particle(), IMP::atom::Mass::get_is_setup(), IMP::atom::Mass::setup_particle(), IMP::atom::Mass::Mass(), IMP::atom::MolecularDynamics::MolecularDynamics(), IMP::atom::Molecule::do_setup_particle(), IMP::atom::Molecule::Molecule(), IMP::atom::Molecule::get_is_setup(), IMP::atom::Molecule::setup_particle(), IMP::atom::Molecule::setup_particle(), IMP::atom::RemoveRigidMotionOptimizerState::RemoveRigidMotionOptimizerState(), IMP::atom::RemoveTranslationOptimizerState::RemoveTranslationOptimizerState(), IMP::atom::Representation::do_setup_particle(), IMP::atom::Representation::get_is_setup(), IMP::atom::Representation::setup_particle(), IMP::atom::Representation::setup_particle(), IMP::atom::Representation::Representation(), IMP::atom::Residue::do_setup_particle(), IMP::atom::Residue::do_setup_particle(), IMP::atom::Residue::Residue(), IMP::atom::Residue::get_is_setup(), IMP::atom::Residue::setup_particle(), IMP::atom::Residue::setup_particle(), IMP::atom::Residue::setup_particle(), IMP::atom::Residue::setup_particle(), IMP::atom::RigidBodyDiffusion::do_setup_particle(), IMP::atom::RigidBodyDiffusion::RigidBodyDiffusion(), IMP::atom::RigidBodyDiffusion::get_is_setup(), IMP::atom::RigidBodyDiffusion::setup_particle(), IMP::atom::SameResiduePairFilter::do_get_inputs(), IMP::atom::SameResiduePairFilter::get_value_index(), IMP::atom::SameResiduePairFilter::get_value_index(), IMP::atom::SecondaryStructureResidue::do_setup_particle(), IMP::atom::SecondaryStructureResidue::SecondaryStructureResidue(), IMP::atom::SecondaryStructureResidue::get_is_setup(), IMP::atom::SecondaryStructureResidue::setup_particle(), IMP::atom::Selection::search(), IMP::atom::Selection::set_hierarchies(), IMP::atom::Selection::Selection(), IMP::atom::Simulator::Simulator(), IMP::atom::SoapPairFilter::do_get_inputs(), IMP::atom::SoapPairFilter::get_value_index(), IMP::atom::SoapPairFilter::get_value_index(), IMP::atom::State::do_setup_particle(), IMP::atom::State::get_is_setup(), IMP::atom::State::setup_particle(), IMP::atom::State::State(), IMP::atom::StereochemistryPairFilter::do_get_inputs(), IMP::atom::StereochemistryPairFilter::get_value_index(), IMP::atom::StereochemistryPairFilter::get_value_index(), IMP::atom::VelocityScalingOptimizerState::VelocityScalingOptimizerState(), IMP::atom::WritePDBOptimizerState::WritePDBOptimizerState(), IMP::container::ConsecutivePairFilter::do_get_inputs(), IMP::container::ConsecutivePairFilter::get_value_index(), IMP::container::ConsecutivePairFilter::get_value_index(), IMP::container::ExclusiveConsecutivePairContainer::get_contains(), IMP::container::ExclusiveConsecutivePairFilter::do_get_inputs(), IMP::container::ExclusiveConsecutivePairFilter::get_value_index(), IMP::container::ExclusiveConsecutivePairFilter::get_value_index(), IMP::container::InContainerPairFilter::do_get_inputs(), IMP::container::InContainerPairFilter::get_value_index(), IMP::container::InContainerPairFilter::get_value_index(), IMP::container::InContainerQuadFilter::do_get_inputs(), IMP::container::InContainerQuadFilter::get_value_index(), IMP::container::InContainerQuadFilter::get_value_index(), IMP::container::InContainerSingletonFilter::do_get_inputs(), IMP::container::InContainerSingletonFilter::get_value_index(), IMP::container::InContainerSingletonFilter::get_value_index(), IMP::container::InContainerTripletFilter::do_get_inputs(), IMP::container::InContainerTripletFilter::get_value_index(), IMP::container::InContainerTripletFilter::get_value_index(), IMP::container::ListPairContainer::ListPairContainer(), IMP::container::ListQuadContainer::ListQuadContainer(), IMP::container::ListSingletonContainer::ListSingletonContainer(), IMP::container::ListTripletContainer::ListTripletContainer(), IMP::container::MinimumPairScore::do_create_current_decomposition(), IMP::container::MinimumPairScore::do_get_inputs(), IMP::container::MinimumPairScore::evaluate_if_good_indexes(), IMP::container::MinimumPairScore::evaluate_index(), IMP::container::MinimumPairScore::evaluate_indexes(), IMP::container::MinimumQuadScore::do_create_current_decomposition(), IMP::container::MinimumQuadScore::do_get_inputs(), IMP::container::MinimumQuadScore::evaluate_if_good_indexes(), IMP::container::MinimumQuadScore::evaluate_index(), IMP::container::MinimumQuadScore::evaluate_indexes(), IMP::container::MinimumSingletonScore::do_create_current_decomposition(), IMP::container::MinimumSingletonScore::do_get_inputs(), IMP::container::MinimumSingletonScore::evaluate_if_good_indexes(), IMP::container::MinimumSingletonScore::evaluate_index(), IMP::container::MinimumSingletonScore::evaluate_indexes(), IMP::container::MinimumTripletScore::do_create_current_decomposition(), IMP::container::MinimumTripletScore::do_get_inputs(), IMP::container::MinimumTripletScore::evaluate_if_good_indexes(), IMP::container::MinimumTripletScore::evaluate_index(), IMP::container::MinimumTripletScore::evaluate_indexes(), IMP::container::PairContainerSet::PairContainerSet(), IMP::container::QuadContainerSet::QuadContainerSet(), IMP::container::SingletonContainerSet::SingletonContainerSet(), IMP::container::TripletContainerSet::TripletContainerSet(), IMP::core::AllSamePairPredicate::do_get_inputs(), IMP::core::AllSamePairPredicate::get_value_index(), IMP::core::AllSamePairPredicate::get_value_index(), IMP::core::AllSameQuadPredicate::do_get_inputs(), IMP::core::AllSameQuadPredicate::get_value_index(), IMP::core::AllSameQuadPredicate::get_value_index(), IMP::core::AllSameSingletonPredicate::do_get_inputs(), IMP::core::AllSameSingletonPredicate::get_value_index(), IMP::core::AllSameSingletonPredicate::get_value_index(), IMP::core::AllSameTripletPredicate::do_get_inputs(), IMP::core::AllSameTripletPredicate::get_value_index(), IMP::core::AllSameTripletPredicate::get_value_index(), IMP::core::AngleTripletScore::do_get_inputs(), IMP::core::AngleTripletScore::evaluate_if_good_indexes(), IMP::core::AngleTripletScore::evaluate_index(), IMP::core::AngleTripletScore::evaluate_indexes(), IMP::core::AttributeSingletonPredicate::do_get_inputs(), IMP::core::AttributeSingletonPredicate::get_value_index(), IMP::core::AttributeSingletonPredicate::get_value_index(), IMP::core::BallMover::BallMover(), IMP::core::BallMover::BallMover(), IMP::core::BoxSweepClosePairsFinder::do_get_inputs(), IMP::core::BoxSweepClosePairsFinder::get_close_pairs(), IMP::core::BoxSweepClosePairsFinder::get_close_pairs(), IMP::core::Centroid::do_setup_particle(), IMP::core::Centroid::do_setup_particle(), IMP::core::Centroid::Centroid(), IMP::core::Centroid::get_is_setup(), IMP::core::Centroid::setup_particle(), IMP::core::Centroid::setup_particle(), IMP::core::CentroidOfRefined::apply_index(), IMP::core::CentroidOfRefined::apply_indexes(), IMP::core::CentroidOfRefined::do_get_inputs(), IMP::core::CentroidOfRefined::do_get_outputs(), IMP::core::ChecksScoreState::ChecksScoreState(), IMP::core::ChildrenRefiner::do_get_inputs(), IMP::core::ClosePairsFinder::get_close_pairs(), IMP::core::ClosePairsFinder::get_close_pairs(), IMP::core::ClosePairsPairScore::get_close_pairs(), IMP::core::ClosePairsPairScore::create_current_decomposition(), IMP::core::ClosePairsPairScore::do_get_inputs(), IMP::core::ClosePairsPairScore::evaluate_if_good_index(), IMP::core::ClosePairsPairScore::evaluate_if_good_indexes(), IMP::core::ClosePairsPairScore::evaluate_index(), IMP::core::ClosePairsPairScore::evaluate_indexes(), IMP::core::CoinFlipPairPredicate::do_get_inputs(), IMP::core::CoinFlipPairPredicate::get_value_index(), IMP::core::CoinFlipPairPredicate::get_value_index(), IMP::core::CoinFlipQuadPredicate::do_get_inputs(), IMP::core::CoinFlipQuadPredicate::get_value_index(), IMP::core::CoinFlipQuadPredicate::get_value_index(), IMP::core::CoinFlipSingletonPredicate::do_get_inputs(), IMP::core::CoinFlipSingletonPredicate::get_value_index(), IMP::core::CoinFlipSingletonPredicate::get_value_index(), IMP::core::CoinFlipTripletPredicate::do_get_inputs(), IMP::core::CoinFlipTripletPredicate::get_value_index(), IMP::core::CoinFlipTripletPredicate::get_value_index(), IMP::core::ConjugateGradients::ConjugateGradients(), IMP::core::ConstantPairPredicate::do_get_inputs(), IMP::core::ConstantPairPredicate::get_value_index(), IMP::core::ConstantPairPredicate::get_value_index(), IMP::core::ConstantQuadPredicate::do_get_inputs(), IMP::core::ConstantQuadPredicate::get_value_index(), IMP::core::ConstantQuadPredicate::get_value_index(), IMP::core::ConstantSingletonPredicate::do_get_inputs(), IMP::core::ConstantSingletonPredicate::get_value_index(), IMP::core::ConstantSingletonPredicate::get_value_index(), IMP::core::ConstantTripletPredicate::do_get_inputs(), IMP::core::ConstantTripletPredicate::get_value_index(), IMP::core::ConstantTripletPredicate::get_value_index(), IMP::core::Cover::do_setup_particle(), IMP::core::Cover::do_setup_particle(), IMP::core::Cover::Cover(), IMP::core::Cover::get_is_setup(), IMP::core::Cover::setup_particle(), IMP::core::Cover::setup_particle(), IMP::core::CoverRefined::apply_index(), IMP::core::CoverRefined::apply_indexes(), IMP::core::CoverRefined::do_get_inputs(), IMP::core::CoverRefined::do_get_outputs(), IMP::core::DerivativesFromRefined::apply_index(), IMP::core::DerivativesFromRefined::apply_indexes(), IMP::core::DerivativesFromRefined::do_get_inputs(), IMP::core::DerivativesFromRefined::do_get_outputs(), IMP::core::DerivativesToRefined::apply_index(), IMP::core::DerivativesToRefined::apply_indexes(), IMP::core::DerivativesToRefined::do_get_inputs(), IMP::core::DerivativesToRefined::do_get_outputs(), IMP::core::DistancePairScore::do_get_inputs(), IMP::core::DistancePairScore::evaluate_index(), IMP::core::FixedRefiner::do_get_inputs(), IMP::core::Gaussian::do_setup_particle(), IMP::core::Gaussian::do_setup_particle(), IMP::core::Gaussian::Gaussian(), IMP::core::Gaussian::get_is_setup(), IMP::core::Gaussian::setup_particle(), IMP::core::Gaussian::setup_particle(), IMP::core::GenericAttributeSingletonScore::do_get_inputs(), IMP::core::GenericAttributeSingletonScore::evaluate_if_good_indexes(), IMP::core::GenericAttributeSingletonScore::evaluate_index(), IMP::core::GenericAttributeSingletonScore::evaluate_indexes(), IMP::core::GenericBoundingBox3DSingletonScore::do_get_inputs(), IMP::core::GenericBoundingBox3DSingletonScore::evaluate_if_good_indexes(), IMP::core::GenericBoundingBox3DSingletonScore::evaluate_index(), IMP::core::GenericBoundingBox3DSingletonScore::evaluate_indexes(), IMP::core::GenericDistanceToSingletonScore::do_get_inputs(), IMP::core::GenericDistanceToSingletonScore::evaluate_if_good_indexes(), IMP::core::GenericDistanceToSingletonScore::evaluate_index(), IMP::core::GenericDistanceToSingletonScore::evaluate_indexes(), IMP::core::GridClosePairsFinder::do_get_inputs(), IMP::core::GridClosePairsFinder::get_close_pairs(), IMP::core::GridClosePairsFinder::get_close_pairs(), IMP::core::HarmonicDistancePairScore::do_get_inputs(), IMP::core::HarmonicDistancePairScore::evaluate_index(), IMP::core::HarmonicSphereDistancePairScore::do_get_inputs(), IMP::core::HarmonicSphereDistancePairScore::evaluate_index(), IMP::core::HarmonicUpperBoundSphereDiameterPairScore::do_get_inputs(), IMP::core::HarmonicUpperBoundSphereDiameterPairScore::evaluate_if_good_indexes(), IMP::core::HarmonicUpperBoundSphereDiameterPairScore::evaluate_index(), IMP::core::HarmonicUpperBoundSphereDiameterPairScore::evaluate_indexes(), IMP::core::HarmonicUpperBoundSphereDistancePairScore::do_get_inputs(), IMP::core::HarmonicUpperBoundSphereDistancePairScore::evaluate_index(), IMP::core::Hierarchy::do_setup_particle(), IMP::core::Hierarchy::do_setup_particle(), IMP::core::Hierarchy::do_setup_particle(), IMP::core::Hierarchy::Hierarchy(), IMP::core::Hierarchy::get_is_setup(), IMP::core::Hierarchy::setup_particle(), IMP::core::Hierarchy::setup_particle(), IMP::core::Hierarchy::setup_particle(), IMP::core::InBoundingBox3DSingletonPredicate::do_get_inputs(), IMP::core::InBoundingBox3DSingletonPredicate::get_value_index(), IMP::core::InBoundingBox3DSingletonPredicate::get_value_index(), IMP::core::IsCollisionPairPredicate::do_get_inputs(), IMP::core::IsCollisionPairPredicate::get_value_index(), IMP::core::KClosePairsPairScore::get_close_pairs(), IMP::core::KClosePairsPairScore::create_current_decomposition(), IMP::core::KClosePairsPairScore::do_get_inputs(), IMP::core::KClosePairsPairScore::evaluate_if_good_index(), IMP::core::KClosePairsPairScore::evaluate_if_good_indexes(), IMP::core::KClosePairsPairScore::evaluate_index(), IMP::core::KClosePairsPairScore::evaluate_indexes(), IMP::core::LeavesRefiner::do_get_inputs(), IMP::core::MCCGSampler::MCCGSampler(), IMP::core::MonteCarlo::MonteCarlo(), IMP::core::MonteCarloMover::MonteCarloMover(), IMP::core::NearestNeighborsClosePairsFinder::do_get_inputs(), IMP::core::NearestNeighborsClosePairsFinder::get_close_pairs(), IMP::core::NearestNeighborsClosePairsFinder::get_close_pairs(), IMP::core::NonRigidMember::NonRigidMember(), IMP::core::NonRigidMember::get_is_setup(), IMP::core::NormalMover::NormalMover(), IMP::core::NormalMover::NormalMover(), IMP::core::NormalizedSphereDistancePairScore::do_get_inputs(), IMP::core::NormalizedSphereDistancePairScore::evaluate_if_good_indexes(), IMP::core::NormalizedSphereDistancePairScore::evaluate_index(), IMP::core::NormalizedSphereDistancePairScore::evaluate_indexes(), IMP::core::OrderedTypePairPredicate::do_get_inputs(), IMP::core::OrderedTypePairPredicate::get_value_index(), IMP::core::OrderedTypePairPredicate::get_value_index(), IMP::core::OrderedTypeQuadPredicate::do_get_inputs(), IMP::core::OrderedTypeQuadPredicate::get_value_index(), IMP::core::OrderedTypeQuadPredicate::get_value_index(), IMP::core::OrderedTypeSingletonPredicate::do_get_inputs(), IMP::core::OrderedTypeSingletonPredicate::get_value_index(), IMP::core::OrderedTypeSingletonPredicate::get_value_index(), IMP::core::OrderedTypeTripletPredicate::do_get_inputs(), IMP::core::OrderedTypeTripletPredicate::get_value_index(), IMP::core::OrderedTypeTripletPredicate::get_value_index(), IMP::core::PairConstraint::PairConstraint(), IMP::core::PairRestraint::PairRestraint(), IMP::core::PredicateSingletonScore::do_get_inputs(), IMP::core::PredicateSingletonScore::evaluate_if_good_indexes(), IMP::core::PredicateSingletonScore::evaluate_index(), IMP::core::PredicateSingletonScore::evaluate_indexes(), IMP::core::QuadConstraint::QuadConstraint(), IMP::core::QuadRestraint::QuadRestraint(), IMP::core::QuadraticClosePairsFinder::do_get_inputs(), IMP::core::QuadraticClosePairsFinder::get_are_close(), IMP::core::QuadraticClosePairsFinder::get_close_pairs(), IMP::core::QuadraticClosePairsFinder::get_close_pairs(), IMP::core::Reference::do_setup_particle(), IMP::core::Reference::Reference(), IMP::core::Reference::get_is_setup(), IMP::core::Reference::setup_particle(), IMP::core::RefinedPairsPairScore::do_get_inputs(), IMP::core::RefinedPairsPairScore::evaluate_if_good_indexes(), IMP::core::RefinedPairsPairScore::evaluate_index(), IMP::core::RefinedPairsPairScore::evaluate_indexes(), IMP::core::RigidBody::do_setup_particle(), IMP::core::RigidBody::do_setup_particle(), IMP::core::RigidBody::RigidBody(), IMP::core::RigidBody::get_is_setup(), IMP::core::RigidBody::setup_particle(), IMP::core::RigidBody::setup_particle(), IMP::core::RigidBodyMember::RigidBodyMember(), IMP::core::RigidBodyMember::get_is_setup(), IMP::core::RigidBodyMover::RigidBodyMover(), IMP::core::RigidBodyTunneler::RigidBodyTunneler(), IMP::core::RigidBodyTunneler::get_reduced_coordinates(), IMP::core::RigidBodyTunneler::get_reduced_coordinates(), IMP::core::RigidBodyTunneler::set_reduced_coordinates(), IMP::core::RigidBodyUmbrella::RigidBodyUmbrella(), IMP::core::RigidBodyUmbrella::RigidBodyUmbrella(), IMP::core::RigidClosePairsFinder::do_get_inputs(), IMP::core::RigidClosePairsFinder::get_close_pairs(), IMP::core::RigidClosePairsFinder::get_close_pairs(), IMP::core::RigidClosePairsFinder::get_close_pairs(), IMP::core::RigidMember::RigidMember(), IMP::core::RigidMember::get_is_setup(), IMP::core::SingletonConstraint::SingletonConstraint(), IMP::core::SingletonRestraint::SingletonRestraint(), IMP::core::SoftSpherePairScore::do_get_inputs(), IMP::core::SoftSpherePairScore::evaluate_index(), IMP::core::SphereDistancePairScore::do_get_inputs(), IMP::core::SphereDistancePairScore::evaluate_index(), IMP::core::SphereDistanceToSingletonScore::do_get_inputs(), IMP::core::SphereDistanceToSingletonScore::evaluate_if_good_indexes(), IMP::core::SphereDistanceToSingletonScore::evaluate_index(), IMP::core::SphereDistanceToSingletonScore::evaluate_indexes(), IMP::core::SteepestDescent::SteepestDescent(), IMP::core::TableRefiner::do_get_inputs(), IMP::core::Transform::apply_index(), IMP::core::Transform::apply_indexes(), IMP::core::Transform::do_get_inputs(), IMP::core::Transform::do_get_outputs(), IMP::core::TransformationAndReflectionSymmetry::apply_index(), IMP::core::TransformationAndReflectionSymmetry::apply_indexes(), IMP::core::TransformationAndReflectionSymmetry::do_get_inputs(), IMP::core::TransformationAndReflectionSymmetry::do_get_outputs(), IMP::core::TransformationSymmetry::apply_index(), IMP::core::TransformationSymmetry::apply_indexes(), IMP::core::TransformationSymmetry::do_get_inputs(), IMP::core::TransformationSymmetry::do_get_outputs(), IMP::core::TransformedDistancePairScore::do_get_inputs(), IMP::core::TransformedDistancePairScore::evaluate_if_good_indexes(), IMP::core::TransformedDistancePairScore::evaluate_index(), IMP::core::TransformedDistancePairScore::evaluate_indexes(), IMP::core::TripletConstraint::TripletConstraint(), IMP::core::TripletRestraint::TripletRestraint(), IMP::core::Typed::do_setup_particle(), IMP::core::Typed::get_is_setup(), IMP::core::Typed::setup_particle(), IMP::core::Typed::Typed(), IMP::core::TypedPairScore::do_get_inputs(), IMP::core::TypedPairScore::evaluate_if_good_indexes(), IMP::core::TypedPairScore::evaluate_index(), IMP::core::TypedPairScore::evaluate_indexes(), IMP::core::UnorderedTypePairPredicate::do_get_inputs(), IMP::core::UnorderedTypePairPredicate::get_value_index(), IMP::core::UnorderedTypePairPredicate::get_value_index(), IMP::core::UnorderedTypeQuadPredicate::do_get_inputs(), IMP::core::UnorderedTypeQuadPredicate::get_value_index(), IMP::core::UnorderedTypeQuadPredicate::get_value_index(), IMP::core::UnorderedTypeSingletonPredicate::do_get_inputs(), IMP::core::UnorderedTypeSingletonPredicate::get_value_index(), IMP::core::UnorderedTypeSingletonPredicate::get_value_index(), IMP::core::UnorderedTypeTripletPredicate::do_get_inputs(), IMP::core::UnorderedTypeTripletPredicate::get_value_index(), IMP::core::UnorderedTypeTripletPredicate::get_value_index(), IMP::core::WeightedDerivativesToRefined::apply_index(), IMP::core::WeightedDerivativesToRefined::apply_indexes(), IMP::core::WeightedDerivativesToRefined::do_get_inputs(), IMP::core::WeightedDerivativesToRefined::do_get_outputs(), IMP::core::WeightedSphereDistancePairScore::do_get_inputs(), IMP::core::WeightedSphereDistancePairScore::evaluate_if_good_indexes(), IMP::core::WeightedSphereDistancePairScore::evaluate_index(), IMP::core::WeightedSphereDistancePairScore::evaluate_indexes(), IMP::core::XYZ::do_setup_particle(), IMP::core::XYZ::get_is_setup(), IMP::core::XYZ::setup_particle(), IMP::core::XYZ::setup_particle(), IMP::core::XYZ::XYZ(), IMP::core::XYZR::do_setup_particle(), IMP::core::XYZR::do_setup_particle(), IMP::core::XYZR::do_setup_particle(), IMP::core::XYZR::XYZR(), IMP::core::XYZR::get_is_setup(), IMP::core::XYZR::setup_particle(), IMP::core::XYZR::setup_particle(), IMP::core::XYZR::setup_particle(), IMP::display::Colored::do_setup_particle(), IMP::display::Colored::Colored(), IMP::display::Colored::get_is_setup(), IMP::display::Colored::setup_particle(), IMP::display::RestraintGeometry::RestraintGeometry(), IMP::display::WriteOptimizerState::WriteOptimizerState(), IMP::domino::BranchAndBoundSampler::BranchAndBoundSampler(), IMP::domino::BranchAndBoundSampler::BranchAndBoundSampler(), IMP::domino::DiscreteSampler::DiscreteSampler(), IMP::domino::DominoSampler::DominoSampler(), IMP::domino::DominoSampler::DominoSampler(), IMP::em2d::Em2DRestraint::Em2DRestraint(), IMP::em2d::Fine2DRegistrationRestraint::Fine2DRegistrationRestraint(), IMP::em2d::Fine2DRegistrationRestraint::setup(), IMP::em2d::ProjectionParameters::do_setup_particle(), IMP::em2d::ProjectionParameters::ProjectionParameters(), IMP::em2d::ProjectionParameters::set_proper_ranges_for_keys(), IMP::em2d::ProjectionParameters::get_is_setup(), IMP::em2d::ProjectionParameters::setup_particle(), IMP::em::Voxel::do_setup_particle(), IMP::em::Voxel::get_is_setup(), IMP::em::Voxel::setup_particle(), IMP::em::Voxel::Voxel(), IMP::example::ExampleDecorator::do_setup_particle(), IMP::example::ExampleDecorator::get_is_setup(), IMP::example::ExampleDecorator::setup_particle(), IMP::example::ExampleDecorator::ExampleDecorator(), IMP::example::ExamplePairScore::do_get_inputs(), IMP::example::ExamplePairScore::evaluate_if_good_indexes(), IMP::example::ExamplePairScore::evaluate_index(), IMP::example::ExamplePairScore::evaluate_indexes(), IMP::example::ExampleRestraint::ExampleRestraint(), IMP::example::ExampleSingletonModifier::apply_index(), IMP::example::ExampleSingletonModifier::apply_indexes(), IMP::example::ExampleSingletonModifier::do_get_inputs(), IMP::example::ExampleSingletonModifier::do_get_outputs(), IMP::gsl::ConjugateGradients::ConjugateGradients(), IMP::gsl::GSLOptimizer::GSLOptimizer(), IMP::gsl::QuasiNewton::QuasiNewton(), IMP::gsl::Simplex::Simplex(), IMP::isd::AmbiguousNOERestraint::AmbiguousNOERestraint(), IMP::isd::AmbiguousRestraint::AmbiguousRestraint(), IMP::isd::AmbiguousRestraint::AmbiguousRestraint(), IMP::isd::CrossLinkMSRestraint::CrossLinkMSRestraint(), IMP::isd::CrossLinkMSRestraint::CrossLinkMSRestraint(), IMP::isd::CrossLinkMSRestraint::CrossLinkMSRestraint(), IMP::isd::GaussianProcessInterpolationRestraint::GaussianProcessInterpolationRestraint(), IMP::isd::HybridMonteCarlo::HybridMonteCarlo(), IMP::isd::LogWrapper::LogWrapper(), IMP::isd::LogWrapper::LogWrapper(), IMP::isd::MarginalHBondRestraint::MarginalHBondRestraint(), IMP::isd::MarginalNOERestraint::MarginalNOERestraint(), IMP::isd::MolecularDynamics::MolecularDynamics(), IMP::isd::MolecularDynamicsMover::MolecularDynamicsMover(), IMP::isd::NOERestraint::NOERestraint(), IMP::isd::Nuisance::do_setup_particle(), IMP::isd::Nuisance::Nuisance(), IMP::isd::Nuisance::get_is_setup(), IMP::isd::Nuisance::setup_particle(), IMP::isd::Nuisance::setup_particle(), IMP::isd::RepulsiveDistancePairScore::do_get_inputs(), IMP::isd::RepulsiveDistancePairScore::evaluate_if_good_indexes(), IMP::isd::RepulsiveDistancePairScore::evaluate_index(), IMP::isd::RepulsiveDistancePairScore::evaluate_indexes(), IMP::isd::Scale::do_setup_particle(), IMP::isd::Scale::Scale(), IMP::isd::Scale::get_is_setup(), IMP::isd::Scale::setup_particle(), IMP::isd::Scale::setup_particle(), IMP::isd::Switching::do_setup_particle(), IMP::isd::Switching::Switching(), IMP::isd::Switching::get_is_setup(), IMP::isd::Switching::setup_particle(), IMP::isd::Switching::setup_particle(), IMP::isd::TALOSRestraint::TALOSRestraint(), IMP::isd::TALOSRestraint::TALOSRestraint(), IMP::isd::TALOSRestraint::TALOSRestraint(), IMP::isd::TALOSRestraint::TALOSRestraint(), IMP::isd::UniformPrior::UniformPrior(), IMP::isd::Weight::do_setup_particle(), IMP::isd::Weight::Weight(), IMP::isd::Weight::get_is_setup(), IMP::isd::Weight::setup_particle(), IMP::isd::vonMisesKappaConjugateRestraint::vonMisesKappaConjugateRestraint(), IMP::isd::vonMisesKappaJeffreysRestraint::vonMisesKappaJeffreysRestraint(), IMP::kernel::AttributeOptimizer::AttributeOptimizer(), IMP::kernel::Configuration::Configuration(), IMP::kernel::Configuration::Configuration(), IMP::kernel::ConfigurationSet::ConfigurationSet(), IMP::kernel::Constraint::Constraint(), IMP::kernel::Container::Container(), IMP::kernel::Decorator::Decorator(), IMP::kernel::ModelObject::set_model(), IMP::kernel::ModelObject::ModelObject(), IMP::kernel::Optimizer::Optimizer(), IMP::kernel::OptimizerState::OptimizerState(), IMP::kernel::PairContainer::PairContainer(), IMP::kernel::PairModifier::apply_index(), IMP::kernel::PairModifier::apply_indexes(), IMP::kernel::PairPredicate::get_value_index(), IMP::kernel::PairPredicate::get_value_index(), IMP::kernel::PairPredicate::operator()(), IMP::kernel::PairScore::create_current_decomposition(), IMP::kernel::PairScore::evaluate_if_good_index(), IMP::kernel::PairScore::evaluate_if_good_indexes(), IMP::kernel::PairScore::evaluate_index(), IMP::kernel::PairScore::evaluate_indexes(), IMP::kernel::PairScore::do_create_current_decomposition(), IMP::kernel::Particle::Particle(), IMP::kernel::Particle::Particle(), IMP::kernel::ParticleInputs::get_inputs(), IMP::kernel::ParticleInputs::do_get_inputs(), IMP::kernel::ParticleOutputs::get_outputs(), IMP::kernel::ParticleOutputs::do_get_outputs(), IMP::kernel::QuadContainer::QuadContainer(), IMP::kernel::QuadModifier::apply_index(), IMP::kernel::QuadModifier::apply_indexes(), IMP::kernel::QuadPredicate::get_value_index(), IMP::kernel::QuadPredicate::get_value_index(), IMP::kernel::QuadPredicate::operator()(), IMP::kernel::QuadScore::create_current_decomposition(), IMP::kernel::QuadScore::evaluate_if_good_index(), IMP::kernel::QuadScore::evaluate_if_good_indexes(), IMP::kernel::QuadScore::evaluate_index(), IMP::kernel::QuadScore::evaluate_indexes(), IMP::kernel::QuadScore::do_create_current_decomposition(), IMP::kernel::Refiner::get_refined_indexes(), IMP::kernel::Refiner::get_refined_indexes_by_ref(), IMP::kernel::Restraint::Restraint(), IMP::kernel::RestraintSet::RestraintSet(), IMP::kernel::RestraintSet::RestraintSet(), IMP::kernel::RestraintsAdaptor::get(), IMP::kernel::Sampler::Sampler(), IMP::kernel::ScoreState::ScoreState(), IMP::kernel::ScoringFunction::ScoringFunction(), IMP::kernel::ScoringFunctionAdaptor::get(), IMP::kernel::SingletonContainer::SingletonContainer(), IMP::kernel::SingletonModifier::apply_index(), IMP::kernel::SingletonModifier::apply_indexes(), IMP::kernel::SingletonPredicate::get_value_index(), IMP::kernel::SingletonPredicate::get_value_index(), IMP::kernel::SingletonPredicate::operator()(), IMP::kernel::SingletonScore::create_current_decomposition(), IMP::kernel::SingletonScore::evaluate_if_good_index(), IMP::kernel::SingletonScore::evaluate_if_good_indexes(), IMP::kernel::SingletonScore::evaluate_index(), IMP::kernel::SingletonScore::evaluate_indexes(), IMP::kernel::SingletonScore::do_create_current_decomposition(), IMP::kernel::TripletContainer::TripletContainer(), IMP::kernel::TripletModifier::apply_index(), IMP::kernel::TripletModifier::apply_indexes(), IMP::kernel::TripletPredicate::get_value_index(), IMP::kernel::TripletPredicate::get_value_index(), IMP::kernel::TripletPredicate::operator()(), IMP::kernel::TripletScore::create_current_decomposition(), IMP::kernel::TripletScore::evaluate_if_good_index(), IMP::kernel::TripletScore::evaluate_if_good_indexes(), IMP::kernel::TripletScore::evaluate_index(), IMP::kernel::TripletScore::evaluate_indexes(), IMP::kernel::TripletScore::do_create_current_decomposition(), IMP::kernel::Undecorator::Undecorator(), IMP::kinematics::KinematicForest::KinematicForest(), IMP::kinematics::KinematicForest::KinematicForest(), IMP::kinematics::KinematicNode::do_setup_particle(), IMP::kinematics::KinematicNode::KinematicNode(), IMP::kinematics::KinematicNode::get_is_setup(), IMP::kinematics::KinematicNode::setup_particle(), IMP::kinematics::KinematicNode::setup_particle(), IMP::kinematics::KinematicNode::setup_particle(), IMP::kinematics::LocalPlanner::LocalPlanner(), IMP::kinematics::PathLocalPlanner::PathLocalPlanner(), IMP::kinematics::RRT::RRT(), IMP::misc::CommonEndpointPairFilter::do_get_inputs(), IMP::misc::CommonEndpointPairFilter::get_value_index(), IMP::misc::CommonEndpointPairFilter::get_value_index(), IMP::misc::CustomXYZR::do_setup_particle(), IMP::misc::CustomXYZR::do_setup_particle(), IMP::misc::CustomXYZR::do_setup_particle(), IMP::misc::CustomXYZR::CustomXYZR(), IMP::misc::CustomXYZR::get_is_setup(), IMP::misc::CustomXYZR::setup_particle(), IMP::misc::CustomXYZR::setup_particle(), IMP::misc::CustomXYZR::setup_particle(), IMP::misc::LogPairScore::do_get_inputs(), IMP::misc::LogPairScore::evaluate_index(), IMP::misc::LowestRefinedPairScore::do_get_inputs(), IMP::misc::LowestRefinedPairScore::evaluate_if_good_indexes(), IMP::misc::LowestRefinedPairScore::evaluate_index(), IMP::misc::LowestRefinedPairScore::evaluate_indexes(), IMP::misc::MetricClosePairsFinder::get_close_pairs_internal(), IMP::misc::MetricClosePairsFinder::get_close_pairs_internal(), IMP::misc::MetricClosePairsFinder::get_close_pairs_internal(), IMP::misc::MetricClosePairsFinder::get_index(), IMP::misc::MetricClosePairsFinder::do_get_inputs(), IMP::misc::MetricClosePairsFinder::get_close_pairs(), IMP::misc::MetricClosePairsFinder::get_close_pairs(), IMP::misc::SoftCylinderPairScore::do_get_inputs(), IMP::misc::SoftCylinderPairScore::evaluate_if_good_indexes(), IMP::misc::SoftCylinderPairScore::evaluate_index(), IMP::misc::SoftCylinderPairScore::evaluate_indexes(), IMP::misc::StateAdaptor::StateAdaptor(), IMP::multifit::AnchorsData::setup_secondary_structure(), IMP::pmi::CompositeRestraint::CompositeRestraint(), IMP::pmi::Resolution::setup_particle(), IMP::pmi::Resolution::Resolution(), IMP::pmi::SigmoidRestraintSphere::SigmoidRestraintSphere(), IMP::pmi::Symmetric::setup_particle(), IMP::pmi::Symmetric::Symmetric(), IMP::pmi::TransformMover::TransformMover(), IMP::pmi::TransformMover::TransformMover(), IMP::pmi::Uncertainty::setup_particle(), IMP::pmi::Uncertainty::Uncertainty(), IMP::rmf::HierarchyLoadLink::add_link_recursive(), IMP::rmf::HierarchyLoadLink::create_recursive(), IMP::rmf::HierarchyLoadLink::do_create(), IMP::rmf::HierarchyLoadLink::do_link_particle(), IMP::rmf::HierarchyLoadLink::do_load_hierarchy(), IMP::rmf::HierarchyLoadLink::do_setup_particle(), IMP::rmf::SaveOptimizerState::SaveOptimizerState(), IMP::rmf::SimpleLoadLink::do_create(), IMP::rmf::SimpleLoadLink::create(), IMP::score_functor::AddScores::get_inputs(), IMP::score_functor::AddScores::get_is_trivially_zero(), IMP::score_functor::AddScores::get_maximum_range(), IMP::score_functor::AddScores::get_score(), IMP::score_functor::AddScores::get_score_and_derivative(), IMP::score_functor::DistancePairScore::do_get_inputs(), IMP::score_functor::DistancePairScore::evaluate_if_good_indexes(), IMP::score_functor::DistancePairScore::evaluate_index(), IMP::score_functor::DistancePairScore::evaluate_indexes(), IMP::score_functor::Harmonic::get_score(), IMP::score_functor::Harmonic::get_score_and_derivative(), IMP::score_functor::HarmonicLowerBound::get_is_trivially_zero(), IMP::score_functor::HarmonicLowerBound::get_maximum_range(), IMP::score_functor::HarmonicLowerBound::get_score(), IMP::score_functor::HarmonicLowerBound::get_score_and_derivative(), IMP::score_functor::HarmonicUpperBound::get_score(), IMP::score_functor::HarmonicUpperBound::get_score_and_derivative(), IMP::score_functor::LinearLowerBound::get_is_trivially_zero(), IMP::score_functor::LinearLowerBound::get_maximum_range(), IMP::score_functor::LinearLowerBound::get_score(), IMP::score_functor::LinearLowerBound::get_score_and_derivative(), IMP::score_functor::OpenCubicSpline::get_is_trivially_zero(), IMP::score_functor::OpenCubicSpline::get_maximum_range(), IMP::score_functor::OpenCubicSpline::get_score(), IMP::score_functor::OpenCubicSpline::get_score_and_derivative(), IMP::score_functor::OrientedSoap::get_inputs(), IMP::score_functor::OrientedSoap::get_is_trivially_zero(), IMP::score_functor::OrientedSoap::get_maximum_range(), IMP::score_functor::OrientedSoap::get_score(), IMP::score_functor::OrientedSoap::get_score_and_derivative(), IMP::score_functor::Shift::get_is_trivially_zero(), IMP::score_functor::Shift::get_maximum_range(), IMP::score_functor::Shift::get_score(), IMP::score_functor::Shift::get_score_and_derivative(), IMP::score_functor::SingletonStatistical::get_score(), IMP::score_functor::SphereDistance::get_rsum(), IMP::score_functor::SphereDistance::get_is_trivially_zero(), IMP::score_functor::SphereDistance::get_maximum_range(), IMP::score_functor::SphereDistance::get_score(), IMP::score_functor::SphereDistance::get_score_and_derivative(), IMP::score_functor::Statistical::get_is_trivially_zero(), IMP::score_functor::Statistical::get_maximum_range(), IMP::score_functor::Statistical::get_score(), IMP::score_functor::Statistical::get_score_and_derivative(), IMP::score_functor::UnaryFunctionEvaluate::get_score(), IMP::score_functor::UnaryFunctionEvaluate::get_score_and_derivative(), IMP::score_functor::WeightScore::get_score(), IMP::score_functor::WeightScore::get_score_and_derivative(), IMP::atom::read_mol2(), IMP::atom::read_pdb(), IMP::atom::read_multimodel_pdb(), IMP::atom::read_psipred(), IMP::atom::create_protein(), IMP::atom::create_protein(), IMP::atom::get_resolution(), IMP::atom::setup_coarse_secondary_structure_residue(), IMP::atom::setup_coarse_secondary_structure_residues(), IMP::core::create_rigid_bodies(), IMP::core::create_xyzr_particles(), IMP::core::get_initial_reference_frame(), IMP::em::density2particles(), IMP::example::optimize_assembly(), IMP::kernel::get_dependency_graph(), IMP::kernel::get_particles(), IMP::kernel::get_pruned_dependency_graph(), IMP::kernel::make_predicate_equal(), IMP::kernel::make_predicate_not_equal(), IMP::multifit::create_coarse_molecule_from_density(), IMP::multifit::create_coarse_molecule_from_molecule(), IMP::multifit::create_coarse_molecules_from_molecules(), IMP::rmf::create_hierarchies(), IMP::rmf::create_particles(), IMP::rmf::create_restraints()
IMP::kernel::ModelObject	IMP::kernel::Model::check_dependency_invariants(), IMP::kernel::Model::do_add_dependencies(), IMP::kernel::Model::do_add_model_object(), IMP::kernel::Model::do_check_inputs_and_outputs(), IMP::kernel::Model::do_check_not_in_readers_and_writers(), IMP::kernel::Model::do_check_readers_and_writers(), IMP::kernel::Model::do_check_required_score_states(), IMP::kernel::Model::do_clear_dependencies(), IMP::kernel::Model::do_clear_required_score_states(), IMP::kernel::Model::do_get_has_dependencies(), IMP::kernel::Model::do_get_has_required_score_states(), IMP::kernel::Model::do_get_required_score_states(), IMP::kernel::Model::do_remove_model_object(), IMP::kernel::Model::do_set_has_dependencies(), IMP::kernel::Model::do_set_has_required_score_states(), IMP::kernel::Model::get_ancestor_score_states(), IMP::kernel::Model::get_dependency_graph_inputs(), IMP::kernel::Model::get_dependency_graph_outputs(), IMP::kernel::Model::get_descendent_score_states(), IMP::kernel::get_dependent_particles(), IMP::kernel::get_dependent_restraints(), IMP::kernel::get_dependent_score_states(), IMP::kernel::get_required_score_states()
IMP::kernel::Optimizer	IMP::kernel::Optimizer::set_optimizer_state_optimizer(), IMP::kernel::OptimizerState::set_optimizer()
IMP::kernel::OptimizerState	IMP::kernel::Optimizer::remove_optimizer_state(), IMP::kernel::Optimizer::add_optimizer_state(), IMP::kernel::Optimizer::set_optimizer_state_optimizer()
IMP::kernel::PairContainer	IMP::core::NeighborsTable::NeighborsTable(), IMP::kernel::PairContainerAdaptor::PairContainerAdaptor()
IMP::kernel::PairContainerAdaptor	IMP::container::PairsRestraint::PairsRestraint()
IMP::kernel::PairModifier	IMP::kernel::PairContainer::apply(), IMP::kernel::PairContainer::apply_generic(), IMP::kernel::PairContainer::do_apply()
IMP::kernel::PairScore	IMP::container::PairsRestraint::PairsRestraint(), IMP::container::PredicatePairsRestraint::set_score(), IMP::container::PredicatePairsRestraint::set_unknown_score()
IMP::kernel::Particle	IMP::atom::BondEndpointsRefiner::get_can_refine(), IMP::atom::BondEndpointsRefiner::get_refined(), IMP::atom::BondGeometry::BondGeometry(), IMP::atom::CHARMMParameters::add_angle(), IMP::atom::CHARMMParameters::add_dihedral(), IMP::atom::SecondaryStructureResidue::setup_particle(), IMP::atom::Selection::Selection(), IMP::atom::Simulator::remove_particle(), IMP::atom::Simulator::add_particle(), IMP::container::DynamicListSingletonContainer::add_particle(), IMP::container::InContainerSingletonFilter::get_value(), IMP::core::AllSameSingletonPredicate::get_value(), IMP::core::AngleRestraint::AngleRestraint(), IMP::core::AttributeSingletonPredicate::get_value(), IMP::core::ChildrenRefiner::get_can_refine(), IMP::core::ChildrenRefiner::get_refined(), IMP::core::CoinFlipSingletonPredicate::get_value(), IMP::core::ConstantSingletonPredicate::get_value(), IMP::core::DihedralRestraint::DihedralRestraint(), IMP::core::DistanceRestraint::DistanceRestraint(), IMP::core::FixedRefiner::get_can_refine(), IMP::core::FixedRefiner::get_refined(), IMP::core::InBoundingBox3DSingletonPredicate::get_value(), IMP::core::LeavesRefiner::get_can_refine(), IMP::core::LeavesRefiner::get_refined(), IMP::core::OrderedTypeSingletonPredicate::get_value(), IMP::core::QuadraticClosePairsFinder::get_are_close(), IMP::core::RigidBody::add_member_internal(), IMP::core::RigidBody::teardown_constraints(), IMP::core::RigidBodyDerivativeGeometry::RigidBodyDerivativeGeometry(), IMP::core::RigidBodyFrameGeometry::RigidBodyFrameGeometry(), IMP::core::RigidBodyTorque::extract_geometry(), IMP::core::RigidBodyTorque::RigidBodyTorque(), IMP::core::SingletonConstraint::SingletonConstraint(), IMP::core::SingletonRestraint::SingletonRestraint(), IMP::core::TableRefiner::add_particle(), IMP::core::TableRefiner::get_can_refine(), IMP::core::TableRefiner::get_refined(), IMP::core::TableRefiner::remove_particle(), IMP::core::TableRefiner::set_particle(), IMP::core::TypedPairScore::set_particle_type(), IMP::core::UnorderedTypeSingletonPredicate::get_value(), IMP::core::XYZDerivativeGeometry::XYZDerivativeGeometry(), IMP::core::XYZRGeometry::XYZRGeometry(), IMP::display::SingletonGeometry::SingletonGeometry(), IMP::domino::CompoundStates::load_particle_state(), IMP::domino::DiscreteSampler::set_particle_states(), IMP::domino::DisjointSetsSubsetFilterTable::get_index(), IMP::domino::IndexStates::load_particle_state(), IMP::domino::ListSubsetFilterTable::get_number_of_particle_states(), IMP::domino::ListSubsetFilterTable::set_allowed_states(), IMP::domino::NestedRigidBodyStates::load_particle_state(), IMP::domino::ParticleStates::load_particle_state(), IMP::domino::ParticleStatesTable::get_has_particle(), IMP::domino::ParticleStatesTable::get_particle_states(), IMP::domino::ParticleStatesTable::set_particle_states(), IMP::domino::PermutationStates::load_particle_state(), IMP::domino::RecursiveStates::RecursiveStates(), IMP::domino::RecursiveStates::load_particle_state(), IMP::domino::RigidBodyStates::load_particle_state(), IMP::domino::XYZStates::load_particle_state(), IMP::em2d::DummyRestraint::DummyRestraint(), IMP::em2d::GridStates::load_particle_state(), IMP::em2d::ProjectionParametersScoreState::ProjectionParametersScoreState(), IMP::em2d::ProjectionStates::load_particle_state(), IMP::em::DensityFillingRestraint::add_particle(), IMP::em::DensityFillingRestraint::remove_particle(), IMP::em::EnvelopePenetrationRestraint::add_particle(), IMP::em::EnvelopePenetrationRestraint::remove_particle(), IMP::em::FitRestraint::add_particle(), IMP::em::FitRestraint::remove_particle(), IMP::em::PCAFitRestraint::add_particle(), IMP::em::PCAFitRestraint::remove_particle(), IMP::example::ExampleConstraint::ExampleConstraint(), IMP::isd::AmbiguousNOERestraint::AmbiguousNOERestraint(), IMP::isd::Covariance1DFunction::Covariance1DFunction(), IMP::isd::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint(), IMP::isd::CysteineCrossLinkRestraint::CysteineCrossLinkRestraint(), IMP::isd::CysteineCrossLinkRestraint::add_contribution(), IMP::isd::FretRestraint::get_current_center(), IMP::isd::FretRestraint::get_current_centers(), IMP::isd::FretRestraint::FretRestraint(), IMP::isd::FretRestraint::FretRestraint(), IMP::isd::FretRestraint::FretRestraint(), IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation(), IMP::isd::GaussianRestraint::GaussianRestraint(), IMP::isd::GaussianRestraint::GaussianRestraint(), IMP::isd::GaussianRestraint::GaussianRestraint(), IMP::isd::GaussianRestraint::GaussianRestraint(), IMP::isd::GaussianRestraint::GaussianRestraint(), IMP::isd::GaussianRestraint::GaussianRestraint(), IMP::isd::GaussianRestraint::GaussianRestraint(), IMP::isd::GeneralizedGuinierPorodFunction::GeneralizedGuinierPorodFunction(), IMP::isd::Linear1DFunction::Linear1DFunction(), IMP::isd::LognormalRestraint::LognormalRestraint(), IMP::isd::LognormalRestraint::LognormalRestraint(), IMP::isd::LognormalRestraint::LognormalRestraint(), IMP::isd::LognormalRestraint::LognormalRestraint(), IMP::isd::LognormalRestraint::LognormalRestraint(), IMP::isd::LognormalRestraint::LognormalRestraint(), IMP::isd::LognormalRestraint::LognormalRestraint(), IMP::isd::MarginalHBondRestraint::add_contribution(), IMP::isd::MarginalNOERestraint::add_contribution(), IMP::isd::Nuisance::set_lower(), IMP::isd::Nuisance::set_upper(), IMP::isd::TALOSRestraint::TALOSRestraint(), IMP::isd::TALOSRestraint::TALOSRestraint(), IMP::isd::TALOSRestraint::TALOSRestraint(), IMP::isd::TALOSRestraint::TALOSRestraint(), IMP::isd::WeightMover::WeightMover(), IMP::isd::WeightRestraint::WeightRestraint(), IMP::isd::vonMisesKappaConjugateRestraint::vonMisesKappaConjugateRestraint(), IMP::isd::vonMisesKappaJeffreysRestraint::vonMisesKappaJeffreysRestraint(), IMP::kernel::Model::add_particle_internal(), IMP::kernel::Model::remove_particle(), IMP::kernel::ParticleAdaptor::ParticleAdaptor(), IMP::kernel::ParticleAdaptor::ParticleAdaptor(), IMP::kernel::ParticleAdaptor::ParticleAdaptor(), IMP::kernel::ParticleAdaptor::ParticleAdaptor(), IMP::kernel::ParticleIndexAdaptor::ParticleIndexAdaptor(), IMP::kernel::ParticleInputs::get_input_containers(), IMP::kernel::ParticleInputs::get_input_particles(), IMP::kernel::ParticleOutputs::get_output_containers(), IMP::kernel::ParticleOutputs::get_output_particles(), IMP::kernel::Refiner::refined_begin(), IMP::kernel::Refiner::refined_end(), IMP::kernel::Refiner::get_can_refine(), IMP::kernel::Refiner::get_number_of_refined(), IMP::kernel::Refiner::get_refined(), IMP::kernel::Refiner::get_refined(), IMP::kernel::ScopedAddCacheAttribute::ScopedAddCacheAttribute(), IMP::kernel::ScopedAddCacheAttribute::set(), IMP::kernel::ScopedSetAttribute::ScopedSetAttribute(), IMP::kernel::ScopedSetAttribute::set(), IMP::kernel::SingletonModifier::apply(), IMP::kernel::SingletonPredicate::get_value(), IMP::kernel::SingletonScore::evaluate(), IMP::kinematics::KinematicForest::reset_root(), IMP::kinematics::KinematicForest::get_children(), IMP::kinematics::KinematicForest::get_parent(), IMP::multifit::DummyRestraint::DummyRestraint(), IMP::multifit::FittingStates::load_particle_state(), IMP::multifit::ProbabilisticAnchorGraph::get_are_probabilities_for_particle_set(), IMP::multifit::ProbabilisticAnchorGraph::get_particle_anchors(), IMP::multifit::ProbabilisticAnchorGraph::get_particle_probabilities(), IMP::multifit::ProbabilisticAnchorGraph::set_particle_probabilities_on_anchors(), IMP::multifit::RadiusOfGyrationRestraint::add_particle(), IMP::multifit::RadiusOfGyrationRestraint::remove_particle(), IMP::multifit::WeightedExcludedVolumeRestraint::add_particle(), IMP::multifit::WeightedExcludedVolumeRestraint::remove_particle(), IMP::rmf::HierarchyLoadLink::do_add_link(), IMP::rmf::HierarchyLoadLink::do_load_one(), IMP::rmf::HierarchySaveLink::do_add(), IMP::rmf::HierarchySaveLink::do_save_one(), IMP::rmf::HierarchySaveLink::get_type(), IMP::saxs::DeltaDistributionFunction::calculate_derivative_distribution(), IMP::saxs::FormFactorTable::get_dummy_form_factor(), IMP::saxs::FormFactorTable::get_dummy_form_factors(), IMP::saxs::FormFactorTable::get_form_factor(), IMP::saxs::FormFactorTable::get_form_factors(), IMP::saxs::FormFactorTable::get_radius(), IMP::saxs::FormFactorTable::get_vacuum_form_factor(), IMP::saxs::FormFactorTable::get_vacuum_form_factors(), IMP::saxs::FormFactorTable::get_volume(), IMP::saxs::FormFactorTable::get_form_factor_atom_type(), IMP::symmetry::BallMover::BallMover(), IMP::atom::setup_as_approximation(), IMP::base::get_vector_geometry(), IMP::base::get_vector_geometry(), IMP::base::set_vector_geometry(), IMP::base::set_vector_geometry(), IMP::em::local_rigid_fitting(), IMP::em::local_rigid_fitting_around_point(), IMP::em::local_rigid_fitting_around_points(), IMP::kernel::get_vector_geometry(), IMP::kernel::set_vector_geometry(), IMP::multifit::get_close_to_point(), IMP::rmf::add_particle()
IMP::kernel::ParticleAdaptor	IMP::atom::Angle::Angle(), IMP::atom::Angle::get_is_setup(), IMP::atom::Angle::setup_particle(), IMP::atom::Atom::Atom(), IMP::atom::Atom::get_is_setup(), IMP::atom::Atom::setup_particle(), IMP::atom::Atom::setup_particle(), IMP::atom::Bond::Bond(), IMP::atom::Bond::get_is_setup(), IMP::atom::Bonded::Bonded(), IMP::atom::Bonded::get_is_setup(), IMP::atom::Bonded::setup_particle(), IMP::atom::CHARMMAtom::CHARMMAtom(), IMP::atom::CHARMMAtom::get_is_setup(), IMP::atom::CHARMMAtom::setup_particle(), IMP::atom::CenterOfMass::CenterOfMass(), IMP::atom::CenterOfMass::get_is_setup(), IMP::atom::CenterOfMass::setup_particle(), IMP::atom::CenterOfMass::setup_particle(), IMP::atom::Chain::Chain(), IMP::atom::Chain::get_is_setup(), IMP::atom::Chain::setup_particle(), IMP::atom::Chain::setup_particle(), IMP::atom::Chain::setup_particle(), IMP::atom::Charged::Charged(), IMP::atom::Charged::get_is_setup(), IMP::atom::Charged::setup_particle(), IMP::atom::Charged::setup_particle(), IMP::atom::Copy::get_is_setup(), IMP::atom::Copy::setup_particle(), IMP::atom::Copy::Copy(), IMP::atom::Diffusion::Diffusion(), IMP::atom::Diffusion::get_is_setup(), IMP::atom::Diffusion::setup_particle(), IMP::atom::Diffusion::setup_particle(), IMP::atom::Diffusion::setup_particle(), IMP::atom::Dihedral::Dihedral(), IMP::atom::Dihedral::get_is_setup(), IMP::atom::Dihedral::setup_particle(), IMP::atom::Domain::get_is_setup(), IMP::atom::Domain::setup_particle(), IMP::atom::Domain::setup_particle(), IMP::atom::Domain::Domain(), IMP::atom::Fragment::get_is_setup(), IMP::atom::Fragment::setup_particle(), IMP::atom::Fragment::setup_particle(), IMP::atom::Fragment::setup_particle(), IMP::atom::Fragment::Fragment(), IMP::atom::Hierarchy::Hierarchy(), IMP::atom::LennardJones::LennardJones(), IMP::atom::LennardJones::get_is_setup(), IMP::atom::LennardJones::setup_particle(), IMP::atom::LennardJones::setup_particle(), IMP::atom::Mass::get_is_setup(), IMP::atom::Mass::setup_particle(), IMP::atom::Mass::Mass(), IMP::atom::Molecule::Molecule(), IMP::atom::Molecule::get_is_setup(), IMP::atom::Molecule::setup_particle(), IMP::atom::Molecule::setup_particle(), IMP::atom::Representation::get_is_setup(), IMP::atom::Representation::setup_particle(), IMP::atom::Representation::setup_particle(), IMP::atom::Representation::Representation(), IMP::atom::Residue::Residue(), IMP::atom::Residue::get_is_setup(), IMP::atom::Residue::setup_particle(), IMP::atom::Residue::setup_particle(), IMP::atom::Residue::setup_particle(), IMP::atom::Residue::setup_particle(), IMP::atom::RigidBodyDiffusion::RigidBodyDiffusion(), IMP::atom::RigidBodyDiffusion::get_is_setup(), IMP::atom::RigidBodyDiffusion::setup_particle(), IMP::atom::SecondaryStructureResidue::SecondaryStructureResidue(), IMP::atom::SecondaryStructureResidue::get_is_setup(), IMP::atom::SecondaryStructureResidue::setup_particle(), IMP::atom::State::get_is_setup(), IMP::atom::State::setup_particle(), IMP::atom::State::State(), IMP::core::Centroid::Centroid(), IMP::core::Centroid::get_is_setup(), IMP::core::Centroid::setup_particle(), IMP::core::Centroid::setup_particle(), IMP::core::Cover::Cover(), IMP::core::Cover::get_is_setup(), IMP::core::Cover::setup_particle(), IMP::core::Cover::setup_particle(), IMP::core::Gaussian::Gaussian(), IMP::core::Gaussian::get_is_setup(), IMP::core::Gaussian::setup_particle(), IMP::core::Gaussian::setup_particle(), IMP::core::Hierarchy::Hierarchy(), IMP::core::Hierarchy::get_is_setup(), IMP::core::Hierarchy::setup_particle(), IMP::core::Hierarchy::setup_particle(), IMP::core::Hierarchy::setup_particle(), IMP::core::NonRigidMember::NonRigidMember(), IMP::core::NonRigidMember::get_is_setup(), IMP::core::Reference::Reference(), IMP::core::Reference::get_is_setup(), IMP::core::Reference::setup_particle(), IMP::core::RigidBody::RigidBody(), IMP::core::RigidBody::get_is_setup(), IMP::core::RigidBody::setup_particle(), IMP::core::RigidBody::setup_particle(), IMP::core::RigidBodyMember::RigidBodyMember(), IMP::core::RigidBodyMember::get_is_setup(), IMP::core::RigidMember::RigidMember(), IMP::core::RigidMember::get_is_setup(), IMP::core::Typed::get_is_setup(), IMP::core::Typed::setup_particle(), IMP::core::Typed::Typed(), IMP::core::XYZ::get_is_setup(), IMP::core::XYZ::setup_particle(), IMP::core::XYZ::setup_particle(), IMP::core::XYZ::XYZ(), IMP::core::XYZR::XYZR(), IMP::core::XYZR::get_is_setup(), IMP::core::XYZR::setup_particle(), IMP::core::XYZR::setup_particle(), IMP::core::XYZR::setup_particle(), IMP::display::Colored::Colored(), IMP::display::Colored::get_is_setup(), IMP::display::Colored::setup_particle(), IMP::em2d::ProjectionParameters::ProjectionParameters(), IMP::em2d::ProjectionParameters::get_is_setup(), IMP::em2d::ProjectionParameters::setup_particle(), IMP::em::Voxel::get_is_setup(), IMP::em::Voxel::setup_particle(), IMP::em::Voxel::Voxel(), IMP::example::ExampleDecorator::get_is_setup(), IMP::example::ExampleDecorator::setup_particle(), IMP::example::ExampleDecorator::ExampleDecorator(), IMP::isd::Nuisance::Nuisance(), IMP::isd::Nuisance::get_is_setup(), IMP::isd::Nuisance::setup_particle(), IMP::isd::Nuisance::setup_particle(), IMP::isd::Scale::Scale(), IMP::isd::Scale::get_is_setup(), IMP::isd::Scale::setup_particle(), IMP::isd::Scale::setup_particle(), IMP::isd::Switching::Switching(), IMP::isd::Switching::get_is_setup(), IMP::isd::Switching::setup_particle(), IMP::isd::Switching::setup_particle(), IMP::isd::Weight::Weight(), IMP::isd::Weight::get_is_setup(), IMP::isd::Weight::setup_particle(), IMP::kernel::Decorator::Decorator(), IMP::kinematics::KinematicNode::KinematicNode(), IMP::kinematics::KinematicNode::get_is_setup(), IMP::kinematics::KinematicNode::setup_particle(), IMP::kinematics::KinematicNode::setup_particle(), IMP::kinematics::KinematicNode::setup_particle(), IMP::misc::CustomXYZR::CustomXYZR(), IMP::misc::CustomXYZR::get_is_setup(), IMP::misc::CustomXYZR::setup_particle(), IMP::misc::CustomXYZR::setup_particle(), IMP::misc::CustomXYZR::setup_particle(), IMP::pmi::Resolution::get_is_setup(), IMP::pmi::Resolution::setup_particle(), IMP::pmi::Resolution::Resolution(), IMP::pmi::Symmetric::get_is_setup(), IMP::pmi::Symmetric::setup_particle(), IMP::pmi::Symmetric::Symmetric(), IMP::pmi::Uncertainty::get_is_setup(), IMP::pmi::Uncertainty::setup_particle(), IMP::pmi::Uncertainty::Uncertainty()
IMP::kernel::ParticleIndexAdaptor	IMP::atom::Representation::add_representation(), IMP::core::Reference::setup_particle(), IMP::core::Reference::setup_particle(), IMP::core::RigidBody::add_member(), IMP::core::RigidBodyMember::get_is_setup(), IMP::core::RigidMember::get_is_setup(), IMP::isd::CrossLinkMSRestraint::CrossLinkMSRestraint(), IMP::pmi::SigmoidRestraintSphere::SigmoidRestraintSphere(), IMP::pmi::TransformMover::add_rigid_body_particle(), IMP::pmi::TransformMover::add_xyz_particle()
IMP::kernel::ParticleIndexesAdaptor	IMP::atom::Hierarchy::setup_particle(), IMP::atom::RemoveRigidMotionOptimizerState::RemoveRigidMotionOptimizerState(), IMP::atom::RemoveTranslationOptimizerState::RemoveTranslationOptimizerState(), IMP::atom::VelocityScalingOptimizerState::VelocityScalingOptimizerState(), IMP::atom::WritePDBOptimizerState::WritePDBOptimizerState(), IMP::core::RigidBody::do_setup_particle(), IMP::core::RigidBody::setup_particle(), IMP::core::RigidBody::setup_particle(), IMP::pmi::CompositeRestraint::CompositeRestraint(), IMP::pmi::CompositeRestraint::add_composite_particle()
IMP::kernel::QuadContainer	IMP::kernel::QuadContainerAdaptor::QuadContainerAdaptor()
IMP::kernel::QuadContainerAdaptor	IMP::container::QuadsRestraint::QuadsRestraint()
IMP::kernel::QuadModifier	IMP::kernel::QuadContainer::apply(), IMP::kernel::QuadContainer::apply_generic(), IMP::kernel::QuadContainer::do_apply()
IMP::kernel::QuadScore	IMP::container::PredicateQuadsRestraint::set_score(), IMP::container::PredicateQuadsRestraint::set_unknown_score(), IMP::container::QuadsRestraint::QuadsRestraint()
IMP::kernel::Restraint	IMP::core::IncrementalScoringFunction::create_data(), IMP::core::MinimumRestraint::add_restraint(), IMP::core::MinimumRestraint::remove_restraint(), IMP::display::RestraintGeometry::RestraintGeometry(), IMP::display::RestraintGeometry::RestraintGeometry(), IMP::domino::RestraintCache::add_restraint_internal(), IMP::domino::RestraintCache::add_restraint_set_child_internal(), IMP::domino::RestraintCache::get_subset(), IMP::domino::RestraintCache::get_score(), IMP::domino::RestraintCache::get_score(), IMP::domino::RestraintCache::get_slice(), IMP::domino::RestraintCache::load_last_score(), IMP::isd::AmbiguousRestraint::AmbiguousRestraint(), IMP::kernel::Model::get_maximum_score(), IMP::kernel::Model::set_maximum_score(), IMP::kernel::RestraintSet::remove_restraint(), IMP::kernel::RestraintSet::add_restraint(), IMP::kernel::RestraintSet::on_add(), IMP::kernel::RestraintSet::on_remove(), IMP::kernel::RestraintsAdaptor::get(), IMP::kernel::RestraintsAdaptor::RestraintsAdaptor(), IMP::kernel::ScoreAccumulator::ScoreAccumulator(), IMP::kernel::ScoringFunctionAdaptor::get(), IMP::kernel::ScoringFunctionAdaptor::ScoringFunctionAdaptor(), IMP::rmf::add_restraint()
IMP::kernel::RestraintSet	IMP::display::RestraintSetGeometry::RestraintSetGeometry(), IMP::domino::RestraintCache::add_restraint_internal(), IMP::domino::RestraintCache::add_restraint_set_child_internal(), IMP::domino::RestraintCache::add_restraint_set_internal(), IMP::kernel::RestraintSet::on_remove(), IMP::domino::get_restraints()
IMP::kernel::RestraintsAdaptor	IMP::core::RestraintsScoringFunction::RestraintsScoringFunction(), IMP::core::RestraintsScoringFunction::RestraintsScoringFunction(), IMP::domino::RestraintCache::add_restraints(), IMP::domino::RestraintScoreSubsetFilterTable::RestraintScoreSubsetFilterTable()
IMP::kernel::ScoreAccumulator	IMP::example::ExampleRestraint::do_add_score_and_derivatives(), IMP::kernel::Restraint::add_score_and_derivatives(), IMP::kernel::Restraint::do_add_score_and_derivatives(), IMP::kernel::ScoreAccumulator::ScoreAccumulator(), IMP::kernel::ScoreAccumulator::ScoreAccumulator(), IMP::kernel::ScoringFunction::do_add_score_and_derivatives()
IMP::kernel::ScoreState	IMP::kernel::Model::remove_score_state(), IMP::kernel::Model::add_score_state(), IMP::kernel::Model::do_add_score_state(), IMP::kernel::Model::do_check_update_order(), IMP::kernel::Model::do_remove_score_state()
IMP::kernel::ScoringFunction	IMP::kernel::ScoringFunctionAdaptor::get(), IMP::kernel::ScoringFunctionAdaptor::ScoringFunctionAdaptor(), IMP::kernel::create_decomposition()
IMP::kernel::ScoringFunctionAdaptor	IMP::kernel::Optimizer::set_scoring_function(), IMP::kernel::Sampler::set_scoring_function(), IMP::kernel::show_restraint_hierarchy()
IMP::kernel::SingletonContainer	IMP::container::ConnectingPairContainer::ConnectingPairContainer(), IMP::kernel::SingletonContainerAdaptor::SingletonContainerAdaptor()
IMP::kernel::SingletonContainerAdaptor	IMP::container::SingletonsRestraint::SingletonsRestraint()
IMP::kernel::SingletonModifier	IMP::kernel::SingletonContainer::apply(), IMP::kernel::SingletonContainer::apply_generic(), IMP::kernel::SingletonContainer::do_apply()
IMP::kernel::SingletonScore	IMP::container::PredicateSingletonsRestraint::set_score(), IMP::container::PredicateSingletonsRestraint::set_unknown_score(), IMP::container::SingletonsRestraint::SingletonsRestraint()
IMP::kernel::TripletContainer	IMP::kernel::TripletContainerAdaptor::TripletContainerAdaptor()
IMP::kernel::TripletContainerAdaptor	IMP::container::TripletsRestraint::TripletsRestraint()
IMP::kernel::TripletModifier	IMP::kernel::TripletContainer::apply(), IMP::kernel::TripletContainer::apply_generic(), IMP::kernel::TripletContainer::do_apply()
IMP::kernel::TripletScore	IMP::container::PredicateTripletsRestraint::set_score(), IMP::container::PredicateTripletsRestraint::set_unknown_score(), IMP::container::TripletsRestraint::TripletsRestraint()
IMP::kernel::Undecorator	IMP::kernel::Model::add_undecorator()

IMP.kinematics

Class	Users
IMP::kinematics::DOFsSampler	IMP::kinematics::LocalPlanner::LocalPlanner(), IMP::kinematics::PathLocalPlanner::PathLocalPlanner(), IMP::kinematics::RRT::RRT()
IMP::kinematics::Joint	IMP::kinematics::CompositeJoint::add_downstream_joint(), IMP::kinematics::CompositeJoint::add_upstream_joint(), IMP::kinematics::KinematicForest::add_edge(), IMP::kinematics::KinematicNode::do_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::add_out_joint(), IMP::kinematics::KinematicNode::set_in_joint()
IMP::kinematics::KinematicForest	IMP::kinematics::Joint::set_owner_kf(), IMP::kinematics::KinematicForestScoreState::KinematicForestScoreState(), IMP::kinematics::KinematicNode::do_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::KinematicNode::setup_particle()
IMP::kinematics::LocalPlanner	IMP::kinematics::RRT::RRT()

IMP.misc

Class	Users
IMP::misc::CustomXYZR	IMP::misc::get_distance(), IMP::misc::get_sphere_d_geometry(), IMP::misc::set_sphere_d_geometry()
IMP::misc::LogPairScore	IMP::misc::LogPairScore::IMP_PAIR_SCORE_METHODS()

IMP.modeller

Class	Users
IMP::modeller::BinormalTerm	IMP::modeller::MultipleBinormalRestraint::add_term()

IMP.multifit

Class	Users
IMP::multifit::AnchorsData	IMP::multifit::ProteinsAnchorsSamplingSpace::set_anchors(), IMP::multifit::get_anchor_indices_matching_secondary_structure(), IMP::multifit::write_cmm(), IMP::multifit::write_txt()
IMP::multifit::AssemblyHeader	IMP::multifit::SettingsData::set_assembly_header()
IMP::multifit::ComponentHeader	IMP::multifit::SettingsData::add_component_header(), IMP::multifit::SettingsData::remove_component_header()
IMP::multifit::DataPointsAssignment	IMP::multifit::get_segment_maximum(), IMP::multifit::get_segment_maximum(), IMP::multifit::write_chimera(), IMP::multifit::write_pdb(), IMP::multifit::write_segment_as_mrc(), IMP::multifit::write_segment_as_pdb(), IMP::multifit::write_segments_as_mrc(), IMP::multifit::write_segments_as_pdb()
IMP::multifit::ProteinsAnchorsSamplingSpace	IMP::multifit::Ensemble::Ensemble(), IMP::multifit::ProteomicsEMAlignmentAtomic::ProteomicsEMAlignmentAtomic(), IMP::multifit::get_part_of_sampling_space(), IMP::multifit::load_ensemble(), IMP::multifit::write_protein_anchors_mapping()
IMP::multifit::ProteomicsData	IMP::multifit::ProteinsAnchorsSamplingSpace::ProteinsAnchorsSamplingSpace(), IMP::multifit::get_partial_proteomics_data(), IMP::multifit::read_protein_anchors_mapping()
IMP::multifit::SettingsData	IMP::multifit::Ensemble::Ensemble(), IMP::multifit::ProteomicsEMAlignmentAtomic::ProteomicsEMAlignmentAtomic(), IMP::multifit::get_partial_assembly_setting_data(), IMP::multifit::load_ensemble(), IMP::multifit::write_settings()

IMP.rotamer

Class	Users
IMP::rotamer::RotamerLibrary	IMP::rotamer::RotamerCalculator::RotamerCalculator()

IMP.saxs

Class	Users
IMP::saxs::DeltaDistributionFunction	IMP::saxs::DerivativeCalculator::compute_intensity_derivatives()
IMP::saxs::DerivativeCalculator	IMP::saxs::RigidBodiesProfileHandler::compute_derivatives()
IMP::saxs::FormFactorTable	IMP::saxs::Profile::set_ff_table(), IMP::saxs::compute_profile(), IMP::saxs::get_form_factors()
IMP::saxs::Profile	IMP::saxs::ChiFreeScore::compute_offset(), IMP::saxs::ChiFreeScore::compute_scale_factor(), IMP::saxs::ChiFreeScore::compute_score(), IMP::saxs::ChiScore::compute_offset(), IMP::saxs::ChiScore::compute_scale_factor(), IMP::saxs::ChiScore::compute_score(), IMP::saxs::ChiScore::compute_score(), IMP::saxs::ChiScoreLog::compute_offset(), IMP::saxs::ChiScoreLog::compute_scale_factor(), IMP::saxs::ChiScoreLog::compute_score(), IMP::saxs::ChiScoreLog::compute_score(), IMP::saxs::DerivativeCalculator::DerivativeCalculator(), IMP::saxs::DerivativeCalculator::compute_chisquare_derivative(), IMP::saxs::DerivativeCalculator::compute_chisquare_derivative(), IMP::saxs::DerivativeCalculator::compute_gaussian_effect_size(), IMP::saxs::DerivativeCalculator::precompute_derivative_helpers(), IMP::saxs::DerivativeCalculator::compute_sinc_cos(), IMP::saxs::Profile::add(), IMP::saxs::Profile::add(), IMP::saxs::Profile::add_partial_profiles(), IMP::saxs::Profile::add_partial_profiles(), IMP::saxs::Profile::copy_errors(), IMP::saxs::Profile::downsample(), IMP::saxs::Profile::resample(), IMP::saxs::ProfileFitter::ProfileFitter(), IMP::saxs::ProfileFitter::ProfileFitter(), IMP::saxs::ProfileFitter::compute_offset(), IMP::saxs::ProfileFitter::compute_scale_factor(), IMP::saxs::ProfileFitter::compute_score(), IMP::saxs::ProfileFitter::compute_score(), IMP::saxs::ProfileFitter::fit_profile(), IMP::saxs::ProfileFitter::resample(), IMP::saxs::ProfileFitter::write_SAXS_fit_file(), IMP::saxs::ProfileFitter::search_fit_parameters(), IMP::saxs::RadiusOfGyrationRestraint::RadiusOfGyrationRestraint(), IMP::saxs::Restraint::Restraint(), IMP::saxs::RigidBodiesProfileHandler::compute_derivatives(), IMP::saxs::RigidBodiesProfileHandler::compute_profile(), IMP::saxs::WeightedProfileFitter::WeightedProfileFitter()
IMP::saxs::RadialDistributionFunction	IMP::saxs::Profile::distribution_2_profile(), IMP::saxs::Profile::profile_2_distribution(), IMP::saxs::Profile::squared_distribution_2_profile(), IMP::saxs::Profile::squared_distributions_2_partial_profiles(), IMP::saxs::RadialDistributionFunction::add(), IMP::saxs::RadialDistributionFunction::fit(), IMP::saxs::RadialDistributionFunction::R_factor_score(), IMP::saxs::RadialDistributionFunction::write_fit_file()

IMP.statistics

Class	Users
IMP::statistics::Embedding	IMP::statistics::EuclideanMetric::EuclideanMetric(), IMP::statistics::RecursivePartitionalClusteringEmbedding::RecursivePartitionalClusteringEmbedding(), IMP::statistics::create_bin_based_clustering(), IMP::statistics::create_centrality_clustering(), IMP::statistics::create_connectivity_clustering(), IMP::statistics::create_lloyds_kmeans(), IMP::statistics::get_centroids(), IMP::statistics::get_representatives()
IMP::statistics::HistogramD	IMP::statistics::show_histogram()
IMP::statistics::Metric	IMP::statistics::RecursivePartitionalClusteringMetric::RecursivePartitionalClusteringMetric(), IMP::statistics::create_centrality_clustering(), IMP::statistics::create_connectivity_clustering(), IMP::statistics::create_diameter_clustering(), IMP::statistics::create_gromos_clustering()
IMP::statistics::PartitionalClustering	IMP::statistics::RecursivePartitionalClusteringEmbedding::RecursivePartitionalClusteringEmbedding(), IMP::statistics::RecursivePartitionalClusteringEmbedding::create_full_clustering(), IMP::statistics::RecursivePartitionalClusteringMetric::RecursivePartitionalClusteringMetric(), IMP::statistics::RecursivePartitionalClusteringMetric::create_full_clustering(), IMP::statistics::get_centroids(), IMP::statistics::get_representatives(), IMP::statistics::validate_partitional_clustering()