Factory Index

Functions that create objects of a given type:

• IMP::algebra::BoundingBoxD:
  • IMP::algebra::BoundingBoxD::operator+=()
  • IMP::algebra::BoundingBoxD::operator+=()
  • IMP::algebra::BoundingBoxD::operator+=()
  • IMP::algebra::BoundingBoxD::get_bounding_box()
  • IMP::algebra::BoundingBoxD::get_cube_kd()
  • IMP::algebra::BoundingBoxD::get_unit_bounding_box_kd()
  • IMP::algebra::Cone3D::get_bounding_box()
  • IMP::algebra::Cylinder3D::get_bounding_box()
  • IMP::algebra::DefaultEmbeddingD::get_bounding_box()
  • IMP::algebra::DefaultEmbeddingD::get_bounding_box()
  • IMP::algebra::Ellipsoid3D::get_bounding_box()
  • IMP::algebra::GridD::get_bounding_box()
  • IMP::algebra::LogEmbeddingD::get_bounding_box()
  • IMP::algebra::LogEmbeddingD::get_bounding_box()
  • IMP::algebra::Plane3D::get_bounding_box()
  • IMP::algebra::Segment3D::get_bounding_box()
  • IMP::algebra::SpherePatch3D::get_bounding_box()
  • IMP::display::BoundingBoxGeometry::get_geometry()
  • IMP::em::SampledDensityMap::calculate_particles_bounding_box()
  • IMP::statistics::HistogramD::get_bounding_box()
  • IMP::algebra::get_transformed()
  • IMP::atom::get_bounding_box()
  • IMP::core::get_bounding_box()
  • IMP::em::get_bounding_box()
  • IMP::em::get_bounding_box()
  • IMP::kernel::get_bounding_box_d_geometry()
• IMP::algebra::Cone3D:
  • IMP::algebra::Cone3D::get_cone_3d_geometry()
• IMP::algebra::Cylinder3D:
  • IMP::algebra::Cylinder3D::get_cylinder_3d_geometry()
  • IMP::display::CylinderGeometry::get_geometry()
• IMP::algebra::DenseGridStorageD:
  • IMP::algebra::DenseGridStorageD::operator=()
  • IMP::em::get_grid()
• IMP::algebra::Ellipsoid3D:
  • IMP::algebra::Ellipsoid3D::get_ellipsoid_3d_geometry()
  • IMP::display::EllipsoidGeometry::get_geometry()
• IMP::algebra::ExtendedGridIndexD:
  • IMP::algebra::BoundedGridRangeD::get_extended_indexes()
  • IMP::algebra::BoundedGridRangeD::get_end_index()
  • IMP::algebra::BoundedGridRangeD::get_maximum_extended_index()
  • IMP::algebra::BoundedGridRangeD::get_minimum_extended_index()
  • IMP::algebra::DefaultEmbeddingD::get_extended_index()
  • IMP::algebra::ExtendedGridIndexD::get_offset()
  • IMP::algebra::ExtendedGridIndexD::get_uniform_offset()
  • IMP::algebra::GridD::get_nearest_extended_index()
  • IMP::algebra::GridD::get_extended_index()
  • IMP::algebra::LogEmbeddingD::get_extended_index()
  • IMP::algebra::SparseGridStorageD::get_maximum_extended_index()
  • IMP::algebra::SparseGridStorageD::get_minimum_extended_index()
  • IMP::algebra::UnboundedGridRangeD::get_extended_indexes()
• IMP::algebra::FixedXYZ:
  • IMP::algebra::get_fixed_xyz_from_rotation()
• IMP::algebra::FixedZXZ:
  • IMP::algebra::FixedZXZ::get_fixed_zxz_from_rotation()
  • IMP::algebra::get_fixed_zxz_from_rotation()
• IMP::algebra::FixedZYZ:
  • IMP::algebra::FixedZYZ::get_fixed_zyz_from_rotation()
  • IMP::algebra::get_fixed_zyz_from_rotation()
• IMP::algebra::GridD:
  • IMP::em::get_grid()
• IMP::algebra::GridIndexD:
  • IMP::algebra::BoundedGridRangeD::get_all_indexes()
  • IMP::algebra::BoundedGridRangeD::get_indexes()
  • IMP::algebra::BoundedGridRangeD::get_index()
  • IMP::algebra::DefaultEmbeddingD::get_index()
  • IMP::algebra::GridD::get_nearest_index()
  • IMP::algebra::GridD::add_voxel()
  • IMP::algebra::LogEmbeddingD::get_index()
  • IMP::algebra::SparseGridStorageD::get_all_indexes()
  • IMP::algebra::SparseGridStorageD::get_indexes()
  • IMP::algebra::SparseGridStorageD::add_voxel()
  • IMP::algebra::SparseGridStorageD::get_index()
• IMP::algebra::Plane3D:
  • IMP::algebra::Cone3D::get_base_plane()
  • IMP::algebra::Plane3D::get_opposite()
  • IMP::algebra::Plane3D::get_plane_3d_geometry()
  • IMP::algebra::SpherePatch3D::get_plane()
• IMP::algebra::ReferenceFrame3D:
  • IMP::algebra::ReferenceFrame3D::get_global_reference_frame()
  • IMP::algebra::ReferenceFrame3D::get_local_reference_frame()
  • IMP::core::RigidBody::get_reference_frame()
  • IMP::display::ReferenceFrameGeometry::get_geometry()
  • IMP::domino::RigidBodyStates::get_reference_frame()
  • IMP::algebra::get_transformed()
  • IMP::core::get_initial_reference_frame()
• IMP::algebra::Rotation2D:
  • IMP::algebra::Rotation2D::get_inverse()
  • IMP::algebra::Transformation2D::get_rotation()
  • IMP::algebra::compose()
  • IMP::algebra::get_identity_rotation_2d()
  • IMP::algebra::get_random_rotation_2d()
  • IMP::algebra::get_rotation_to_x_axis()
• IMP::algebra::Rotation3D:
  • IMP::algebra::Ellipsoid3D::get_rotation()
  • IMP::algebra::FixedXYZ::get_rotation_from_fixed_xyz()
  • IMP::algebra::FixedZYZ::get_rotation_from_fixed_zyz()
  • IMP::algebra::Rotation3D::get_rotation_from_fixed_zxz()
  • IMP::algebra::Rotation3D::get_inverse()
  • IMP::algebra::Rotation3D::operator*()
  • IMP::algebra::Rotation3D::operator/()
  • IMP::algebra::Rotation3D::operator/=()
  • IMP::algebra::Rotation3D::compose()
  • IMP::algebra::Rotation3D::get_identity_rotation_3d()
  • IMP::algebra::Rotation3D::get_interpolated()
  • IMP::algebra::Rotation3D::get_random_rotation_3d()
  • IMP::algebra::Rotation3D::get_random_rotation_3d()
  • IMP::algebra::Rotation3D::get_rotation_about_axis()
  • IMP::algebra::Rotation3D::get_rotation_from_matrix()
  • IMP::algebra::Rotation3D::get_rotation_from_vector4d()
  • IMP::algebra::Rotation3D::get_rotation_taking_first_to_second()
  • IMP::algebra::Transformation3D::get_rotation()
  • IMP::em2d::GridStates::get_orientation()
  • IMP::em2d::ProjectionParameters::get_rotation()
  • IMP::em2d::RegistrationResult::get_rotation()
  • IMP::em::PCAAligner::get_rotation_matrix()
  • IMP::algebra::get_rotation_from_fixed_xyz()
  • IMP::algebra::get_rotation_from_fixed_zxz()
  • IMP::algebra::get_rotation_from_fixed_zyz()
  • IMP::algebra::compose()
  • IMP::algebra::get_identity_rotation_3d()
  • IMP::algebra::get_interpolated()
  • IMP::algebra::get_random_rotation_3d()
  • IMP::algebra::get_random_rotation_3d()
  • IMP::algebra::get_rotation_about_axis()
  • IMP::algebra::get_rotation_from_matrix()
  • IMP::algebra::get_rotation_from_vector4d()
  • IMP::algebra::get_rotation_from_x_y_axes()
  • IMP::algebra::get_rotation_taking_first_to_second()
• IMP::algebra::Segment3D:
  • IMP::algebra::Cylinder3D::get_segment()
  • IMP::algebra::Segment3D::get_shortest_segment()
  • IMP::algebra::Segment3D::get_segment_3d_geometry()
  • IMP::core::RigidBodyTorque::extract_geometry()
  • IMP::core::RigidBodyTorque::get_geometry()
  • IMP::display::SegmentGeometry::get_geometry()
  • IMP::algebra::get_shortest_segment()
  • IMP::algebra::get_shortest_segment()
• IMP::algebra::SphereD:
  • IMP::algebra::get_unit_sphere_kd()
• IMP::algebra::SpherePatch3D:
  • IMP::algebra::SpherePatch3D::get_sphere_patch_3d_geometry()
• IMP::algebra::Transformation2D:
  • IMP::algebra::Transformation2D::get_inverse()
  • IMP::algebra::Transformation2D::operator*()
  • IMP::algebra::Transformation2D::operator*=()
  • IMP::algebra::Transformation2D::operator/()
  • IMP::algebra::Transformation2D::operator/=()
  • IMP::algebra::Transformation2D::compose()
  • IMP::algebra::Transformation2D::get_identity_transformation_2d()
  • IMP::algebra::Transformation2D::get_rotation_about_point()
  • IMP::algebra::compose()
  • IMP::algebra::get_identity_transformation_2d()
  • IMP::algebra::get_rotation_about_point()
  • IMP::algebra::get_transformation_aligning_pair()
• IMP::algebra::Transformation3D:
  • IMP::algebra::Ellipsoid3D::get_transformation()
  • IMP::algebra::ReferenceFrame3D::get_inverse()
  • IMP::algebra::ReferenceFrame3D::get_transformation_from()
  • IMP::algebra::ReferenceFrame3D::get_transformation_to()
  • IMP::algebra::Transformation3D::get_inverse()
  • IMP::algebra::Transformation3D::operator*()
  • IMP::algebra::Transformation3D::operator*=()
  • IMP::algebra::Transformation3D::operator/()
  • IMP::algebra::Transformation3D::operator/=()
  • IMP::algebra::Transformation3D::compose()
  • IMP::algebra::Transformation3D::get_identity_transformation_3d()
  • IMP::algebra::Transformation3D::get_rotation_about_point()
  • IMP::core::NonRigidMember::get_internal_transformation()
  • IMP::core::RigidMember::get_internal_transformation()
  • IMP::domino::NestedRigidBodyStates::get_transformation()
  • IMP::em::EnvelopeFitRestraint::get_transformation()
  • IMP::em::FittingSolutions::get_transformation()
  • IMP::multifit::FittingSolutionRecord::get_dock_transformation()
  • IMP::multifit::FittingSolutionRecord::get_fit_transformation()
  • IMP::algebra::get_transformation_aligning_first_to_second()
  • IMP::algebra::compose()
  • IMP::algebra::get_identity_transformation_3d()
  • IMP::algebra::get_random_local_transformation()
  • IMP::algebra::get_rotation_about_point()
  • IMP::algebra::get_transformation_3d()
  • IMP::algebra::get_transformation_from_first_to_second()
  • IMP::algebra::get_transformation_from_first_triangle_to_second()
  • IMP::cnmultifit::calc_transformation_around_axis()
  • IMP::core::get_transformation_aligning_first_to_second()
• IMP::algebra::Triangle3D:
  • IMP::algebra::Triangle3D::get_largest_triangle()
  • IMP::display::TriangleGeometry::get_geometry()
  • IMP::algebra::get_largest_triangle()
• IMP::algebra::VectorD:
  • IMP::algebra::BoundingBoxD::get_corner()
  • IMP::algebra::DefaultEmbeddingD::get_center()
  • IMP::algebra::DefaultEmbeddingD::get_center()
  • IMP::algebra::DefaultEmbeddingD::get_origin()
  • IMP::algebra::DefaultEmbeddingD::get_unit_cell()
  • IMP::algebra::LogEmbeddingD::get_center()
  • IMP::algebra::LogEmbeddingD::get_center()
  • IMP::algebra::LogEmbeddingD::get_origin()
  • IMP::algebra::LogEmbeddingD::get_unit_cell()
  • IMP::algebra::PrincipalComponentAnalysisD::get_centroid()
  • IMP::algebra::PrincipalComponentAnalysisD::get_principal_component()
  • IMP::algebra::PrincipalComponentAnalysisD::get_principal_components()
  • IMP::algebra::PrincipalComponentAnalysisD::get_principal_values()
  • IMP::algebra::SphereD::get_random_vector_in()
  • IMP::algebra::SphereD::get_center()
  • IMP::algebra::VectorD::get_unit_vector()
  • IMP::core::RigidBody::get_rotational_derivatives()
  • IMP::example::ExampleTemplateClassD::get_point()
  • IMP::multifit::GeometricHash::from_bucket()
  • IMP::statistics::HistogramD::get_mean()
  • IMP::statistics::HistogramD::get_standard_deviation()
  • IMP::algebra::get_random_vector_in()
  • IMP::algebra::get_basis_vector_kd()
  • IMP::algebra::get_ones_vector_kd()
  • IMP::algebra::get_zero_vector_kd()
• IMP::atom::Angle:
  • IMP::atom::Angle::decorate_particle()
  • IMP::atom::Angle::setup_particle()
• IMP::atom::Atom:
  • IMP::atom::Atom::decorate_particle()
  • IMP::atom::Atom::setup_particle()
  • IMP::atom::Atom::setup_particle()
  • IMP::atom::Atom::setup_particle()
  • IMP::atom::CHARMMBondEndpoint::get_atom()
  • IMP::atom::Hierarchy::get_as_atom()
  • IMP::atom::Hierarchy::get_atom()
  • IMP::atom::get_atom()
• IMP::atom::AtomType:
  • IMP::atom::Atom::get_atom_type()
  • IMP::atom::AtomType::add_atom_type()
  • IMP::atom::get_atom_type()
  • IMP::atom::add_atom_type()
• IMP::atom::Bond:
  • IMP::atom::Bond::decorate_particle()
  • IMP::atom::BondGraph::get_bond()
  • IMP::atom::Bonded::get_bond()
  • IMP::atom::Bonded::create_bond()
  • IMP::atom::Bonded::create_bond()
  • IMP::atom::Bonded::create_custom_bond()
  • IMP::atom::Bonded::get_bond()
  • IMP::atom::create_bond()
  • IMP::atom::create_bond()
  • IMP::atom::create_custom_bond()
  • IMP::atom::get_bond()
• IMP::atom::Bonded:
  • IMP::atom::Bond::get_bonded()
  • IMP::atom::Bonded::get_bonded()
  • IMP::atom::Bonded::decorate_particle()
  • IMP::atom::Bonded::setup_particle()
• IMP::atom::CHARMMAtom:
  • IMP::atom::CHARMMAtom::decorate_particle()
  • IMP::atom::CHARMMAtom::setup_particle()
• IMP::atom::CHARMMAtomTopology:
  • IMP::atom::CHARMMResidueTopologyBase::get_atom()
  • IMP::atom::CHARMMResidueTopologyBase::get_atom()
  • IMP::atom::CHARMMResidueTopologyBase::get_atom()
• IMP::atom::CHARMMBondEndpoint:
  • IMP::atom::CHARMMConnection::get_endpoint()
• IMP::atom::CHARMMConnection:
  • IMP::atom::CHARMMResidueTopologyBase::get_angle()
  • IMP::atom::CHARMMResidueTopologyBase::get_bond()
  • IMP::atom::CHARMMResidueTopologyBase::get_dihedral()
  • IMP::atom::CHARMMResidueTopologyBase::get_improper()
• IMP::atom::CHARMMIdealResidueTopology:
  • IMP::atom::CHARMMParameters::get_residue_topology()
• IMP::atom::CHARMMInternalCoordinate:
  • IMP::atom::CHARMMResidueTopologyBase::get_internal_coordinate()
• IMP::atom::CHARMMParameters:
  • IMP::atom::CHARMMTopology::get_parameters()
  • IMP::atom::get_all_atom_CHARMM_parameters()
  • IMP::atom::get_heavy_atom_CHARMM_parameters()
• IMP::atom::CHARMMPatch:
  • IMP::atom::CHARMMParameters::get_patch()
• IMP::atom::CHARMMResidueTopology:
  • IMP::atom::CHARMMSegmentTopology::get_residue()
• IMP::atom::CHARMMSegmentTopology:
  • IMP::atom::CHARMMTopology::get_segment()
• IMP::atom::CHARMMTopology:
  • IMP::atom::CHARMMParameters::create_topology()
• IMP::atom::Chain:
  • IMP::atom::Chain::decorate_particle()
  • IMP::atom::Chain::setup_particle()
  • IMP::atom::Chain::setup_particle()
  • IMP::atom::Chain::setup_particle()
  • IMP::atom::Hierarchy::get_as_chain()
  • IMP::atom::get_chain()
• IMP::atom::Charged:
  • IMP::atom::Charged::decorate_particle()
  • IMP::atom::Charged::setup_particle()
  • IMP::atom::Charged::setup_particle()
• IMP::atom::Copy:
  • IMP::atom::Copy::decorate_particle()
  • IMP::atom::Copy::setup_particle()
• IMP::atom::Diffusion:
  • IMP::atom::Diffusion::decorate_particle()
  • IMP::atom::Diffusion::setup_particle()
  • IMP::atom::Diffusion::setup_particle()
  • IMP::atom::Diffusion::setup_particle()
• IMP::atom::Dihedral:
  • IMP::atom::Dihedral::decorate_particle()
  • IMP::atom::Dihedral::setup_particle()
• IMP::atom::Domain:
  • IMP::atom::Domain::decorate_particle()
  • IMP::atom::Domain::setup_particle()
  • IMP::atom::Domain::setup_particle()
  • IMP::atom::Hierarchy::get_as_domain()
• IMP::atom::ElementTable:
  • IMP::atom::get_element_table()
• IMP::atom::Fragment:
  • IMP::atom::Fragment::decorate_particle()
  • IMP::atom::Fragment::setup_particle()
  • IMP::atom::Fragment::setup_particle()
  • IMP::atom::Hierarchy::get_as_fragment()
• IMP::atom::Hierarchy:
  • IMP::atom::CHARMMTopology::create_hierarchy()
  • IMP::atom::Hierarchy::read_pdb()
  • IMP::atom::Hierarchy::get_child()
  • IMP::atom::Hierarchy::get_parent()
  • IMP::atom::Hierarchy::decorate_particle()
  • IMP::atom::Hierarchy::setup_particle()
  • IMP::atom::Hierarchy::setup_particle()
  • IMP::atom::Hierarchy::setup_particle()
  • IMP::atom::Hierarchy::create_clone()
  • IMP::atom::Hierarchy::create_clone_one()
  • IMP::atom::Hierarchy::create_fragment()
  • IMP::atom::Hierarchy::create_protein()
  • IMP::atom::Hierarchy::get_residue()
  • IMP::atom::Hierarchy::get_root()
  • IMP::atom::Residue::get_next_residue()
  • IMP::atom::Residue::get_previous_residue()
  • IMP::atom::create_simplified_along_backbone()
  • IMP::atom::create_simplified_along_backbone()
  • IMP::atom::read_mol2()
  • IMP::atom::read_pdb()
  • IMP::atom::read_pdb()
  • IMP::atom::create_clone()
  • IMP::atom::create_clone_one()
  • IMP::atom::create_fragment()
  • IMP::atom::create_protein()
  • IMP::atom::create_protein()
  • IMP::atom::get_next_residue()
  • IMP::atom::get_previous_residue()
  • IMP::atom::get_residue()
  • IMP::atom::get_root()
  • IMP::multifit::create_coarse_molecule_from_density()
  • IMP::multifit::create_coarse_molecule_from_molecule()
• IMP::atom::LennardJones:
  • IMP::atom::LennardJones::decorate_particle()
  • IMP::atom::LennardJones::setup_particle()
• IMP::atom::Mass:
  • IMP::atom::Hierarchy::get_as_mass()
  • IMP::atom::Mass::decorate_particle()
  • IMP::atom::Mass::setup_particle()
• IMP::atom::Molecule:
  • IMP::atom::Hierarchy::get_as_molecule()
  • IMP::atom::Molecule::decorate_particle()
  • IMP::atom::Molecule::setup_particle()
  • IMP::atom::Molecule::setup_particle()
• IMP::atom::Residue:
  • IMP::atom::Hierarchy::get_as_residue()
  • IMP::atom::Hierarchy::get_residue()
  • IMP::atom::Residue::decorate_particle()
  • IMP::atom::Residue::setup_particle()
  • IMP::atom::Residue::setup_particle()
  • IMP::atom::Residue::setup_particle()
  • IMP::atom::get_residue()
• IMP::atom::ResidueType:
  • IMP::atom::CHARMMParameters::parse_residue_line()
  • IMP::atom::Residue::get_residue_type()
  • IMP::atom::get_residue_type()
  • IMP::atom::get_residue_type()
• IMP::atom::RigidBodyDiffusion:
  • IMP::atom::RigidBodyDiffusion::decorate_particle()
  • IMP::atom::RigidBodyDiffusion::setup_particle()
• IMP::atom::SecondaryStructureResidue:
  • IMP::atom::SecondaryStructureResidue::decorate_particle()
  • IMP::atom::SecondaryStructureResidue::setup_particle()
  • IMP::atom::SecondaryStructureResidue::setup_particle()
  • IMP::atom::setup_coarse_secondary_structure_residue()
• IMP::atom::StereochemistryPairFilter:
  • IMP::atom::CHARMMStereochemistryRestraint::get_pair_filter()
• IMP::base::LRUCache:
  • IMP::domino::RestraintCache::Generator::operator()()
• IMP::base::Object:
  • IMP::kernel::Model::get_data()
• IMP::base::TextOutput:
  • IMP::base::create_temporary_file()
  • IMP::base::get_log_target()
• IMP::base::Tracker:
  • IMP::base::TrackedObject::get_tracker()
• IMP::base::Vector:
  • IMP::algebra::BoundedGridRangeD::get_all_indexes()
  • IMP::algebra::BoundedGridRangeD::get_indexes()
  • IMP::algebra::BoundedGridRangeD::get_extended_indexes()
  • IMP::algebra::DenseGridStorageD::get_all_voxels()
  • IMP::algebra::PrincipalComponentAnalysisD::get_principal_components()
  • IMP::algebra::SparseGridStorageD::get_all_indexes()
  • IMP::algebra::SparseGridStorageD::get_indexes()
  • IMP::algebra::UnboundedGridRangeD::get_extended_indexes()
  • IMP::base::ConstVector::ConstVector()
  • IMP::base::LRUCache::get_keys()
  • IMP::base::Tracker::get_tracked()
  • IMP::core::MSConnectivityRestraint::ExperimentalTree::Node::get_label()
  • IMP::kernel::Container::get_all_possible_indexes()
  • IMP::kernel::Container::get_all_possible_particles()
  • IMP::kernel::Key::get_all_strings()
  • IMP::kernel::Model::get_particles()
  • IMP::kernel::ModelObject::get_interactions()
  • IMP::kernel::ModelObject::do_get_interactions()
  • IMP::kernel::PairModifier::get_input_particles()
  • IMP::kernel::PairModifier::get_output_particles()
  • IMP::kernel::PairPredicate::get_input_particles()
  • IMP::kernel::PairScore::get_input_particles()
  • IMP::kernel::QuadModifier::get_input_particles()
  • IMP::kernel::QuadModifier::get_output_particles()
  • IMP::kernel::QuadPredicate::get_input_particles()
  • IMP::kernel::QuadScore::get_input_particles()
  • IMP::kernel::Refiner::get_input_particles()
  • IMP::kernel::Refiner::get_refined()
  • IMP::kernel::Restraint::get_input_particles()
  • IMP::kernel::ScoreState::get_input_particles()
  • IMP::kernel::ScoreState::get_output_particles()
  • IMP::kernel::SingletonContainer::get_indexes()
  • IMP::kernel::SingletonContainer::get_particles()
  • IMP::kernel::SingletonContainer::get_range_indexes()
  • IMP::kernel::SingletonModifier::get_input_particles()
  • IMP::kernel::SingletonModifier::get_output_particles()
  • IMP::kernel::SingletonPredicate::get_input_particles()
  • IMP::kernel::SingletonScore::get_input_particles()
  • IMP::kernel::TripletModifier::get_input_particles()
  • IMP::kernel::TripletModifier::get_output_particles()
  • IMP::kernel::TripletPredicate::get_input_particles()
  • IMP::kernel::TripletScore::get_input_particles()
  • IMP::multifit::GeometricHash::neighbors_data()
  • IMP::rmf::SimpleLoadLink::create()
  • IMP::kernel::get_required_particles()
  • IMP::kernel::get_dependent_particles()
  • IMP::kernel::get_input_particles()
  • IMP::kernel::get_output_particles()
  • IMP::kernel::write_particles_to_buffer()
  • IMP::kernel::get_indexes()
  • IMP::kernel::get_particles()
• IMP::base::VersionInfo:
  • IMP::base::Object::get_version_info()
  • IMP::em::EnvelopeScore::get_version_info()
  • IMP::em::PCAAligner::get_version_info()
• IMP::container::ClosePairContainer:
  • IMP::example::create_excluded_volume()
• IMP::container::DynamicListPairContainer:
  • IMP::container::DistributePairsScoreState::add_predicate()
• IMP::container::DynamicListQuadContainer:
  • IMP::container::DistributeQuadsScoreState::add_predicate()
• IMP::container::DynamicListSingletonContainer:
  • IMP::container::DistributeSingletonsScoreState::add_predicate()
• IMP::container::DynamicListTripletContainer:
  • IMP::container::DistributeTripletsScoreState::add_predicate()
• IMP::container::PairContainerSet:
  • IMP::container::PairContainerSet::get_set()
• IMP::container::QuadContainerSet:
  • IMP::container::QuadContainerSet::get_set()
• IMP::container::SingletonContainerSet:
  • IMP::container::SingletonContainerSet::get_set()
• IMP::container::TripletContainerSet:
  • IMP::container::TripletContainerSet::get_set()
• IMP::core::Centroid:
  • IMP::core::Centroid::decorate_particle()
  • IMP::core::Centroid::setup_particle()
  • IMP::core::Centroid::setup_particle()
• IMP::core::ConnectivityRestraint:
  • IMP::restrainer::SimpleConnectivity::get_restraint()
• IMP::core::Cover:
  • IMP::core::Cover::decorate_particle()
  • IMP::core::Cover::setup_particle()
  • IMP::core::Cover::setup_particle()
• IMP::core::DataObject:
  • IMP::multifit::ComplementarityRestraint::get_grid_object()
• IMP::core::DiameterRestraint:
  • IMP::restrainer::SimpleDiameter::get_restraint()
• IMP::core::DistanceRestraint:
  • IMP::restrainer::SimpleDistance::get_restraint()
• IMP::core::ExcludedVolumeRestraint:
  • IMP::restrainer::SimpleExcludedVolume::get_restraint()
• IMP::core::HarmonicUpperBound:
  • IMP::restrainer::SimpleConnectivity::get_harmonic_upper_bound()
  • IMP::restrainer::SimpleDiameter::get_harmonic_upper_bound()
  • IMP::restrainer::SimpleDistance::get_harmonic_upper_bound()
• IMP::core::Hierarchy:
  • IMP::core::Hierarchy::get_child()
  • IMP::core::Hierarchy::get_parent()
  • IMP::core::Hierarchy::decorate_particle()
  • IMP::core::Hierarchy::setup_particle()
  • IMP::core::Hierarchy::setup_particle()
  • IMP::core::Hierarchy::get_root()
  • IMP::core::get_root()
• IMP::core::HierarchyTraits:
  • IMP::atom::Hierarchy::get_traits()
  • IMP::core::Hierarchy::get_decorator_traits()
  • IMP::core::Hierarchy::get_traits()
  • IMP::core::Hierarchy::get_default_decorator_traits()
  • IMP::core::Hierarchy::get_default_traits()
• IMP::core::IncrementalScoringFunction:
  • IMP::core::MonteCarlo::get_incremental_scoring_function()
• IMP::core::MonteCarloMover:
  • IMP::core::MonteCarlo::get_mover()
  • IMP::example::create_serial_mover()
• IMP::core::NonRigidMember:
  • IMP::core::NonRigidMember::decorate_particle()
• IMP::core::Reference:
  • IMP::core::Reference::decorate_particle()
  • IMP::core::Reference::setup_particle()
• IMP::core::RigidBody:
  • IMP::core::NonRigidMember::get_rigid_body()
  • IMP::core::RigidBody::decorate_particle()
  • IMP::core::RigidBody::setup_particle()
  • IMP::core::RigidBody::setup_particle()
  • IMP::core::RigidBody::create_compatible_rigid_body()
  • IMP::core::RigidBody::create_rigid_body()
  • IMP::core::RigidMember::get_rigid_body()
  • IMP::atom::create_compatible_rigid_body()
  • IMP::atom::create_rigid_body()
  • IMP::atom::create_rigid_body()
• IMP::core::RigidMember:
  • IMP::core::RigidMember::decorate_particle()
• IMP::core::SphereDistancePairScore:
  • IMP::restrainer::SimpleConnectivity::get_sphere_distance_pair_score()
• IMP::core::Typed:
  • IMP::core::Typed::decorate_particle()
  • IMP::core::Typed::setup_particle()
• IMP::core::XYZ:
  • IMP::atom::Hierarchy::get_as_xyz()
  • IMP::core::XYZ::decorate_particle()
  • IMP::core::XYZ::setup_particle()
  • IMP::core::XYZ::setup_particle()
• IMP::core::XYZR:
  • IMP::atom::Hierarchy::get_as_xyzr()
  • IMP::atom::Selection::create_cover()
  • IMP::core::XYZR::decorate_particle()
  • IMP::core::XYZR::setup_particle()
  • IMP::core::XYZR::setup_particle()
  • IMP::core::XYZR::setup_particle()
  • IMP::core::XYZR::setup_particle()
  • IMP::atom::create_cover()
• IMP::display::BoundingBoxGeometry:
  • IMP::display::create_geometry()
• IMP::display::Color:
  • IMP::display::Color::get_jet_color()
  • IMP::display::Color::get_hot_color()
  • IMP::display::Color::get_rgb_color()
  • IMP::display::Color::get_grey_color()
  • IMP::display::Color::get_gnuplot_color()
  • IMP::display::Color::get_interpolated_rgb()
  • IMP::display::Colored::get_color()
  • IMP::display::Geometry::get_color()
  • IMP::display::PairGeometry::get_color()
  • IMP::display::SingletonGeometry::get_color()
  • IMP::display::get_jet_color()
  • IMP::display::get_hot_color()
  • IMP::display::get_rgb_color()
  • IMP::display::get_grey_color()
  • IMP::display::get_gnuplot_color()
  • IMP::display::get_display_color()
  • IMP::display::get_interpolated_rgb()
• IMP::display::Colored:
  • IMP::display::Colored::decorate_particle()
  • IMP::display::Colored::setup_particle()
• IMP::display::CylinderGeometry:
  • IMP::display::create_geometry()
• IMP::display::EllipsoidGeometry:
  • IMP::display::create_geometry()
• IMP::display::Geometry:
  • IMP::display::WriteOptimizerState::get_geometry()
• IMP::display::PointGeometry:
  • IMP::display::create_geometry()
• IMP::display::PolygonGeometry:
  • IMP::display::create_geometry()
• IMP::display::ReferenceFrameGeometry:
  • IMP::display::create_geometry()
• IMP::display::SegmentGeometry:
  • IMP::display::create_geometry()
• IMP::display::SphereGeometry:
  • IMP::display::create_geometry()
• IMP::display::TriangleGeometry:
  • IMP::display::create_geometry()
• IMP::display::Writer:
  • IMP::display::WriterAdaptor::get_writer()
  • IMP::display::WriterAdaptor::operator->()
  • IMP::display::create_writer()
• IMP::domino::Assignment:
  • IMP::domino::AssignmentContainer::get_assignment()
  • IMP::domino::Order::get_subset_ordered()
  • IMP::domino::Slice::get_sliced()
  • IMP::domino::get_nearest_assignment()
• IMP::domino::AssignmentsTable:
  • IMP::domino::DiscreteSampler::get_assignments_table_to_use()
• IMP::domino::ParticleStates:
  • IMP::domino::ParticleStatesTable::get_particle_states()
• IMP::domino::ParticleStatesTable:
  • IMP::domino::DiscreteSampler::get_particle_states_table()
  • IMP::domino::RestraintCache::Generator::get_particle_states_table()
  • IMP::multifit::ProteomicsEMAlignmentAtomic::set_particle_states_table()
• IMP::domino::Slice:
  • IMP::domino::RestraintCache::get_slice()
  • IMP::domino::get_slice()
• IMP::domino::Subset:
  • IMP::domino::ParticleStatesTable::get_subset()
  • IMP::domino::RestraintCache::get_subset()
  • IMP::domino::Slice::get_sliced()
  • IMP::domino::get_difference()
  • IMP::domino::get_intersection()
  • IMP::domino::get_union()
• IMP::domino::SubsetFilter:
  • IMP::domino::SubsetFilterTable::get_subset_filter()
• IMP::domino::SubsetFilterTable:
  • IMP::domino::DiscreteSampler::get_subset_filter_table()
• IMP::em2d::Image:
  • IMP::em2d::ProjectionStates::get_projection()
• IMP::em2d::ProjectionParameters:
  • IMP::em2d::ProjectionParameters::decorate_particle()
  • IMP::em2d::ProjectionParameters::setup_particle()
• IMP::em2d::RegistrationResult:
  • IMP::em2d::Fine2DRegistrationRestraint::get_final_registration()
• IMP::em::DensityHeader:
  • IMP::em::DensityHeader::create_density_header()
  • IMP::em::DensityMap::get_header()
  • IMP::em::DensityMap::get_header_writable()
  • IMP::em::create_density_header()
• IMP::em::DensityMap:
  • IMP::em::DensityMap::get_resampled()
  • IMP::em::DensityMap::get_transformed()
  • IMP::em::DensityMap::get_transformed()
  • IMP::em::DensityMap::read_map()
  • IMP::em::DensityMap::read_map()
  • IMP::em::DensityMap::get_cropped()
  • IMP::em::DensityMap::get_cropped()
  • IMP::em::DensityMap::pad_margin()
  • IMP::multifit::FFTFitting::crop_margin()
  • IMP::cnmultifit::build_cn_dens_assembly()
  • IMP::em::binarize()
  • IMP::em::create_density_map()
  • IMP::em::create_density_map()
  • IMP::em::create_density_map()
  • IMP::em::create_density_map()
  • IMP::em::get_binarized_interior()
  • IMP::em::get_max_map()
  • IMP::em::get_resampled()
  • IMP::em::get_segment()
  • IMP::em::get_segment()
  • IMP::em::get_segment_by_masking()
  • IMP::em::get_threshold_map()
  • IMP::em::get_transformed()
  • IMP::em::get_transformed()
  • IMP::em::interpolate_map()
  • IMP::em::mask_and_norm()
  • IMP::em::multiply()
  • IMP::em::read_map()
  • IMP::em::read_map()
  • IMP::multifit::create_hit_map()
  • IMP::multifit::grid2map()
  • IMP::multifit::remove_background()
  • IMP::restrainer::load_em_density_map()
• IMP::em::FitRestraint:
  • IMP::restrainer::SimpleEMFit::get_restraint()
• IMP::em::FittingSolutions:
  • IMP::cnmultifit::fit_cn_assembly()
  • IMP::cnmultifit::fit_cn_assembly()
  • IMP::cnmultifit::symmetry_local_fitting()
  • IMP::em::compute_fitting_scores()
  • IMP::em::compute_fitting_scores()
  • IMP::em::local_rigid_fitting()
  • IMP::em::local_rigid_fitting_around_point()
  • IMP::em::local_rigid_fitting_around_points()
  • IMP::em::local_rigid_fitting_grid_search()
  • IMP::multifit::convert_multifit_to_em_format()
  • IMP::multifit::fitting_clustering()
  • IMP::multifit::pca_based_rigid_fitting()
  • IMP::multifit::pca_based_rigid_fitting()
• IMP::em::ImageHeader:
  • IMP::em2d::Image::get_header()
• IMP::em::KernelParameters:
  • IMP::em::SampledDensityMap::get_kernel_params()
• IMP::em::RadiusDependentKernelParameters:
  • IMP::em::KernelParameters::get_params()
  • IMP::em::KernelParameters::set_params()
• IMP::em::SampledDensityMap:
  • IMP::em::FitRestraint::get_model_dens_map()
  • IMP::em::SampledDensityMap::particles2binarized_density()
  • IMP::em::SampledDensityMap::particles2density()
  • IMP::em::particles2binarized_density()
  • IMP::em::particles2density()
• IMP::em::SurfaceShellDensityMap:
  • IMP::em::SampledDensityMap::particles2surface()
  • IMP::em::particles2surface()
• IMP::em::Voxel:
  • IMP::em::Voxel::decorate_particle()
  • IMP::em::Voxel::setup_particle()
• IMP::example::ExampleDecorator:
  • IMP::example::ExampleDecorator::decorate_particle()
  • IMP::example::ExampleDecorator::setup_particle()
• IMP::isd::MolecularDynamics:
  • IMP::isd::HybridMonteCarlo::get_md()
  • IMP::isd::MolecularDynamicsMover::get_md()
• IMP::isd::Nuisance:
  • IMP::isd::Nuisance::decorate_particle()
  • IMP::isd::Nuisance::setup_particle()
• IMP::isd::Scale:
  • IMP::isd::Scale::decorate_particle()
  • IMP::isd::Scale::setup_particle()
• IMP::isd::Switching:
  • IMP::isd::Switching::decorate_particle()
  • IMP::isd::Switching::setup_particle()
• IMP::kernel::ConfigurationSet:
  • IMP::kernel::Sampler::create_sample()
  • IMP::kernel::Sampler::do_sample()
• IMP::kernel::DerivativeAccumulator:
  • IMP::kernel::ScoreAccumulator::get_derivative_accumulator()
• IMP::kernel::Key:
  • IMP::kernel::Key::operator+()
  • IMP::kernel::Key::operator++()
  • IMP::kernel::Key::operator–()
  • IMP::kernel::Key::add_alias()
  • IMP::misc::CustomXYZR::get_decorator_traits()
  • IMP::misc::CustomXYZR::get_default_decorator_traits()
• IMP::kernel::Model:
  • IMP::kernel::ConfigurationSet::get_model()
  • IMP::kernel::Decorator::get_model()
  • IMP::kernel::ModelObject::get_model()
  • IMP::kernel::Optimizer::get_model()
  • IMP::kernel::Sampler::get_model()
• IMP::kernel::Optimizer:
  • IMP::kernel::OptimizerState::get_optimizer()
• IMP::kernel::OptimizerState:
  • IMP::kernel::Optimizer::get_optimizer_state()
• IMP::kernel::Particle:
  • IMP::kernel::Decorator::get_particle()
  • IMP::kernel::Model::get_particle()
  • IMP::kernel::Refiner::get_refined()
  • IMP::kernel::SingletonContainer::get_particle()
• IMP::kernel::Restraint:
  • IMP::kernel::Restraint::create_current_decomposition()
  • IMP::kernel::Restraint::create_decomposition()
  • IMP::kernel::RestraintSet::get_restraint()
• IMP::kernel::ScoreAccumulator:
  • IMP::kernel::ScoringFunction::get_score_accumulator()
  • IMP::kernel::ScoringFunction::get_score_accumulator_if_below()
  • IMP::kernel::ScoringFunction::get_score_accumulator_if_good()
• IMP::kernel::ScoreState:
  • IMP::kernel::Model::get_score_state()
• IMP::kernel::ScoringFunction:
  • IMP::kernel::Model::create_model_scoring_function()
  • IMP::kernel::Optimizer::get_scoring_function()
  • IMP::kernel::Restraint::create_scoring_function()
  • IMP::kernel::Restraint::create_internal_scoring_function()
  • IMP::kernel::Sampler::get_scoring_function()
  • IMP::kernel::ScoringFunctionAdaptor::get()
  • IMP::kernel::ScoringFunctionAdaptor::get()
  • IMP::kernel::ScoringFunctionAdaptor::get()
  • IMP::kernel::ScoringFunctionAdaptor::get()
  • IMP::kernel::ScoringFunctionAdaptor::get()
• IMP::misc::CustomXYZR:
  • IMP::misc::CustomXYZR::decorate_particle()
  • IMP::misc::CustomXYZR::setup_particle()
  • IMP::misc::CustomXYZR::setup_particle()
  • IMP::misc::CustomXYZR::setup_particle()
• IMP::multifit::AssemblyHeader:
  • IMP::multifit::SettingsData::get_assembly_header()
• IMP::multifit::ComponentHeader:
  • IMP::multifit::SettingsData::get_component_header()
• IMP::multifit::ProteinsAnchorsSamplingSpace:
  • IMP::multifit::get_part_of_sampling_space()
  • IMP::multifit::read_protein_anchors_mapping()
• IMP::multifit::SettingsData:
  • IMP::multifit::get_partial_assembly_setting_data()
  • IMP::multifit::read_settings()
• IMP::restrainer::SimpleConnectivity:
  • IMP::restrainer::SimpleConnectivity::create_simple_connectivity_on_molecules()
  • IMP::restrainer::create_simple_connectivity_on_rigid_bodies()
• IMP::restrainer::SimpleDiameter:
  • IMP::restrainer::SimpleDiameter::create_simple_diameter()
• IMP::restrainer::SimpleDistance:
  • IMP::restrainer::SimpleDistance::create_simple_distance()
• IMP::restrainer::SimpleEMFit:
  • IMP::restrainer::SimpleEMFit::create_simple_em_fit()
  • IMP::restrainer::SimpleEMFit::create_simple_em_fit()
• IMP::restrainer::SimpleExcludedVolume:
  • IMP::restrainer::SimpleExcludedVolume::create_simple_excluded_volume_on_molecules()
  • IMP::restrainer::SimpleExcludedVolume::create_simple_excluded_volume_on_rigid_bodies()
• IMP::rotamer::ResidueRotamer:
  • IMP::rotamer::RotamerCalculator::get_rotamer()
• IMP::saxs::DeltaDistributionFunction:
  • IMP::saxs::DerivativeCalculator::precompute_derivative_helpers()
• IMP::saxs::FormFactorTable:
  • IMP::saxs::default_form_factor_table()
• IMP::statistics::Histogram:
  • IMP::cnmultifit::my_get_density_histogram()
  • IMP::multifit::get_density_histogram()
• IMP::statistics::HistogramD:
  • IMP::statistics::HistogramD::get_frequencies()
  • IMP::statistics::HistogramD::get_probability_distribution_function()
• IMP::statistics::PartitionalClustering:
  • IMP::statistics::RecursivePartitionalClusteringEmbedding::create_full_clustering()
  • IMP::statistics::RecursivePartitionalClusteringMetric::create_full_clustering()
  • IMP::statistics::create_centrality_clustering()
  • IMP::statistics::create_centrality_clustering()
  • IMP::statistics::create_connectivity_clustering()
  • IMP::statistics::create_diameter_clustering()
• IMP::statistics::PartitionalClusteringWithCenter:
  • IMP::statistics::create_bin_based_clustering()
  • IMP::statistics::create_connectivity_clustering()
  • IMP::statistics::create_lloyds_kmeans()