Argument Index

Functions that take objects of a given type as arguments:

• IMP::algebra::BoundingBoxD:
  • IMP::algebra::BoundingBoxD::get_contains()
  • IMP::algebra::BoundingBoxD::operator+()
  • IMP::algebra::BoundingBoxD::operator+=()
  • IMP::algebra::BoundingBoxD::get_edges()
  • IMP::algebra::BoundingBoxD::get_interiors_intersect()
  • IMP::algebra::BoundingBoxD::get_intersection()
  • IMP::algebra::BoundingBoxD::get_maximum_length()
  • IMP::algebra::BoundingBoxD::get_union()
  • IMP::algebra::BoundingBoxD::get_vertices()
  • IMP::algebra::BoundingBoxD::get_volume()
  • 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::GridD()
  • IMP::algebra::GridD::GridD()
  • IMP::algebra::GridD::set_bounding_box()
  • IMP::algebra::LogEmbeddingD::initialize_from_box()
  • IMP::algebra::LogEmbeddingD::LogEmbeddingD()
  • IMP::algebra::VectorD::get_random_vector_in()
  • IMP::algebra::VectorD::get_random_vector_on()
  • 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::em::DensityHeader::create_density_header()
  • 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_transformed()
  • IMP::core::create_bounding_box_3d_singleton_score()
  • IMP::display::create_geometry()
  • IMP::em::create_density_header()
• IMP::algebra::Cone3D:
  • IMP::algebra::Cone3D::get_uniform_surface_cover()
  • 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_random_vector_in()
  • IMP::algebra::Cylinder3D::get_uniform_surface_cover()
  • IMP::algebra::Cylinder3D::get_grid_surface_cover()
  • 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::GridD:
  • IMP::algebra::GridD::get_trilinearly_interpolated()
  • 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::algebra::GridIndexD:
  • IMP::algebra::DefaultEmbeddingD::get_center()
  • IMP::algebra::DefaultEmbeddingD::get_bounding_box()
  • 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::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_distance()
  • 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::ReferenceFrame3D::get_global_reference_frame()
  • IMP::algebra::ReferenceFrame3D::get_local_reference_frame()
  • IMP::core::RigidBody::add_member_internal()
  • IMP::core::RigidBody::set_reference_frame()
  • IMP::core::RigidBody::set_reference_frame_lazy()
  • 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::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::Transformation2D::get_rotation_about_point()
  • IMP::algebra::compose()
  • IMP::algebra::get_rotation_about_point()
• IMP::algebra::Rotation3D:
  • IMP::algebra::Ellipsoid3D::Ellipsoid3D()
  • IMP::algebra::FixedZXZ::get_fixed_zxz_from_rotation()
  • IMP::algebra::FixedZYZ::get_fixed_zyz_from_rotation()
  • IMP::algebra::Rotation3D::operator*()
  • IMP::algebra::Rotation3D::operator/()
  • IMP::algebra::Rotation3D::operator/=()
  • IMP::algebra::Rotation3D::compose()
  • IMP::algebra::Rotation3D::get_axis_and_angle()
  • IMP::algebra::Rotation3D::get_distance()
  • IMP::algebra::Rotation3D::get_interpolated()
  • IMP::algebra::Rotation3D::get_random_rotation_3d()
  • IMP::algebra::Transformation3D::Transformation3D()
  • IMP::algebra::Transformation3D::get_rotation_about_point()
  • IMP::em2d::ProjectionParameters::set_rotation()
  • IMP::em2d::RegistrationResult::RegistrationResult()
  • IMP::em2d::RegistrationResult::set_rotation()
  • IMP::algebra::get_fixed_zyz_from_rotation()
  • IMP::algebra::get_fixed_zxz_from_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_shortest_segment()
  • IMP::algebra::Segment3D::get_bounding_box()
  • IMP::algebra::Segment3D::get_distance()
  • IMP::algebra::Segment3D::get_distance()
  • 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_random_vector_in()
  • IMP::algebra::SphereD::get_random_vector_in()
  • IMP::algebra::SphereD::get_random_vector_on()
  • IMP::algebra::SphereD::get_uniform_surface_cover()
  • IMP::algebra::SphereD::get_contains()
  • IMP::algebra::SphereD::get_distance()
  • IMP::algebra::SphereD::get_interiors_intersect()
  • IMP::algebra::SphereD::get_power_distance()
  • 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_d_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::VectorD::get_uniform_surface_cover()
  • 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::algebra::Transformation2D::compose()
  • 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::algebra::Transformation3D::compose()
  • IMP::atom::RMSDCalculator::get_rmsd()
  • IMP::atom::RMSDCalculator::get_squared_rmsd()
  • IMP::core::NonRigidMember::set_internal_transformation()
  • IMP::core::RigidBody::transform()
  • IMP::core::RigidMember::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::DensityMap::get_transformed()
  • IMP::em::DensityMap::get_transformed()
  • IMP::em::DensityMap::get_transformed_into()
  • IMP::em::EnvelopeScore::is_penetrating()
  • IMP::em::EnvelopeScore::score()
  • IMP::em::FittingSolutions::add_solution()
  • IMP::em::FittingSolutions::multiply()
  • IMP::multifit::FittingSolutionRecord::set_dock_transformation()
  • IMP::multifit::FittingSolutionRecord::set_fit_transformation()
  • IMP::algebra::compose()
  • IMP::algebra::get_transformed()
  • IMP::algebra::get_transformed()
  • IMP::atom::get_rmsd()
  • IMP::atom::get_rmsd()
  • 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::VectorD:
  • 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::add_voxel()
  • 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::Rotation3D::get_rotation_from_vector4d()
  • IMP::algebra::SphereD::SphereD()
  • IMP::algebra::SphereD::get_contains()
  • IMP::algebra::VectorD::check_compatible_vector()
  • IMP::algebra::VectorD::get_scalar_product()
  • IMP::algebra::VectorD::compare()
  • IMP::algebra::VectorD::get_distance()
  • IMP::algebra::VectorD::get_elementwise_product()
  • IMP::algebra::VectorD::get_elementwise_product()
  • IMP::algebra::VectorD::get_squared_distance()
  • IMP::algebra::VectorD::get_vector_d_geometry()
  • IMP::algebra::VectorD::operator*()
  • IMP::algebra::VectorD::set_vector_d_geometry()
  • IMP::algebra::VectorInputD::VectorInputD()
  • IMP::algebra::VectorInputD< 1 >::VectorInputD()
  • 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::algebra::get_l2_norm()
  • IMP::algebra::get_l1_norm()
  • IMP::algebra::get_linf_norm()
  • 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::VectorInputD:
  • IMP::algebra::BoundingBoxD::BoundingBoxD()
  • IMP::algebra::BoundingBoxD::BoundingBoxD()
  • IMP::statistics::HistogramD::add()
  • IMP::statistics::HistogramD::get_standard_deviation()
• IMP::atom::Atom:
  • 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::atom::Hierarchy::get_residue()
  • IMP::atom::get_residue()
• IMP::atom::AtomType:
  • 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::Hierarchy::get_atom()
  • 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::Bonded::create_bond()
  • IMP::atom::Bonded::destroy_bond()
  • IMP::atom::create_bond()
  • IMP::atom::destroy_bond()
• IMP::atom::BondPairContainer:
  • IMP::atom::BondPairContainer::IMP_IMPLEMENT_PAIR_CONTAINER()
• IMP::atom::Bonded:
  • 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::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::Chain:
  • IMP::atom::Chain::setup_particle()
  • IMP::atom::create_simplified_along_backbone()
• IMP::atom::Domain:
  • IMP::atom::Domain::setup_particle()
• IMP::atom::ForceFieldParameters:
  • IMP::atom::ForceFieldParameters::add_bonds()
  • IMP::atom::ForceFieldParameters::add_radii()
  • IMP::atom::add_bonds()
  • IMP::atom::add_radii()
• IMP::atom::Fragment:
  • IMP::atom::Fragment::setup_particle()
• IMP::atom::Hierarchy:
  • IMP::atom::Bond::get_internal_bonds()
  • 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::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::ForceFieldParameters::add_bonds()
  • IMP::atom::ForceFieldParameters::add_radii()
  • IMP::atom::Hierarchy::add_child()
  • IMP::atom::Hierarchy::create_clone()
  • IMP::atom::Hierarchy::create_clone_one()
  • IMP::atom::Hierarchy::destroy()
  • IMP::atom::Hierarchy::get_bounding_sphere()
  • IMP::atom::Hierarchy::get_by_type()
  • IMP::atom::Hierarchy::get_hierarchy_tree()
  • IMP::atom::Hierarchy::get_leaves()
  • IMP::atom::Hierarchy::get_residue()
  • IMP::atom::Hierarchy::get_root()
  • IMP::atom::Hierarchy::setup_as_approximation()
  • IMP::atom::Hierarchy::show()
  • IMP::atom::ProteinLigandRestraint::initialize()
  • IMP::atom::ProteinLigandRestraint::ProteinLigandRestraint()
  • IMP::atom::ProteinLigandRestraint::ProteinLigandRestraint()
  • IMP::atom::Selection::check_nonradius()
  • IMP::atom::Selection::operator()()
  • IMP::atom::Selection::Selection()
  • IMP::atom::Selection::Selection()
  • IMP::multifit::Ensemble::add_component_and_fits()
  • IMP::multifit::FFTFitting::prepare_probe()
  • IMP::multifit::FFTFitting::do_global_fitting()
  • IMP::multifit::FFTFitting::do_local_fitting()
  • IMP::multifit::MergeTreeBuilder::increase_edge()
  • IMP::restrainer::SimpleEMFit::create_simple_em_fit()
  • IMP::rotamer::RotamerCalculator::transform()
  • IMP::atom::add_dope_score_data()
  • IMP::atom::create_simplified_along_backbone()
  • IMP::atom::get_molecule_name()
  • IMP::atom::get_residue_indexes()
  • IMP::atom::get_residue_type()
  • IMP::atom::get_chain_id()
  • IMP::atom::get_atom_type()
  • IMP::atom::get_domain_name()
  • IMP::atom::get_copy_index()
  • IMP::atom::write_mol2()
  • IMP::atom::read_pdb()
  • IMP::atom::add_protein_ligand_score_data()
  • IMP::atom::show_molecular_hiearchy()
  • 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::destroy()
  • IMP::atom::get_bounding_box()
  • IMP::atom::get_bounding_sphere()
  • IMP::atom::get_by_type()
  • IMP::atom::get_chain()
  • IMP::atom::get_charmm_untyped_atoms()
  • IMP::atom::get_hierarchy_tree()
  • IMP::atom::get_internal_bonds()
  • IMP::atom::get_is_heterogen()
  • IMP::atom::get_leaves()
  • IMP::atom::get_residue()
  • IMP::atom::get_root()
  • 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::fitting_clustering()
  • 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::setup_particle()
• IMP::atom::PDBSelector:
  • IMP::atom::AndPDBSelector::AndPDBSelector()
  • IMP::atom::Hierarchy::read_pdb()
  • 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::Hierarchy::get_atom()
  • IMP::atom::Residue::setup_particle()
  • IMP::atom::Residue::get_next_residue()
  • IMP::atom::Residue::get_phi_dihedral_atoms()
  • IMP::atom::Residue::get_previous_residue()
  • IMP::atom::Residue::get_psi_dihedral_atoms()
  • 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::set_residue_type()
  • 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_one_letter_code()
• IMP::atom::SecondaryStructureResidue:
  • IMP::atom::get_secondary_structure_match_score()
• IMP::atom::Selection:
  • IMP::atom::Hierarchy::get_leaves()
  • IMP::atom::Selection::create_cover()
  • IMP::atom::Selection::create_distance_restraint()
  • IMP::atom::Selection::create_internal_connectivity_restraint()
  • IMP::atom::Selection::create_internal_connectivity_restraint()
  • IMP::atom::Selection::get_mass()
  • IMP::atom::Selection::get_radius_of_gyration()
  • IMP::atom::Selection::get_surface_area()
  • IMP::atom::Selection::get_volume()
  • 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_surface_area()
  • IMP::atom::get_volume()
• IMP::atom::Simulator:
  • IMP::atom::Simulator::IMP_OPTIMIZER()
  • IMP::rmf::SaveOptimizerState::set_simulator()
• IMP::atom::SmoothingFunction:
  • IMP::atom::CoulombPairScore::CoulombPairScore()
  • IMP::atom::LennardJonesPairScore::LennardJonesPairScore()
• IMP::base::Array:
  • IMP::base::Array::compare()
  • 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::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::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::Shift::get_maximum_range()
  • IMP::score_functor::Shift::get_score()
  • IMP::score_functor::Shift::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::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::operator[]()
  • IMP::base::IndexVector::operator[]()
  • IMP::base::get_as_unsigned_int()
  • IMP::base::resize_to_fit()
• IMP::base::LRUCache:
  • IMP::domino::RestraintCache::Generator::operator()()
• IMP::base::Object:
  • IMP::base::Object::compare()
  • IMP::base::Object::add_live_object()
  • IMP::base::Object::remove_live_object()
  • 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::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::Showable:
  • IMP::base::operator<<()
• IMP::base::TextInput:
  • IMP::algebra::SphereD::read_spheres()
  • IMP::algebra::VectorD::read_pts()
  • IMP::atom::CHARMMParameters::read_parameter_file()
  • IMP::atom::CHARMMParameters::read_topology_file()
  • IMP::atom::CHARMMParameters::CHARMMParameters()
  • IMP::atom::DopePairScore::DopePairScore()
  • IMP::atom::Hierarchy::read_pdb()
  • IMP::atom::ProteinLigandAtomPairScore::ProteinLigandAtomPairScore()
  • IMP::atom::ProteinLigandRestraint::ProteinLigandRestraint()
  • IMP::core::StatisticalPairScore::StatisticalPairScore()
  • IMP::core::StatisticalPairScore::StatisticalPairScore()
  • IMP::score_functor::Dope::Dope()
  • 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_pdb()
  • IMP::atom::read_multimodel_pdb()
  • IMP::atom::read_multimodel_pdb()
  • IMP::atom::read_psipred()
  • IMP::atom::read_psipred()
• IMP::base::TextOutput:
  • IMP::algebra::SphereD::write_spheres()
  • IMP::algebra::VectorD::write_pts()
  • IMP::base::SetLogTarget::SetLogTarget()
  • IMP::base::SetLogTarget::set()
  • IMP::core::WriteRestraintScoresOptimizerState::WriteRestraintScoresOptimizerState()
  • IMP::display::BildWriter::BildWriter()
  • IMP::display::CMMWriter::CMMWriter()
  • 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::base::set_log_target()
  • IMP::multifit::write_connolly_surface()
• IMP::base::Tracker:
  • IMP::base::TrackedObject::TrackedObject()
  • IMP::base::TrackedObject::set_tracker()
• IMP::base::Vector:
  • IMP::algebra::BoundingBoxD::BoundingBoxD()
  • IMP::algebra::NearestNeighborD::NearestNeighborD()
  • IMP::algebra::PrincipalComponentAnalysisD::PrincipalComponentAnalysisD()
  • IMP::atom::CHARMMConnection::CHARMMConnection()
  • IMP::atom::CHARMMInternalCoordinate::CHARMMInternalCoordinate()
  • IMP::atom::CHARMMParameters::parse_dihedrals_parameters_line()
  • IMP::base::ConstVector::ConstVector()
  • IMP::base::SparseSymmetricPairMemoizer::SparseSymmetricPairMemoizer()
  • IMP::core::ConjugateGradients::get_score()
  • IMP::core::ConjugateGradients::line_search()
  • IMP::core::MSConnectivityRestraint::ExperimentalTree::desc_to_label()
  • IMP::domino::PairListSubsetFilterTable::fill()
  • IMP::kernel::PairModifier::get_inputs()
  • IMP::kernel::PairModifier::get_outputs()
  • IMP::kernel::PairModifier::do_get_inputs()
  • IMP::kernel::PairModifier::do_get_outputs()
  • IMP::kernel::PairPredicate::get_inputs()
  • IMP::kernel::PairPredicate::do_get_inputs()
  • IMP::kernel::PairScore::get_inputs()
  • IMP::kernel::PairScore::do_get_inputs()
  • IMP::kernel::QuadModifier::get_inputs()
  • IMP::kernel::QuadModifier::get_outputs()
  • IMP::kernel::QuadModifier::do_get_inputs()
  • IMP::kernel::QuadModifier::do_get_outputs()
  • IMP::kernel::QuadPredicate::get_inputs()
  • IMP::kernel::QuadPredicate::do_get_inputs()
  • IMP::kernel::QuadScore::get_inputs()
  • IMP::kernel::QuadScore::do_get_inputs()
  • IMP::kernel::Refiner::get_inputs()
  • IMP::kernel::Refiner::do_get_inputs()
  • IMP::kernel::SingletonContainerAdaptor::SingletonContainerAdaptor()
  • IMP::kernel::SingletonModifier::apply_indexes()
  • IMP::kernel::SingletonModifier::get_inputs()
  • IMP::kernel::SingletonModifier::get_outputs()
  • IMP::kernel::SingletonModifier::do_get_inputs()
  • IMP::kernel::SingletonModifier::do_get_outputs()
  • IMP::kernel::SingletonPredicate::get_inputs()
  • IMP::kernel::SingletonPredicate::get_value()
  • IMP::kernel::SingletonPredicate::get_value_index()
  • IMP::kernel::SingletonPredicate::do_get_inputs()
  • IMP::kernel::SingletonScore::evaluate_if_good_indexes()
  • IMP::kernel::SingletonScore::evaluate_indexes()
  • IMP::kernel::SingletonScore::get_inputs()
  • IMP::kernel::SingletonScore::do_get_inputs()
  • IMP::kernel::TripletModifier::get_inputs()
  • IMP::kernel::TripletModifier::get_outputs()
  • IMP::kernel::TripletModifier::do_get_inputs()
  • IMP::kernel::TripletModifier::do_get_outputs()
  • IMP::kernel::TripletPredicate::get_inputs()
  • IMP::kernel::TripletPredicate::do_get_inputs()
  • IMP::kernel::TripletScore::get_inputs()
  • IMP::kernel::TripletScore::do_get_inputs()
  • IMP::multifit::GeometricHash::neighbors()
  • IMP::rmf::SimpleLoadLink::link()
  • IMP::rmf::SimpleSaveLink::add()
  • IMP::algebra::get_principal_components()
  • IMP::kernel::write_particles_to_buffer()
  • IMP::kernel::read_particles_from_buffer()
  • IMP::kernel::get_indexes()
  • IMP::kernel::get_particles()
• IMP::base::map:
  • IMP::domino::RestraintCache::add_restraint_internal()
  • IMP::domino::RestraintCache::add_restraint_set_internal()
  • IMP::domino::RestraintCache::get_subset()
• IMP::cnmultifit::AlignSymmetric:
  • IMP::cnmultifit::fit_cn_assembly()
• IMP::container::AllBipartitePairContainer:
  • IMP::container::AllBipartitePairContainer::IMP_IMPLEMENT_PAIR_CONTAINER()
• IMP::container::AllPairContainer:
  • IMP::container::AllPairContainer::IMP_IMPLEMENT_PAIR_CONTAINER()
• IMP::container::CloseBipartitePairContainer:
  • IMP::container::CloseBipartitePairContainer::IMP_PAIR_CONTAINER()
• IMP::container::ClosePairContainer:
  • IMP::container::ClosePairContainer::IMP_PAIR_CONTAINER()
  • IMP::container::get_slack_estimate()
• IMP::container::ConnectingPairContainer:
  • IMP::container::ConnectingPairContainer::IMP_IMPLEMENT_PAIR_CONTAINER()
• IMP::container::ConsecutivePairContainer:
  • IMP::container::ConsecutivePairContainer::IMP_IMPLEMENT_PAIR_CONTAINER()
  • IMP::container::ConsecutivePairFilter::ConsecutivePairFilter()
• IMP::container::DynamicListPairContainer:
  • IMP::container::IMP_OBJECTS()
• IMP::container::DynamicListQuadContainer:
  • IMP::container::IMP_OBJECTS()
• IMP::container::DynamicListSingletonContainer:
  • IMP::container::IMP_OBJECTS()
• IMP::container::DynamicListTripletContainer:
  • IMP::container::IMP_OBJECTS()
• IMP::container::ExclusiveConsecutivePairContainer:
  • IMP::container::ExclusiveConsecutivePairContainer::IMP_IMPLEMENT_PAIR_CONTAINER()
• IMP::container::ListPairContainer:
  • IMP::container::IMP_OBJECTS()
• IMP::container::ListQuadContainer:
  • IMP::container::IMP_OBJECTS()
• IMP::container::ListSingletonContainer:
  • IMP::container::IMP_OBJECTS()
• IMP::container::ListTripletContainer:
  • IMP::container::IMP_OBJECTS()
• IMP::container::PairsRestraint:
  • IMP::container::IMP_OBJECTS()
• IMP::container::QuadsRestraint:
  • IMP::container::IMP_OBJECTS()
• IMP::container::SingletonsRestraint:
  • IMP::container::IMP_OBJECTS()
• IMP::container::TripletsRestraint:
  • IMP::container::IMP_OBJECTS()
• IMP::core::Centroid:
  • IMP::core::Centroid::IMP_CONSTRAINT_DECORATOR_DECL()
• IMP::core::ClosePairsFinder:
  • IMP::container::ClosePairContainer::ClosePairContainer()
  • IMP::core::RigidClosePairsFinder::RigidClosePairsFinder()
• IMP::core::ConnectivityRestraint:
  • IMP::restrainer::SimpleConnectivity::SimpleConnectivity()
• IMP::core::Cover:
  • IMP::core::Cover::IMP_CONSTRAINT_DECORATOR_DECL()
• IMP::core::DiameterRestraint:
  • IMP::restrainer::SimpleDiameter::SimpleDiameter()
• IMP::core::DihedralRestraint:
  • IMP::core::DihedralRestraint::IMP_RESTRAINT()
• IMP::core::DistanceRestraint:
  • IMP::restrainer::SimpleDistance::SimpleDistance()
• IMP::core::ExcludedVolumeRestraint:
  • IMP::restrainer::SimpleExcludedVolume::SimpleExcludedVolume()
• IMP::core::HarmonicUpperBound:
  • IMP::restrainer::SimpleConnectivity::SimpleConnectivity()
  • IMP::restrainer::SimpleDiameter::SimpleDiameter()
  • IMP::restrainer::SimpleDistance::SimpleDistance()
• 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::Hierarchy::get_all_descendants()
  • IMP::core::Hierarchy::get_internal()
  • IMP::core::Hierarchy::get_leaves()
  • IMP::core::Hierarchy::get_root()
  • IMP::core::Hierarchy::show()
  • IMP::core::HierarchyVisitor::operator()()
  • IMP::core::ModifierVisitor::operator()()
  • IMP::core::RigidBody::create_compatible_rigid_body()
  • 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::Hierarchy()
  • IMP::core::Hierarchy::Hierarchy()
  • IMP::core::Hierarchy::Hierarchy()
  • IMP::core::Hierarchy::decorate_particle()
  • IMP::core::Hierarchy::particle_is_instance()
  • 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::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::RigidBody::transform()
  • 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::multifit::ComplementarityRestraint::get_grid_object()
  • IMP::saxs::DerivativeCalculator::compute_all_derivatives()
  • 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::SoftSpherePairScore:
  • IMP::core::ExcludedVolumeRestraint::ExcludedVolumeRestraint()
• IMP::core::SphereDistancePairScore:
  • IMP::restrainer::SimpleConnectivity::SimpleConnectivity()
• IMP::core::XYZ:
  • IMP::atom::Angle::setup_particle()
  • IMP::atom::Dihedral::setup_particle()
  • IMP::core::AngleRestraint::AngleRestraint()
  • IMP::core::XYZ::get_vector_to()
  • IMP::core::XYZ::get_dihedral()
  • IMP::core::XYZ::get_distance()
  • IMP::core::XYZDerivativeGeometry::XYZDerivativeGeometry()
  • IMP::core::get_dihedral()
  • IMP::core::get_distance()
  • IMP::core::get_vector_d_geometry()
  • IMP::core::set_vector_d_geometry()
  • IMP::core::transform()
• IMP::core::XYZR:
  • IMP::core::XYZR::get_distance()
  • IMP::core::XYZR::set_enclosing_radius()
  • IMP::core::XYZR::set_enclosing_sphere()
  • IMP::core::XYZRGeometry::XYZRGeometry()
  • IMP::core::get_distance()
  • IMP::core::get_sphere_d_geometry()
  • IMP::core::set_enclosing_radius()
  • IMP::core::set_enclosing_sphere()
  • IMP::core::set_sphere_d_geometry()
• IMP::display::BoundingBoxGeometry:
  • IMP::display::GeometryProcessor::handle_bounding_box()
• IMP::display::Color:
  • IMP::display::BildWriter::handle()
  • IMP::display::BildWriter::handle_cylinder()
  • IMP::display::BildWriter::handle_point()
  • IMP::display::BildWriter::handle_polygon()
  • IMP::display::BildWriter::handle_segment()
  • IMP::display::BildWriter::handle_sphere()
  • IMP::display::BildWriter::handle_triangle()
  • IMP::display::BoundingBoxGeometry::BoundingBoxGeometry()
  • IMP::display::BoundingBoxGeometry::BoundingBoxGeometry()
  • IMP::display::CMMWriter::handle_point()
  • IMP::display::CMMWriter::handle_sphere()
  • 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::Color::get_interpolated_rgb()
  • IMP::display::Colored::setup_particle()
  • IMP::display::Colored::set_color()
  • 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::BildWriter::handle_cylinder()
  • 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::BildWriter::handle_point()
  • IMP::display::CMMWriter::handle_point()
  • 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::BildWriter::handle_polygon()
  • IMP::display::ChimeraWriter::handle_polygon()
  • IMP::display::GeometryProcessor::handle_polygon()
  • IMP::display::PymolWriter::handle_polygon()
• IMP::display::SegmentGeometry:
  • IMP::display::BildWriter::handle_segment()
  • 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::BildWriter::handle_sphere()
  • IMP::display::CMMWriter::handle_sphere()
  • 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::BildWriter::handle_triangle()
  • 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::Assignment:
  • IMP::domino::AssignmentContainer::add_assignment()
  • IMP::domino::Order::get_list_ordered()
  • IMP::domino::RestraintCache::get_score()
  • IMP::domino::RestraintCache::get_score()
  • IMP::domino::RestraintCache::load_last_score()
  • IMP::domino::Slice::get_sliced()
  • IMP::domino::SubsetFilter::get_is_ok()
  • IMP::domino::SubsetFilter::get_next_state()
  • 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::CappedAssignmentContainer::CappedAssignmentContainer()
  • IMP::domino::DominoSampler::load_vertex_assignments()
  • IMP::domino::DominoSampler::load_vertex_assignments()
  • IMP::domino::ListAssignmentsTable::set_assignments()
  • IMP::domino::RangeViewAssignmentContainer::RangeViewAssignmentContainer()
  • 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::RestraintCache::Generator::Generator()
  • 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::RestraintCache::Generator::add_to_set()
  • IMP::domino::swap()
• IMP::domino::Subset:
  • IMP::domino::AssignmentsTable::load_assignments()
  • IMP::domino::DiscreteSampler::do_get_sample_assignments()
  • IMP::domino::DiscreteSampler::get_sample_assignments()
  • IMP::domino::HeapAssignmentContainer::HeapAssignmentContainer()
  • IMP::domino::ListAssignmentsTable::set_assignments()
  • IMP::domino::MinimumRestraintScoreSubsetFilterTable::get_restraints()
  • IMP::domino::Order::Order()
  • IMP::domino::PairListSubsetFilterTable::fill()
  • IMP::domino::ReadAssignmentContainer::ReadAssignmentContainer()
  • IMP::domino::ReadHDF5AssignmentContainer::ReadHDF5AssignmentContainer()
  • 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::RestraintCache::Generator::add_restraint()
  • 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::example::ExampleSubsetFilterTable::get_indexes()
  • 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::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::PolarResamplingParameters:
  • IMP::em2d::do_resample_polar()
  • IMP::em2d::do_resample_polar()
• 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::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::get_density()
  • IMP::em::DensityMap::get_resampled()
  • IMP::em::DensityMap::get_transformed()
  • IMP::em::DensityMap::get_transformed()
  • IMP::em::DensityMap::get_transformed_into()
  • IMP::em::DensityMap::write_map()
  • IMP::em::DensityMap::write_map()
  • 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::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::FFTFitting::do_global_fitting()
  • IMP::multifit::FFTFitting::do_local_fitting()
  • IMP::multifit::ProteomicsEMAlignmentAtomic::set_density_map()
  • IMP::restrainer::SimpleEMFit::create_simple_em_fit()
  • IMP::restrainer::SimpleEMFit::create_simple_em_fit()
  • IMP::cnmultifit::build_cn_dens_assembly()
  • IMP::cnmultifit::fit_cn_assembly()
  • IMP::cnmultifit::fit_cn_assembly()
  • IMP::cnmultifit::my_get_density_histogram()
  • IMP::cnmultifit::symmetry_local_fitting()
  • 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_density_histogram()
  • IMP::multifit::get_segment_maximum()
  • 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::FitRestraint:
  • IMP::restrainer::SimpleEMFit::SimpleEMFit()
• IMP::em::FittingSolutions:
  • IMP::multifit::convert_em_to_multifit_format()
  • IMP::multifit::fitting_clustering()
• 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::DensityMap::read_map()
  • IMP::em::DensityMap::write_map()
  • 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::isd::BivariateFunction:
  • IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation()
• IMP::isd::GaussianProcessInterpolation:
  • IMP::isd::GaussianProcessInterpolationRestraint::GaussianProcessInterpolationRestraint()
• IMP::isd::ISDRestraint:
  • IMP::isd::LogicalORRestraint::LogicalORRestraint()
• IMP::isd::UnivariateFunction:
  • IMP::isd::GaussianProcessInterpolation::GaussianProcessInterpolation()
• IMP::kernel::Configuration:
  • IMP::kernel::Configuration::Configuration()
• IMP::kernel::ConfigurationSet:
  • IMP::kernel::SaveToConfigurationSetOptimizerState::SaveToConfigurationSetOptimizerState()
• IMP::kernel::DerivativeAccumulator:
  • IMP::core::MSConnectivityRestraint::unprotected_evaluate()
  • IMP::kernel::Constraint::do_after_evaluate()
  • IMP::kernel::Constraint::do_update_derivatives()
  • IMP::kernel::Container::do_after_evaluate()
  • 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::multifit::WeightedExcludedVolumeRestraint::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::kernel::Model:
  • 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::GenericScopedRemoveScoreState::setup()
  • IMP::kernel::GenericScopedRemoveScoreState::GenericScopedRemoveScoreState()
  • IMP::kernel::GenericScopedRemoveScoreState::set()
  • IMP::kernel::GenericScopedScoreState::GenericScopedScoreState()
  • IMP::kernel::GenericScopedScoreState::set()
  • IMP::kernel::ModelObject::ModelObject()
  • IMP::kernel::Optimizer::Optimizer()
  • IMP::kernel::Optimizer::set_model()
  • IMP::kernel::PairContainer::PairContainer()
  • IMP::kernel::PairModifier::apply_index()
  • IMP::kernel::PairModifier::apply_indexes()
  • IMP::kernel::PairModifier::get_inputs()
  • IMP::kernel::PairModifier::get_outputs()
  • IMP::kernel::PairModifier::do_get_inputs()
  • IMP::kernel::PairModifier::do_get_outputs()
  • IMP::kernel::PairPredicate::get_inputs()
  • IMP::kernel::PairPredicate::get_value_index()
  • IMP::kernel::PairPredicate::get_value_index()
  • IMP::kernel::PairPredicate::operator()()
  • IMP::kernel::PairPredicate::do_get_inputs()
  • 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::get_inputs()
  • IMP::kernel::PairScore::do_create_current_decomposition()
  • IMP::kernel::PairScore::do_get_inputs()
  • IMP::kernel::Particle::Particle()
  • IMP::kernel::Particle::Particle()
  • IMP::kernel::QuadContainer::QuadContainer()
  • IMP::kernel::QuadModifier::apply_index()
  • IMP::kernel::QuadModifier::apply_indexes()
  • IMP::kernel::QuadModifier::get_inputs()
  • IMP::kernel::QuadModifier::get_outputs()
  • IMP::kernel::QuadModifier::do_get_inputs()
  • IMP::kernel::QuadModifier::do_get_outputs()
  • IMP::kernel::QuadPredicate::get_inputs()
  • IMP::kernel::QuadPredicate::get_value_index()
  • IMP::kernel::QuadPredicate::get_value_index()
  • IMP::kernel::QuadPredicate::operator()()
  • IMP::kernel::QuadPredicate::do_get_inputs()
  • 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::get_inputs()
  • IMP::kernel::QuadScore::do_create_current_decomposition()
  • IMP::kernel::QuadScore::do_get_inputs()
  • IMP::kernel::Refiner::get_inputs()
  • IMP::kernel::Refiner::do_get_inputs()
  • IMP::kernel::Restraint::Restraint()
  • IMP::kernel::RestraintSet::RestraintSet()
  • IMP::kernel::Sampler::Sampler()
  • IMP::kernel::ScoreState::ScoreState()
  • IMP::kernel::ScoringFunction::ScoringFunction()
  • IMP::kernel::ScoringFunctionAdaptor::get()
  • IMP::kernel::ScoringFunctionAdaptor::ScoringFunctionAdaptor()
  • IMP::kernel::SingletonContainer::SingletonContainer()
  • IMP::kernel::SingletonModifier::apply_index()
  • IMP::kernel::SingletonModifier::apply_indexes()
  • IMP::kernel::SingletonModifier::get_inputs()
  • IMP::kernel::SingletonModifier::get_outputs()
  • IMP::kernel::SingletonModifier::do_get_inputs()
  • IMP::kernel::SingletonModifier::do_get_outputs()
  • IMP::kernel::SingletonPredicate::get_inputs()
  • IMP::kernel::SingletonPredicate::get_value_index()
  • IMP::kernel::SingletonPredicate::get_value_index()
  • IMP::kernel::SingletonPredicate::operator()()
  • IMP::kernel::SingletonPredicate::do_get_inputs()
  • 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::get_inputs()
  • IMP::kernel::SingletonScore::do_create_current_decomposition()
  • IMP::kernel::SingletonScore::do_get_inputs()
  • IMP::kernel::TripletContainer::TripletContainer()
  • IMP::kernel::TripletModifier::apply_index()
  • IMP::kernel::TripletModifier::apply_indexes()
  • IMP::kernel::TripletModifier::get_inputs()
  • IMP::kernel::TripletModifier::get_outputs()
  • IMP::kernel::TripletModifier::do_get_inputs()
  • IMP::kernel::TripletModifier::do_get_outputs()
  • IMP::kernel::TripletPredicate::get_inputs()
  • IMP::kernel::TripletPredicate::get_value_index()
  • IMP::kernel::TripletPredicate::get_value_index()
  • IMP::kernel::TripletPredicate::operator()()
  • IMP::kernel::TripletPredicate::do_get_inputs()
  • 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::get_inputs()
  • IMP::kernel::TripletScore::do_create_current_decomposition()
  • IMP::kernel::TripletScore::do_get_inputs()
  • IMP::kernel::Undecorator::Undecorator()
  • 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::kernel::ModelObject:
  • IMP::kernel::get_required_particles()
  • IMP::kernel::get_required_score_states()
  • IMP::kernel::get_dependent_particles()
  • IMP::kernel::get_dependent_restraints()
  • IMP::kernel::get_dependent_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::kernel::PairContainerAdaptor::PairContainerAdaptor()
• IMP::kernel::PairModifier:
  • IMP::kernel::PairContainer::do_apply()
  • IMP::kernel::PairContainer::apply()
  • IMP::kernel::PairContainer::apply_generic()
• IMP::kernel::Particle:
  • IMP::atom::Angle::Angle()
  • IMP::atom::Angle::decorate_particle()
  • IMP::atom::Atom::Atom()
  • IMP::atom::Atom::decorate_particle()
  • IMP::atom::Bond::Bond()
  • IMP::atom::Bond::decorate_particle()
  • IMP::atom::Bonded::Bonded()
  • IMP::atom::Bonded::decorate_particle()
  • IMP::atom::CHARMMAtom::CHARMMAtom()
  • IMP::atom::CHARMMAtom::decorate_particle()
  • IMP::atom::Chain::Chain()
  • IMP::atom::Chain::decorate_particle()
  • IMP::atom::Charged::Charged()
  • IMP::atom::Charged::decorate_particle()
  • IMP::atom::Copy::decorate_particle()
  • IMP::atom::Copy::Copy()
  • IMP::atom::Diffusion::Diffusion()
  • IMP::atom::Diffusion::decorate_particle()
  • IMP::atom::Dihedral::Dihedral()
  • IMP::atom::Dihedral::decorate_particle()
  • IMP::atom::Domain::decorate_particle()
  • IMP::atom::Domain::Domain()
  • IMP::atom::Fragment::decorate_particle()
  • IMP::atom::Fragment::Fragment()
  • IMP::atom::LennardJones::LennardJones()
  • IMP::atom::LennardJones::decorate_particle()
  • IMP::atom::Mass::decorate_particle()
  • IMP::atom::Mass::Mass()
  • IMP::atom::Molecule::Molecule()
  • IMP::atom::Molecule::decorate_particle()
  • IMP::atom::Residue::Residue()
  • IMP::atom::Residue::decorate_particle()
  • IMP::atom::RigidBodyDiffusion::RigidBodyDiffusion()
  • IMP::atom::RigidBodyDiffusion::decorate_particle()
  • IMP::atom::SecondaryStructureResidue::SecondaryStructureResidue()
  • IMP::atom::SecondaryStructureResidue::decorate_particle()
  • IMP::core::Centroid::Centroid()
  • IMP::core::Centroid::decorate_particle()
  • IMP::core::Cover::Cover()
  • IMP::core::Cover::decorate_particle()
  • IMP::core::Hierarchy::Hierarchy()
  • IMP::core::Hierarchy::decorate_particle()
  • IMP::core::NonRigidMember::NonRigidMember()
  • IMP::core::NonRigidMember::decorate_particle()
  • IMP::core::Reference::Reference()
  • IMP::core::Reference::decorate_particle()
  • IMP::core::RigidBody::RigidBody()
  • IMP::core::RigidBody::decorate_particle()
  • IMP::core::RigidMember::RigidMember()
  • IMP::core::RigidMember::decorate_particle()
  • IMP::core::Typed::decorate_particle()
  • IMP::core::Typed::Typed()
  • IMP::core::XYZ::decorate_particle()
  • IMP::core::XYZ::XYZ()
  • IMP::core::XYZR::XYZR()
  • IMP::core::XYZR::decorate_particle()
  • IMP::display::Colored::decorate_particle()
  • IMP::display::Colored::Colored()
  • IMP::em2d::ProjectionParameters::ProjectionParameters()
  • IMP::em2d::ProjectionParameters::decorate_particle()
  • IMP::em::Voxel::decorate_particle()
  • IMP::em::Voxel::Voxel()
  • IMP::example::ExampleDecorator::decorate_particle()
  • IMP::example::ExampleDecorator::ExampleDecorator()
  • IMP::isd::Nuisance::Nuisance()
  • IMP::isd::Nuisance::decorate_particle()
  • IMP::isd::Scale::Scale()
  • IMP::isd::Scale::decorate_particle()
  • IMP::isd::Switching::Switching()
  • IMP::isd::Switching::decorate_particle()
  • IMP::kernel::Decorator::Decorator()
  • IMP::kernel::Decorator::particle_is_instance()
  • IMP::kernel::PairModifier::get_input_containers()
  • IMP::kernel::PairModifier::get_input_particles()
  • IMP::kernel::PairModifier::get_output_containers()
  • IMP::kernel::PairModifier::get_output_particles()
  • IMP::kernel::PairPredicate::get_input_containers()
  • IMP::kernel::PairPredicate::get_input_particles()
  • IMP::kernel::PairScore::get_input_containers()
  • IMP::kernel::PairScore::get_input_particles()
  • IMP::kernel::QuadModifier::get_input_containers()
  • IMP::kernel::QuadModifier::get_input_particles()
  • IMP::kernel::QuadModifier::get_output_containers()
  • IMP::kernel::QuadModifier::get_output_particles()
  • IMP::kernel::QuadPredicate::get_input_containers()
  • IMP::kernel::QuadPredicate::get_input_particles()
  • IMP::kernel::QuadScore::get_input_containers()
  • IMP::kernel::QuadScore::get_input_particles()
  • IMP::kernel::Refiner::refined_begin()
  • IMP::kernel::Refiner::refined_end()
  • IMP::kernel::Refiner::get_can_refine()
  • IMP::kernel::Refiner::get_input_containers()
  • IMP::kernel::Refiner::get_input_particles()
  • 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::SingletonContainer::get_contains_particle()
  • IMP::kernel::SingletonModifier::apply()
  • IMP::kernel::SingletonModifier::get_input_containers()
  • IMP::kernel::SingletonModifier::get_input_particles()
  • IMP::kernel::SingletonModifier::get_output_containers()
  • IMP::kernel::SingletonModifier::get_output_particles()
  • IMP::kernel::SingletonPredicate::get_input_containers()
  • IMP::kernel::SingletonPredicate::get_input_particles()
  • IMP::kernel::SingletonPredicate::get_value()
  • IMP::kernel::SingletonScore::evaluate()
  • IMP::kernel::SingletonScore::get_input_containers()
  • IMP::kernel::SingletonScore::get_input_particles()
  • IMP::kernel::TripletModifier::get_input_containers()
  • IMP::kernel::TripletModifier::get_input_particles()
  • IMP::kernel::TripletModifier::get_output_containers()
  • IMP::kernel::TripletModifier::get_output_particles()
  • IMP::kernel::TripletPredicate::get_input_containers()
  • IMP::kernel::TripletPredicate::get_input_particles()
  • IMP::kernel::TripletScore::get_input_containers()
  • IMP::kernel::TripletScore::get_input_particles()
  • IMP::misc::CustomXYZR::CustomXYZR()
  • IMP::misc::CustomXYZR::decorate_particle()
  • IMP::kernel::get_bounding_box_d_geometry()
  • IMP::kernel::get_sphere_d_geometry()
  • IMP::kernel::get_vector_d_geometry()
  • IMP::kernel::set_sphere_d_geometry()
  • IMP::kernel::set_vector_d_geometry()
• IMP::kernel::QuadContainer:
  • IMP::kernel::QuadContainerAdaptor::QuadContainerAdaptor()
• IMP::kernel::QuadModifier:
  • IMP::kernel::QuadContainer::do_apply()
  • IMP::kernel::QuadContainer::apply()
  • IMP::kernel::QuadContainer::apply_generic()
• IMP::kernel::Restraint:
  • IMP::kernel::GenericScopedRemoveRestraint::setup()
  • IMP::kernel::Model::get_restraint_statistics()
  • IMP::kernel::RestraintSet::remove_restraint()
  • IMP::kernel::RestraintSet::add_restraint()
  • IMP::kernel::RestraintSet::on_add()
  • IMP::kernel::RestraintSet::on_remove()
  • IMP::kernel::ScoreAccumulator::ScoreAccumulator()
  • IMP::kernel::ScoringFunctionAdaptor::get()
  • IMP::kernel::ScoringFunctionAdaptor::ScoringFunctionAdaptor()
• IMP::kernel::RestraintSet:
  • IMP::kernel::GenericScopedRemoveRestraint::setup()
  • IMP::kernel::GenericScopedRemoveRestraint::GenericScopedRemoveRestraint()
  • IMP::kernel::GenericScopedRemoveRestraint::set()
  • IMP::kernel::GenericScopedRestraint::GenericScopedRestraint()
  • IMP::kernel::GenericScopedRestraint::set()
  • IMP::kernel::RestraintSet::on_remove()
• IMP::kernel::ScoreAccumulator:
  • 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::GenericScopedRemoveScoreState::setup()
  • IMP::kernel::Model::remove_score_state()
  • IMP::kernel::Model::add_score_state()
  • IMP::kernel::Model::add_to_update_after_time()
  • IMP::kernel::Model::add_to_update_before_time()
• 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::kernel::SingletonContainerAdaptor::SingletonContainerAdaptor()
• IMP::kernel::SingletonModifier:
  • IMP::kernel::SingletonContainer::do_apply()
  • IMP::kernel::SingletonContainer::apply()
  • IMP::kernel::SingletonContainer::apply_generic()
• IMP::kernel::TripletContainer:
  • IMP::kernel::TripletContainerAdaptor::TripletContainerAdaptor()
• IMP::kernel::TripletModifier:
  • IMP::kernel::TripletContainer::do_apply()
  • IMP::kernel::TripletContainer::apply()
  • IMP::kernel::TripletContainer::apply_generic()
• IMP::kernel::Undecorator:
  • IMP::kernel::Model::add_undecorator()
• 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_SIMPLE_PAIR_SCORE()
• IMP::modeller::BinormalTerm:
  • IMP::modeller::MultipleBinormalRestraint::add_term()
• IMP::modeller::MultipleBinormalRestraint:
  • IMP::modeller::MultipleBinormalRestraint::IMP_RESTRAINT()
• IMP::multifit::AssemblyHeader:
  • IMP::multifit::SettingsData::set_assembly_header()
• IMP::multifit::ComplementarityRestraint:
  • IMP::multifit::ComplementarityRestraint::IMP_RESTRAINT()
• 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::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::RotamerLibrary:
  • IMP::rotamer::RotamerCalculator::RotamerCalculator()
• IMP::saxs::DeltaDistributionFunction:
  • IMP::saxs::DerivativeCalculator::compute_intensity_derivatives()
• IMP::saxs::FormFactorTable:
  • IMP::saxs::Profile::set_ff_table()
  • IMP::saxs::get_form_factors()
• IMP::saxs::Profile:
  • 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_all_derivatives()
  • IMP::saxs::DerivativeCalculator::compute_gaussian_effect_size()
  • IMP::saxs::DerivativeCalculator::compute_chisquare_derivative()
  • IMP::saxs::DerivativeCalculator::compute_chisquare_derivative()
  • IMP::saxs::DerivativeCalculator::precompute_derivative_helpers()
  • IMP::saxs::DerivativeCalculator::compute_profile_difference()
  • IMP::saxs::DerivativeCalculator::compute_sinc_cos()
  • IMP::saxs::Profile::add()
  • IMP::saxs::Profile::add_partial_profiles()
  • IMP::saxs::Profile::sum_partial_profiles()
  • IMP::saxs::ProfileFitter::compute_score()
  • IMP::saxs::ProfileFitter::compute_score()
  • IMP::saxs::ProfileFitter::fit_profile()
  • IMP::saxs::ProfileFitter::resample()
  • IMP::saxs::ProfileFitter::search_fit_parameters()
  • IMP::saxs::ProfileFitter::write_SAXS_fit_file()
  • IMP::saxs::ProfileFitter::ProfileFitter()
  • IMP::saxs::ProfileFitter::compute_offset()
  • IMP::saxs::ProfileFitter::compute_scale_factor()
  • IMP::saxs::RadiusOfGyrationRestraint::RadiusOfGyrationRestraint()
  • IMP::saxs::Restraint::Restraint()
  • IMP::saxs::Restraint::compute_profile()
• 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::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::HistogramD::show_histogram()
  • 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::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()