| acetylenic_CH | Model of acetylenic X-CH |
| alignment_t | Change-of-basis ("cb") matrix for joint alignment and its inverse |
| angle | Residual and gradient calculations for angle restraint |
| angle_proxy | Grouping of indices into array of sites (i_seqs) and angle_params |
| approx_equal | Element-wise comparison with a given absolute tolerance |
| aromatic_CH_or_amide_NH | Model of aromatic C-H or amide N-H |
| asu | Access to general contiguous reciprocal space asymmetric units |
| asu_cache | Asymmetric unit cache to facilitate speed optimizations |
| asu_clusters | Determination of clusters of points with interactions defined by pair_asu_table |
| asu_mapping | Mapping of a site to an asymmetric unit |
| asu_mapping_index | Grouping of indices for site in asu_mappings container |
| asu_mapping_index_pair | Grouping of indices for pair of sites in asu_mappings container |
| asu_mapping_index_pair_and_diff | Asu_mapping_index_pair plus difference vector and distance squared |
| asu_mappings | Container for mapping of sites to an asymmetric unit |
| asym_index | Selection of an asymmetric Miller index |
| atom | Atom attributes |
| atom_data | Holder for atom attributes (to be held by a shared_ptr) |
| atom_group | Atom_group attributes |
| atom_group_data | Holder for atom_group attributes (to be held by a shared_ptr) |
| atom_label_columns_formatter | Not available in Python |
| atom_mask | Radial shell flat solvent mask and structure factors |
| auto_array | Like std::auto_ptr, but with delete[] |
| axis_and_angle_from_matrix | Numerically robust computation of rotation axis and angle |
| base | |
| base | Coefficients for the Analytical Approximation to the Scattering Factor |
| basic_statistics | Collection of basic statistics such as min, max, mean, variance |
| batch | Safe access to CMtz::MTZBAT* owned by an iotbx::mtz::object |
| bidiagonal_2x2_decomposition | Special SVD for the 2x2 case |
| bidiagonal_decomposition | Golub-Kahan decomposition of a bidiagonal matrix B |
| bidiagonalisation | Decomposition U^T A V = B where B is bibidiagonal and U,V orthogonal |
| body_t | Abstract body type |
| bond | Residual and gradient calculations for harmonically restrained bonds |
| bond_asu_proxy | Grouping of asu_mapping_index_pair and bond_params |
| bond_params | Grouping of bond parameters distance_ideal and weight |
| bond_similarity | Residual and gradient calculations for harmonically restrained bonds |
| bond_similarity_proxy | |
| bond_simple_proxy | Grouping of indices into array of sites (i_seqs) and bond_params |
| bond_sorted_asu_proxies | Generation of sorted bond proxies |
| bond_sym_proxy | Grouping of bond_simple_proxy and symmetry operation (rt_mx_ji) |
| brick | Parallelepiped that contains an asymmetric unit |
| brick_point | A "point" of a brick |
| cartesian | Class for cartesian (orthogonal, real) coordinates |
| chain | Chain attributes |
| chain_data | Holder for chain attributes (to be held by a shared_ptr) |
| change_of_basis_op | Change-of-basis (transformation) operator |
| characteristic | Characteristic wavelengths of commonly used x-ray tube target materials |
| characteristic_iterator | Iterator over characteristic wavelengths |
| chebyshev_base | Chebyshev Base class |
| chebyshev_fitter | A chebyshev polynome for coefficient fitting purposes |
| chebyshev_lsq | Some functionality for least squares fitting |
| chebyshev_polynome | Chebyshev polynome, witrh derivative with respect to x |
| chebyshev_smooth | A chebyshev polynome with gibbs damping |
| chebyshev_smooth_fitter | The derivative of the chebyshev polynomial wrt to the coeficients |
| chebyshev_smooth_lsq | Some functionality for least squares fitting |
| chirality | Residual and gradient calculations for chirality restraint |
| chirality_proxy | Grouping of indices into array of sites (i_seqs) and parameters |
| column | Safe access to CMtz::MTZCOL* owned by an iotbx::mtz::dataset |
| columns_73_76_evaluator | Detects old-style PDB files with the PDB access code in columns 73-76 |
| complex_group | Result type for family of object::extract_* functions |
| complex_to_complex | Complex-to-complex Fast Fourier Transformation |
| complex_to_complex_3d | 3-dimensional complex-to-complex Fast Fourier Transformation |
| conformer | Conformer attributes |
| conformer_data | Holder for conformer attributes (to be held by a shared_ptr) |
| const_ref1 | Emulation of 1-dimensional FORTRAN arrays with offset 1 |
| const_ref1 | Emulation of 1-dimensional FORTRAN arrays with offset 1 |
| constraints | Handling of symmetry constraints for tensors of rank 2 |
| continued_fraction | Continued fraction as rational number |
| core | |
| core | Generic coordination sequence algorithm |
| cos_repulsion_function | Energy(delta) = max_residual*((cos(pi*delta)+1)/2)**exponent |
| crystal | Safe access to CMtz::MTZXTAL* owned by an iotbx::mtz::object |
| crystal_orientation | Class for the handling of crystal orientation matrix |
| cut | Plane in 3D for representation of faces of the asymmetric unit polyhedron |
| data_group | Result type for family of object::extract_* functions |
| dataset | Safe access to CMtz::MTZSET* owned by an iotbx::mtz::crystal |
| demmel_kahan_rotations | |
| depth_first_search | |
| dihedral | Residual and gradient calculations for dihedral angle restraint |
| dihedral_proxy | Grouping of indices into array of sites (i_seqs) and dihedral_params |
| direct_space_asu | Direct space asymmetric unit |
| dps_core | Autoindexing of observed reciprocal space vectors using DPS algorithm |
| drop_convergence_test | Convergence test based on monitoring an objective function |
| eigensystem | Group of associated eigenvectors and eigenvalues |
| ellipsoid_to_sphere_transform | |
| end_of_line | End-of-line |
| erf_engine | Port of http://www.netlib.org/specfun/erf (as of 2003 Dec 03) |
| error | All iotbx exceptions are derived from this class |
| error | All mmtbx exceptions are derived from this class |
| error | All cctbx exceptions are derived from this class |
| error | All scitbx exceptions are derived from this class |
| error | Generic exception class for lbfgs error messages |
| error | All smtbx exceptions are derived from this class |
| error | All gltbx exceptions are derived from this class |
| error_base | Exception which can plug into the SCITBX_ERROR_UTILS_ASSERT trickery |
| error_degenerate_unit_cell_parameters | Specific exception to indicate failure of reduction algorithm |
| error_improper_input_data | Specific exception class |
| error_improper_input_parameter | Specific exception class |
| error_index | Special class for "Index out of range." exceptions |
| error_index | Special class for "Index out of range." exceptions |
| error_index | Special class for "Index out of range." exceptions |
| error_index | Special class for "Index out of range." exceptions |
| error_index | Special class for "Index out of range." exceptions |
| error_index | Special class for "Index out of range." exceptions |
| error_internal_error | Specific exception class |
| error_iteration_limit_exceeded | Specific exception to indicate failure of reduction algorithm |
| error_line_search_failed | Specific exception class |
| error_line_search_failed_rounding_errors | Specific exception class |
| error_non_crystallographic_rotation_matrix_encountered | Specific exception to indicate failure of group multiplication |
| error_rational_vector | Special class for rational vector exceptions |
| error_search_direction_not_descent | Specific exception class |
| expand_to_p1_complex | Expands an array of Miller indices and associated complex data to P1 symmetry |
| expand_to_p1_hendrickson_lattman | Expands an array of Miller indices and associated Hendrickson-Lattman coefficients to P1 symmetry |
| expand_to_p1_obs | Expands an array of Miller indices and associated observations (data, sigmas) to P1 symmetry |
| expand_to_p1_phases | Expands an array of Miller indices and associated phases to P1 symmetry |
| expand_to_p1_scalar | Expands an array of Miller indices and associated scalar data (e.g. bool, int, double) to P1 symmetry |
| f_calc_modulus | The modulus of complex structure factors |
| f_calc_modulus_square | The modulus squared of complex structure factors |
| f_sq_as_f_xtal_3_7 | |
| factor_beta_u_iso | Factorization into isotropic and remaining anisotropic contributions |
| factor_u_cart_u_iso | Factorization into isotropic and remaining anisotropic contributions |
| factor_u_cif_u_iso | Factorization into isotropic and remaining anisotropic contributions |
| factor_u_star_u_iso | Factorization into isotropic and remaining anisotropic contributions |
| factorization | Determination of prime factors for both complex-to-complex and real-to-complex transforms |
| failure_info | Info about a failure during a Cholesky process |
| fast_less_than | Definition of fast comparison for use in, e.g., std::map<miller::index<> > |
| fast_minimum_reduction | Fast minimum-lengths cell reduction |
| fast_nv1995 | Fast computation of the translation function (correlation of intensities) |
| fast_pair_generator | Fast algorithm for generating pairs of next neighbors |
| fast_terms | Computation of fast translation function terms |
| few_scatterer_constraints | Constraints on some parameters of a few scatterers |
| find_affine | Find affine normalizers of triclinic and monoclinic space groups |
| float_asu | Floating-point parameterization of an asymmetric unit |
| float_cut_plane | Floating-point parameterization of a cut plane |
| floating_point_epsilon | Dynamic determination of the smallest floating point number such that 1 + floating_point_epsilon() differs from 1 |
| fortran_int | Stream manipulator following FORTRAN Iw editing |
| fortran_int_parser | Parser following FORTRAN Iw editing of input fields |
| fortran_int_parser | Parser following FORTRAN Iw editing of input fields |
| fortran_real | Stream manipulator following FORTRAN Fw.d editing |
| fortran_real_parser | Parser following FORTRAN Fw.d editing of input fields |
| fortran_real_parser | Parser following FORTRAN Fw.d editing of input fields |
| fp_fdp | Helper class for passing f' (f-prime) and f" (f-double-prime) |
| fractional | Class for fractional coordinates |
| from_map | Extracts structure factors from a 3-dimensional complex map |
| functor_absolute | Helper function object for array operations |
| functor_approx_equal | Helper function object for array operations |
| functor_fmod_positive | Helper function object for array operations |
| functor_pow2 | Helper function object for array operations |
| gaussian_repulsion_function | Energy(delta) = max_residual*exp(-delta**2/f_sq) |
| geometrical_hydrogens | Base class for all geometrically constrained hydrogen's -XHn |
| gilbert_peierls_lu_factorization | LU decomposition with partial pivoting |
| gill_murray_wright_decomposition_in_place | Computes PAP^{T} + E = LDL^{T} |
| golay_24_12_generator | Generator for the 4096 binary words of the Golay (24,12) code |
| grid_point | Class for grid_point coordinates |
| grid_symop | Symmetry operator optimized for grid |
| hendrickson_lattman | Grouping of Hendrickson-Lattman coefficients |
| hexagonal_sampling_generator | Generator for sampling based on a hexagonal close packing |
| histogram | Histogram of an array of scalar values |
| hkl_columns | Result type for object::get_hkl_columns() |
| hr_ht_cache | The miller indices  and the scalars  where  spans the elements of a space group  |
| hr_ht_group | A pair  where is a symmetry element |
| icosahedron | Cartesian coordinates of points on a sphere |
| image_divider | Class for breaking a detector image into component modules |
| imaginary | An imaginary number |
| imaginary_unit_t | The complex number i |
| in_generic_space_group | |
| in_origin_centric_space_group | |
| incremental_d_star_sq | Helper class for optimizing d_star_sq computations in loops over a grid of Miller indices |
| index | Miller index class |
| index_generator | Efficient, easy-to-use algorithm for building an asymmetric unit of Miller indices up to a given high-resolution limit or up to a given maximum Miller index |
| index_span | Determines min(indices[i]) and max(indices[i])+1, i=1..3, for an array of Miller indices |
| index_table_layout_adaptor | Support for common layouts of tables of asymmetric Miller indices |
| info | Translates atom name alias to reference name |
| initialiser | Syntactic sugar to initialise arrays |
| input | Processing of PDB strings |
| input_atom_labels | Efficient processing of input atom labels |
| inverse_power_repulsion_function | Energy(delta) = k_rep*vdw_distance/(delta**irexp) repulsive function |
| is_singular_revolute | Helper |
| isotropic_form_factor_mixin | Helper |
| it1992 | Coefficients for the Analytical Approximation to the Scattering Factor |
| it1992_iterator | Iterator over table of Coefficients for the Analytical Approximation to the Scattering Factor, International Tables 1992 |
| joint_t | Abstract joint model |
| l_l_transpose_decomposition_in_place | Cholesky decomposition A = L L^T in place |
| least_squares_residual | A functor representing a least-squares residual |
| levenberg_marquardt | C++ wrapper for MINPACK lmder |
| line_info | Facilitates fast processing and comprehensive error messages |
| lmder | C++ port of lmder |
| local_scaling_nikonov | |
| lq_decomposition | Householder LQ decomposition |
| machine_dependent_base | Port of http://www.netlib.org/specfun/erf (as of 2003 Dec 03) |
| many_scatterer_constraints | A set of constraints on some parameters of several scatterers |
| mapping | Pair of wyckoff::position and a symmetry operation |
| mass_points_cache | Helper |
| mat2 | Matrix class (2x2) |
| mat3 | Matrix class (3x3) |
| matrix | A sparse matrix, represented by a sequence of sparse columns |
| maximum_likelihood_criterion | Maximum-likelihood target function and gradients |
| maximum_likelihood_criterion_hl | Maximum-likelihood target function and gradients |
| median_functor | Functor returning a given quantile of a list of data |
| median_statistics | Median and dispersion around it |
| mersenne_twister | Wrapper for boost/random/mersenne_twister.hpp |
| min_sym_equiv_distance_info | Algorithm for finding the shortest distance between two sites under application of space group symmetry |
| minimizer | Interface to the LBFGS minimizer |
| minimizer | High-level interface to L-BFGS-B Version 2.1 |
| minimum_covering_sphere_3d | Minimum covering sphere of a set of 3-dimensional points |
| model | Model attributes |
| model | Torsion-angle refinement and dynamics model |
| model_data | Holder for model attributes (to be held by a shared_ptr) |
| more_statistics | Determines higher order statistical central moments |
| neutron_news_1992_table | Access to neutron bound scattering lengths & cross-sections |
| neutron_news_1992_table_iterator | Iterator over neutron_news_1992_table entries |
| node | Grouping of symmetry operations characterizing a node in a graph of bonded sites |
| non_parametric_bootstrap | Resampling class |
| non_parametric_bootstrap_as_int | Resampling class |
| nonbonded | Residual and gradient calculations for nonbonded restraints |
| nonbonded_asu_proxy | Grouping of asu_mapping_index_pair and vdw_distance |
| nonbonded_params | Grouping of parameters for the generation of nonbonded pair interactions |
| nonbonded_simple_proxy | Grouping of indices into array of sites (i_seqs) and vdw_distance |
| nonbonded_sorted_asu_proxies | Generation of sorted nonbonded proxies |
| norm_accumulator | LAPACK-style norm of a vector: overflow- and underflow-resilient |
| normal_equations_for_generic_residuals | Normal equations for generic non-linear least-squares |
| normal_equations_for_linear_least_squares | Normal equations for linear least-squares |
| normal_equations_separating_scale_factor | Normal equations for least-squares fit with an overall scale |
| numeric_limits | Extension of std::numeric_limits for LAPACK-style floating point info |
| object | Wrapper for CMtz::MTZ* |
| observations_group | Result type for family of object::extract_* functions |
| optional_copy | Optional allocation of value with new, with value-copy semantics |
| packed_l_accessor | Accessor for the lower diagonal of a square matrix packed by row |
| packed_u_accessor | Accessor for the upper diagonal of a square matrix packed by row |
| pair_asu_table | Managed table of pair interactions based on direct_space_asu::asu_mappings |
| pairwise_global | Based on implementation by Kevin Cowtan |
| parameter_indices | Position of the various derivatives or shifts in an array |
| parameter_map | An array of parameter_indices |
| parse_string | Class for communicating string parsing errors |
| phase_info | Handling of phase restrictions and optional evaluation of conditions for systematically absent reflections |
| phase_integrator | |
| planarity | Residual and gradient calculations for planarity restraint |
| planarity_proxy | Grouping of indices into array of sites (i_seqs) and weights |
| polyhedral_BH | Model of BH as part of a polyhedral fragment (Boron cages e.g.) |
| position | Information for Wyckoff positions |
| principal_axes_of_inertia | |
| principal_axes_of_inertia_2d | |
| product | Product of Given rotations  |
| prolsq_repulsion_function | General repulsive function (see PROLSQ and CNS) |
| proto_cylinder | A prototype of a cylinder stored in a diplay list |
| proto_ellipsoid | A prototype of an ellispoid stored in a display list |
| python_file_buffer | A stream buffer getting data from and putting data into a Python file object |
| qr_decomposition | Householder QR decomposition |
| random_gauss_adaptor | Helper |
| random_matrix_generator | A sequence of random sparse matrices |
| range_loop | Helper for looping over index ranges |
| real_symmetric | Group of associated eigenvectors and eigenvalues |
| real_to_complex | Real-to-complex Fast Fourier Transformation |
| real_to_complex_3d | 3-dimensional real-to-complex Fast Fourier Transformation |
| ref1 | Emulation of 1-dimensional FORTRAN arrays with offset 1 |
| ref2 | Emulation of 2-dimensional FORTRAN arrays with offset 1 |
| ref_owning_shared | Like af::ref but it owns the shared array it refers to |
| ref_owning_versa | Like af::ref but it owns the versa array it refers to |
| reference_asu | Contiguous reciprocal space asymmetric units for the 230 reference settings |
| reflection | Householder reflection P = I - beta v v^T |
| remainder_and_quotient | Quotient and remainder of x/y for floating point x and y |
| residue | Residue attributes |
| residue_data | Holder for residue attributes (to be held by a shared_ptr) |
| residue_group | Residue_group attributes |
| residue_group_data | Holder for residue_group attributes (to be held by a shared_ptr) |
| revolute | Revolute (one degree of freedom) body model (see Featherstone RBDA 2007) |
| revolute | Revolute (one degree of freedom) joint model (see Featherstone RBDA 2007) |
| revolute_alignment | See code |
| root | Root attributes |
| root_data | Holder for root attributes (to be held by a shared_ptr) |
| rot_mx | 3x3 rotation matrix |
| rot_mx_info | Class for grouping information about rotation matrices |
| rotation | Givens rotation |
| rotation_angles | Class for determining if a Miller index diffracts |
| rt_mx | Rotation-Translation matrix |
| rt_mx_from_string | Parser for xyz expressions |
| scatterer | Information about an atom that is needed for a structure factor calculation |
| search_symmetry | Parameterization of search symmetries |
| search_symmetry_flags | Grouping of flags determining the symmetry of search spaces |
| secondary_CH2 | Model of X-CH2-Y |
| shell_asu_tables_actions | Actions for the generation of higher-level (nonbonded) interactions |
| simple_pair_generator | Simple O(N^2) algorithm for generating pairs of next neighbors |
| site_constraints | Handling of site symmetry coordinate constraints |
| site_symmetry | Numerically robust algorithm for the determination of site-symmetries |
| site_symmetry_ops | Base class for site_symmetry, holding the essential results |
| six_dof | Six degree-of-freedom body model (see Featherstone RBDA 2007) |
| six_dof | Six degree-of-freedom joint model (see Featherstone RBDA 2007) |
| six_dof_alignment | See code |
| smooth_bootstrap | Resampling class |
| solve_in_place | Umbrella for A x = b solvers in place |
| sorted_asu_proxies | Managed group of simple proxies and asu proxies |
| space_group | Space group operations |
| space_group_symbol_iterator | Iterator for the 530 tabulated space group representations |
| space_group_symbols | Class for the handling of space group symbols of various types |
| space_group_type | Computation and use of change-of-basis matrix to reference setting |
| spherical | Spherical (three degrees of freedom) body model (see Featherstone RBDA 2007) |
| spherical | Spherical (three degrees of freedom) joint model (see Featherstone RBDA 2007) |
| spherical_alignment | See code |
| ss_vec_mod | Entry in list of structure seminvariant vectors and moduli |
| staggered_terminal_tetrahedral_XHn | Model of Z-Y-XHn with tetrahedral angles |
| statistics | Determines simple map statistics |
| sticky_fortran_int | Stream manipulator following FORTRAN Iw editing |
| sticky_fortran_real | Stream manipulator following FORTRAN Fw.d editing |
| structure_seminvariants | Structure-seminvariant vector and moduli |
| sum | Sum of Gaussian terms plus a constant |
| sym_equiv_index | Class for symmetrically equivalent Miller indices |
| sym_equiv_indices | Class for the handling of symmetrically equivalent Miller indices |
| sym_equiv_sites | Container for symmetrically equivalent coordinates |
| sym_mat2 | Symmetric 2x2 matrix class |
| sym_mat3 | Symmetric 3x3 matrix class |
| symmetry | Grouping of unit cell and space group |
| symmetry_flags | Grouping of flags determining the symmetry of the translation function |
| system_model | RBDA Tab. 4.3, p. 87 |
| table | Access to Henke tables |
| table | Access to table of ionic radii |
| table | Tiny Periodic System of Elements |
| table | Table of Wyckoff positions |
| table | Access to Sasaki tables |
| table | Access to table of covalent radii |
| table_entry | Entry in table of N-Gaussian approximations |
| table_iterator | Iterator over Sasaki tables |
| table_iterator | Iterator over Henke tables |
| table_iterator | Iterator over table entries |
| table_iterator | Iterator over table of radii |
| table_iterator | Iterator over table of radii |
| term | Gaussian term: a Exp[-b x^2] |
| term_table_actions | Actions for simple counting |
| terminal_tetrahedral_XHn | Model of Y-XHn with tetrahedral angles |
| terminal_trihedral_XH2 | Model of terminal Z-Y=XH2 (ethylenic CH2 or amide NH2) |
| tertiary_CH | Model of tertiary CH |
| three_shells | Buffer for nodes in three shells |
| to_map | Copies a structure factor array to a 3-dimensional complex map |
| tr_vec | Translation vector |
| tr_vec_12 | Constructor for initialization of constants |
| traditional_convergence_test | Traditional LBFGS convergence test |
| translation_part_info | Analysis of the translation part of a rotation-translation matrix |
| translational | Translational (three degrees of freedom) joint model (see Featherstone RBDA 2007) |
| translational | Translational (three degrees of freedom) body model (see Featherstone RBDA 2007) |
| translational_alignment | See code |
| triangulation | Triangulation of an isosurface of a scalar field |
| triplet_generator | Triplets for direct methods (reciprocal-space squaring) |
| triplet_phase_relation | Triplet phase relation h = k + h-k |
| u_transpose_u_decomposition_in_place | Cholesky decomposition A = U^T U in place |
| unit_cell | Class for the handling of unit cell information |
| vec2 | Two-dimensional vector |
| vec3 | Three-dimensional vector |
| vector | |
| vector::const_iterator | Const iterator over the records |
| vector::element_const_reference | A const reference to an element of given index |
| vector::element_reference | A reference to an element of given index |
| vector::iterator | Iterator over the records |
| weighted_triplet_phase_relation | Weighted triplet phase relation |
| wk1995 | Coefficients for the Analytical Approximation to the Scattering Factor |
| wk1995_iterator | Iterator over table of Coefficients for the Analytical Approximation to the Scattering Factor, Waasmaier & Kirfel 1995 |
| zero_dof | Zero degree-of-freedom joint model |
| zero_dof | Zero degree-of-freedom body model |
| zero_dof_alignment | See code |
