Package Contents
		burzlaff_zimmermann_dewolff close_packing coordination_sequences direct_space_asu find_best_cell reindex tst_ext

Classes
		__builtin__.object show_distances sym_pair symmetry special_position_settings _clustering_mix_in(__builtin__.object) distance_based_clustering incremental_clustering   class distance_based_clustering(_clustering_mix_in)       Method resolution order: distance_based_clustering _clustering_mix_in __builtin__.object Methods defined here: __init__(self, special_position_settings, sites_cart, distance_cutoff, discard_special_positions=False) Methods inherited from _clustering_mix_in: sites_cart(self) tidy_index_groups_in_place(self) Data descriptors inherited from _clustering_mix_in: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class incremental_clustering(_clustering_mix_in)       Method resolution order: incremental_clustering _clustering_mix_in __builtin__.object Methods defined here: __init__(self, special_position_settings, sites_cart, distance_cutoffs, scores=None, discard_special_positions=False, discard_not_strictly_inside_asu=False, initial_required_cluster_size=0) Methods inherited from _clustering_mix_in: sites_cart(self) tidy_index_groups_in_place(self) Data descriptors inherited from _clustering_mix_in: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class show_distances(__builtin__.object)       Methods defined here: __init__(self, pair_asu_table, site_labels=None, sites_frac=None, sites_cart=None, show_cartesian=False, keep_pair_asu_table=False, out=None) Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class special_position_settings(symmetry)       Method resolution order: special_position_settings symmetry __builtin__.object Methods defined here: __init__(self, crystal_symmetry, min_distance_sym_equiv=0.5, u_star_tolerance=0, assert_min_distance_sym_equiv=True) assert_min_distance_sym_equiv(self) asu_mappings(self, buffer_thickness, sites_frac=None, sites_cart=None, site_symmetry_table=None, asu_is_inside_epsilon=None) change_basis(self, cb_op) incremental_pairs(self, distance_cutoff, asu_is_inside_epsilon=None, asu_mappings_buffer_thickness=-1, cubicle_epsilon=-1) min_distance_sym_equiv(self) pair_asu_table(self, distance_cutoff, sites_frac=None, sites_cart=None, site_symmetry_table=None, asu_mappings_buffer_thickness=None, asu_is_inside_epsilon=None, distance_cutoff_epsilon=None) site_cluster_analysis(self, min_distance=None, min_cross_distance=None, min_self_distance=None, general_positions_only=False, estimated_reduction_factor=4, asu_is_inside_epsilon=None, asu_mappings_buffer_thickness=-1, min_cubicle_edge=5, cubicle_epsilon=-1) site_symmetry(self, site=None, site_cart=None) site_symmetry_table(self, sites_frac=None, sites_cart=None) sym_equiv_sites(self, site) u_star_tolerance(self) Methods inherited from symmetry: as_reference_setting(self) average_b_cart(self, b_cart) average_u_cart(self, u_cart) best_cell(self, angular_tolerance=None) build_miller_set(self, anomalous_flag, d_min, d_max=None) cell_equivalent_p1(self) change_of_basis_op_to_best_cell(self, angular_tolerance=None, best_monoclinic_beta=True) change_of_basis_op_to_inverse_hand(self) change_of_basis_op_to_minimum_cell(self) change_of_basis_op_to_niggli_cell(self, relative_epsilon=None, iteration_limit=None) change_of_basis_op_to_primitive_setting(self) change_of_basis_op_to_reference_setting(self) customized_copy(self, unit_cell=<class libtbx.utils.Keep at 0xae51d0>, space_group_info=<class libtbx.utils.Keep at 0xae51d0>) direct_space_asu(self) gridding(self, d_min=None, resolution_factor=None, step=None, symmetry_flags=None, mandatory_factors=None, max_prime=5, assert_shannon_sampling=True) inverse_hand(self) is_compatible_unit_cell(self) is_patterson_symmetry(self) is_similar_symmetry(self, other, relative_length_tolerance=0.01, absolute_angle_tolerance=1.0) join_symmetry(self, other_symmetry, force=False) minimum_cell(self) niggli_cell(self, relative_epsilon=None, iteration_limit=None) patterson_symmetry(self) primitive_setting(self) reflection_intensity_symmetry(self, anomalous_flag) show_summary(self, f=None, prefix='') space_group(self) space_group_info(self) special_position_settings(self, min_distance_sym_equiv=0.5, u_star_tolerance=0, assert_min_distance_sym_equiv=True) subtract_continuous_allowed_origin_shifts(self, translation_cart) unit_cell(self) Data descriptors inherited from symmetry: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class sym_pair(__builtin__.object)       Methods defined here: __init__(self, i_seq, j_seq, rt_mx_ji) i_seqs(self) Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)   class symmetry(__builtin__.object)       Methods defined here: __init__(self, unit_cell=None, space_group_symbol=None, space_group_info=None, space_group=None, assert_is_compatible_unit_cell=True, force_compatible_unit_cell=True) as_reference_setting(self) asu_mappings(self, buffer_thickness, asu_is_inside_epsilon=None) average_b_cart(self, b_cart) average_u_cart(self, u_cart) best_cell(self, angular_tolerance=None) build_miller_set(self, anomalous_flag, d_min, d_max=None) cell_equivalent_p1(self) change_basis(self, cb_op) change_of_basis_op_to_best_cell(self, angular_tolerance=None, best_monoclinic_beta=True) change_of_basis_op_to_inverse_hand(self) change_of_basis_op_to_minimum_cell(self) change_of_basis_op_to_niggli_cell(self, relative_epsilon=None, iteration_limit=None) change_of_basis_op_to_primitive_setting(self) change_of_basis_op_to_reference_setting(self) customized_copy(self, unit_cell=<class libtbx.utils.Keep at 0xae51d0>, space_group_info=<class libtbx.utils.Keep at 0xae51d0>) direct_space_asu(self) gridding(self, d_min=None, resolution_factor=None, step=None, symmetry_flags=None, mandatory_factors=None, max_prime=5, assert_shannon_sampling=True) inverse_hand(self) is_compatible_unit_cell(self) is_patterson_symmetry(self) is_similar_symmetry(self, other, relative_length_tolerance=0.01, absolute_angle_tolerance=1.0) join_symmetry(self, other_symmetry, force=False) minimum_cell(self) niggli_cell(self, relative_epsilon=None, iteration_limit=None) patterson_symmetry(self) primitive_setting(self) reflection_intensity_symmetry(self, anomalous_flag) show_summary(self, f=None, prefix='') space_group(self) space_group_info(self) special_position_settings(self, min_distance_sym_equiv=0.5, u_star_tolerance=0, assert_min_distance_sym_equiv=True) subtract_continuous_allowed_origin_shifts(self, translation_cart) unit_cell(self) Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)

Functions
		cluster_erosion(sites_cart, box_size, fraction_to_be_retained) coordination_sequences_shell_asu_tables(...) coordination_sequences_shell_asu_tables( (pair_asu_table)pair_asu_table, (int)max_shell) -> tuple :       C++ signature :         std::vector<cctbx::crystal::pair_asu_table<double, int>, std::allocator<cctbx::crystal::pair_asu_table<double, int> > > coordination_sequences_shell_asu_tables(cctbx::crystal::pair_asu_table<double, int>,unsigned int) coordination_sequences_simple(...) coordination_sequences_simple( (pair_asu_table)pair_asu_table, (int)max_shell) -> stl_vector_unsigned :       C++ signature :         scitbx::af::shared<std::vector<unsigned int, std::allocator<unsigned int> > > coordination_sequences_simple(cctbx::crystal::pair_asu_table<double, int>,unsigned int) correct_special_position(crystal_symmetry, special_op, site_frac=None, site_cart=None, tolerance=0.10000000000000001, error_message='Corrupt gradient calculations.') During refinement it is essential to reset special positions because otherwise rounding error accumulate over many cycles. get_distances(...) get_distances( (pair_sym_table)pair_sym_table, (object)orthogonalization_matrix, (vec3_double)sites_frac) -> double :       C++ signature :         scitbx::af::shared<double> get_distances(scitbx::af::const_ref<std::map<unsigned int, std::vector<cctbx::sgtbx::rt_mx, std::allocator<cctbx::sgtbx::rt_mx> >, std::less<unsigned int>, std::allocator<std::pair<unsigned int const, std::vector<cctbx::sgtbx::rt_mx, std::allocator<cctbx::sgtbx::rt_mx> > > > >, scitbx::af::trivial_accessor>,scitbx::mat3<double>,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>)   get_distances( (pair_sym_table)pair_sym_table, (vec3_double)sites_cart) -> double :       C++ signature :         scitbx::af::shared<double> get_distances(scitbx::af::const_ref<std::map<unsigned int, std::vector<cctbx::sgtbx::rt_mx, std::allocator<cctbx::sgtbx::rt_mx> >, std::less<unsigned int>, std::allocator<std::pair<unsigned int const, std::vector<cctbx::sgtbx::rt_mx, std::allocator<cctbx::sgtbx::rt_mx> > > > >, scitbx::af::trivial_accessor>,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>) neighbors_max_memory_allocation_get(...) neighbors_max_memory_allocation_get() -> int :       C++ signature :         unsigned long neighbors_max_memory_allocation_get() neighbors_max_memory_allocation_set(...) neighbors_max_memory_allocation_set( (int)number_of_bytes) -> None :       C++ signature :         void neighbors_max_memory_allocation_set(unsigned long) non_crystallographic_symmetry(sites_cart=None, sites_cart_min=None, sites_cart_max=None, default_buffer_layer=0.5, min_unit_cell_length=0) select_crystal_symmetry(from_command_line=None, from_parameter_file=None, from_coordinate_files=[None], from_reflection_files=[None]) Select/construct a crystal symmetry from a list of various options