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- Method resolution order:
- smtbx_structure_enhancements
- libtbx.object_oriented_patterns.injector
- cctbx.xray.structure.structure
- cctbx.crystal.special_position_settings
- cctbx.crystal.symmetry
- __builtin__.object
Methods defined here:
- parameter_map(self)
Data descriptors inherited from libtbx.object_oriented_patterns.injector:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
Data and other attributes inherited from libtbx.object_oriented_patterns.injector:
- __metaclass__ = <class 'libtbx.object_oriented_patterns.__metaclass__'>
Methods inherited from cctbx.xray.structure.structure:
- __getitem__(self, slice_object)
- __init__(self, special_position_settings=None, scatterers=None, site_symmetry_table=None, scattering_type_registry=None, crystal_symmetry=None)
- add_scatterer(self, scatterer, site_symmetry_ops=None, insert_at_index=None)
- add_scatterers(self, scatterers, site_symmetry_table=None)
- adjust_occupancy(self, occ_max, occ_min, selection=None)
- adjust_u_iso(self)
- all_selection(self)
- apply_rigid_body_shift(self, rot, trans, selection=None)
- apply_rigid_body_shift_obj(self, sites_cart, sites_frac, rot, trans, selection, unit_cell, atomic_weights)
- apply_shift(self, shift, recompute_site_symmetries=False)
- apply_special_position_ops_d_target_d_site(self, d_target_d_site)
- apply_symmetry_sites(self)
- apply_symmetry_u_stars(self)
- as_cif_simple(self, out=None)
- as_cns_sdb_file = xray_structure_as_cns_sdb_file(self, file=None, description=None, comment=None, action=None, segid=None, group=None)
- as_emma_model(self)
- as_pdb_file(self, remark=None, remarks=[], fractional_coordinates=False, resname=None, connect=None)
- asu_mappings(self, buffer_thickness, asu_is_inside_epsilon=None)
- asymmetric_unit_in_p1(self)
- atomic_weights(self)
- b_iso_min_max_mean(self)
- center_of_mass(self, atomic_weights=None)
- change_basis(self, cb_op)
- change_hand(self)
- closest_distances(self, sites_frac, distance_cutoff, use_selection=None)
- concatenate(self, other)
- concatenate_inplace(self, other)
- conservative_pair_proxies(self, bond_sym_table, conserve_angles)
- convert_to_anisotropic(self, selection=None)
- convert_to_isotropic(self, selection=None)
- coordinate_degrees_of_freedom_counts(self, selection=None)
- crystal_symmetry(self)
- cubic_unit_cell_around_centered_scatterers(self, buffer_size)
- deep_copy_scatterers(self)
- difference_vectors_cart(self, other)
- distances(self, other, selection=None)
- element_selection(self, *elements)
- erase_scatterers(self)
- expand_to_p1(self, append_number_to_labels=False)
- extract_u_cart_plus_u_iso(self)
- extract_u_iso_or_u_equiv(self)
- grads_and_curvs_target_simple(self, miller_indices, da_db, daa_dbb_dab)
- hd_selection(self)
- is_positive_definite_u(self, u_cart_tolerance=None)
- label_regex_selection(self, label_regex)
- label_selection(self, *labels)
- max_distance(self, other, selection=None)
- mean_distance(self, other, selection=None)
- min_distance(self, other, selection=None)
- min_u_cart_eigenvalue(self)
- n_grad_u_aniso(self)
- n_grad_u_iso(self)
- n_parameters(self)
- n_parameters_XXX(self)
- n_undefined_multiplicities(self)
- orthorhombic_unit_cell_around_centered_scatterers(self, buffer_size)
- pair_asu_table(self, distance_cutoff=None, asu_mappings_buffer_thickness=None, asu_is_inside_epsilon=None)
- principal_axes_of_inertia(self, atomic_weights=None)
- random_remove_sites_selection(self, fraction)
- random_shift_sites(self, max_shift_cart=0.20000000000000001)
- re_apply_symmetry(self, i_scatterer)
- replace_scatterers(self, scatterers, site_symmetry_table='existing')
- replace_sites_cart(self, new_sites)
- replace_sites_frac(self, new_sites)
- rms_difference(self, other)
- scale_adp(self, factor, selection=None)
- scatterer_flags(self)
- scatterers(self)
- scattering_type_registry(self, custom_dict=None, d_min=None, table=None, types_without_a_scattering_contribution=None)
- scattering_types(self)
- scattering_types_counts_and_occupancy_sums(self)
- select(self, selection, negate=False)
- select_inplace(self, selection)
- set_b_iso(self, value=None, values=None, selection=None)
- set_inelastic_form_factors(self, photon, table, set_use_fp_fdp=True)
- set_occupancies(self, value, selection=None)
- set_scatterer_flags(self, scatterer_flags)
- set_sites_cart(self, sites_cart)
- set_sites_frac(self, sites_frac)
- set_u_cart(self, u_cart, selection=None)
- set_u_iso(self, value=None, values=None, selection=None)
- shake_adp(self, b_max=None, b_min=None, spread=10.0, aniso_spread=0.10000000000000001, keep_anisotropic=False, random_u_cart_scale=1.0, selection=None)
- shake_adp_if_all_equal(self, b_iso_tolerance=0.10000000000000001)
- shake_occupancies(self, selection=None)
- shake_sites_in_place(self, rms_difference=None, mean_distance=None, selection=None)
- shift_occupancies(self, q_shift, selection=None)
- shift_us(self, u_shift=None, b_shift=None, selection=None)
- show_distances(self, distance_cutoff=None, asu_mappings_buffer_thickness=None, asu_is_inside_epsilon=None, pair_asu_table=None, show_cartesian=False, keep_pair_asu_table=False, out=None)
- show_scatterer_flags_summary(self, out=None)
- show_scatterers(self, f=None)
- show_special_position_shifts(self, sites_frac_original=None, sites_cart_original=None, out=None, prefix='')
- show_summary(self, f=None, prefix='')
- show_u_statistics(self, text='', out=None, use_hydrogens=False)
- site_symmetry_table(self)
- sites_cart(self)
- sites_frac(self)
- sites_mod_positive(self)
- sites_mod_short(self)
- sort(self, by_value='occupancy', reverse=False)
- special_position_indices(self)
- structure_factors(self, anomalous_flag=None, d_min=None, algorithm=None, cos_sin_table=False, quality_factor=None, u_base=None, b_base=None, wing_cutoff=None)
- switch_to_neutron_scattering_dictionary(self)
- tidy_us(self, u_min=9.9999999999999995e-07, u_max=6.9658313754107217)
- translate(self, x=0, y=0, z=0)
- use_u_aniso(self)
- use_u_iso(self)
Class methods inherited from cctbx.xray.structure.structure:
- from_shelx(cls, file=None, filename=None, set_grad_flags=True) from libtbx.object_oriented_patterns.__metaclass__
Methods inherited from cctbx.crystal.special_position_settings:
- assert_min_distance_sym_equiv(self)
- incremental_pairs(self, distance_cutoff, asu_is_inside_epsilon=None, asu_mappings_buffer_thickness=-1, cubicle_epsilon=-1)
- min_distance_sym_equiv(self)
- 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)
- sym_equiv_sites(self, site)
- u_star_tolerance(self)
Methods inherited from cctbx.crystal.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)
- 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)
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