| | |
- __builtin__.object
-
- array_info
- binned_data
- merge_equivalents
- cctbx.crystal.symmetry(__builtin__.object)
-
- set
-
- array
- cctbx.maptbx.crystal_gridding(__builtin__.object)
-
- fft_map
- crystal_symmetry_is_compatible_with_symmetry_from_file
- cctbx_miller_ext.binner(cctbx_miller_ext.binning)
-
- binner
class array(set) |
| | |
- Method resolution order:
- array
- set
- cctbx.crystal.symmetry
- __builtin__.object
Methods defined here:
- __abs__(self)
- __add__(self, other)
- __getitem__(self, slice_object)
- __imul__(self, other)
- __init__(self, miller_set, data=None, sigmas=None)
- __iter__(self)
- __mul__(self, other)
- adopt_set(self, other, assert_is_similar_symmetry=True)
- amplitudes(self)
- anomalous_differences(self)
- anomalous_signal(self, use_binning=False)
- sqrt((<||F(+)|-|F(-)||**2>)/(1/2(<|F(+)|>**2+<|F(-)|>**2)))
- apply_scaling(self, target_max=None, factor=None)
- arg(self, deg=False)
- as_amplitude_array(self)
- as_double(self)
- as_intensity_array(self)
- as_mtz_dataset(self, column_root_label, column_types=None, label_decorator=None, title=None, crystal_name='crystal', project_name='project', dataset_name='dataset', wavelength=1.0)
- as_non_anomalous_array(self)
- as_phases_phs(self, out, scale_amplitudes=True, phases=None, phases_deg=None, figures_of_merit=None)
- average_bijvoet_mates(self)
- change_basis(self, cb_op, deg=None)
- complete_array(self, d_min_tolerance=9.9999999999999995e-07, d_min=None, d_max=None, new_data_value=-1, new_sigmas_value=-1)
- concatenate(self, other)
- conjugate(self)
- copy(self)
- correlation(self, other, use_binning=False, assert_is_similar_symmetry=True)
- count_and_fraction_in_bins(self, data_value_to_count, count_not_equal=False)
- crystal_symmetry_is_compatible_with_symmetry_from_file(self, unit_cell_relative_length_tolerance=0.02, unit_cell_absolute_angle_tolerance=3.0, working_point_group=None)
- customized_copy(self, miller_set=<class libtbx.utils.Keep at 0x8d05f0>, data=<class libtbx.utils.Keep at 0x8d05f0>, sigmas=<class libtbx.utils.Keep at 0x8d05f0>, crystal_symmetry=<class libtbx.utils.Keep at 0x8d05f0>, indices=<class libtbx.utils.Keep at 0x8d05f0>, anomalous_flag=<class libtbx.utils.Keep at 0x8d05f0>, unit_cell=<class libtbx.utils.Keep at 0x8d05f0>, space_group_info=<class libtbx.utils.Keep at 0x8d05f0>, observation_type=<class libtbx.utils.Keep at 0x8d05f0>)
- data(self)
- deep_copy(self)
- discard_sigmas(self)
- eliminate_sys_absent(self, integral_only=False, log=None, prefix='')
- enforce_positive_amplitudes(self, i_sig_level=-4.0)
- Takes in an intensity array (including negatives) and spits out amplitudes.
The basic assumption is that
P(Itrue) \propto exp(-(Itrue-Iobs)**2/(2*s))
where Itrue>=0 (positivity constraint on error free amplitudes).
For amplitudes, this results in
P(Ftrue) \propto 2 Ftrue exp( -(Ftrue**2-Iobs)**2/(2s) )
A Gaussian approximation is fitted to the Mode of this distribution.
An analytical solution exists and is implemented below.
This method does not require any Wilson statistics assumptions.
- expand_to_p1(self, phase_deg=None)
- export_as_cns_hkl(self, file_object, file_name=None, info=[], array_names=None, r_free_flags=None)
- f_as_f_sq(self)
- f_obs_minus_f_calc(self, f_obs_factor, f_calc)
- f_sq_as_f(self, algorithm='xtal_3_7', tolerance=9.9999999999999995e-07)
- fft_map(self, resolution_factor=0.33333333333333331, d_min=None, grid_step=None, symmetry_flags=None, mandatory_factors=None, max_prime=5, assert_shannon_sampling=True, f_000=None)
- generate_bijvoet_mates(self)
- hemisphere_acentrics(self, plus_or_minus)
- hemispheres_acentrics(self)
- i_over_sig_i(self, use_binning=False, return_fail=None)
- <I/sigma_I>
- info(self)
- is_bool_array(self)
- is_complex_array(self)
- is_hendrickson_lattman_array(self)
- is_integer_array(self)
- is_real_array(self)
- is_xray_amplitude_array(self)
- is_xray_intensity_array(self)
- is_xray_reconstructed_amplitude_array(self)
- map_correlation(self, other)
- map_to_asu(self, deg=None)
- matching_set(self, other, data_substitute, sigmas_substitute=None, assert_is_similar_symmetry=True)
- mean(self, use_binning=False, use_multiplicities=False, squared=False, rms=False)
- mean_of_intensity_divided_by_epsilon(self, use_binning=False, return_fail=None)
- <I/epsilon>
- mean_of_squared_sigma_divided_by_epsilon(self, use_binning=False, return_fail=None)
- <sigma^2/epsilon>
- mean_phase_error(self, phase_source)
- mean_sq(self, use_binning=False, use_multiplicities=False)
- mean_weighted_phase_error(self, phase_source)
- measurability(self, use_binning=False, cutoff=3.0, return_fail=None)
- Fraction of reflections for which (|delta I|/sigma_dI) > cutoff
and min(I_plus/sigma_plus,I_min/sigma_min) > cutoff
- merge_equivalents(self)
- min_f_over_sigma(self)
- norm(self)
- observation_type(self)
- patterson_map(self, resolution_factor=0.33333333333333331, d_min=None, symmetry_flags=None, mandatory_factors=None, max_prime=5, assert_shannon_sampling=True, f_000=None, sharpening=False, origin_peak_removal=False)
- patterson_symmetry(self)
- phase_entropy(self, exponentiate=False, return_binned_data=False, return_mean=False)
- Phase entropy as measured in terms of an base-360 entropy (base-2 for centrics).
An entropy of 0, indicates that the phase uncertainity is as low as possible.
An entropy of 1 however, indicates that the uncertainty is maximal: all phases are equally likely!
Options: return_binned_data -> Determines if you receive a binned object rather then a raw array
exponentiate -> whether or not to exponentiate the entropy. This will return a phase uncertainty in degrees (or the 'alphabet size')
- phase_integrals(self, n_steps=None, integrator=None)
- phase_transfer(self, phase_source, epsilon=1e-10, deg=False, phase_integrator_n_steps=None)
- Combines phases of phase_source with self's data if real (keeping the sign of self's data) or with self's amplitudes if complex.
Centric reflections are forced to be compatible with the phase
restrictions.
phase_source can be a miller.array or a plain flex array.
epsilon is only used when phase_source is a complex array. If both the
real and the imaginary part of phase_source[i] < epsilon the phase is
assumed to be 0.
deg is only used if phase_source is an array of doubles.
deg=True indicates that the phases are given in degrees,
deg=False indicates phases are given in radians.
phase_integrator_n_steps is only used if phase_source is an
array of Hendrickson-Lattman coefficients. The centroid
phases are determined on the fly using the given step size.
- phased_translation_function_coeff(self, phase_source, f_calc, fom=None)
- phases(self, deg=False)
- quasi_normalize_structure_factors(self, d_star_power=1)
- quasi_normalized_as_normalized(self)
- r1_factor(self, other, assume_index_matching=False)
- sum ||F| - |F'|| / sum |F|
where F is data() and F' is other.data()
- r_free_flags_accumulation(self)
- randomize_phases(self)
- remove_patterson_origin_peak(self)
- rms(self, use_binning=False, use_multiplicities=False)
- rms_filter(self, cutoff_factor, use_binning=False, use_multiplicities=False, negate=False)
- second_moment(self, use_binning=False)
- <data^2>/(<data>)^2
- second_moment_of_intensities(self, use_binning=False)
- <I^2>/(<I>)^2 (2.0 for untwinned, 1.5 for twinned data)
- select(self, selection, negate=False, anomalous_flag=None)
- set(self, crystal_symmetry=<class libtbx.utils.Keep at 0x8d05f0>, indices=<class libtbx.utils.Keep at 0x8d05f0>, anomalous_flag=<class libtbx.utils.Keep at 0x8d05f0>, unit_cell=<class libtbx.utils.Keep at 0x8d05f0>, space_group_info=<class libtbx.utils.Keep at 0x8d05f0>)
- set_info(self, info)
- set_observation_type(self, observation_type)
- set_observation_type_xray_amplitude(self)
- set_observation_type_xray_intensity(self)
- show_array(self, f=None, prefix='', deg=None)
- Listing of Miller indices and data
- show_r_free_flags_info(self, n_bins=10, binner_range='used', out=None, prefix='')
- show_summary(self, f=None, prefix='')
- sigma_filter(self, cutoff_factor, negate=False)
- sigmas(self)
- sigmas_are_sensible(self, critical_ratio=0.75, epsilon=9.9999999999999995e-07)
- size(self)
- sort_permutation(self, by_value='resolution', reverse=False)
- statistical_mean(self, use_binning=0)
- wilson_plot(self, use_binning=False)
- <data^2>
- wilson_ratio(self, use_binning=False)
- (<F>)^2/<F^2> (0.785 for untwinned, 0.885 for twinned data)
Methods inherited from set:
- all_selection(self)
- anomalous_flag(self)
- array(self, data=None, sigmas=None)
- as_non_anomalous_set(self)
- auto_anomalous(self, min_n_bijvoet_pairs=None, min_fraction_bijvoet_pairs=None)
- binner(self)
- centric_flags(self)
- clear_binner(self)
- combine(self, other, scale=True, scale_for_lones=1)
- common_set(self, other, assert_is_similar_symmetry=True)
- common_sets(self, other, assert_is_similar_symmetry=True)
- complete_set(self, d_min_tolerance=9.9999999999999995e-07, d_min=None, d_max=None)
- completeness(self, use_binning=False, d_min_tolerance=9.9999999999999995e-07, return_fail=None, d_max=None)
- crystal_gridding(self, resolution_factor=0.33333333333333331, d_min=None, grid_step=None, symmetry_flags=None, mandatory_factors=None, max_prime=5, assert_shannon_sampling=True)
- crystal_symmetry(self)
- d_max_min(self)
- d_min(self)
- d_spacings(self)
- d_star_cubed(self)
- d_star_sq(self)
- epsilons(self)
- f_obs_minus_xray_structure_f_calc(self, f_obs_factor, xray_structure, structure_factor_algorithm=None, cos_sin_table=False, quality_factor=None, u_base=None, b_base=None, wing_cutoff=None, exp_table_one_over_step_size=None)
- generate_r_free_flags(self, fraction=0.10000000000000001, max_free=2000, lattice_symmetry_max_delta=5.0, use_lattice_symmetry=False)
- generate_r_free_flags_basic(self, fraction=0.10000000000000001, max_free=2000)
- generate_r_free_flags_on_lattice_symmetry(self, fraction=0.10000000000000001, max_free=2000, max_delta=5.0, return_integer_array=False, n_partitions=None)
- indices(self)
- is_unique_set_under_symmetry(self)
- lone_set(self, other, assert_is_similar_symmetry=True)
- lone_sets(self, other, assert_is_similar_symmetry=True)
- match_bijvoet_mates(self)
- match_indices(self, other, assert_is_similar_symmetry=True)
- min_max_d_star_sq(self)
- multiplicities(self)
- n_bijvoet_pairs(self)
- random_phases_compatible_with_phase_restrictions(self, deg=False)
- reflection_intensity_symmetry(self)
- remove_systematic_absences(self, negate=False)
- resolution_filter(self, d_max=0, d_min=0, negate=0)
- resolution_filter_selection(self, d_max=0, d_min=0)
- resolution_range(self)
- select_acentric(self)
- select_centric(self)
- setup_binner(self, d_max=0, d_min=0, auto_binning=False, reflections_per_bin=0, n_bins=0)
- setup_binner_counting_sorted(self, d_max=0, d_min=0, reflections_per_bin=None, d_tolerance=1e-10)
- setup_binner_d_star_sq_step(self, auto_binning=True, d_max=None, d_min=None, d_star_sq_step=None)
- show_comprehensive_summary(self, f=None, prefix='')
- Comprehensive Miller set or array summary
- sin_theta_over_lambda_sq(self)
- sort(self, by_value='resolution', reverse=False)
- structure_factors_from_map(self, map, in_place_fft=False)
- structure_factors_from_scatterers(self, xray_structure, algorithm=None, cos_sin_table=False, grid_resolution_factor=0.33333333333333331, quality_factor=None, u_base=None, b_base=None, wing_cutoff=None, exp_table_one_over_step_size=None)
- sys_absent_flags(self, integral_only=False)
- two_theta(self, wavelength, deg=False)
- unique_under_symmetry(self)
- unique_under_symmetry_selection(self)
- use_binner_of(self, other)
- use_binning(self, binning)
- use_binning_of(self, other)
Methods inherited from cctbx.crystal.symmetry:
- 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_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)
- 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)
- primitive_setting(self)
- 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 cctbx.crystal.symmetry:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
|
class array_info(__builtin__.object) |
| | |
Methods defined here:
- __init__(self, source=None, source_type=None, history=None, labels=None, merged=False, systematic_absences_eliminated=False, crystal_symmetry_from_file=None)
- __str__(self)
- as_string_part_2(self)
- customized_copy(self, source=<class libtbx.utils.Keep at 0x8d05f0>, source_type=<class libtbx.utils.Keep at 0x8d05f0>, history=<class libtbx.utils.Keep at 0x8d05f0>, labels=<class libtbx.utils.Keep at 0x8d05f0>, merged=<class libtbx.utils.Keep at 0x8d05f0>, systematic_absences_eliminated=<class libtbx.utils.Keep at 0x8d05f0>, crystal_symmetry_from_file=<class libtbx.utils.Keep at 0x8d05f0>)
- label_string(self)
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
|
class binned_data(__builtin__.object) |
| | |
Methods defined here:
- __init__(self, binner, data, data_fmt=None)
- show(self, data_fmt=None, show_bin_number=True, show_d_range=True, show_counts=True, show_unused=True, f=None, prefix='')
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
|
class binner(cctbx_miller_ext.binner) |
| | |
- Method resolution order:
- binner
- cctbx_miller_ext.binner
- cctbx_miller_ext.binning
- Boost.Python.instance
- __builtin__.object
Methods defined here:
- __getinitargs__(self)
- __init__(self, binning, miller_set)
- bin_legend(self, i_bin, show_bin_number=True, show_d_range=True, show_counts=True)
- counts_complete(self, include_centric=True, include_acentric=True, d_min_tolerance=9.9999999999999995e-07)
- counts_given(self)
- n_bin_d_too_large(self)
- n_bin_d_too_large_or_small(self)
- n_bin_d_too_small(self)
- show_data(self, data, data_fmt=None, show_bin_number=True, show_d_range=True, show_counts=True, show_unused=True, f=None, prefix='')
- show_summary(self, show_bin_number=True, show_d_range=True, show_counts=True, f=None, prefix='')
Methods inherited from cctbx_miller_ext.binner:
- __reduce__ = (...)
- array_indices(...)
- array_indices( (binner)arg1, (int)arg2) -> size_t :
C++ signature :
scitbx::af::shared<unsigned long> array_indices(cctbx::miller::binner {lvalue},unsigned long)
- bin_centers(...)
- bin_centers( (binner)arg1, (float)arg2) -> double :
C++ signature :
scitbx::af::shared<double> bin_centers(cctbx::miller::binner {lvalue},double)
- bin_indices(...)
- bin_indices( (binner)arg1) -> size_t :
C++ signature :
scitbx::af::shared<unsigned long> bin_indices(cctbx::miller::binner {lvalue})
- count(...)
- count( (binner)arg1, (int)arg2) -> int :
C++ signature :
unsigned long count(cctbx::miller::binner {lvalue},unsigned long)
- counts(...)
- counts( (binner)arg1) -> size_t :
C++ signature :
scitbx::af::shared<unsigned long> counts(cctbx::miller::binner {lvalue})
- interpolate(...)
- interpolate( (binner)arg1, (object)arg2, (float)arg3) -> double :
C++ signature :
scitbx::af::shared<double> interpolate(cctbx::miller::binner {lvalue},scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,double)
- miller_indices(...)
- miller_indices( (binner)arg1) -> miller_index :
C++ signature :
scitbx::af::shared<cctbx::miller::index<int> > miller_indices(cctbx::miller::binner {lvalue})
- selection(...)
- selection( (binner)arg1, (int)arg2) -> bool :
C++ signature :
scitbx::af::shared<bool> selection(cctbx::miller::binner {lvalue},unsigned long)
Data and other attributes inherited from cctbx_miller_ext.binner:
- __safe_for_unpickling__ = True
Methods inherited from cctbx_miller_ext.binning:
- bin_d_min(...)
- bin_d_min( (binning)arg1, (int)arg2) -> float :
C++ signature :
double bin_d_min(cctbx::miller::binning {lvalue},unsigned long)
- bin_d_range(...)
- bin_d_range( (binning)arg1, (int)arg2) -> tuple :
C++ signature :
scitbx::af::tiny<double, 2ul> bin_d_range(cctbx::miller::binning {lvalue},unsigned long)
- d_max(...)
- d_max( (binning)arg1) -> float :
C++ signature :
double d_max(cctbx::miller::binning {lvalue})
- d_min(...)
- d_min( (binning)arg1) -> float :
C++ signature :
double d_min(cctbx::miller::binning {lvalue})
- get_i_bin(...)
- get_i_bin( (binning)arg1, (float)arg2) -> int :
C++ signature :
unsigned long get_i_bin(cctbx::miller::binning {lvalue},double)
get_i_bin( (binning)arg1, (object)arg2) -> int :
C++ signature :
unsigned long get_i_bin(cctbx::miller::binning {lvalue},cctbx::miller::index<int>)
- i_bin_d_too_large(...)
- i_bin_d_too_large( (binning)arg1) -> int :
C++ signature :
unsigned long i_bin_d_too_large(cctbx::miller::binning {lvalue})
- i_bin_d_too_small(...)
- i_bin_d_too_small( (binning)arg1) -> int :
C++ signature :
unsigned long i_bin_d_too_small(cctbx::miller::binning {lvalue})
- limits(...)
- limits( (binning)arg1) -> double :
C++ signature :
scitbx::af::shared<double> limits(cctbx::miller::binning {lvalue})
- n_bins_all(...)
- n_bins_all( (binning)arg1) -> int :
C++ signature :
unsigned long n_bins_all(cctbx::miller::binning {lvalue})
- n_bins_used(...)
- n_bins_used( (binning)arg1) -> int :
C++ signature :
unsigned long n_bins_used(cctbx::miller::binning {lvalue})
- range_all(...)
- range_all( (binning)arg1) -> object :
C++ signature :
boost::python::api::object range_all(cctbx::miller::binning)
- range_used(...)
- range_used( (binning)arg1) -> object :
C++ signature :
boost::python::api::object range_used(cctbx::miller::binning)
- unit_cell(...)
- unit_cell( (binning)arg1) -> unit_cell :
C++ signature :
cctbx::uctbx::unit_cell unit_cell(cctbx::miller::binning {lvalue})
Data descriptors inherited from Boost.Python.instance:
- __dict__
- __weakref__
Data and other attributes inherited from Boost.Python.instance:
- __new__ = <built-in method __new__ of Boost.Python.class object at 0x2aaaac5444a0>
- T.__new__(S, ...) -> a new object with type S, a subtype of T
|
class fft_map(cctbx.maptbx.crystal_gridding) |
| | |
- Method resolution order:
- fft_map
- cctbx.maptbx.crystal_gridding
- __builtin__.object
Methods defined here:
- __init__(self, crystal_gridding, fourier_coefficients, f_000=None)
- anomalous_flag(self)
- apply_sigma_scaling(self)
- apply_volume_scaling(self)
- as_xplor_map = cctbx_miller_fft_map_as_xplor_map(self, file_name, title_lines=['cctbx.miller.fft_map'], gridding_first=None, gridding_last=None, average=None, standard_deviation=None)
- complex_map(self)
- peak_search(self, parameters=None, verify_symmetry=True)
- real_map(self)
- real_map_unpadded(self)
- statistics(self)
Methods inherited from cctbx.maptbx.crystal_gridding:
- change_space_group(self, space_group_info)
- crystal_symmetry(self)
- d_min(self)
- mandatory_factors(self)
- max_prime(self)
- n_grid_points(self)
- n_real(self)
- resolution_factor(self)
- space_group(self)
- space_group_info(self)
- symmetry_flags(self)
- tags(self)
- unit_cell(self)
Data descriptors inherited from cctbx.maptbx.crystal_gridding:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
|
class set(cctbx.crystal.symmetry) |
| | |
- Method resolution order:
- set
- cctbx.crystal.symmetry
- __builtin__.object
Methods defined here:
- __getitem__(self, slice_object)
- __init__(self, crystal_symmetry, indices, anomalous_flag=None)
- all_selection(self)
- anomalous_flag(self)
- array(self, data=None, sigmas=None)
- as_non_anomalous_set(self)
- auto_anomalous(self, min_n_bijvoet_pairs=None, min_fraction_bijvoet_pairs=None)
- binner(self)
- centric_flags(self)
- change_basis(self, cb_op)
- clear_binner(self)
- combine(self, other, scale=True, scale_for_lones=1)
- common_set(self, other, assert_is_similar_symmetry=True)
- common_sets(self, other, assert_is_similar_symmetry=True)
- complete_set(self, d_min_tolerance=9.9999999999999995e-07, d_min=None, d_max=None)
- completeness(self, use_binning=False, d_min_tolerance=9.9999999999999995e-07, return_fail=None, d_max=None)
- concatenate(self, other)
- copy(self)
- crystal_gridding(self, resolution_factor=0.33333333333333331, d_min=None, grid_step=None, symmetry_flags=None, mandatory_factors=None, max_prime=5, assert_shannon_sampling=True)
- crystal_symmetry(self)
- customized_copy(self, crystal_symmetry=<class libtbx.utils.Keep at 0x8d05f0>, indices=<class libtbx.utils.Keep at 0x8d05f0>, anomalous_flag=<class libtbx.utils.Keep at 0x8d05f0>, unit_cell=<class libtbx.utils.Keep at 0x8d05f0>, space_group_info=<class libtbx.utils.Keep at 0x8d05f0>)
- d_max_min(self)
- d_min(self)
- d_spacings(self)
- d_star_cubed(self)
- d_star_sq(self)
- deep_copy(self)
- epsilons(self)
- expand_to_p1(self)
- f_obs_minus_xray_structure_f_calc(self, f_obs_factor, xray_structure, structure_factor_algorithm=None, cos_sin_table=False, quality_factor=None, u_base=None, b_base=None, wing_cutoff=None, exp_table_one_over_step_size=None)
- generate_r_free_flags(self, fraction=0.10000000000000001, max_free=2000, lattice_symmetry_max_delta=5.0, use_lattice_symmetry=False)
- generate_r_free_flags_basic(self, fraction=0.10000000000000001, max_free=2000)
- generate_r_free_flags_on_lattice_symmetry(self, fraction=0.10000000000000001, max_free=2000, max_delta=5.0, return_integer_array=False, n_partitions=None)
- indices(self)
- is_unique_set_under_symmetry(self)
- lone_set(self, other, assert_is_similar_symmetry=True)
- lone_sets(self, other, assert_is_similar_symmetry=True)
- map_to_asu(self)
- match_bijvoet_mates(self)
- match_indices(self, other, assert_is_similar_symmetry=True)
- min_max_d_star_sq(self)
- multiplicities(self)
- n_bijvoet_pairs(self)
- patterson_symmetry(self)
- random_phases_compatible_with_phase_restrictions(self, deg=False)
- reflection_intensity_symmetry(self)
- remove_systematic_absences(self, negate=False)
- resolution_filter(self, d_max=0, d_min=0, negate=0)
- resolution_filter_selection(self, d_max=0, d_min=0)
- resolution_range(self)
- select(self, selection, negate=False, anomalous_flag=None)
- select_acentric(self)
- select_centric(self)
- setup_binner(self, d_max=0, d_min=0, auto_binning=False, reflections_per_bin=0, n_bins=0)
- setup_binner_counting_sorted(self, d_max=0, d_min=0, reflections_per_bin=None, d_tolerance=1e-10)
- setup_binner_d_star_sq_step(self, auto_binning=True, d_max=None, d_min=None, d_star_sq_step=None)
- show_comprehensive_summary(self, f=None, prefix='')
- Comprehensive Miller set or array summary
- show_summary(self, f=None, prefix='')
- Minimal Miller set summary
- sin_theta_over_lambda_sq(self)
- size(self)
- sort(self, by_value='resolution', reverse=False)
- sort_permutation(self, by_value='resolution', reverse=False)
- structure_factors_from_map(self, map, in_place_fft=False)
- structure_factors_from_scatterers(self, xray_structure, algorithm=None, cos_sin_table=False, grid_resolution_factor=0.33333333333333331, quality_factor=None, u_base=None, b_base=None, wing_cutoff=None, exp_table_one_over_step_size=None)
- sys_absent_flags(self, integral_only=False)
- two_theta(self, wavelength, deg=False)
- unique_under_symmetry(self)
- unique_under_symmetry_selection(self)
- use_binner_of(self, other)
- use_binning(self, binning)
- use_binning_of(self, other)
Methods inherited from cctbx.crystal.symmetry:
- 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_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)
- 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)
- primitive_setting(self)
- 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 cctbx.crystal.symmetry:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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