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- __builtin__.object
-
- core
- info
- manager_mixin
-
- manager
- phaser_sad_target_functor
- resolution_bin
- target_attributes
- target_functor
- target_result_mixin
-
- target_result
class core(__builtin__.object) |
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Methods defined here:
- __getstate__(self)
- __init__(self, f_calc=None, f_mask=None, k_sol=0.0, b_sol=0.0, u_star=[0, 0, 0, 0, 0, 0], ss=None, fmodel=None)
- __setstate__(self, state)
- update(self, f_calc=None, f_mask=None, k_sol=None, b_sol=None, u_star=None)
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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class info(__builtin__.object) |
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Methods defined here:
- __init__(self, fmodel, free_reflections_per_bin=140, max_number_of_bins=30)
- export_bins_table_data(self, title='Statistics by resolution bin')
- # re-arrange binned statistics for phenix GUI (or logfile)
- show_all(self, header='', out=None)
- show_fom_pher_alpha_beta_in_bins(self, out=None)
- show_remark_3(self, out=None)
- show_rfactors_targets_in_bins(self, out=None)
- show_rfactors_targets_scales_overall(self, header=None, out=None)
- show_rwork_rfree_number_completeness(self, prefix='', title=None, out=None)
- show_targets(self, out=None, text='')
- statistics_in_resolution_bins(self, fmodel, free_reflections_per_bin, max_number_of_bins)
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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class manager(manager_mixin) |
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- Method resolution order:
- manager
- manager_mixin
- __builtin__.object
Methods defined here:
- __getstate__(self)
- __init__(self, f_obs=None, r_free_flags=None, b_cart=[0.0, 0.0, 0.0, 0.0, 0.0, 0.0], k_sol=0.0, b_sol=0.0, sf_and_grads_accuracy_params=None, target_name='ml', abcd=None, alpha_beta_params=None, xray_structure=None, f_mask=None, f_calc=None, mask_params=None, trust_xray_structure=False, update_xray_structure=True, use_f_model_scaled=False, mask_manager=None, twin_law=None, twin_fraction=0, max_number_of_bins=30, filled_f_obs_selection=None, _target_memory=None)
- __setstate__(self, state)
- adopt_external_b_iso_adjustments(self, overall_b_iso_shift)
- alpha_beta(self, f_obs=None, f_model=None)
- alpha_beta_t(self)
- alpha_beta_w(self, only_if_required_by_target=False)
- apply_back_b_iso(self)
- b_cart(self)
- b_iso(self)
- b_sol(self)
- combine_phases(self, n_steps=360)
- combined_hl_coefficients(self)
- compute_f_calc(self, miller_array=None)
- core_data_work(self)
- deep_copy(self)
- determine_n_bins(self, free_reflections_per_bin, max_n_bins=None, min_n_bins=1, min_refl_per_bin=100)
- electron_density_map(self, fill_missing_f_obs=False, filled_f_obs_file_name=None, fill_mode=None, reverse_scale=True)
- explain_members(self, out=None, prefix='', suffix='')
- export(self, out=None, format='mtz')
- export_filled_f_obs(self, file_name)
- f_bulk(self)
- f_bulk_t(self)
- f_bulk_w(self)
- f_calc(self)
- f_calc_t(self)
- f_calc_w(self)
- f_mask(self)
- f_mask_t(self)
- f_mask_w(self)
- f_model(self)
- f_model_free(self)
- f_model_free_twin_mate(self)
- f_model_phases_as_hl_coefficients(self)
- f_model_scaled_with_k1(self)
- f_model_scaled_with_k1_t(self)
- f_model_scaled_with_k1_w(self)
- f_model_twin_mate(self)
- f_model_work(self)
- f_model_work_twin_mate(self)
- f_obs_scaled_with_k2(self)
- f_star_w_star(self)
- f_star_w_star_obj(self)
- f_star_w_star_test(self)
- f_star_w_star_work(self)
- fb_cart(self)
- fb_cart_t(self)
- fb_cart_work(self)
- fft_vs_direct(self, reflections_per_bin=250, n_bins=0, out=None)
- figures_of_merit(self)
- figures_of_merit_work(self)
- fill_missing_f_obs(self, fill_mode)
- info(self, free_reflections_per_bin=None, max_number_of_bins=None)
- k_sol(self)
- k_sol_b_sol(self)
- map_calculation_helper(self, free_reflections_per_bin=100, interpolation=True, need_alpha_and_fom=True, reverse_scale=True)
- model_error_ml(self)
- optimize_mask_and_update_solvent_and_scale(self, params=None, out=None, verbose=-1)
- outlier_selection(self, show=False, log=None)
- phase_errors(self)
- phase_errors_test(self)
- phase_errors_work(self)
- r_all(self)
- r_free(self, d_min=None, d_max=None, selection=None)
- r_overall_low_high(self, d=6.0)
- r_work(self, d_min=None, d_max=None, selection=None)
- remove_filled_f_obs(self)
- remove_outliers(self, show=False, log=None)
- resolution_filter(self, d_max=0, d_min=0, update_xray_structure=False)
- scale_k1(self, selection=None)
- scale_k1_t(self, selection=None)
- scale_k1_w(self, selection=None)
- scale_k2(self, selection=None)
- scale_k2_t(self, selection=None)
- scale_k2_w(self, selection=None)
- scale_k3_t(self, selection=None)
- scale_k3_w(self, selection=None)
- scale_ml(self)
- scale_ml_wrapper(self)
- select(self, selection, update_xray_structure=False)
- set_target_name(self, target_name)
- show_mask_optimization_statistics(self, prefix='', out=None)
- show_rwork_in_bins(self, reflections_per_bin, title, log)
- sigmaa(self, f_obs=None, f_model=None)
- target_attributes(self)
- target_functor(self)
- twin_test(self, cut_off=3.5)
- u_star(self)
- update(self, f_calc=None, f_obs=None, f_mask=None, r_free_flags=None, b_cart=None, k_sol=None, b_sol=None, sf_and_grads_accuracy_params=None, target_name=None, abcd=None, alpha_beta_params=None, twin_fraction=None, xray_structure=None, mask_params=None)
- update_core(self, f_calc=None, f_mask=None, f_calc_twin=None, f_mask_twin=None, b_cart=None, u_star=None, k_sol=None, b_sol=None)
- update_r_free_flags(self, r_free_flags)
- update_solvent_and_scale(self, params=None, out=None, verbose=None)
- update_twin_fraction(self)
- update_xray_structure(self, xray_structure=None, update_f_calc=False, update_f_mask=False, force_update_f_mask=False, out=None, k_sol=None, b_sol=None, b_cart=None)
- wilson_b(self, force_update=False)
Data descriptors defined here:
- structure_factor_gradients_w
- target_name
Data and other attributes defined here:
- target_names = {'ls_wexp_k1': <mmtbx.f_model.target_attributes object at 0x25da210>, 'ls_wexp_k2': <mmtbx.f_model.target_attributes object at 0x25da250>, 'ls_wexp_kunit': <mmtbx.f_model.target_attributes object at 0x25da290>, 'ls_wff_k1': <mmtbx.f_model.target_attributes object at 0x25da2d0>, 'ls_wff_k1_fixed': <mmtbx.f_model.target_attributes object at 0x25da390>, 'ls_wff_k1ask3_fixed': <mmtbx.f_model.target_attributes object at 0x25da3d0>, 'ls_wff_k2': <mmtbx.f_model.target_attributes object at 0x25da310>, 'ls_wff_kunit': <mmtbx.f_model.target_attributes object at 0x25da350>, 'ls_wunit_k1': <mmtbx.f_model.target_attributes object at 0x25c7f10>, 'ls_wunit_k1_fixed': <mmtbx.f_model.target_attributes object at 0x25da190>, ...}
Methods inherited from manager_mixin:
- one_time_gradients_wrt_atomic_parameters(self, **keyword_args)
- target_t(self)
- target_w(self)
Data descriptors inherited from manager_mixin:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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class resolution_bin(__builtin__.object) |
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Methods defined here:
- __init__(self, i_bin=None, d_range=None, completeness=None, alpha_work=None, beta_work=None, r_work=None, r_free=None, target_work=None, target_free=None, n_work=None, n_free=None, mean_f_obs=None, fom_work=None, scale_k1_work=None, pher_work=None, pher_free=None)
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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