mmtbx.f_model
index
/net/chevy/raid1/nat/src/cctbx_project/mmtbx/f_model.py

 
Modules
       
mmtbx.scaling.absolute_scaling
cctbx.adptbx
boost
mmtbx.bulk_solvent.bulk_solvent_and_scaling
mmtbx.bulk_solvent
cctbx
mmtbx_f_model_ext
cctbx.array_family.flex
iotbx
libtbx
mmtbx.map_tools
cctbx.maptbx
mmtbx.masks
math
mmtbx.max_lik
mmtbx.max_lik.maxlik
cctbx.miller
mmtbx
os
mmtbx.scaling.outlier_rejection
scitbx
cctbx.sgtbx
sys
cctbx.xray

 
Classes
       
__builtin__.object
arrays
manager_kbu
manager_mixin
manager
mask_result
mmtbx.f_model_info.info(__builtin__.object)
info
mmtbx.f_model_info.resolution_bin(__builtin__.object)
resolution_bin

 
class arrays(__builtin__.object)
     Methods defined here:
__init__(self, core, f_obs, r_free_flags, hl_coeffs=None, core_twin=None, twin_fraction=None)
update_core(self, core=None, core_twin=None, twin_fraction=None)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class info(mmtbx.f_model_info.info)
    # XXX backwards compatibility 2011-02-08
 
 
Method resolution order:
info
mmtbx.f_model_info.info
__builtin__.object

Methods inherited from mmtbx.f_model_info.info:
__init__(self, fmodel, free_reflections_per_bin=140, max_number_of_bins=30, n_bins=None)
as_cif_block(self, cif_block=None)
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, n_bins=None)

Data descriptors inherited from mmtbx.f_model_info.info:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class manager(manager_mixin)
    
Method resolution order:
manager
manager_mixin
__builtin__.object

Methods defined here:
__getstate__(self)
__init__(self, f_obs=None, r_free_flags=None, f_mask=None, f_part1=None, f_part2=None, f_calc=None, abcd=None, sf_and_grads_accuracy_params=None, target_name='ml', alpha_beta_params=None, xray_structure=None, mask_params=None, use_f_model_scaled=False, mask_manager=None, twin_law=None, twin_fraction=0, max_number_of_bins=30, bin_selections=None, k_mask=None, k_isotropic=None, k_anisotropic=None, k_anisotropic_twin=None, k_sol=None, b_sol=None, b_cart=None, _target_memory=None, n_resolution_bins_output=None, f_part_1_updated_for_purpose=None)
__setstate__(self, state)
alpha_beta(self, f_obs=None, f_model=None)
alpha_beta_t(self)
alpha_beta_w(self, only_if_required_by_target=False)
alpha_beta_with_restrained_n_calc(self)
anomalous_map(self, **kwds)
apply_scale_k1_to_f_obs(self, threshold=10)
check_f_mask_all_zero(self)
classical_dm_map_coefficients(self)
combine_phases(self, n_steps=360, map_calculation_helper=None)
combined_hl_coefficients(self, map_calculation_helper)
compute_f_calc(self, miller_array=None, twin=False, xray_structure=None)
compute_f_part1(self, params, log=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, update_f_part1)
explain_members(self, out=None, prefix='', suffix='')
export(self, out=None, format='mtz')
export_f_obs_flags_as_mtz(self, file_name, merge_anomalous=False, include_hendrickson_lattman=True)
Dump all input data to an MTZ file using standard column labels.  This may
be useful when running modules or programs that require an MTZ file as
input (rather than taking f_model.manager or the Miller arrays directly).
f_bulk(self)
f_bulk_t(self)
f_bulk_w(self)
f_calc(self)
f_calc_t(self)
f_calc_twin(self)
f_calc_w(self)
f_masks(self)
f_masks_twin(self)
f_model(self)
f_model_free(self)
f_model_no_scales(self)
f_model_phases_as_hl_coefficients(self, map_calculation_helper, k_blur=None, b_blur=None)
f_model_phases_as_hl_coeffs_array(self)
f_model_scaled_with_k1(self)
f_model_scaled_with_k1_composite_work_free(self)
f_model_scaled_with_k1_t(self)
f_model_scaled_with_k1_w(self)
f_model_work(self)
f_obs(self)
f_obs_free(self)
f_obs_vs_f_model(self, log=None)
f_obs_work(self)
f_part1(self)
f_part1_twin(self)
f_part2(self)
f_part2_twin(self)
f_star_w_star(self)
f_star_w_star_obj(self)
fft_vs_direct(self, reflections_per_bin=250, n_bins=0, out=None)
figures_of_merit(self)
figures_of_merit_work(self)
filter_by_delta_fofc(self)
filter_by_fom(self, fom_threshold=0.2)
fmodel_kbu(self)
fmodel_kbu_twin(self)
fofc_map(self, **kwds)
fom(self)
hl_coeffs(self)
info(self, free_reflections_per_bin=None, max_number_of_bins=None, n_bins=None)
is_twin_fmodel_manager(self)
k_anisotropic(self)
k_anisotropic_test(self)
k_anisotropic_work(self)
k_isotropic(self)
k_isotropic_work(self)
k_masks(self)
k_sol_b_sol_from_k_mask(self)
map_calculation_helper(self, free_reflections_per_bin=100, interpolation=True)
map_coefficients(self, **kwds)
model_error_ml(self)
n_obs_n_calc(self, update_nobs_ncalc=True)
optimize_mask(self, params=None, thorough=False, out=None, nproc=1)
outlier_selection(self, show=False, log=None, use_model=True)
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_free_flags(self)
r_overall_low_high(self, d=6.0)
r_work(self, d_min=None, d_max=None, selection=None)
r_work_low(self, size=500, reverse=False)
remove_outliers(self, show=False, log=None, use_model=True)
remove_unreliable_atoms_and_update(self, min_map_value=0.5, min_cc=0.7)
Identify and remove 'unreliably' pleaced atoms, and create a new fmodel
with updated xray_structure.
resolution_filter(self, d_max=0, d_min=0)
resolve_dm_map_coefficients(self)
scale_k1(self, selection=None)
scale_k1_t(self, selection=None)
scale_k1_w(self, selection=None)
scale_k1_w_for_twin_targets(self)
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_wrapper(self)
select(self, selection=None, in_place=False, deep_copy_xray_structure=True)
set_target_name(self, target_name)
show(self, log=None, suffix=None, show_header=True, show_approx=True)
show_mask_optimization_statistics(self, prefix='', out=None)
sigmaa(self, f_obs=None, f_model=None)
target_attributes(self)
target_functor(self, alpha_beta=None)
top_largest_f_obs_f_model_differences(self, threshold_percent, n_slots=10000)
try_mask_params(self, args)
# XXX parallel routine
two_fofc_map(self, **kwds)
update(self, f_calc=None, f_obs=None, f_mask=None, r_free_flags=None, f_part1=None, k_mask=None, k_anisotropic=None, k_anisotropic_twin=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_all_scales(self, update_f_part1_for, refine_threshold=True, apply_back_trace=False, params=None, nproc=None, cycles=None, fast=True, optimize_mask=False, refine_hd_scattering=True, bulk_solvent_and_scaling=True, remove_outliers=True, show=False, map_neg_cutoff=None, verbose=None, log=None)
update_core(self, f_calc=None, f_mask=None, f_calc_twin=None, f_mask_twin=None, f_part1=None, f_part2=None, f_part1_twin=None, f_part2_twin=None, k_anisotropic=None, k_anisotropic_twin=None, k_isotropic=None, k_mask=None)
update_f_hydrogens(self, log=None)
update_f_part1(self, purpose, map_neg_cutoff=None, refinement_neg_cutoff=-2.5, refine_threshold=True)
update_f_part1_all(self, purpose, map_neg_cutoff=None, refinement_neg_cutoff=-2.5, refine_threshold=True)
update_solvent_and_scale(self, params=None, out=None, verbose=None, optimize_mask=False, nproc=1, fast=True, apply_back_trace=False)
update_twin_fraction(self)
update_xray_structure(self, xray_structure=None, update_f_calc=False, update_f_mask=False, force_update_f_mask=False)
wilson_b(self, force_update=False)

Data descriptors defined here:
structure_factor_gradients_w
target_name

Data and other attributes defined here:
n_calc = None
n_obs = None
set_scale_switch = 0
set_sigmaa = None

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)

 
class manager_kbu(__builtin__.object)
     Methods defined here:
__init__(self, f_obs, f_calc, f_masks, ss, f_part1=None, f_part2=None, k_sols=[0.0], b_sol=0.0, u_star=[0, 0, 0, 0, 0, 0])
b_cart(self)
b_sol(self)
check_f_mask_all_zero(self)
core_data_work(self)
deep_copy(self)
k_anisotropic(self)
k_isotropic(self)
k_mask(self)
k_masks(self)
k_sol(self, i)
k_sols(self)
r_factor(self)
select(self, selection)
u_star(self)
update(self, k_sols=None, b_sol=None, b_cart=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)

 
class manager_mixin(__builtin__.object)
     Methods defined here:
one_time_gradients_wrt_atomic_parameters(self, **keyword_args)
target_t(self)
target_w(self)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class mask_result(__builtin__.object)
     Methods defined here:
__init__(self, r_solv, r_shrink, r_work, r_free, r_work_low)
show(self, out)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
class resolution_bin(mmtbx.f_model_info.resolution_bin)
    
Method resolution order:
resolution_bin
mmtbx.f_model_info.resolution_bin
__builtin__.object

Methods inherited from mmtbx.f_model_info.resolution_bin:
__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, cc_work=None, cc_free=None)

Data descriptors inherited from mmtbx.f_model_info.resolution_bin:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)

 
Functions
       
StringIO(...)
StringIO([s]) -- Return a StringIO-like stream for reading or writing
kb_range(x_max, x_min, step)
n_as_s(format, value)
show_histogram(data, n_slots, log)
show_times(out=None)

 
Data
        Auto = <libtbx.AutoType object>
alpha_beta_master_params = <libtbx.phil.scope object>
division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
sf_and_grads_accuracy_master_params = <libtbx.phil.scope object>
time_alpha_beta = 0.0
time_bulk_solvent_and_scale = 0.0
time_f_calc = 0.0
time_fmodel_core_data = 0.0
time_foms = 0.0
time_gradients_wrt_atomic_parameters = 0.0
time_mask = 0.0
time_phase_errors = 0.0
time_r_factors = 0.0
time_show = 0.0
time_target = 0.0