mmtbx.utils
index
/net/chevy/raid1/nat/src/cctbx_project/mmtbx/utils/__init__.py

 
Package Contents
       
fab_elbow_angle
ncs_utils
rotatable_bonds
tst_ncs_utils
tst_switch_rotamers

 
Classes
       
__builtin__.object
detect_hydrogen_nomenclature_problem
determine_data_and_flags
experimental_data_target_and_gradients
extract_box_around_model_and_map
f_000
fmodel_from_xray_structure
guess_observation_type
pdb_file
process_command_line_args
process_pdb_file_srv
set_map_to_value
shift_origin
states
xray_structures_from_processed_pdb_file

 
class detect_hydrogen_nomenclature_problem(__builtin__.object)
    This allows us to avoid the following problems:
1) a bug in automatic linking which deletes the monomer library definition
   for HD22 for an N-linked Asn, even though it may not actually be replaced
   by a sugar link.
2) general issues with hydrogen nomenclature
 
  Methods defined here:
__init__(self, pdb_file, cif_files=())

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

 
class determine_data_and_flags(__builtin__.object)
     Methods defined here:
__init__(self, reflection_file_server, parameters=None, data_parameter_scope='', flags_parameter_scope='', data_description=None, working_point_group=None, symmetry_safety_check=None, remark_r_free_flags_md5_hexdigest=None, extract_r_free_flags=True, keep_going=False, log=None, prefer_anomalous=None, force_non_anomalous=False)
data_as_f_obs(self, f_obs)
extract_data(self)
extract_flags(self, data, data_description='R-free flags')
flags_as_r_free_flags(self, f_obs, r_free_flags, missing_show_max_lines=10)
get_r_free_flags(self)
verify_r_free_flags_md5_hexdigest(self, ignore_pdb_hexdigest, current, records)

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

 
class experimental_data_target_and_gradients(__builtin__.object)
     Methods defined here:
__init__(self, fmodel, alpha_beta=None)
grad_occ(self)
grad_sites_cart(self)
group_occupancy_grads(self, pdb_hierarchy=None, residues_per_window=None, selections=None)
show(self, log=None)
target(self)
update_xray_structure(self, xray_structure, alpha_beta=None)

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

 
class extract_box_around_model_and_map(__builtin__.object)
     Methods defined here:
__init__(self, xray_structure, map_data, box_cushion, pdb_hierarchy=None, selection_radius=None, selection_string=None, selection=None, map_data_2=None, assert_pdb_hierarchy_and_xray_structure_equal=True)
box_map_coefficients(self, d_min, resolution_factor)
box_map_coefficients_as_fft_map(self, d_min, resolution_factor)
map_coefficients(self, d_min, resolution_factor, file_name='box.mtz')
write_ccp4_map(self, file_name='box.ccp4')
write_pdb_file(self, file_name)
write_xplor_map(self, file_name='box.xplor')

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

 
class f_000(__builtin__.object)
     Methods defined here:
__init__(self, xray_structure=None, unit_cell_volume=None, solvent_fraction=None, mean_solvent_density=0.35)

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

 
class fmodel_from_xray_structure(__builtin__.object)
     Methods defined here:
Sorry_high_resolution_is_not_defined(self)
__init__(self, xray_structure, f_obs=None, params=None, r_free_flags_fraction=None, add_sigmas=False, twin_law=None, twin_fraction=None, target='ml', out=None)
write_to_file(self, file_name)

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

 
class guess_observation_type(__builtin__.object)
     Methods defined here:
__init__(self, f_obs, label, xray_structure, r_free_flags=None)
find_best(self, results)
get_r_factor(self, f_obs, f_calc, scattering_table, xray_structure, twin_switch_tolerance, skip_twin_detection)
mtz_object(self)

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

Data and other attributes defined here:
data_size = 500

 
class pdb_file(__builtin__.object)
     Methods defined here:
__init__(self, pdb_file_names, crystal_symmetry=None, cif_objects=[], log=None, ignore_unknown_nonbonded_energy_types=False, use_neutron_distances=False)
set_ppf(self, stop_if_duplicate_labels=True, log=None)

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

 
class process_command_line_args(__builtin__.object)
     Methods defined here:
__init__(self, args, cmd_cs=None, master_params=None, log=None, home_scope=None, suppress_symmetry_related_errors=False)
get_reflection_file_server(self)

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

 
class process_pdb_file_srv(__builtin__.object)
     Methods defined here:
__init__(self, crystal_symmetry=None, pdb_parameters=None, pdb_interpretation_params=None, stop_for_unknowns=None, log=None, cif_objects=None, cif_parameters=None, mon_lib_srv=None, ener_lib=None, use_neutron_distances=False, for_dihedral_reference=False)
process_pdb_files(self, pdb_file_names=None, raw_records=None, stop_if_duplicate_labels=True, for_dihedral_reference=False, allow_missing_symmetry=False)

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

 
class set_map_to_value(__builtin__.object)
     Methods defined here:
__init__(self, map_data, xray_structure, atom_radius, value)
write_xplor_map(self, file_name)

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

 
class shift_origin(__builtin__.object)
     Methods defined here:
__init__(self, map_data, pdb_hierarchy, crystal_symmetry)
show_shifted(self)

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

 
class states(__builtin__.object)
     Methods defined here:
__init__(self, xray_structure, pdb_hierarchy)
add(self, sites_cart)
write(self, file_name)

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

 
class xray_structures_from_processed_pdb_file(__builtin__.object)
     Methods defined here:
__init__(self, processed_pdb_file, scattering_table, d_min, log=None)

Data descriptors defined here:
__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
apply_twin_fraction(...)
apply_twin_fraction( (object)amplitude_data_part_one, (object)amplitude_data_part_two, (float)twin_fraction) -> double :
 
    C++ signature :
        scitbx::af::shared<double> apply_twin_fraction(scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,double)
assert_model_is_consistent(model)
assert_water_is_consistent(model)
assert_xray_structures_equal(x1, x2, selection=None, sites=True, adp=True, occupancies=True, elements=True, scattering_types=True, eps=1e-06)
assign_chain_ids(pdb_hierarchy, seg_dict)
atom_selection(all_chain_proxies, string, allow_empty_selection=False)
check_for_duplicate_chain_ids(pdb_hierarchy)
combine_hd_exchangable(hierarchy)
compare_hierarchy(hierarchy, scatterers, cell)
correct_drifted_waters(...)
correct_drifted_waters( (vec3_double)sites_frac_all, (vec3_double)sites_frac_peaks, (bool)water_selection, (unit_cell)unit_cell) -> None :
 
    C++ signature :
        void correct_drifted_waters(scitbx::af::ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<scitbx::vec3<double>, scitbx::af::trivial_accessor>,scitbx::af::const_ref<bool, scitbx::af::trivial_accessor>,cctbx::uctbx::unit_cell)
create_twin_mate(...)
create_twin_mate( (miller_index)miller_indices, (object)twin_law_matrix) -> miller_index :
 
    C++ signature :
        scitbx::af::shared<cctbx::miller::index<int> > create_twin_mate(scitbx::af::const_ref<cctbx::miller::index<int>, scitbx::af::trivial_accessor>,scitbx::mat3<double>)
d_min_from_map(map_data, unit_cell, resolution_factor=0.25)
data_and_flags_master_params(master_scope_name=None)
determine_experimental_phases(reflection_file_server, parameters, log, parameter_scope, working_point_group, symmetry_safety_check, ignore_all_zeros=True)
equivalent_sigma_from_cumulative_histogram_match(map_1, map_2, sigma_1, tail_cutoff=3, step=1, verbose=True)
explain_how_to_generate_array_of_r_free_flags(log, flags_parameter_scope)
extract_tls_and_u_total_from_pdb(f_obs, r_free_flags, xray_structure, tls_selections, tls_groups)
find_bare_chains_with_segids(pdb_hierarchy)
find_overlapping_selections(selections, selection_strings)
fmodel_manager(f_obs, xray_structure=None, r_free_flags=None, f_mask=None, f_calc=None, ignore_r_free_flags=False, target_name='ml', k_mask=None, k_anisotropic=None, hl_coeff=None, use_f_model_scaled=False, twin_law=None, detwin_mode=None, detwin_map_types=None, alpha_beta_params=None, sf_and_grads_accuracy_params=<libtbx.phil.scope_extract object>, mask_params=None, max_number_of_resolution_bins=None, n_resolution_bins_output=None)
fmodel_simple(f_obs, update_f_part1_for, xray_structures, scattering_table, r_free_flags=None, target_name='ml', bulk_solvent_and_scaling=True, bss_params=None, mask_params=None, twin_laws=None, skip_twin_detection=False, twin_switch_tolerance=2.0, outliers_rejection=True, bulk_solvent_correction=True, anisotropic_scaling=True, log=None)
force_unique_chain_ids(pdb_hierarchy)
generate_two_character_ids()
get_atom_selection(pdb_file_name, selection_string, iselection=False)
get_atom_selections(all_chain_proxies, xray_structure, selection_strings=None, iselection=True, one_group_per_residue=False, allow_empty_selection=False, hydrogens_only=False, one_selection_array=False, parameter_name=None)
miller_array_symmetry_safety_check(miller_array, data_description, working_point_group, symmetry_safety_check, log)
model_simple(pdb_file_names, log=None, normalization=True, cif_objects=[], crystal_symmetry=None, plain_pairs_radius=5, refinement_flags=None, scattering_table=None, d_min=None)
optimize_h(fmodel, mon_lib_srv, pdb_hierarchy=None, model=None, log=None, verbose=True)
print_header(line, out=None)
print_programs_start_header(log, text)
remove_selections(selection, other, size)
rms_b_iso_or_b_equiv_bonded(restraints_manager, xray_structure, ias_selection=None)
seg_id_to_chain_id(pdb_hierarchy)
select_water_by_distance(...)
select_water_by_distance( (vec3_double)sites_frac_all, (std_string)element_symbols_all, (size_t)water_selection_o, (float)dist_max, (float)dist_min_mac, (float)dist_min_sol, (unit_cell)unit_cell) -> size_t :
 
    C++ signature :
        scitbx::af::shared<unsigned long> select_water_by_distance(scitbx::af::shared<scitbx::vec3<double> >,scitbx::af::shared<std::string>,scitbx::af::shared<unsigned long>,double,double,double,cctbx::uctbx::unit_cell)
set_log(args, out=<open file '<stdout>', mode 'w'>, replace_stderr=True)
setup_scattering_dictionaries(scattering_table, xray_structure, d_min, log=None, all_chain_proxies=None)
structure_factors_from_map(map_data, unit_cell_lengths, n_real, crystal_symmetry, resolution_factor=0.25)
switch_rotamers(pdb_hierarchy, mode, selection=None)
write_pdb_file(xray_structure, pdb_hierarchy, pdb_atoms=None, write_cryst1_record=True, selection=None, atoms_reset_serial=True, out=None, return_pdb_string=False)
xtriage(f_obs)

 
Data
        cif_params = <libtbx.phil.scope object>
data_and_flags_str = ' file_name = None\n .type=path\n .short_c...short_caption = Number of resolution shells\n\n }\n'
data_and_flags_str_part1 = ' file_name = None\n .type=path\n .short_cap...(Iobs) rejection criterion\n .expert_level = 0\n'
data_and_flags_str_part2 = ' file_name = None\n .type=path\n .short_cap...n refinement (work and test)\n .expert_level=0\n'
division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
experimental_phases_params = <libtbx.phil.scope object>
experimental_phases_params_str = ' file_name=None\n .type=path\n .short_capti...\n .style = renderer:draw_hl_label_widget bold\n'
map_coefficents_params_str = ' file_name=None\n .type=path\n .short_capti...oefficients file\n labels=None\n .type=strings\n'
neutron_data_str = 'neutron_data\n .help=Scope of neutron data and n...t_caption = Number of resolution shells\n\n }\n\n}\n\n'
pdb_params = <libtbx.phil.scope object>
xray_data_str = 'xray_data\n .help=Scope of X-ray data and free-R...rt_caption = Number of resolution shells\n\n }\n\n}\n'