iotbx.reflection_file_utils
index
/net/chevy/raid1/nat/src/cctbx_project/iotbx/reflection_file_utils.py

 
Modules
       
cctbx.array_family.flex
libtbx
math
cctbx.miller
os
iotbx.reflection_file_reader
sys

 
Classes
       
__builtin__.object
get_r_free_flags_score
get_r_free_flags_scores
label_table
process_raw_data
reflection_file_server

 
class get_r_free_flags_score(__builtin__.object)
     Methods defined here:
__init__(self, test_flag_value, n, n_free, miller_array_info)

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

 
class get_r_free_flags_scores(__builtin__.object)
     Methods defined here:
__init__(self, miller_arrays, test_flag_value)

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

 
class label_table(__builtin__.object)
     Methods defined here:
__init__(self, miller_arrays, err=None)
match_data_label(self, label, command_line_switch, f=None)
scores(self, label=None, labels=None)
select_array(self, label, command_line_switch, f=None)
show_possible_choices(self, f=None, scores=None, minimum_score=None, parameter_name=None)

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

 
class process_raw_data(__builtin__.object)
    Automation wrapper - prepares single-wavelength experimental data (and
optional R-free flags and experimental phases) for any future step in the
structure determination process.  Used in Phenix for ligand pipeline and
automated re-refinement of PDB entries.
 
  Methods defined here:
__init__(self, obs, r_free_flags, test_flag_value, phases=None, d_min=None, d_max=None, r_free_flags_params=None, merge_anomalous=False, log=<open file '<stdout>', mode 'w'>, verbose=True)
data_and_flags(self)
data_labels(self)
flags_are_new(self)
fraction_free(self)
n_obs(self)
phase_labels(self)
r_free_flags_as_boolean_array(self)
r_free_flags_label(self)
write_mtz_file(self, file_name, title=None, wavelength=None, single_dataset=True)

Data descriptors defined here:
f_obs
phases
r_free_flags
test_flag_value

 
class reflection_file_server(__builtin__.object)
     Methods defined here:
__init__(self, crystal_symmetry=None, force_symmetry=None, reflection_files=None, err=None)
get_amplitudes(self, file_name, labels, convert_to_amplitudes_if_necessary, parameter_scope, parameter_name, return_all_valid_arrays=False, minimum_score=1, strict=False)
get_experimental_phases(self, file_name, labels, ignore_all_zeros, parameter_scope, parameter_name='labels', return_all_valid_arrays=False, minimum_score=1)
get_miller_array(self, labels, file_name=None)
get_miller_arrays(self, file_name)
get_phases_deg(self, file_name, labels, convert_to_phases_if_necessary, original_phase_units, parameter_scope, parameter_name, return_all_valid_arrays=False, minimum_score=1)
get_r_free_flags(self, file_name, label, test_flag_value, disable_suitability_test, parameter_scope, return_all_valid_arrays=False, minimum_score=1)
get_xray_data(self, file_name, labels, ignore_all_zeros, parameter_scope, parameter_name='labels', return_all_valid_arrays=False, minimum_score=1, prefer_anomalous=None, prefer_amplitudes=None)

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

 
Functions
       
change_space_group(file_name, space_group_info)
Update the space group in an MTZ file, writing it in place.
cif_status_flags_as_int_r_free_flags(miller_array, test_flag_value)
construct_output_file_name(input_file_names, user_file_name, file_type_label, file_extension, extension_seperator='.')
extract_miller_array_from_file(file_name, label=None, type=None, log=None)
find_labels(search_labels, info_string)
get_amplitude_scores(miller_arrays, strict=False)
get_experimental_phases_scores(miller_arrays, ignore_all_zeros)
get_phase_scores(miller_arrays)
get_xray_data_scores(miller_arrays, ignore_all_zeros, prefer_anomalous=None, prefer_amplitudes=None)
guess_r_free_flag_value(miller_array, test_flag_value=None)
load_f_obs_and_r_free(file_name, anomalous_flag=False, phases=False)
Automation wrapper for reading in MTZ files generated by the process_raw_data
class.
looks_like_r_free_flags_info(array_info)
make_joined_set(miller_arrays)
presumably_from_mtz_FQDQY(miller_array)
select_array(parameter_name, labels, miller_arrays, data_scores, err, error_message_no_array, error_message_not_a_suitable_array, error_message_multiple_equally_suitable)
sort_arrays_by_score(miller_arrays, array_scores, minimum_score)

 
Data
        division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)