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

# TODO: confirm old_test_flag_value if ambiguous

 
Modules
       
iotbx
os
random
re
string
sys
warnings

 
Classes
       
__builtin__.object
process_arrays
libtbx.slots_getstate_setstate(__builtin__.object)
array_input

 
class array_input(libtbx.slots_getstate_setstate)
    
Method resolution order:
array_input
libtbx.slots_getstate_setstate
__builtin__.object

Methods defined here:
__init__(self, params, input_files=None)
resolve_unit_cell(self)

Data descriptors defined here:
array_types
file_names
miller_arrays

Methods inherited from libtbx.slots_getstate_setstate:
__getstate__(self)
__setstate__(self, state)

 
class process_arrays(__builtin__.object)
     Methods defined here:
__init__(self, params, input_files=None, inputs_object=None, log=<open file '<stdout>', mode 'w'>, accumulation_callback=None, symmetry_callback=None)
add_array_to_mtz_dataset(self, output_array, default_label, column_types, out=<open file '<stdout>', mode 'w'>)
finish(self)
show(self, out=<open file '<stdout>', mode 'w'>)

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

 
Functions
       
check_and_warn_about_incomplete_r_free_flags(combined_set)
collect_symmetries(file_names)
# XXX the requirement for defined crystal symmetry in phil input files is
# problematic for automation, where labels and operations are very
# standardized.  so I added this to identify unique symmetry information
# in the collected input files.
export_r_free_flags(miller_array, test_flag_value)
generate_params(file_name, miller_array, include_resolution=False)
get_best_resolution(miller_arrays, input_symm=None)
get_original_array_types(input_file, original_labels)
get_r_free_as_bool(*args, **kwds)
get_r_free_stats(*args, **kwds)
#-----------------------------------------------------------------------
# TODO get rid of these two (need to make sure they aren't imported elsewhere)
guess_array_output_labels(miller_array)
is_rfree_array(miller_array, array_info)
modify_array(miller_array, array_name, array_params, array_info=None, verbose=True, debug=False, log=<open file '<stdout>', mode 'w'>)
Perform various manipulations on a Miller array.  This can be applied to
any data type, although certain options are limited to experimental data.
modify_experimental_data_array(miller_array, array_name, array_params, log=<open file '<stdout>', mode 'w'>)
Manipulations common to amplitude and intensity arrays only.
resolve_symmetry(file_symmetries, current_space_group, current_unit_cell)
run(args, out=<open file '<stdout>', mode 'w'>)
#-----------------------------------------------------------------------
usage(out=<open file '<stdout>', mode 'w'>, attributes_level=0)
validate_column_root_label(miller_array, root_label, array_name)
Check the root MTZ label for a Miller array to ensure consistency with
data type - this is done after the array has been processed.
validate_output_labels(miller_array, array_name, array_params, output_labels)
Check output labels for consistency with selected options (done before the
array undergoes most modifications).
validate_params(params)

 
Data
        DEBUG = False
division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
master_phil = <libtbx.phil.scope object>