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 reflection_file_server exceptions.Sorry(exceptions.Exception) Sorry_No_array_of_the_required_type Sorry_Not_a_suitable_array   class Sorry_No_array_of_the_required_type(exceptions.Sorry)       Method resolution order: Sorry_No_array_of_the_required_type exceptions.Sorry exceptions.Exception exceptions.BaseException __builtin__.object Methods inherited from exceptions.Sorry: __del__(self) __init__(self, *args, **keyword_args) __str__(self) reset_tracebacklimit(self) Data descriptors inherited from exceptions.Sorry: __weakref__ list of weak references to the object (if defined) Data and other attributes inherited from exceptions.Exception: __new__ = <built-in method __new__ of type object at 0x722c00> T.__new__(S, ...) -> a new object with type S, a subtype of T Methods inherited from exceptions.BaseException: __delattr__(...) x.__delattr__('name') <==> del x.name __getattribute__(...) x.__getattribute__('name') <==> x.name __getitem__(...) x.__getitem__(y) <==> x[y] __getslice__(...) x.__getslice__(i, j) <==> x[i:j]   Use of negative indices is not supported. __reduce__(...) __repr__(...) x.__repr__() <==> repr(x) __setattr__(...) x.__setattr__('name', value) <==> x.name = value __setstate__(...) Data descriptors inherited from exceptions.BaseException: __dict__ args message exception message   class Sorry_Not_a_suitable_array(exceptions.Sorry)       Method resolution order: Sorry_Not_a_suitable_array exceptions.Sorry exceptions.Exception exceptions.BaseException __builtin__.object Methods inherited from exceptions.Sorry: __del__(self) __init__(self, *args, **keyword_args) __str__(self) reset_tracebacklimit(self) Data descriptors inherited from exceptions.Sorry: __weakref__ list of weak references to the object (if defined) Data and other attributes inherited from exceptions.Exception: __new__ = <built-in method __new__ of type object at 0x722c00> T.__new__(S, ...) -> a new object with type S, a subtype of T Methods inherited from exceptions.BaseException: __delattr__(...) x.__delattr__('name') <==> del x.name __getattribute__(...) x.__getattribute__('name') <==> x.name __getitem__(...) x.__getitem__(y) <==> x[y] __getslice__(...) x.__getslice__(i, j) <==> x[i:j]   Use of negative indices is not supported. __reduce__(...) __repr__(...) x.__repr__() <==> repr(x) __setattr__(...) x.__setattr__('name', value) <==> x.name = value __setstate__(...) Data descriptors inherited from exceptions.BaseException: __dict__ args message exception message   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 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) get_experimental_phases(self, file_name, labels, ignore_all_zeros, parameter_scope, parameter_name='labels') 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) get_r_free_flags(self, file_name, label, test_flag_value, disable_suitability_test, parameter_scope) get_valid_xray_data(self, file_name=None, labels='', ignore_all_zeros=False, parameter_scope='', parameter_name='labels', minimum_score=1) # most of the parameters here are placeholders. --nat get_xray_data(self, file_name, labels, ignore_all_zeros, parameter_scope, parameter_name='labels') Data descriptors defined here: __dict__ dictionary for instance variables (if defined) __weakref__ list of weak references to the object (if defined)

Functions
		construct_output_file_name(input_file_names, user_file_name, file_type_label, file_extension, extension_seperator='.') find_labels(search_labels, info_string) get_amplitude_scores(miller_arrays) get_experimental_phases_scores(miller_arrays, ignore_all_zeros) get_phase_scores(miller_arrays) get_xray_data_scores(miller_arrays, ignore_all_zeros) looks_like_r_free_flags_info(array_info) 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)