iotbx.mtz
index
/net/chevy/raid1/nat/src/cctbx_project/iotbx/mtz/__init__.py

 
Package Contents
       
crystal_symmetry_from_mtz
extract_from_symmetry_lib
tst
tst_dano
tst_ext
tst_extract_from_symmetry_lib
tst_miller_dict
tst_unmerged

 
Classes
       
__builtin__.object
label_decorator
ccp4_label_decorator
libtbx.slots_getstate_setstate(__builtin__.object)
column_values_and_selection_valid

 
class ccp4_label_decorator(label_decorator)
    # XXX this will generate output labels recognizable by the Coot auto-open
# command, but only for specific root label types.
 
 
Method resolution order:
ccp4_label_decorator
label_decorator
__builtin__.object

Methods defined here:
phases(self, root_label, anomalous_sign=None)

Methods inherited from label_decorator:
__init__(self, anomalous_plus_suffix='(+)', anomalous_minus_suffix='(-)', sigmas_prefix='SIG', sigmas_suffix='', delta_anomalous_prefix='DANO', delta_anomalous_suffix='', delta_anomalous_isym_prefix='ISYM', delta_anomalous_isym_suffix='', phases_prefix='PHI', phases_suffix='', hendrickson_lattman_suffix_list=['A', 'B', 'C', 'D'])
anomalous(self, root_label, sign=None)
delta_anomalous(self, root_label)
delta_anomalous_isym(self, root_label)
delta_anomalous_sigmas(self, root_label)
hendrickson_lattman(self, root_label, i_coeff, anomalous_sign=None)
sigmas(self, root_label, anomalous_sign=None)

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

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

Methods defined here:
__init__(O, values, selection_valid)
as_tuple(O)

Data descriptors defined here:
selection_valid
values

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

 
class label_decorator(__builtin__.object)
     Methods defined here:
__init__(self, anomalous_plus_suffix='(+)', anomalous_minus_suffix='(-)', sigmas_prefix='SIG', sigmas_suffix='', delta_anomalous_prefix='DANO', delta_anomalous_suffix='', delta_anomalous_isym_prefix='ISYM', delta_anomalous_isym_suffix='', phases_prefix='PHI', phases_suffix='', hendrickson_lattman_suffix_list=['A', 'B', 'C', 'D'])
anomalous(self, root_label, sign=None)
delta_anomalous(self, root_label)
delta_anomalous_isym(self, root_label)
delta_anomalous_sigmas(self, root_label)
hendrickson_lattman(self, root_label, i_coeff, anomalous_sign=None)
phases(self, root_label, anomalous_sign=None)
sigmas(self, root_label, anomalous_sign=None)

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

 
Functions
       
are_anomalous_labels(sign, labels)
ccp4_liberr_verbosity(...)
ccp4_liberr_verbosity( (int)level) -> int :
 
    C++ signature :
        int ccp4_liberr_verbosity(int)
cmtz_struct_sizes(...)
cmtz_struct_sizes() -> size_t :
 
    C++ signature :
        scitbx::af::shared<unsigned long> cmtz_struct_sizes()
column_group(crystal_symmetry_from_file, crystal_symmetry, base_array_info, primary_column_type, labels, group, observation_type)
default_column_types(miller_array)
format_min_max(func, values)
is_anomalous_label(sign, label)
mend_non_conforming_anomalous_column_types(all_types, all_labels)
miller_array_as_mtz_dataset(self, column_root_label, column_types=None, label_decorator=None, title=None, crystal_name='crystal', project_name='project', dataset_name='dataset', wavelength=0.0)
tidy_show_column_data_format_keyword(input)

 
Data
        anomalous_label_patterns = {'+': ('+', 'PLUS'), '-': ('-', 'MINU')}
column_type_as_miller_array_type_hints = {'A': 'hendrickson_lattman', 'B': 'batch_number', 'D': 'anomalous_difference', 'E': 'normalized_amplitude', 'F': 'amplitude', 'G': 'amplitude', 'H': 'miller_index', 'I': 'integer', 'J': 'intensity', 'K': 'intensity', ...}
column_type_legend = {'A': 'phase probability coefficients (Hendrickson/Lattman)', 'B': 'BATCH number', 'D': 'anomalous difference', 'E': 'normalized amplitude', 'F': 'amplitude', 'G': 'F(+) or F(-)', 'H': 'index h,k,l', 'I': 'integer', 'J': 'intensity', 'K': 'I(+) or I(-)', ...}
column_type_legend_source = 'ccp4/doc/mtzformat.doc'
division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
expected_cmtz_struct_sizes = ((56, 84, 176, 500, 12336, 12488), (64, 88, 184, 504, 12336, 12528), (56, 84, 176, 500, 12340, 12492), (64, 88, 184, 504, 12340, 12536), (136, 84, 176, 500, 12340, 12504), (144, 88, 184, 504, 12340, 12560))
show_column_data_format_keywords = ['human_readable', 'machine_readable', 'spreadsheet']