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

 
Modules
       
cPickle
os
re
sys

 
Classes
       
__builtin__.object
any_file_fast_input
any_file_input
directory_input
group_files
exceptions.Sorry(exceptions.Exception)
FormatError

 
class FormatError(exceptions.Sorry)
    
Method resolution order:
FormatError
exceptions.Sorry
exceptions.Exception
exceptions.BaseException
__builtin__.object

Methods inherited from exceptions.Sorry:
reset_module(self)

Data descriptors inherited from exceptions.Sorry:
__weakref__
list of weak references to the object (if defined)

Data and other attributes inherited from exceptions.Sorry:
__orig_module__ = 'libtbx.utils'

Methods inherited from exceptions.Exception:
__init__(...)
x.__init__(...) initializes x; see help(type(x)) for signature

Data and other attributes inherited from exceptions.Exception:
__new__ = <built-in method __new__ of type object>
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__(...)
__str__(...)
x.__str__() <==> str(x)
__unicode__(...)

Data descriptors inherited from exceptions.BaseException:
__dict__
args
message

 
class any_file_fast_input(__builtin__.object)
     Methods defined here:
__init__(self, file_name, valid_types)

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:
__descriptions__ = {'aln': 'Sequence alignment', 'ccp4_map': 'CCP4 map', 'cif': 'Restraints', 'hhr': 'HHpred alignment', 'hkl': 'Reflections', 'img': 'Detector image', 'mtz': 'Reflections (MTZ)', 'pdb': 'Model', 'phil': 'Parameters', 'pkl': 'Python pickle', ...}
__extensions__ = {'aln': ['aln', 'ali', 'clustal'], 'ccp4_map': ['ccp4', 'map'], 'cif': ['cif', 'mmcif'], 'hhr': ['hhr'], 'hkl': ['mtz', 'hkl', 'sca', 'cns', 'xplor', 'cv', 'ref', 'fobs'], 'img': ['img', 'osc', 'mccd', 'cbf'], 'map': ['xplor', 'map', 'ccp4'], 'mtz': ['mtz'], 'pdb': ['pdb', 'ent'], 'phil': ['params', 'eff', 'def', 'phil', 'param'], ...}

 
class any_file_input(__builtin__.object)
     Methods defined here:
__init__(self, file_name, get_processed_file, valid_types, force_type, raise_sorry_if_errors=False, raise_sorry_if_not_expected_format=False)
assert_file_type(self, expected_type)
check_file_type(self, expected_type=None, multiple_formats=())
crystal_symmetry(self)
Extract the crystal symmetry (if any).  Only valid for model (PDB/mmCIF)
and reflection files.
file_info(self, show_file_size=True)
show_summary(self, out=<open file '<stdout>', mode 'w'>)
try_all_types(self)
try_as_aln(self)
try_as_ccp4_map(self)
try_as_cif(self)
try_as_hhr(self)
try_as_hkl(self)
try_as_img(self)
try_as_pdb(self)
PDB parser, actually tries both 'classic' PDB and mmCIF formats.
try_as_phil(self)
try_as_pkl(self)
try_as_seq(self)
try_as_txt(self)
try_as_xml(self)
try_as_xplor_map(self)

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

Data and other attributes defined here:
__descriptions__ = {'aln': 'Sequence alignment', 'ccp4_map': 'CCP4 map', 'cif': 'Restraints', 'hhr': 'HHpred alignment', 'hkl': 'Reflections', 'img': 'Detector image', 'mtz': 'Reflections (MTZ)', 'pdb': 'Model', 'phil': 'Parameters', 'pkl': 'Python pickle', ...}
__extensions__ = {'aln': ['aln', 'ali', 'clustal'], 'ccp4_map': ['ccp4', 'map'], 'cif': ['cif', 'mmcif'], 'hhr': ['hhr'], 'hkl': ['mtz', 'hkl', 'sca', 'cns', 'xplor', 'cv', 'ref', 'fobs'], 'img': ['img', 'osc', 'mccd', 'cbf'], 'map': ['xplor', 'map', 'ccp4'], 'mtz': ['mtz'], 'pdb': ['pdb', 'ent'], 'phil': ['params', 'eff', 'def', 'phil', 'param'], ...}

 
class directory_input(__builtin__.object)
     Methods defined here:
__init__(self, dir_name)
file_info(self, show_file_size=False)

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

 
class group_files(__builtin__.object)
     Methods defined here:
__init__(self, file_names, template_format='pdb', group_by_directory=True)

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

 
Functions
       
any_file(file_name, get_processed_file=False, valid_types=['pdb', 'hkl', 'cif', 'pkl', 'seq', 'phil', 'aln', 'txt', 'xplor_map', 'ccp4_map'], allow_directories=False, force_type=None, input_class=None, raise_sorry_if_errors=False, raise_sorry_if_not_expected_format=False)
Main input method, wrapper for any_file_input class.
any_file_fast(file_name, get_processed_file=False, valid_types=['pdb', 'hkl', 'cif', 'pkl', 'seq', 'phil', 'aln', 'txt', 'xplor_map', 'ccp4_map'], allow_directories=False, force_type=None, input_class=None)
mimics any_file, but without parsing - will instead guess the file type from
the extension.  for most output files produced by cctbx/phenix this is
relatively safe; for files of unknown provenance it is less effective.
find_closest_base_name(file_name, base_name, templates)
get_wildcard_string(format)
get_wildcard_strings(formats, include_any=True)
guess_file_type(file_name, extensions={'aln': ['aln', 'ali', 'clustal'], 'ccp4_map': ['ccp4', 'map'], 'cif': ['cif', 'mmcif'], 'hhr': ['hhr'], 'hkl': ['mtz', 'hkl', 'sca', 'cns', 'xplor', 'cv', 'ref', 'fobs'], 'img': ['img', 'osc', 'mccd', 'cbf'], 'map': ['xplor', 'map', 'ccp4'], 'mtz': ['mtz'], 'pdb': ['pdb', 'ent'], 'phil': ['params', 'eff', 'def', 'phil', 'param'], ...})
sort_by_file_type(file_names, sort_order=None)
splitext(file_name)
strip_shelx_format_extension(file_name)

 
Data
        ascii_types = ['hkl', 'xplor_map', 'pdb', 'cif', 'phil', 'hhr', 'aln', 'seq', 'xml', 'txt']
binary_types = ['hkl', 'ccp4_map', 'img', 'pkl']
compression_extensions = ['gz', 'Z', 'bz2', 'zip']
division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
standard_file_descriptions = {'aln': 'Sequence alignment', 'ccp4_map': 'CCP4 map', 'cif': 'Restraints', 'hhr': 'HHpred alignment', 'hkl': 'Reflections', 'img': 'Detector image', 'mtz': 'Reflections (MTZ)', 'pdb': 'Model', 'phil': 'Parameters', 'pkl': 'Python pickle', ...}
standard_file_extensions = {'aln': ['aln', 'ali', 'clustal'], 'ccp4_map': ['ccp4', 'map'], 'cif': ['cif', 'mmcif'], 'hhr': ['hhr'], 'hkl': ['mtz', 'hkl', 'sca', 'cns', 'xplor', 'cv', 'ref', 'fobs'], 'img': ['img', 'osc', 'mccd', 'cbf'], 'map': ['xplor', 'map', 'ccp4'], 'mtz': ['mtz'], 'pdb': ['pdb', 'ent'], 'phil': ['params', 'eff', 'def', 'phil', 'param'], ...}
standard_file_types = ['hkl', 'ccp4_map', 'xplor_map', 'pdb', 'cif', 'phil', 'hhr', 'aln', 'seq', 'xml', 'pkl', 'txt']
supported_file_types = ['pdb', 'hkl', 'cif', 'pkl', 'seq', 'phil', 'aln', 'txt', 'xplor_map', 'ccp4_map']