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

 
Modules
       
os

 
Classes
       
__builtin__.object
auto_convert_map_coefficients
map_info
server
write_ccp4_maps_wrapper
exceptions.RuntimeError(exceptions.StandardError)
MapNotFound

 
class MapNotFound(exceptions.RuntimeError)
    
Method resolution order:
MapNotFound
exceptions.RuntimeError
exceptions.StandardError
exceptions.Exception
exceptions.BaseException
__builtin__.object

Data descriptors defined here:
__weakref__
list of weak references to the object (if defined)

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

Data and other attributes inherited from exceptions.RuntimeError:
__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 auto_convert_map_coefficients(__builtin__.object)
     Methods defined here:
__init__(self, mtz_file, pdb_file=None, resolution_factor=0.25)

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

 
class map_info(__builtin__.object)
     Methods defined here:
__getattr__(self, name)
__init__(self, map_coeffs, map_type, map_name=None)
fft_map(self, resolution_factor)
is_anomalous_map(self)
is_difference_map(self)
is_filled_map(self)
is_fobs_map(self)
is_neutron_map(self)

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

 
class server(__builtin__.object)
    Manager for files containing map coefficients (either as complex arrays or
separate F, PHI, and optional FOM).  Once an MTZ file or collection of
Miller arrays is loaded, individual maps can be quickly retrieved, and it
includes built-in recognition of standard map labels used in PHENIX (and
CCP4).
 
  Methods defined here:
__init__(self, file_name=None, miller_arrays=())
auto_open_maps(self, use_filled=True)
contains_amplitude_and_phase(self)
contains_map_coefficients(self)
convert_all_map_coefficients(self, **kwds)
convert_anomalous_map(self, **kwds)
convert_any_map(self, f_label, phi_label, fom_label, **kwds)
convert_ccp4_map(self, **kwds)
convert_complex_map(self, map_label, **kwds)
convert_phenix_maps(self, file_base, **kwds)
convert_resolve_map(self, **kwds)
convert_solve_map(self, **kwds)
get_amplitudes_and_phases(self, f_label=None, phi_label=None, fom_label=None)
get_anomalous_map(self)
get_ccp4_maps(self)
get_pdb_file(self, file_name)
get_phenix_maps(self, keep_column_labels=False)
get_resolve_map(self)
get_solve_map(self)
is_anomalous_map(self)
is_ccp4_style_difference_map(self)
is_ccp4_style_map(self)
is_cctbx_maps(self)
is_phenix_refine_maps(self)
is_resolve_map(self)
is_solve_map(self)

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

 
class write_ccp4_maps_wrapper(__builtin__.object)
    Callable object for running map conversions in parallel (probably overkill,
but anything we can do to take advantage of multiple CPUs is worth trying).
 
  Methods defined here:
__init__(self, pdb_hierarchy, map_coeffs, output_files, resolution_factor)
run(self)

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

 
Functions
       
combine_f_phi_and_fom(f, phi, fom=None, weighted=True)
convert_any_map_coeffs(mtz_file, **kwds)
convert_ccp4_map(mtz_file, **kwds)
convert_map_coefficients(map_coefficients, mtz_file, **kwds)
Convert the map coefficients in an MTZ file created by phenix.maps or
phenix.refine (and related applications).  The parameter block expected in
map_coefficients is actually in mmtbx/maps/__init__.py, but the I/O belongs
here.
convert_phenix_maps(file_base, **kwds)
convert_resolve_map(mtz_file, **kwds)
########################################################################
# convenience functions
convert_solve_map(mtz_file, **kwds)
get_map_summary(map, resolution_factor=0.25)
write_ccp4_map(sites_cart, unit_cell, map_data, n_real, file_name, buffer=10)
write_map_coefficients_generic(map_coeffs, map_types, file_name)
# FIXME this is probably too much code duplication...
# used by phenix.composite_omit_map, etc.
write_map_coeffs(fwt_coeffs, delfwt_coeffs, file_name, anom_coeffs=None, fmodel_coeffs=None)
Convenience function for writing out 2mFo-DFc and mFo-DFc (and, optionally,
anomalous difference) map coefficients with predefined labels, which will
be recognized by the auto-open function in Coot.

 
Data
        MAP_TYPE_ANOMALOUS = 4
MAP_TYPE_DIFF = 2
MAP_TYPE_FILLED = 64
MAP_TYPE_F_CALC = 32
MAP_TYPE_F_OBS = 1
MAP_TYPE_ISO_DIFF = 8
MAP_TYPE_NEUTRON = 16
division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
standard_map_names = {'2FOFCWT': '2mFo-DFc', '2FOFCWT_no_fill': '2mFo-DFc_no_fill', 'ANOM': 'anomalous', 'FOFCWT': 'mFo-DFc'}