mmtbx.density_modification
index
/net/chevy/raid1/nat/src/cctbx_project/mmtbx/density_modification/__init__.py

 
Package Contents
       
tst_density_modification

 
Classes
       
__builtin__.object
density_modification
dm_stats
local_standard_deviation_map

 
class density_modification(__builtin__.object)
     Methods defined here:
__init__(self, params, f_obs, hl_coeffs_start, ncs_object=None, map_coeffs=None, log=None, as_gui_program=False)
anisotropic_correction(self)
calculate_solvent_mask(self)
compute_map(self)
compute_map_coefficients(self)
compute_phase_source(self, hl_coeffs, n_steps=72)
density_truncation(self)
get_stats(self)
matthews_analysis(self)
miller_array_in_original_setting(self, miller_array)
ncs_averaging(self)
next_cycle(self)
show_cycle_summary(self, out=None)
solvent_adjust(self)
solvent_flattening(self)
solvent_flipping(self)
start_and_end_fom(self)

Data descriptors defined here:
__dict__
dictionary for instance variables (if defined)
__weakref__
list of weak references to the object (if defined)
active_indices
d_min
f_obs_active
hl_coeffs_in_original_setting
map_coeffs_in_original_setting
radius

 
class dm_stats(__builtin__.object)
     Methods defined here:
__init__(self)
add_cycle(self, **kwds)
extract_loggraph(self)
format_summary(self, i_cycle=-1)
get_cycle_stats(self, i_cycle=-1)
get_fom_for_plot(self)

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

 
class local_standard_deviation_map(__builtin__.object)
     Methods defined here:
__init__(self, map_coeffs, radius, mean_solvent_density=0, method=0, symmetry_flags=None, resolution_factor=0.3333333333333333)
histogram(self, n_slots=10000)
mask(self, solvent_fraction)

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

 
Functions
       
StringIO(...)
StringIO([s]) -- Return a StringIO-like stream for reading or writing
phase_error(...)
phase_error( (float)phi1, (float)phi2 [, (bool)deg=False]) -> float :
 
    C++ signature :
        double phase_error(double,double [,bool=False])
 
phase_error( (object)phi1, (object)phi2 [, (bool)deg=False]) -> double :
 
    C++ signature :
        scitbx::af::shared<double> phase_error(scitbx::af::const_ref<double, scitbx::af::trivial_accessor>,scitbx::af::const_ref<double, scitbx::af::trivial_accessor> [,bool=False])
rms(flex_double)

 
Data
        Auto = <libtbx.AutoType object>
division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
master_params_str = '\n solvent_fraction = None\n .type = float\n ...ption = Number of copies in asymmetric unit\n }\n\n'
pi_180 = 0.017453292519943295