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

 
Modules
       
boost
cctbx.array_family.flex
libtbx
cctbx.maptbx
cctbx.miller
mmtbx
mmtbx_f_model_ext
random

 
Classes
       
__builtin__.object
combine
electron_density_map
fo_fc_scales
model_missing_reflections
ncs_averager

 
class combine(__builtin__.object)
     Methods defined here:
__init__(self, fmodel, map_type_str, fo_scale, fc_scale, use_shelx_weight, shelx_weight_parameter, map_calculation_helper=None)
map_coefficients(self, f_model=None)

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

 
class electron_density_map(__builtin__.object)
     Methods defined here:
__init__(self, fmodel, map_calculation_helper=None)
fft_map(self, resolution_factor=0.3333333333333333, symmetry_flags=None, map_coefficients=None, other_fft_map=None, map_type=None, force_anomalous_flag_false=None, acentrics_scale=2.0, centrics_pre_scale=1.0, use_all_data=True)
map_coefficients(self, map_type, acentrics_scale=2.0, centrics_pre_scale=1.0, exclude_free_r_reflections=False, fill_missing=False, fill_missing_method='f_model', ncs_average=False, isotropize=True, sharp=False, post_processing_callback=None, pdb_hierarchy=None, merge_anomalous=None, use_shelx_weight=False, shelx_weight_parameter=1.5)

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

 
class fo_fc_scales(__builtin__.object)
     Methods defined here:
__init__(self, fmodel, map_type_str, acentrics_scale=2.0, centrics_scale=1.0)
Compute x and y for x*Fobs-y*Fmodel given map type string

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

 
class model_missing_reflections(__builtin__.object)
     Methods defined here:
__init__(self, fmodel, coeffs)
get_missing(self, deterministic=False)
get_missing_fast(self)

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

 
class ncs_averager(__builtin__.object)
    # XXX it would be more useful to have this integrated with the rest of the
# code, instead of making map averaging an afterthought.  however, the
# external overhead is currently substantial.
 
  Methods defined here:
__call__(self, map_coeffs, fmodel, generate_new_mask=False, map_type=None)
__init__(self, ncs_object, params=None, log=None, verbose=False)

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

 
Functions
       
anomalous_residual_map_coefficients(fmodel, weighted=False, exclude_free_r_reflections=True)
EXPERIMENTAL
 
Calculates map coefficients showing the difference in anomalous scattering
between F-obs and F-model.  Similar to the Phaser SAD LLG map, but appears
to be less sensitive.
fill_missing_f_obs(coeffs, fmodel, method)
fill_missing_f_obs_1(coeffs, fmodel)
fill_missing_f_obs_2(coeffs, fmodel)
fill_missing_f_obs_3(coeffs, fmodel)
get_phaser_sad_llg_map_coefficients(fmodel, pdb_hierarchy, log=None, verbose=False)
Calculates an anomalous log-likelihood gradient (LLG) map using the SAD
target in Phaser.  This is essentially similar to an anomalous difference-
difference map, but more sensitive.
resolve_dm_map(fmodel, map_coeffs, pdb_inp, use_model_hl, fill, solvent_content=None, solvent_content_attenuator=0.15, mask_cycles=2, minor_cycles=2, input_text=None)
Compute Resolve DM map
sharp_evaluation_target(sites_frac, map_coeffs, resolution_factor=0.25)
sharp_map(sites_frac, map_coeffs, ss=None, b_sharp=None, b_min=-150, b_max=150, step=10)
shelx_weight(f_obs, f_model, weight_parameter=None)

 
Data
        division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
ncs_averaging_params = '\nresolution_factor = 0.25\n .type = float\nuse_mo...= bool\nskip_difference_map = Auto\n .type = bool\n'