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

 
Package Contents
       
alignment
arrays
building (package)
bulk_solvent (package)
cablam (package)
chemical_components (package)
command_line (package)
conformation_dependent_library (package)
den (package)
density_modification (package)
disorder (package)
dynamics (package)
f_model
f_model_info
find_peaks
geometry (package)
geometry_restraints (package)
grow_density
hydrogens (package)
ias (package)
invariant_domain
ions (package)
kinemage (package)
lattice
libtbx_refresh
ligands (package)
map_tools
maps (package)
masks (package)
max_lik (package)
model
model_statistics
model_vs_data
monomer_library (package)
msa
ncs (package)
pdb_distances
pdb_symmetry
pdbtools
polygon (package)
real_space (package)
real_space_correlation
refinement (package)
regression (package)
resolve_resources
restraints
rotamer (package)
rsr (package)
run_tests
scaling (package)
secondary_structure (package)
solvent (package)
superpose
tls (package)
torsion_restraints (package)
twinning (package)
utils (package)
validation (package)
wwpdb (package)
xmanip
xmanip_tasks

 
Classes
       
__builtin__.object
fmodels
map_names

 
class fmodels(__builtin__.object)
     Methods defined here:
__init__(self, fmodel_xray=None, fmodel_neutron=None, xray_scattering_dict=None, neutron_scattering_dict=None, neutron_refinement=None, twin_law=None, log=None)
create_target_functors(self)
fmodel_neutron(self, xray_structure=None)
fmodel_xray(self, xray_structure=None)
prepare_target_functors_for_minimization(self)
pseudo_deep_copy(self)
resolution_filter(self, d_min)
show_comprehensive(self, message='')
show_short(self, log=None)
show_targets(self, log, text='')
target_and_gradients(self, weights, compute_gradients, u_iso_refinable_params=None, occupancy=False)
target_functions_are_invariant_under_allowed_origin_shifts(self)
target_functor_result_neutron(self, compute_gradients)
target_functor_result_xray(self, compute_gradients)
update(self, target_name=None)
update_all_scales(self, update_f_part1_for, refine_threshold, params=None, optimize_mask=False, force_update_f_mask=False, nproc=1, log=None, apply_back_trace=False, refine_hd_scattering=None)
update_xray_structure(self, xray_structure=None, update_f_calc=None, update_f_mask=None, force_update_f_mask=False)

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

 
class map_names(__builtin__.object)
     Methods defined here:
__init__(self, map_name_string)
error(self, s)
format(self)

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:
DFC = ['dfcalc', 'dfcal', 'dfc', 'dfmodel', 'dfmod', 'dfm']
FC = ['fcalc', 'fcal', 'fc', 'fmodel', 'fmod', 'fm']
FILLED = ['+filled', '-filled', 'filled', '+fill', '-fill', 'fill']
FO = ['fobs', 'fob', 'fo']
KICK = ['-kicked', '+kicked', 'kicked', '-kick', '+kick', 'kick']
MFO = ['mfobs', 'mfob', 'mfo']

 
Data
        division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)