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

 
Modules
       
cctbx.array_family.flex
iotbx
cctbx.maptbx
cctbx.miller
mmtbx
os
iotbx.reflection_file_reader
iotbx.reflection_file_utils
sys

 
Classes
       
__builtin__.object
selection_map_statistics_manager

 
class selection_map_statistics_manager(__builtin__.object)
    Utility class for performing repeated calculations on multiple maps.  Useful
in post-refinement validation, ligand fitting, etc. where we want to collect
both CC and values for 2mFo-DFc and mFo-DFc maps.
 
  Methods defined here:
__init__(self, atom_selection, xray_structure, fft_m_real, fft_n_real, atom_radius=1.5, exclude_hydrogens=False)
analyze_map(self, map, model_map=None, min=None, max=None, compare_at_sites_only=False)
Extract statistics for the given map, plus statistics for the model map
if given.  The CC can either be calculated across grid points within the
given radius of the sites, or at the sites directly.

Data descriptors defined here:
atom_radii
atom_selection
fft_m_real
fft_n_real
map_sel
sites
sites_frac

 
Functions
       
StringIO(...)
StringIO([s]) -- Return a StringIO-like stream for reading or writing
broadcast(m, log)
cmd_run(args, command_name, log=None)
compute(pdb_hierarchy, unit_cell, fft_n_real, fft_m_real, map_1, map_2, detail, atom_radius, use_hydrogens, hydrogen_atom_radius)
compute_map_from_model(high_resolution, low_resolution, xray_structure, grid_resolution_factor, crystal_gridding=None)
extract_data_and_flags(params, crystal_symmetry=None)
extract_input_data(hkl_file, params)
extract_input_pdb(pdb_file, params)
extract_map_stats_for_single_atoms(xray_structure, pdb_atoms, fmodel, selection=None)
Memory-efficient routine for harvesting map values for individual atoms
(e.g. waters).  Only one FFT'd map at a time is in memory.
find_suspicious_residues(fmodel, pdb_hierarchy, hetatms_only=True, skip_single_atoms=True, skip_alt_confs=True, min_acceptable_cc=0.8, min_acceptable_2fofc=1.0, max_frac_atoms_below_min=0.5, ignore_resnames=(), log=None)
map_statistics_for_atom_selection(atom_selection, fmodel=None, resolution_factor=0.25, map1=None, map2=None, xray_structure=None, map1_type='2mFo-DFc', map2_type='Fmodel', atom_radius=1.5, exclude_hydrogens=False)
Simple-but-flexible function to give the model-to-map CC and mean density
values (sigma-scaled, unless pre-calculated maps are provided) for any
arbitrary atom selection.
map_statistics_for_fragment(fragment, **kwds)
Shortcut to map_statistics_for_atom_selection using a PDB hierarchy object
to define the atom selection.
master_params()
pdb_to_xrs(pdb_file_name, scattering_table)
set_detail_level_and_radius(detail, atom_radius, d_min)
show(log, results, detail, params=None, map_1_name=None, map_2_name=None)
simple(fmodel, pdb_hierarchy, params=None, log=None, show_results=False)

 
Data
        core_params_str = 'atom_radius = None\n .type = float\n .help = Ato...type = float\nuse_hydrogens = None\n .type = bool\n'
division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
master_params_str = 'atom_radius = None\n .type = float\n .help = Ato... .type=float\nlow_resolution = None\n .type=float\n'