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

 
Package Contents
       
alternate_conformations (package)
extend_sidechains
make_library
tst
tst_extend_sidechains
tst_make_library

 
Classes
       
__builtin__.object
box_build_refine_base
local_density_quality

 
class box_build_refine_base(__builtin__.object)
    Base class for handling functions associated with rebuilding and refinement
of atoms in a box, with the building methods implemented elsewhere.
 
  Methods defined here:
__init__(self, pdb_hierarchy, xray_structure, processed_pdb_file, target_map, selection, d_min, out, cif_objects=(), resolution_factor=0.25, selection_buffer_radius=5, box_cushion=2, target_map_rsr=None, geometry_restraints_manager=None, debug=False)
anneal(self, simulated_annealing_params=None, start_temperature=None, cool_rate=None, number_of_steps=50)
Run real-space simulated annealing using the target map (not the RSR map,
if this is different).  In practice, the non-selection atoms in the box
should almost always be restrained to their current positions, but the
setup is left to the calling code.
cc_model_map(self, selection=None, radius=1.5)
Calculate the correlation coefficient for the current model (in terms of
F(calc) from the xray structure) and the target map, calculated at atomic
positions rather than grid points.  This will be much
less accurate than the CC calculated in the original crystal environment,
with full F(model) including bulk solvent correction.
fit_residue_in_box(self, mon_lib_srv=None, rotamer_manager=None, backbone_sample_angle=20)
geometry_minimization(self, selection=None, bond=True, nonbonded=True, angle=True, dihedral=True, chirality=True, planarity=True, generic_restraints=True, max_number_of_iterations=500, number_of_macro_cycles=5, rmsd_bonds_termination_cutoff=0, rmsd_angles_termination_cutoff=0)
Perform geometry minimization on a selection of boxed atoms.
get_selected_sites(self, selection=None, hydrogens=True)
mean_density_at_sites(self, selection=None)
Compute the mean density of the target map at coordinates for non-hydrogen
atoms.
only_residue(self)
Returns the atom_group object corresponding to the original selection.
Will raise an exception if the selection covers more than one atom_group.
real_space_refine(self, selection=None)
Run simple real-space refinement, returning the optimized weight for the
map target (wx).
restrain_atoms(self, selection, reference_sigma, limit=1.0, reset_first=True, top_out_potential=False)
Apply harmonic reference restraints to the selected atoms, wiping out
any previously existing harmonic restraints.
update_coordinates(self, sites_cart)
Set coordinates for the boxed xray_structure and pdb_hierarchy objects.
update_original_coordinates(self)
Copies the new coordinates from the box to the selected atoms in the
original xray_structure object, and returns the (complete) list of
coordinates.
update_sites_from_pdb_atoms(self)
Update the xray_structure coordinates after manipulating the PDB hierarchy.

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

 
class local_density_quality(__builtin__.object)
    #-----------------------------------------------------------------------
# MAP-RELATED
 
  Methods defined here:
__init__(self, fofc_map, two_fofc_map, sites_cart=None, atom_names=None, unit_cell=None, atom_selection=None, xray_structure=None, radius=2.5)
atoms_below_fofc_map_level(self, sigma_cutoff=-2.5)
atoms_below_two_fofc_map_level(self, sigma_cutoff=-2.5)
atoms_outside_density(self, **kwds)
fraction_of_nearby_grid_points_above_cutoff(self, sigma_cutoff=2.5)
max_fofc_value(self)
number_of_atoms_below_fofc_map_level(self, *args, **kwds)
number_of_atoms_below_two_fofc_map_level(self, *args, **kwds)
number_of_atoms_outside_density(self, *args, **kwds)
show_atoms_outside_density(self, **kwds)

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

 
Functions
       
atom_group_as_hierarchy(atom_group)
Convert an iotbx.pdb.hierarchy.atom_group object to a separate hierarchy
(leaving the original hierarchy untouched), which allows us to use the
pickling capabilities of iotbx.pdb.hierarchy.root.
extract_iselection(pdb_objects)
generate_sidechain_clusters(residue, mon_lib_srv)
Extract Chi angle indices (including rotation axis) from the atom_group
get_difference_maps(fmodel, resolution_factor=0.25)
get_model_map_stats(selection, target_map, model_map, unit_cell, sites_cart, pdb_atoms, local_sampling=False)
Collect basic statistics for a model map and some target map (usually an
mFo-DFc map), including CC, mean, and minimum density at the atomic
positions.
get_nearby_water_selection(pdb_hierarchy, xray_structure, selection, selection_buffer_radius=5)
get_non_hydrogen_atom_indices(pdb_object)
get_restraints_manager(processed_pdb_file, xray_structure, log=<open file '<stdout>', mode 'w'>)
get_window_around_residue(residue, window_size=2)
is_stub_residue(atom_group)
iter_residue_groups(hierarchy)
remove_sidechain_atoms(pdb_objects)
reprocess_pdb(pdb_hierarchy, crystal_symmetry, cif_objects, out)
residue_density_quality(atom_group, unit_cell, two_fofc_map, fofc_map)
residues_are_adjacent(residue1, residue2, max_sep=2.5)
run_real_space_annealing(xray_structure, pdb_hierarchy, selection, target_map, d_min, processed_pdb_file=None, cif_objects=(), resolution_factor=0.25, params=None, wc=1, target_map_rsr=None, rsr_after_anneal=False, reference_sigma=0.5, out=None, debug=False)
Run simulated annealing with a real-space target.  For maximum flexibility,
a separate map may be used for the initial real-space refinement step.
show_chain_resseq_ranges(residues, out=<open file '<stdout>', mode 'w'>, prefix='')
Given a list of residues (either residue_group or atom_group objects),
print a summary of the chains and residue ranges present.

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