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

 
Package Contents
       
tst_ias

 
Classes
       
__builtin__.object
atom
bond_density
extract_ias
find_peak_at_bond
ias
ias_counters
manager

 
class atom(__builtin__.object)
     Methods defined here:
__init__(self, site_cart=None, q=None, b_iso=None, name=None, i_seq=None, element=None)

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

 
class bond_density(__builtin__.object)
     Methods defined here:
__init__(self, data=None, dist=None, ideal_data=None, one_dim_point=None, one_dim_point_predicted=None, peak_data=None, peak_dist=None)

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

 
class extract_ias(__builtin__.object)
     Methods defined here:
__init__(self, xray_structure, bond_proxies_simple, pdb_atoms, planarity_proxies, params, log=None)

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

 
class find_peak_at_bond(__builtin__.object)
     Methods defined here:
__init__(self, map_data, unit_cell, label, site_cart_1, site_cart_2, step=0.005)
find_peak(self, peak_width=0.3, offset=0.1)
set_status(self)

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

 
class ias(__builtin__.object)
     Methods defined here:
__init__(self, atom_1=None, atom_2=None, atom_3=None, site_cart_predicted=None, peak_value=None, peak_position_cart=None, q=None, b_iso=None, name=None, type=None, bond_density=None, status=None)
deep_copy(self)

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

 
class ias_counters(__builtin__.object)
     Methods defined here:
__init__(self, iass)
show(self, out=None)

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

 
class manager(__builtin__.object)
     Methods defined here:
__init__(self, geometry, pdb_atoms, xray_structure, params=None, fmodel=None, file_name=None, log=None)
all_bonds(self, iass, file_name)
iass_as_xray_structure(self, iass)
write_pdb_file(self, out=None)

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

 
Functions
       
add_lone_pairs_for_peptyde_o(site_c, site_o, site_ca, dist_co, R=0.35, ALPHA=66.635468, small=1e-06)
check_at_bond_vector(ias)
ias_position_at_lone_pairs(ias, params)
ias_site_position(site_i, site_j, alp)
set_ias_name_and_predicted_position(iass, params)
set_peaks(iass, fmodel, grid_step, map_type, scaling)
set_status(iass, params)

 
Data
        BH_type = ['IS1', 'IS2', 'IS3']
B_type = ['IS4', 'IS5', 'IS6', 'IS7', 'IS8']
L_type = ['IS10']
R_type = ['IS9']
division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
ias_master_params = <libtbx.phil.scope object>
ias_scattering_dict = {'IS1': <cctbx_eltbx_xray_scattering_ext.gaussian object>, 'IS10': <cctbx_eltbx_xray_scattering_ext.gaussian object>, 'IS2': <cctbx_eltbx_xray_scattering_ext.gaussian object>, 'IS3': <cctbx_eltbx_xray_scattering_ext.gaussian object>, 'IS4': <cctbx_eltbx_xray_scattering_ext.gaussian object>, 'IS5': <cctbx_eltbx_xray_scattering_ext.gaussian object>, 'IS6': <cctbx_eltbx_xray_scattering_ext.gaussian object>, 'IS7': <cctbx_eltbx_xray_scattering_ext.gaussian object>, 'IS8': <cctbx_eltbx_xray_scattering_ext.gaussian object>, 'IS9': <cctbx_eltbx_xray_scattering_ext.gaussian object>}