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

 
Package Contents
       
base_pairing
build (package)
dssp
proteins
tst
tst_base_pairing
utils

 
Classes
       
__builtin__.object
manager

 
class manager(__builtin__.object)
     Methods defined here:
__init__(self, pdb_hierarchy, sec_str_from_pdb_file=None, params=None, assume_hydrogens_all_missing=None, tmp_dir=None, verbose=-1)
alpha_selection(self, **kwds)
# FIXME backwards compatibility
alpha_selections(self, **kwds)
apply_params(self, params)
apply_phil_str(self, phil_string, log=<open file '<stdout>', mode 'w'>, verbose=False)
as_phil_str(self, master_phil=<libtbx.phil.scope object>)
base_pair_selection(self, **kwds)
base_pair_selections(self, limit=None, main_conf_only=False)
beta_selection(self, **kwds)
beta_selections(self, limit=None, main_conf_only=False)
calculate_structure_content(self)
create_hbond_proxies(self, log=<open file '<stdout>', mode 'w'>, hbond_params=None, as_python_objects=False, master_selection=None)
find_approximate_helices(self, log=<open file '<stdout>', mode 'w'>)
find_automatically(self, log=<open file '<stdout>', mode 'w'>)
find_base_pairs(self, log=<open file '<stdout>', mode 'w'>)
find_base_pairs_with_segids(self, log=<open file '<stdout>', mode 'w'>, force=False)
find_sec_str(self, log=<open file '<stdout>', mode 'w'>)
find_sec_str_with_segids(self, log=<open file '<stdout>', mode 'w'>)
get_helix_types(self)
get_simple_bonds(self, selection_phil=None)
helix_selection(self, **kwds)
helix_selections(self, limit=None, main_conf_only=False, alpha_only=False)
initialize(self, log=<open file '<stdout>', mode 'w'>)
selections_as_ints(self)
show_summary(self, out=<open file '<stdout>', mode 'w'>)

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

 
Functions
       
analyze_distances(self, params, pdb_hierarchy=None, log=<open file '<stdout>', mode 'w'>)
calculate_structure_content(pdb_file)
find_nucleic_acids(pdb_hierarchy)
get_ksdssp_exe_path()
get_pdb_hierarchy(file_names)
hydrogen_bond_proxies_from_selections(pdb_hierarchy, params, use_hydrogens, as_python_objects=False, remove_outliers=False, master_selection=None, log=<open file '<stdout>', mode 'w'>)
manager_from_pdb_file(pdb_file)
process_structure(params, processed_pdb_file, tmp_dir, log, assume_hydrogens_all_missing=None)
run_ksdssp(file_name, log=<open file '<stdout>', mode 'w'>)
run_ksdssp_direct(pdb_str)
sec_str_from_phil(phil_str)
sqrt(...)
sqrt(x)
 
Return the square root of x.

 
Data
        default_params = <libtbx.phil.scope_extract object>
division = _Feature((2, 2, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 8192)
sec_str_master_phil = <libtbx.phil.scope object>
sec_str_master_phil_str = '\ninput\n .style = box auto_align\n{\n\n file_name ...\n# TODO\n# planar = False\n# .type = bool\n}\n\n}\n'
ss_group_params_str = '\nhelix\n .multiple = True\n .optional = True\n ....traints which are already backbone-only.\n}\n'
ss_restraint_params_str = '\n verbose = False\n .type = bool\n substitute....type = float\n top_out = False\n .type = bool\n'
ss_tardy_params_str = ''