mmtbx.secondary_structure package

Subpackages

Submodules

mmtbx.secondary_structure.base_pairing module

mmtbx.secondary_structure.dssp module

mmtbx.secondary_structure.proteins module

mmtbx.secondary_structure.proteins.create_helix_hydrogen_bond_proxies(params, pdb_hierarchy, selection_cache, weight, hbond_counts, distance_ideal, distance_cut, remove_outliers, restrain_hbond_angles, log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
mmtbx.secondary_structure.proteins.create_sheet_hydrogen_bond_proxies(sheet_params, pdb_hierarchy, selection_cache, weight, hbond_counts, distance_ideal, distance_cut, remove_outliers, restrain_hbond_angles, log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
class mmtbx.secondary_structure.proteins.find_helices_simple(pdb_hierarchy)

Bases: object

Identify helical regions, defined as any three or more contiguous residues with phi and psi within specified limits:

-120 < phi < -20 -80 < psi < -10

This is much more tolerant of distorted models than KSDSSP, but will still miss helices in poor structures.

as_pdb_records()
as_restraint_group_phil()
as_restraint_groups()
build_selections()
process_break()
push_back(chain_id, resseq)
run()
show(out=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
mmtbx.secondary_structure.proteins.is_approximately_helical(phi, psi)

mmtbx.secondary_structure.utils module

mmtbx.secondary_structure.utils.get_residue_name_from_selection(resi_sele, selection_cache, atoms)
mmtbx.secondary_structure.utils.hydrogen_bond_from_selection_pair(donor_sele, acceptor_sele, selection_cache)

Module contents

mmtbx.secondary_structure.contiguous_ss_selections(pdb_hierarchy)

Return list of atom selections that contiguous split molecule by SS and loops.

mmtbx.secondary_structure.get_ksdssp_exe_path()
class mmtbx.secondary_structure.manager(pdb_hierarchy, atom_selection_cache=None, geometry_restraints_manager=None, sec_str_from_pdb_file=None, params=None, was_initialized=False, mon_lib_srv=None, verbose=-1, show_summary_on=True, log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)

Bases: object

apply_phil_str(phil_string, phil_params=None, annot=None, log=None, verbose=False)
as_phil_str(master_phil=<libtbx.phil.scope object>)
base_pair_selection(**kwds)
base_pair_selections(limit=None, main_conf_only=False)
beta_selection(**kwds)
beta_selections(limit=None, main_conf_only=False)
calculate_structure_content()
create_all_new_restraints(pdb_hierarchy, grm, log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
create_protein_hbond_proxies(annotation=None, log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
find_approximate_helices(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
find_automatically()
find_base_pairs(log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, use_segid=False, segids=None)
find_sec_str(pdb_hierarchy)
static get_default_ss_params()
get_helix_types()
get_simple_bonds(selection_phil=None)
helix_selection(**kwds)
helix_selections(limit=None, main_conf_only=False, alpha_only=False)
initialize()
records_for_pdb_file()
show_summary(log=None)
mmtbx.secondary_structure.run_ksdssp(file_name, log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)
mmtbx.secondary_structure.run_ksdssp_direct(pdb_str)
mmtbx.secondary_structure.sec_str_from_phil(phil_str)