mmtbx.geometry_restraints package¶
Submodules¶
mmtbx.geometry_restraints.c_beta module¶
- mmtbx.geometry_restraints.c_beta.get_c_beta_torsion_proxies(pdb_hierarchy, selection=None, sigma=2.5)¶
- mmtbx.geometry_restraints.c_beta.get_cb_target_angle_pair(resname)¶
mmtbx.geometry_restraints.external module¶
Accessory module for interfacing phenix.refine (or similar programs) with various external third-party software such as AFITT, DivCon, Schrodinger.
- mmtbx.geometry_restraints.external.is_schrodinger_installed(env)¶
Check if Schrodinger is installed and interface requested. Schrodinger is installed if SCHRODINGER env variable is set to root directory and if PHENIX_SCHRODINGER env variable is set.
mmtbx.geometry_restraints.flags module¶
mmtbx.geometry_restraints.hbond module¶
mmtbx.geometry_restraints.ramachandran module¶
- mmtbx.geometry_restraints.ramachandran.is_proxy_present(proxies, n_seq, proxy)¶
- mmtbx.geometry_restraints.ramachandran.load_emsley8k_tables()¶
- mmtbx.geometry_restraints.ramachandran.load_phi_psi_2_tables()¶
- mmtbx.geometry_restraints.ramachandran.load_tables()¶
- class mmtbx.geometry_restraints.ramachandran.ramachandran_manager(pdb_hierarchy, params=None, log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, proxies=None, tables=None, initialize=True)¶
Bases:
object- append_emsley8k_proxies(proxy, n_seq)¶
- append_emsley_proxies(proxy, n_seq)¶
- append_oldfield_proxies(proxy, n_seq)¶
- append_phi_psi_2_proxies(proxy, n_seq)¶
- extract_proxies(hierarchy)¶
- get_n_emsley8k_proxies()¶
- get_n_emsley_proxies()¶
- get_n_oldfield_proxies()¶
- get_n_phi_psi_2_proxies()¶
- get_n_proxies()¶
- proxy_select(n_seq, iselection)¶
- show_sorted(by_value, sites_cart, site_labels=None, proxy_label=None, f=None, prefix='', max_items=None)¶
- target_and_gradients(unit_cell, sites_cart, gradient_array=None)¶
- update_phi_psi_targets(hierarchy)¶
- update_phi_psi_targets_on_init(hierarchy)¶
mmtbx.geometry_restraints.reference module¶
- mmtbx.geometry_restraints.reference.add_coordinate_restraints(sites_cart, selection=None, sigma=0.5, limit=1.0, top_out_potential=False)¶
- mmtbx.geometry_restraints.reference.exclude_outliers_from_reference_restraints_selection(pdb_hierarchy, restraints_selection)¶
- mmtbx.geometry_restraints.reference.generate_torsion_restraints(pdb_hierarchy, sites_cart, selection=None, sigma=2.5, limit=15.0, chi_angles_only=False, top_out_potential=False, origin_id=None)¶
- selection ties up hierarchy with sites cart. Basically, if applied
to hierarchy, remaining atoms should correspond to sites_cart. Therefore it is necessary that len(sites_cart) == len(actual_selection) below. This seems to be done this way to make it possible to use sites_cart from another source (reference model) which is not necessary of the same size as hierarchy.
- mmtbx.geometry_restraints.reference.get_selection_to_sites_map(sites_cart, selection)¶