mmtbx.ias package¶
Module contents¶
- mmtbx.ias.add_lone_pairs_for_peptyde_o(site_c, site_o, site_ca, dist_co, R=0.35, ALPHA=66.635468, small=1e-06)¶
- class mmtbx.ias.atom(site_cart=None, q=None, b_iso=None, name=None, i_seq=None, element=None)¶
Bases:
object
- class mmtbx.ias.bond_density(data=None, dist=None, ideal_data=None, one_dim_point=None, one_dim_point_predicted=None, peak_data=None, peak_dist=None)¶
Bases:
object
- mmtbx.ias.check_at_bond_vector(ias)¶
- class mmtbx.ias.extract_ias(xray_structure, bond_proxies_simple, pdb_atoms, planarity_proxies, params, log=None)¶
Bases:
object
- class mmtbx.ias.find_peak_at_bond(map_data, unit_cell, label, site_cart_1, site_cart_2, step=0.005)¶
Bases:
object- find_peak(peak_width=0.3, offset=0.1)¶
- set_status()¶
- class mmtbx.ias.ias(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)¶
Bases:
object- deep_copy()¶
- mmtbx.ias.ias_position_at_lone_pairs(ias, params)¶
- mmtbx.ias.ias_site_position(site_i, site_j, alp)¶
- class mmtbx.ias.manager(geometry, pdb_atoms, xray_structure, params=None, fmodel=None, file_name=None, log=None)¶
Bases:
object- all_bonds(iass, file_name)¶
- get_ias_selection()¶
- iass_as_xray_structure(iass)¶
- set_ias_selection(ias_selection)¶
- setup_ias_selection()¶
- write_pdb_file(out=None)¶
- mmtbx.ias.set_ias_name_and_predicted_position(iass, params)¶
- mmtbx.ias.set_peaks(iass, fmodel, grid_step, map_type, scaling)¶
- mmtbx.ias.set_status(iass, params)¶