mmtbx.hydrogens package¶

Submodules¶

mmtbx.hydrogens.build_hydrogens module¶

mmtbx.hydrogens.build_hydrogens.add_arg_like_h(site_0, site_1, site_2, d, alpha, flag)¶

mmtbx.hydrogens.build_hydrogens.add_ca_ha1_and_ha2(site_0, site_1, site_2, d0, alpha, beta)¶

mmtbx.hydrogens.build_hydrogens.add_ca_ha1_or_ha2(site_0, site_1, site_2, site_3, d0, alpha, beta, gamma)¶

mmtbx.hydrogens.build_hydrogens.add_hhh(site_0, site_1, d0, alpha, beta)¶

mmtbx.hydrogens.build_hydrogens.add_ring_h(site_0, site_1, site_2, d0, alpha, beta)¶

mmtbx.hydrogens.build_hydrogens.regularize_model(xray_structure, geometry_restraints_manager, max_iterations)¶

mmtbx.hydrogens.build_hydrogens.run(file_name)¶

mmtbx.hydrogens.build_hydrogens.write_atoms(monomer_mapping, atom_number, file_object, new_atom_name=None, new_atom_coordinates=None, crystal_symmetry=None)¶

mmtbx.hydrogens.find module¶

mmtbx.hydrogens.find.all_master_params()¶

mmtbx.hydrogens.find.assert_water_is_consistent(model)¶

mmtbx.hydrogens.find.atom_as_str(atom)¶

mmtbx.hydrogens.find.atom_scat(atom, scat)¶

mmtbx.hydrogens.find.build_dod_and_od(model, fmodels, log=None, params=None)¶

mmtbx.hydrogens.find.build_water_hydrogens_from_map(model, fmodel, params=None, log=None)¶

mmtbx.hydrogens.find.build_water_hydrogens_from_map2(model, fmodel, params=None, log=None)¶

mmtbx.hydrogens.find.choose_h_for_water(unit_cell, o_site, xyz_h, h1_site=None, min_dod_angle=80, max_dod_angle=170)¶

mmtbx.hydrogens.find.distances_to_peaks(xray_structure, sites_frac, peak_heights, distance_cutoff, use_selection=None)¶

mmtbx.hydrogens.find.extract_hoh_peaks(peaks, pdb_hierarchy, pdb_atoms, xray_structure)¶

mmtbx.hydrogens.find.find_hydrogen_peaks(fmodel, pdb_atoms, params, log)¶

mmtbx.hydrogens.find.fit_water(water_and_peaks, xray_structure, params, log)¶

mmtbx.hydrogens.find.get_pdb_oxygen(water_residue_group)¶

class mmtbx.hydrogens.find.h_peak(site_frac, height, dist, scatterer_o, pdb_atom_o, i_seq_o)¶: Bases: object

mmtbx.hydrogens.find.insert_atom_into_model(xs, atom, atom_name, site_frac, occupancy, uiso, element)¶

mmtbx.hydrogens.find.len_peaks(set_of_peaks)¶

mmtbx.hydrogens.find.make_peak_dict(peaks, selection, obs_map, cutoff)¶

mmtbx.hydrogens.find.map_peak_filter(sites_frac, obs_map, cutoff)¶

mmtbx.hydrogens.find.match_dod(unit_cell, xyz_h, min_od=0.5, max_od=1.35, min_dod_angle=85.0, max_dod_angle=170.0)¶

mmtbx.hydrogens.find.match_od(unit_cell, xyz_h, min_od=0.5, max_od=1.35)¶

mmtbx.hydrogens.find.obs_map(fmodel, map_type, resolution_factor=0.25)¶

mmtbx.hydrogens.find.one_water_correlation(model, fmodels, water)¶

mmtbx.hydrogens.find.print_atom(out, atom)¶

mmtbx.hydrogens.find.print_scat(out, s)¶

mmtbx.hydrogens.find.print_scats(xray_structure, fn)¶

mmtbx.hydrogens.find.remove_zero_occupancy(model, min_occupancy=0.05, max_b_iso=80.0)¶

mmtbx.hydrogens.find.run(fmodel, model, log, params=None)¶

mmtbx.hydrogens.find.scatterers_info(scatterers, selection)¶

mmtbx.hydrogens.find.select_one_water(water_residue_group, n_atoms)¶

class mmtbx.hydrogens.find.water_and_peaks(i_seq_o, i_seq_h1, i_seq_h2, peaks_sites_frac)¶: Bases: object

mmtbx.hydrogens.find.water_bond_angle(o, h1, h2)¶

mmtbx.hydrogens.find.water_map_correlations(model, fmodels, log=None)¶

Module contents¶

mmtbx.hydrogens.count_rotatable(selections)¶

mmtbx.hydrogens.fit_rotatable(pdb_hierarchy, xray_structure, map_data, rotatable_h_selection)¶

mmtbx.hydrogens.fit_rotatable2(model, fmodel, use_electron_xh=True)¶: Slow, OMIT map based fitting of rotatable H.

class mmtbx.hydrogens.map_manager(fmodel, map_type)¶

Bases: object

score(sites_cart)¶

update_omit_map(omit_selection)¶

mmtbx.hydrogens.rotatable(pdb_hierarchy, mon_lib_srv, restraints_manager, log, use_shortcut=True)¶: General tool to identify rotatable H, such as C-O-H, C-H3, in any molecule.

mmtbx.hydrogens.run_fit_rotatable(fmodel, ref_model, angular_step, log=None, use_h_omit_map=False, map_type='2mFo-DFc')¶

mmtbx.hydrogens.shortcut(residue, first, log)¶: Avoid TARDY, huge speedup for huge structures!