mmtbx.tls package¶
Submodules¶
mmtbx.tls.command_line module¶
- mmtbx.tls.command_line.run(args, command_name='phenix.tls')¶
mmtbx.tls.ladp module¶
- mmtbx.tls.ladp.check_u_cart(axis, u_cart)¶
- mmtbx.tls.ladp.get_axes_and_atoms_i_seqs(pdb_hierarchy, mon_lib_srv)¶
- mmtbx.tls.ladp.set_ladp(xray_structure, axes_and_atoms_i_seqs, value, depth, enable_recursion=True)¶
mmtbx.tls.tls_as_xyz module¶
- class mmtbx.tls.tls_as_xyz.ensemble_generator(tls_from_motions_object, pdb_hierarchy, xray_structure, n_models, origin, use_states=True, log=None)¶
Bases:
object- write_pdb_file(file_name)¶
- mmtbx.tls.tls_as_xyz.formula_49(r, log, eps=1e-07)¶
Generate shifts from group translation.
- mmtbx.tls.tls_as_xyz.print_step(s, log)¶
- mmtbx.tls.tls_as_xyz.run(pdb_file_name, n_models, log, output_file_name_prefix, eps=1e-07)¶
- mmtbx.tls.tls_as_xyz.step_i__compute_delta_L_r_dp(r, r_L, dx0, dy0, dz0)¶
- mmtbx.tls.tls_as_xyz.step_i__get_dxdydz(r, log, eps=1e-07)¶
Generation of shifts from screw rotations.
mmtbx.tls.tools module¶
- mmtbx.tls.tools.combine_tls_and_u_local(xray_structure, tls_selections, tls_groups)¶
- mmtbx.tls.tools.extract_tls_from_pdb(pdb_inp_tls, model)¶
- mmtbx.tls.tools.finite_differences_grads_of_xray_target_wrt_tls(target_functor, T, L, S, origins, selections, delta=1e-05)¶
- mmtbx.tls.tools.generate_tlsos(selections, xray_structure, value=None, T=None, L=None, S=None)¶
- mmtbx.tls.tools.get_u_cart(o_tfm, origin, sites_cart)¶
- mmtbx.tls.tools.make_tlso_compatible_with_u_positive_definite(xray_structure, selections, max_iterations, number_of_u_nonpositive_definite, eps, number_of_macro_cycles_for_tls_from_uanisos, tlsos=None, refine_T=True, refine_L=True, refine_S=True, out=None)¶
- mmtbx.tls.tools.remark_3_tls(tlsos, selection_strings, out=None)¶
- mmtbx.tls.tools.show_times(out=None)¶
- mmtbx.tls.tools.split_u(xray_structure, tls_selections, offset)¶
- mmtbx.tls.tools.tls_from_pdb_inp(remark_3_records, pdb_hierarchy)¶
- mmtbx.tls.tools.tls_from_u_cart(xray_structure, tlsos_initial, tls_selections, number_of_macro_cycles=100, max_iterations=100)¶
- class mmtbx.tls.tools.tls_from_uaniso_minimizer(uaniso, T_initial, L_initial, S_initial, refine_T, refine_L, refine_S, origin, sites, max_iterations)¶
Bases:
object- compute_functional_and_gradients()¶
- pack(T, L, S)¶
- unpack_x()¶
- mmtbx.tls.tools.tls_from_uanisos(xray_structure, selections, tlsos_initial, number_of_macro_cycles=3000, max_iterations=1000, refine_T=True, refine_L=True, refine_S=True, verbose=-1, enforce_positive_definite_TL=True, out=None)¶
- class mmtbx.tls.tools.tls_from_uiso_minimizer(uiso, T_initial, L_initial, S_initial, refine_T, refine_L, refine_S, origin, sites, max_iterations)¶
Bases:
object- compute_functional_and_gradients()¶
- pack(T, L, S)¶
- unpack_x()¶
- class mmtbx.tls.tools.tls_groups(tlsos=None, selection_strings=None, iselections=None)¶
Bases:
object- as_cif_block(hierarchy, cif_block=None, scattering_type=None)¶
- select(selection, n_atoms)¶
- class mmtbx.tls.tools.tls_refinement(fmodel, model, selections, selections_1d, refine_T, refine_L, refine_S, number_of_macro_cycles, max_number_of_iterations, start_tls_value=None, run_finite_differences_test=False, eps=1e-06, out=None, macro_cycle=None, verbose=True)¶
Bases:
object
- class mmtbx.tls.tools.tls_xray_target_minimizer(fmodel, tlsos_initial, refine_T, refine_L, refine_S, selections, selections_1d, max_iterations, run_finite_differences_test=False, correct_adp=True)¶
Bases:
object- compute_functional_and_gradients()¶
- pack(T, L, S)¶
- unpack_x()¶
- mmtbx.tls.tools.u_cart_from_ensemble(models)¶
- mmtbx.tls.tools.u_cart_from_tls(sites_cart, selections, tlsos)¶
- class mmtbx.tls.tools.u_tls_vs_u_ens(pdb_str, dx=0, dy=0, dz=0, sx=0, sy=0, sz=0, lx=[1, 0, 0], ly=[0, 1, 0], lz=[0, 0, 1], tx=0, ty=0, tz=0, vx=[1, 0, 0], vy=[0, 1, 0], vz=[0, 0, 1], w_M_lx=[0, 0, 0], w_M_ly=[0, 0, 0], w_M_lz=[0, 0, 0], origin=None, n_models=10000, assert_similarity=True, show=False, log=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, write_pdb_files=False, smear_eps=0)¶
Bases:
object
- mmtbx.tls.tools.update_xray_structure_with_tls(xray_structure, selections, tlsos, selections_1d=None, correct_adp=True)¶
- mmtbx.tls.tools.water_in_tls_selections(tls_selections, pdb_hierarchy)¶