mmtbx.solvent package¶
Submodules¶
mmtbx.solvent.ensemble_ordered_solvent module¶
- class mmtbx.solvent.ensemble_ordered_solvent.manager(fmodel, model, verbose=-1, params=None, velocities=None, log=None)¶
Bases:
object- add_new_solvent()¶
- compare_peaks_with_positions()¶
- find_peaks(map_type, map_cutoff)¶
- is_water_last()¶
- move_solvent_to_the_end_of_atom_list()¶
- randomize_new_velocities()¶
- randomize_velocity()¶
- remove_solvent()¶
- reset_solvent(solvent_selection, solvent_xray_structure)¶
- show(message=None)¶
- mmtbx.solvent.ensemble_ordered_solvent.master_params()¶
mmtbx.solvent.ordered_solvent module¶
- mmtbx.solvent.ordered_solvent.filter_by_distance(model, fix_altlocs_and_filter_was_run, dist_min=1.8, dist_max=3.2)¶
- mmtbx.solvent.ordered_solvent.fix_altlocs_and_filter(model, dist_min=1.8, fix_only=False)¶
- mmtbx.solvent.ordered_solvent.get_sphere_selection(sites_cart_all, special_position_settings, radius, i_seq)¶
- mmtbx.solvent.ordered_solvent.get_unique_altloc(exclude)¶
- mmtbx.solvent.ordered_solvent.get_unique_altloc2(available, exclude)¶
- class mmtbx.solvent.ordered_solvent.manager(fmodel, fmodels, model, is_neutron_scat_table, params=<libtbx.phil.scope_extract object>, find_peaks_params=None, log=<colorama.ansitowin32.StreamWrapper object>)¶
Bases:
object- refine_oat()¶
- class mmtbx.solvent.ordered_solvent.maps(fmodel, model, mask_atoms_selection, difference_map_type, model_map_type, data_map_type, grid_step=0.6, radius=2.0)¶
Bases:
object- score_atom(atom, min_cc, min_value)¶
- mmtbx.solvent.ordered_solvent.master_params()¶