mmtbx.den package

Submodules

mmtbx.den.plot_weights module

mmtbx.den.plot_weights.exercise()

mmtbx.den.plot_weights.plot_weights_pyplot(gamma, weight, z)

mmtbx.den.refinement module

class mmtbx.den.refinement.manager(fmodels, model, params, target_weights, macro_cycle, ncs_manager=None, log=None)

Bases: object

adp_refinement(log)

bulk_solvent_and_scale(log)

minimize(ca_only=False)

show_den_opt_summary_cartesian(grid_results)

show_den_opt_summary_torsion(grid_results)

try_den_weight_cartesian(grid_pair)

try_den_weight_torsion(grid_pair)

Module contents

class mmtbx.den.den_restraints(pdb_hierarchy, params, pdb_hierarchy_ref=None, log=None, den_proxies=None)

Bases: object

build_den_proxies(pdb_hierarchy)

build_den_restraints()

check_den_pair_consistency()

count_atoms_per_chain(pdb_hierarchy)

dump_den_network()

find_atom_pairs(pdb_hierarchy, resid_hash)

get_current_eq_distances()

get_den_atom_pairs()

get_n_proxies()

get_optimization_grid()

get_selection_strings()

import_eq_distances(eq_distances)

load_den_network()

output_kinemage(sites_cart)

proxy_select(n_seq, selection)

remove_non_matching_pairs()

select_random_den_restraints()

show_den_summary(sites_cart)

target_and_gradients(unit_cell, sites_cart, gradient_array)

update_eq_distances(sites_cart)

mmtbx.den.distance_squared(a, b)