cctbx.omz.dev module

cctbx.omz.dev.delta_estimation_minus_cos(limit, grad, curv)
class cctbx.omz.dev.dynamic_shift_limit_site(width)

Bases: object

neg, pos estimation: xrefine_pot first_negative_after_min(curv) neg = pos = d_min / 2

pair(x)
width
class cctbx.omz.dev.dynamic_shift_limit_u_iso(d_min)

Bases: object

d_min
pair(x)

neg, pos estimation: xrefine_pot first_negative(curv) d_min y_interc slope

0.5 0.04 1.6 1 0.06 1.5 2 0.2 1.4 3 0.4 1.3 4 0.6 1.2 5 1.4 1.1

cctbx.omz.dev.get_master_phil(iteration_limit=50, show_distances_threshold=0, bulk_solvent_correction=False, grads_mean_sq_threshold=1e-06, f_calc_options_algorithm='*direct fft', additional_phil_string='')
class cctbx.omz.dev.refinement(i_obs, f_obs, xray_structure, params, reference_structure, expected_n_refinable_parameters=None, plot_samples_id=None)

Bases: object

approx_curvs(shift_limit_factor=0.1)
build_bfgs_memory(active_infos)
calc_shelxl_wght_ls(f_cbs, need)
calc_weights_if_needed()
callback_after_step(minimizer)
classic_lbfgs()
compute_functional_and_gradients()
compute_step()
compute_step_just_grads()
compute_step_using_curvs()
developmental_algorithms()
format_rms_info()
get_active_infos(i_start=0)
get_f_calc()
get_f_cbs(f_calc=None)
get_rms_info()
lbfgs_emulation(memory_range=5)
pack_variables(xray_structure=None)
plot_samples(stage)
plot_samples_ix(stage, ix)
r1_factor()
setup_bulk_solvent_correction()
show_dests(dests)
show_rms_info()
update_dests_using_bfgs_formula(dests)
update_fgc(is_iterate=False)
cctbx.omz.dev.run_refinement(structure_ideal, structure_shake, params, i_obs=None, f_obs=None)
class cctbx.omz.dev.shift_limit_pair(neg, pos=None, curv_est_factor=0.1)

Bases: object

curv_est_factor
curv_est_shift(grad)
get(grad)
neg
pos
cctbx.omz.dev.sign0(x)
class cctbx.omz.dev.xfgc_info(work_obj, is_iterate)

Bases: object

approx_quads
check_strong_wolfe(l, pk, ak, c1, c2)
curvs
funcl
grads
is_iterate
x