def update(self, x):
if (self.refine_k): self.kbu.update(k_sols=x)
if (self.refine_b): self.kbu.update(b_sols=x)
if (self.refine_kb):
self.kbu.update(k_sols=x[:len(x) // 2], b_sols=x[len(x) // 2:])
if (self.refine_u):
#u_star = x
u_star = self.adp_constraints.all_params(list(x))
self.kbu.update(u_star=list(u_star))
if (self.use_scale):
sc = bulk_solvent.scale(self.f_obs.data(), self.kbu.data.f_model)
else:
sc = 1.0
self.t_g_c = bulk_solvent.ls_kbp_sol_u_star(f_model=self.kbu.data,
f_obs=self.f_obs.data(),
scale=sc,
kb_sol_grad=self.refine_k
or self.refine_b
or self.refine_kb,
p_sol_grad=False,
u_star_grad=self.refine_u,
kb_sol_curv=self.refine_k
or self.refine_b
or self.refine_kb,
p_sol_curv=False)
def get_k_total(self, selection=None):
if (selection is None):
selection = flex.bool(self.core.k_isotropic.size(), True)
scale = self.core.k_anisotropic.select(selection) * \
self.core.k_isotropic.select(selection) * \
self.core.k_isotropic_exp.select(selection)
scale_k1 = bulk_solvent.scale(self.f_obs.data(),
self.core.f_model.data(), selection)
return scale * scale_k1
def estimate_scale_k1(self, cutoff=4, width=1, min_reflections=500):
cutoff = min(cutoff, self.f_obs.d_min() + width)
sel_high = self.d_spacings.data() < cutoff
sel_high = sel_high & self.selection_work.data()
scale_k1 = 1
if (sel_high.count(True) > min_reflections):
core = self.core.select(selection=sel_high)
f_obs = self.f_obs.select(sel_high)
fm = core.k_isotropic_exp * core.k_anisotropic * (
core.f_calc.data() + core.k_mask() * core.f_mask().data())
scale_k1 = bulk_solvent.scale(f_obs.data(), fm)
return scale_k1
def estimate_scale_k1(self, cutoff=4, width=1, min_reflections=500):
cutoff = min(cutoff, self.f_obs.d_min()+width)
sel_high = self.d_spacings.data()<cutoff
sel_high = sel_high & self.selection_work.data()
scale_k1 = 1
if(sel_high.count(True)>min_reflections):
core = self.core.select(selection = sel_high)
f_obs = self.f_obs.select(sel_high)
fm = core.k_isotropic_exp * core.k_anisotropic * (core.f_calc.data() +
core.k_mask() * core.f_mask().data())
scale_k1 = bulk_solvent.scale(f_obs.data(), fm)
return scale_k1
def _k_isotropic_as_scale_k1(self, r_start, k_mask=None):
k_isotropic = flex.double(self.ss.size(), -1)
if (k_mask is None): k_mask = self.core.k_mask()
core_data = mmtbx.arrays.init(
f_calc=self.core.f_calc,
f_masks=self.core.f_mask(),
k_isotropic_exp=self.core.k_isotropic_exp,
k_anisotropic=self.core.k_anisotropic,
k_masks=k_mask).data
for i_cas, cas in enumerate(self.cores_and_selections):
selection, core, selection_use, sel_work = cas
scale_k1 = bulk_solvent.scale(self.f_obs.data(), core_data.f_model,
sel_work)
k_isotropic = k_isotropic.set_selected(selection, scale_k1)
assert k_isotropic.count(-1.) == 0
return k_isotropic
def _k_isotropic_as_scale_k1(self, r_start, k_mask=None):
k_isotropic = flex.double(self.ss.size(), -1)
if(k_mask is None): k_mask = self.core.k_mask()
core_data = mmtbx.arrays.init(
f_calc = self.core.f_calc,
f_masks = self.core.f_mask(),
k_isotropic_exp = self.core.k_isotropic_exp,
k_anisotropic = self.core.k_anisotropic,
k_masks = k_mask).data
for i_cas, cas in enumerate(self.cores_and_selections):
selection, core, selection_use, sel_work = cas
scale_k1 = bulk_solvent.scale(self.f_obs.data(),
core_data.f_model, sel_work)
k_isotropic = k_isotropic.set_selected(selection, scale_k1)
assert k_isotropic.count(-1.) == 0
#
r = self.try_scale(k_isotropic = k_isotropic, k_mask=k_mask)
if(r<=r_start):
self.core = self.core.update(k_isotropic = k_isotropic, k_masks=k_mask)
r_start = r
return k_isotropic
def update(self, x):
if(self.refine_k): self.kbu.update(k_sols=x)
if(self.refine_b): self.kbu.update(b_sols=x)
if(self.refine_kb):
self.kbu.update(
k_sols=x[:len(x)//2],
b_sols=x[len(x)//2:])
if(self.refine_u):
#u_star = x
u_star = self.adp_constraints.all_params(list(x))
self.kbu.update(u_star = list(u_star))
if(self.use_scale):
sc = bulk_solvent.scale(self.f_obs.data(), self.kbu.data.f_model)
else:
sc = 1.0
self.t_g_c = bulk_solvent.ls_kb_sol_u_star(
f_model = self.kbu.data,
f_obs = self.f_obs.data(),
scale = sc,
kb_sol_grad = self.refine_k or self.refine_b or self.refine_kb,
u_star_grad = self.refine_u,
kb_sol_curv = self.refine_k or self.refine_b or self.refine_kb)
def apply_overall_scale(self):
scale_k1 = bulk_solvent.scale(self.f_obs.data(),
self.core.f_model.data(),
self.selection_work.data())
self.core = self.core.update(k_isotropic=self.core.k_isotropic *
scale_k1)
def apply_overall_scale(self):
scale_k1 = bulk_solvent.scale(self.f_obs.data(),
self.core.f_model.data(), self.selection_work.data())
self.core = self.core.update(k_isotropic = self.core.k_isotropic*scale_k1)
