def _filter_by_sphericity(self):
sel = flex.bool(self.xrs_water.scatterers().size(), False)
for i, site_frac in enumerate(self.xrs_water.sites_frac()):
site_cart = self.unit_cell.orthogonalize(site_frac)
o = maptbx.sphericity_by_heuristics(map_data=self.map_data,
unit_cell=self.unit_cell,
center_cart=site_cart,
radius=1.0)
mi, ma, me = o.rho
#if(self.debug):
# _debug_show_all_plots(
# map_data = self.map_data,
# unit_cell = self.unit_cell,
# center_cart = site_cart,
# radius = 1.0,
# plot_number = str("%d_%4.2f_%4.2f"%(i, o.ccs[0],o2.ccs[0])))
if (o.ccs[0] > self.scc):
sel[i] = True
#print i, "%6.3f %6.3f %6.3f"%mv.min_max_mean().as_tuple(),\
# "%6.3f %6.3f %6.3f"%ccs.min_max_mean().as_tuple(),\
# "%6.3f %6.3f %6.3f"%ccs2.min_max_mean().as_tuple()
# print(hoh_str%(i,i,sc[0],sc[1],sc[2]), file=of)
#else:
# print(hoh_str%(i,i,sc[0],sc[1],sc[2]), file=of2)
# #print i, "%6.3f %6.3f %6.3f"%mv.min_max_mean().as_tuple(),\
# # "%6.3f %6.3f %6.3f"%ccs.min_max_mean().as_tuple(),\
# # "%6.3f %6.3f %6.3f"%ccs2.min_max_mean().as_tuple(), "<<< REJECTED"
self.xrs_water = self.xrs_water.select(sel)
self.ma.add(" peaks left: %d" % self.xrs_water.scatterers().size())
def _show_peak_profiles(self):
for i, site_frac in enumerate(self.sites_frac_water):
site_cart = self.unit_cell.orthogonalize(site_frac)
o = maptbx.sphericity_by_heuristics(map_data=self.map_data,
unit_cell=self.unit_cell,
center_cart=site_cart,
radius=0.5)
o2 = maptbx.sphericity_by_heuristics(map_data=self.map_data,
unit_cell=self.unit_cell,
center_cart=site_cart,
radius=1.0)
_debug_show_all_plots(
map_data=self.map_data,
unit_cell=self.unit_cell,
center_cart=site_cart,
radius=1.0,
plot_number=str("%d_%4.2f_%4.2f" %
(i + 1, o.ccs[0], o2.ccs[0])))
def _filter_by_sphericity(self):
tmp = flex.vec3_double()
for i, site_frac in enumerate(self.sites_frac_water):
site_cart = self.unit_cell.orthogonalize(site_frac)
# XXX make it so it is called once! XXX
o = maptbx.sphericity_by_heuristics(map_data=self.map_data,
unit_cell=self.unit_cell,
center_cart=site_cart,
radius=0.5)
o2 = maptbx.sphericity_by_heuristics(map_data=self.map_data,
unit_cell=self.unit_cell,
center_cart=site_cart,
radius=1.0)
mi, ma, me = o.rho
if (self.debug):
_debug_show_all_plots(
map_data=self.map_data,
unit_cell=self.unit_cell,
center_cart=site_cart,
radius=1.0,
plot_number=str("%d_%4.2f_%4.2f" %
(i, o.ccs[0], o2.ccs[0])))
fl = (mi > 0 and ma > 0 and me > 0 and o.ccs[0] > 0.95
and o2.ccs[0] > 0.90)
if (fl):
tmp.append(site_frac)
#print i, "%6.3f %6.3f %6.3f"%mv.min_max_mean().as_tuple(),\
# "%6.3f %6.3f %6.3f"%ccs.min_max_mean().as_tuple(),\
# "%6.3f %6.3f %6.3f"%ccs2.min_max_mean().as_tuple()
# print(hoh_str%(i,i,sc[0],sc[1],sc[2]), file=of)
#else:
# print(hoh_str%(i,i,sc[0],sc[1],sc[2]), file=of2)
# #print i, "%6.3f %6.3f %6.3f"%mv.min_max_mean().as_tuple(),\
# # "%6.3f %6.3f %6.3f"%ccs.min_max_mean().as_tuple(),\
# # "%6.3f %6.3f %6.3f"%ccs2.min_max_mean().as_tuple(), "<<< REJECTED"
self.sites_frac_water = tmp
self.ma.add(" peaks left: %d" % self.sites_frac_water.size())