def truncate_with_roots(m,
fmodel,
c1,
c2,
cutoff,
scale,
zero_all_interblob_region=True,
as_int=False,
average_peak_volume=None,
selection=None):
assert c1 >= c2
if (average_peak_volume is None):
sites_cart = fmodel.xray_structure.sites_cart()
if (selection is not None):
sites_cart = sites_cart.select(selection)
average_peak_volume = maptbx.peak_volume_estimate(
map_data=m,
sites_cart=sites_cart,
crystal_symmetry=fmodel.xray_structure.crystal_symmetry(),
cutoff=cutoff)
if (average_peak_volume is None
or int(average_peak_volume * scale) - 1 == 0):
return None
average_peak_volume = int(
average_peak_volume * scale /
2) - 1 # XXX "/2" is ad hoc and I don't know why!
co1 = maptbx.connectivity(map_data=m, threshold=c1)
co2 = maptbx.connectivity(map_data=m, threshold=c2)
result = co2.noise_elimination_two_cutoffs(
connectivity_object_at_t1=co1,
elimination_volume_threshold_at_t1=average_peak_volume,
zero_all_interblob_region=zero_all_interblob_region)
if (as_int): return result
else: return result.as_double()
def run_group(symbol):
group = space_group_info(symbol)
elements = ('C', ) * 10
xrs = random_structure.xray_structure(space_group_info=group,
volume_per_atom=50.,
general_positions_only=True,
elements=elements,
min_distance=2.0,
u_iso=0.1)
d_min = 2.
fc = xrs.structure_factors(d_min=d_min).f_calc()
symmetry_flags = None #maptbx.use_space_group_symmetry
fft_map = fc.fft_map(symmetry_flags=symmetry_flags,
resolution_factor=1. / 5)
fft_map.apply_volume_scaling()
map_data = fft_map.real_map_unpadded()
#
r = maptbx.peak_volume_estimate(map_data=map_data,
sites_cart=xrs.sites_cart(),
crystal_symmetry=xrs.crystal_symmetry(),
cutoff=0.3,
atom_radius=1.5)
result.append(r)
def run_group(symbol):
group = space_group_info(symbol);
elements = ('C',)*10
xrs = random_structure.xray_structure(
space_group_info = group,
volume_per_atom = 50.,
general_positions_only = True,
elements = elements,
min_distance = 2.0,
u_iso=0.1)
d_min = 2.
fc = xrs.structure_factors(d_min=d_min).f_calc()
symmetry_flags = None#maptbx.use_space_group_symmetry
fft_map = fc.fft_map(symmetry_flags = symmetry_flags, resolution_factor=1./5)
fft_map.apply_volume_scaling()
map_data = fft_map.real_map_unpadded()
#
r = maptbx.peak_volume_estimate(
map_data = map_data,
sites_cart = xrs.sites_cart(),
crystal_symmetry = xrs.crystal_symmetry(),
cutoff = 0.3,
atom_radius = 1.5)
result.append(r)
def truncate_with_roots(
m, fmodel, c1, c2, cutoff, scale, zero_all_interblob_region=True,
as_int=False, average_peak_volume=None, selection=None):
assert c1>=c2
if(average_peak_volume is None):
sites_cart = fmodel.xray_structure.sites_cart()
if(selection is not None):
sites_cart = sites_cart.select(selection)
average_peak_volume = maptbx.peak_volume_estimate(
map_data = m,
sites_cart = sites_cart,
crystal_symmetry = fmodel.xray_structure.crystal_symmetry(),
cutoff = cutoff)
if(average_peak_volume is None or int(average_peak_volume*scale)-1==0):
return None
average_peak_volume = int(average_peak_volume*scale/2)-1 # XXX "/2" is ad hoc and I don't know why!
co1 = maptbx.connectivity(map_data=m, threshold=c1)
co2 = maptbx.connectivity(map_data=m, threshold=c2)
result = co2.noise_elimination_two_cutoffs(
connectivity_object_at_t1=co1,
elimination_volume_threshold_at_t1=average_peak_volume,
zero_all_interblob_region=zero_all_interblob_region)
if(as_int): return result
else: return result.as_double()