def asu_omit_map_as_sf(m_asu, s, e):
m_asu_omit = maptbx.set_box_copy(value = 0, map_data_to = m_asu,
start = s, end = e)
m_asu_omit.reshape(self.acc_asu)
asu_m_omit = asu_map_ext.asymmetric_map(self.sgt, m_asu_omit, self.n_real)
return self.zero_cmpl_ma.customized_copy(
indices = self.zero_cmpl_ma.indices(),
data = asu_m_omit.structure_factors(self.zero_cmpl_ma.indices()))
def __init__(self,
crystal_gridding,
fmodel,
map_type,
max_boxes,
box_size_as_fraction=None):
sgt = fmodel.f_obs().space_group().type()
assert sgt.number() == 1
def get_map(fmodel, map_type, external_complete_set=None):
f_map = fmodel.electron_density_map().map_coefficients(
map_type=map_type, isotropize=True, fill_missing=False)
fft_map = miller.fft_map(crystal_gridding=crystal_gridding,
fourier_coefficients=f_map)
return fft_map.real_map_unpadded()
f_model = fmodel.f_model_scaled_with_k1()
fft_map = miller.fft_map(crystal_gridding=crystal_gridding,
fourier_coefficients=f_model)
f_model_map_data = fft_map.real_map_unpadded()
zero_complex_ma = f_model.customized_copy(
data=flex.complex_double(f_model.data().size(), 0))
b = maptbx.boxes(fraction=0.3,
n_real=f_model_map_data.focus(),
max_boxes=max_boxes,
log=sys.stdout)
self.map_result = flex.double(flex.grid(b.n_real))
self.r = flex.double()
for s, e in zip(b.starts, b.ends):
f_model_map_data_omit = maptbx.set_box_copy(
value=0, map_data_to=f_model_map_data, start=s, end=e)
f_model_omit = f_model.structure_factors_from_map(
map=f_model_map_data_omit,
use_scale=True,
anomalous_flag=False,
use_sg=False)
fmodel_ = mmtbx.f_model.manager(f_obs=fmodel.f_obs(),
r_free_flags=fmodel.r_free_flags(),
f_calc=f_model_omit,
f_mask=zero_complex_ma)
self.r.append(fmodel_.r_work())
f_map_data = get_map(fmodel=fmodel_, map_type=map_type)
etmp = [e[0] - 1, e[1] - 1,
e[2] - 1] # because .copy() includes right edge
box = maptbx.copy(f_map_data, s, etmp)
box.reshape(flex.grid(box.all()))
maptbx.set_box(map_data_from=box,
map_data_to=self.map_result,
start=s,
end=e)
sd = self.map_result.sample_standard_deviation()
self.map_result = self.map_result / sd
self.map_coefficients = fmodel.f_obs().structure_factors_from_map(
map=self.map_result,
use_scale=True,
anomalous_flag=False,
use_sg=False)
def omit_box(self, s, e, md_asu):
md_asu_omit = maptbx.set_box_copy(value = 0, map_data_to = md_asu,
start = s, end = e)
md_asu_omit.reshape(self.acc)
asu_map_omit = asu_map_ext.asymmetric_map(self.sgt, md_asu_omit, self.n_real)
ma_omit = self.zero_cmpl_ma.customized_copy(
indices = self.zero_cmpl_ma.indices(),
data = asu_map_omit.structure_factors(self.zero_cmpl_ma.indices()))
fft_map = cctbx.miller.fft_map(
crystal_gridding = self.crystal_gridding, fourier_coefficients = ma_omit)
md = fft_map.real_map_unpadded()
asu_map = asu_map_ext.asymmetric_map(self.sgt, md)
md_asu_omit = asu_map.data()
md_asu_omit = md_asu_omit.shift_origin()
return ma_omit, md_asu_omit
def omit_box(self, s, e, md_asu):
md_asu_omit = maptbx.set_box_copy(value=0,
map_data_to=md_asu,
start=s,
end=e)
md_asu_omit.reshape(self.acc)
asu_map_omit = asu_map_ext.asymmetric_map(self.sgt, md_asu_omit,
self.n_real)
ma_omit = self.zero_cmpl_ma.customized_copy(
indices=self.zero_cmpl_ma.indices(),
data=asu_map_omit.structure_factors(self.zero_cmpl_ma.indices()))
fft_map = cctbx.miller.fft_map(crystal_gridding=self.crystal_gridding,
fourier_coefficients=ma_omit)
md = fft_map.real_map_unpadded()
asu_map = asu_map_ext.asymmetric_map(self.sgt, md)
md_asu_omit = asu_map.data()
md_asu_omit = md_asu_omit.shift_origin()
return ma_omit, md_asu_omit
def __init__(
self,
crystal_gridding,
fmodel,
map_type,
max_boxes,
box_size_as_fraction=None):
sgt = fmodel.f_obs().space_group().type()
assert sgt.number() == 1
def get_map(fmodel, map_type, external_complete_set=None):
f_map = fmodel.electron_density_map().map_coefficients(
map_type = map_type,
isotropize = True,
fill_missing = False)
fft_map = miller.fft_map(
crystal_gridding = crystal_gridding,
fourier_coefficients = f_map)
return fft_map.real_map_unpadded()
f_model = fmodel.f_model_scaled_with_k1()
fft_map = miller.fft_map(
crystal_gridding = crystal_gridding,
fourier_coefficients = f_model)
f_model_map_data = fft_map.real_map_unpadded()
zero_complex_ma = f_model.customized_copy(
data = flex.complex_double(f_model.data().size(), 0))
b = maptbx.boxes(
fraction = 0.3,
n_real = f_model_map_data.focus(),
max_boxes=max_boxes,
log=sys.stdout)
self.map_result = flex.double(flex.grid(b.n_real))
self.r = flex.double()
for s,e in zip(b.starts, b.ends):
f_model_map_data_omit = maptbx.set_box_copy(
value = 0,
map_data_to = f_model_map_data,
start = s,
end = e)
f_model_omit = f_model.structure_factors_from_map(
map = f_model_map_data_omit,
use_scale = True,
anomalous_flag = False,
use_sg = False)
fmodel_ = mmtbx.f_model.manager(
f_obs = fmodel.f_obs(),
r_free_flags = fmodel.r_free_flags(),
f_calc = f_model_omit,
f_mask = zero_complex_ma)
self.r.append(fmodel_.r_work())
f_map_data = get_map(fmodel=fmodel_, map_type=map_type)
etmp = [e[0]-1, e[1]-1, e[2]-1] # because .copy() includes right edge
box = maptbx.copy(f_map_data, s, etmp)
box.reshape(flex.grid(box.all()))
maptbx.set_box(
map_data_from = box,
map_data_to = self.map_result,
start = s,
end = e)
sd = self.map_result.sample_standard_deviation()
self.map_result = self.map_result/sd
self.map_coefficients = fmodel.f_obs().structure_factors_from_map(
map = self.map_result,
use_scale = True,
anomalous_flag = False,
use_sg = False)
