def get_atom_radius(xray_structure=None,
d_min=None,
map_data=None,
crystal_symmetry=None,
radius=None):
if (radius is not None): return radius
radii = []
if (d_min is not None):
radii.append(d_min)
if ([xray_structure, crystal_symmetry].count(None) == 0):
assert crystal_symmetry.is_similar_symmetry(
xray_structure.crystal_symmetry())
if ([map_data, crystal_symmetry].count(None) == 0):
d99 = maptbx.d99(map=map_data,
crystal_symmetry=crystal_symmetry).result.d99
radii.append(d99)
if (xray_structure is not None and d_min is not None):
b_iso = adptbx.u_as_b(
flex.mean(xray_structure.extract_u_iso_or_u_equiv()))
o = maptbx.atom_curves(scattering_type="C",
scattering_table="electron")
rad_image = o.image(d_min=d_min,
b_iso=b_iso,
radius_max=max(15., d_min),
radius_step=0.01).radius
radii.append(rad_image)
return max(3, min(10, max(radii)))
def _atom_radius(self):
b_iso = adptbx.u_as_b(
flex.mean(self.xray_structure.extract_u_iso_or_u_equiv()))
o = maptbx.atom_curves(scattering_type="C",
scattering_table="electron")
return o.image(d_min=self.d_min,
b_iso=b_iso,
radius_max=max(15., self.d_min),
radius_step=0.01).radius
def get_atom_radius(xray_structure=None, resolution=None, radius=None):
if(radius is not None): return radius
radii = []
if(resolution is not None):
radii.append(resolution)
if(xray_structure is not None and resolution is not None):
b_iso = adptbx.u_as_b(
flex.mean(xray_structure.extract_u_iso_or_u_equiv()))
o = maptbx.atom_curves(scattering_type="C", scattering_table="electron")
rad_image = o.image(d_min=resolution, b_iso=b_iso,
radius_max=max(15.,resolution), radius_step=0.01).radius
radii.append(rad_image)
return max(3, min(10, max(radii)))
def run():
for i, mxp in enumerate([0, 6]):
o = maptbx.atom_curves(scattering_type="C", scattering_table="wk1995")
b = o.bcr_approx(
d_min=2.0,
b_iso=0,
radius_max=5,
radius_step=0.01,
mxp=mxp,
epsc=0.001,
kpres=0 # BCR params
)
r = rfactor(b.image_values, b.bcr_approx_values)
if (i == 0): assert r > 10, r
else: assert r < 0.3, r
def run():
o = maptbx.atom_curves(scattering_type="C")
result = o.image(d_min=3.0, b_iso=50, radius_step=0.01)
assert approx_equal(result.radius, 2.59, 0.01)
#
o.xray_structure.set_b_iso(value=50)
map_data = get_map_data(xrs=o.xray_structure, d_min=3.0)
image = flex.double()
dim = o.xray_structure.unit_cell().parameters()[0]
for i, r in enumerate(result.radii):
mv = map_data.eight_point_interpolation([r / dim, 0, 0])
image.append(mv)
cc = flex.linear_correlation(x=image, y=result.image_values).coefficient()
assert cc > 0.99
num = flex.sum(flex.abs(flex.abs(image) - flex.abs(result.image_values)))
den = flex.sum(flex.abs(flex.abs(image) + flex.abs(result.image_values)))
r = 100. * 2. * num / den
assert r < 6.
def run(d_min=2.0, radius_max=5, radius_step=0.01):
for i, mxp in enumerate([0, 6]):
o = maptbx.atom_curves(scattering_type="C", scattering_table="wk1995")
b = o.bcr_approx(
d_min=d_min,
radius_max=radius_max,
radius_step=radius_step,
mxp=mxp,
epsc=0.001,
kpres=0 # BCR params
)
r = rfactor(b.image_values, b.bcr_approx_values)
if (i == 0): assert r > 10, r
else: assert r < 0.4, r
#
# b_iso is not 0
#
b_iso = 50
im = o.image(d_min=d_min,
b_iso=b_iso,
radius_max=radius_max,
radius_step=radius_step)
bcr_approx_values = flex.double()
bcr_approx_values_cpp = flex.double()
# c++
sc = xray.scatterer("c", site=(0, 0, 0), u=adptbx.b_as_u(b_iso))
bcr_cpp = ext.bcr_model(scatterer=sc, B=b.B, C=b.C, R=b.R)
calc = ext.calculator(bcr_model=bcr_cpp)
#
for r in im.radii:
first = 0
second = 0
for B, C, R in zip(b.B, b.C, b.R):
if (abs(R) < 1.e-6):
first += bcr.gauss(B=B, C=C, r=r, b_iso=b_iso)
else:
second += C * bcr.chi(B=B, R=R, r=r, b_iso=b_iso)
bcr_approx_values.append(first + second)
bcr_approx_values_cpp.append(calc.rho(r))
r = rfactor(im.image_values, bcr_approx_values)
if (i == 0): assert r > 10, r
else: assert r < 0.4, r
assert approx_equal(bcr_approx_values, bcr_approx_values_cpp)
