def run(args):
def vdw_radii_callback(option, opt_str, value, parser):
# create a dict from space separated string of element types and radii
radii = {}
items = value.split()
assert len(items) % 2 == 0
for i in range(int(len(items) / 2)):
radii.setdefault(items[i * 2], float(items[i * 2 + 1]))
setattr(parser.values, option.dest, radii)
command_line = (option_parser(
usage="smtbx.masks structure reflections [options]"
).enable_symmetry_comprehensive().option(
None, "--solvent_radius", action="store", type="float",
default=1.3).option(
None,
"--shrink_truncation_radius",
action="store",
type="float",
default=1.3).option(None, "--debug", action="store_true").option(
None, "--verbose", action="store_true").option(
None,
"--resolution_factor",
action="store",
type="float",
default=1 / 4).option(
None, "--grid_step", action="store",
type="float").option(
None, "--d_min", action="store",
type="float").option(
None,
"--two_theta_max",
action="store",
type="float").option(
None,
"--cb_op",
action="store",
type="string").option(
None,
"--vdw_radii",
action="callback",
callback=vdw_radii_callback,
type="string",
nargs=1).option(
None,
"--use_space_group_symmetry",
action="store_true")).process(
args=args)
structure_file = command_line.args[0]
ext = os.path.splitext(structure_file)[-1].lower()
if ext in ('.res', '.ins'):
xs = xray.structure.from_shelx(filename=structure_file)
elif ext == '.cif':
xs = xray.structure.from_cif(filename=structure_file)
else:
print "%s: unsupported structure file format {shelx|cif}" % ext
return
reflections_server = reflection_file_utils.reflection_file_server(
crystal_symmetry=xs.crystal_symmetry(),
reflection_files=[
reflection_file_reader.any_reflection_file(command_line.args[1])
])
fo_sq = reflections_server.get_miller_arrays(None)[0]
if command_line.options.cb_op is not None:
cb_op = sgtbx.change_of_basis_op(
sgtbx.rt_mx(command_line.options.cb_op))
fo_sq = fo_sq.change_basis(cb_op).customized_copy(crystal_symmetry=xs)
print "structure file: %s" % command_line.args[0]
print "reflection file: %s" % command_line.args[1]
if command_line.options.debug:
print "debug: %s" % command_line.options.debug
print
xs.show_summary()
print
d_min = command_line.options.d_min
two_theta_max = command_line.options.two_theta_max
assert [d_min, two_theta_max].count(None) > 0
if two_theta_max is not None:
d_min = uctbx.two_theta_as_d(two_theta_max,
wavelength=0.71073,
deg=True)
exercise_masks(
xs,
fo_sq,
solvent_radius=command_line.options.solvent_radius,
shrink_truncation_radius=command_line.options.shrink_truncation_radius,
resolution_factor=command_line.options.resolution_factor,
grid_step=command_line.options.grid_step,
resolution_cutoff=d_min,
atom_radii_table=command_line.options.vdw_radii,
use_space_group_symmetry=command_line.options.use_space_group_symmetry,
debug=command_line.options.debug,
verbose=command_line.options.verbose)
print "OK"
def exercise_functions():
d_star_sq_s = 1.2345
d_star_sq_a = flex.double((1.2345, 0.1234))
two_theta_s = 0.61725
two_theta_a = flex.double((0.61725,0.65432))
# forward conversions
assert approx_equal(
uctbx.d_star_sq_as_stol_sq(d_star_sq_s), d_star_sq_s / 4)
assert approx_equal(
uctbx.d_star_sq_as_stol_sq(d_star_sq_a),
[uctbx.d_star_sq_as_stol_sq(i) for i in d_star_sq_a])
assert approx_equal(
uctbx.d_star_sq_as_two_stol(d_star_sq_s)**2, d_star_sq_s)
assert approx_equal(
uctbx.d_star_sq_as_two_stol(d_star_sq_a),
[uctbx.d_star_sq_as_two_stol(i) for i in d_star_sq_a])
assert approx_equal(
uctbx.d_star_sq_as_stol(d_star_sq_s)**2, d_star_sq_s / 4)
assert approx_equal(
uctbx.d_star_sq_as_stol(d_star_sq_a),
[uctbx.d_star_sq_as_stol(i) for i in d_star_sq_a])
assert approx_equal(
1/(uctbx.d_star_sq_as_d(d_star_sq_s)**2), d_star_sq_s)
assert approx_equal(
uctbx.d_star_sq_as_d(d_star_sq_a),
[uctbx.d_star_sq_as_d(i) for i in d_star_sq_a])
assert approx_equal(
uctbx.d_star_sq_as_two_theta(d_star_sq_s, 1.5),
2 * asin(1.5/2*sqrt(d_star_sq_s)))
assert approx_equal(
uctbx.d_star_sq_as_two_theta(d_star_sq_s, 1.5),
uctbx.d_star_sq_as_two_theta(d_star_sq_s, 1.5, False))
assert approx_equal(
uctbx.d_star_sq_as_two_theta(d_star_sq_a, 1.5),
[uctbx.d_star_sq_as_two_theta(i, 1.5) for i in d_star_sq_a])
assert approx_equal(
uctbx.d_star_sq_as_two_theta(d_star_sq_s, 1.5)*180/pi,
uctbx.d_star_sq_as_two_theta(d_star_sq_s, 1.5, True))
# reverse conversions
for d_star_sq, two_theta in zip(
(d_star_sq_s, d_star_sq_a),(two_theta_s, two_theta_a)):
assert approx_equal(
uctbx.stol_sq_as_d_star_sq(
uctbx.d_star_sq_as_stol_sq(d_star_sq)), d_star_sq)
assert approx_equal(
uctbx.two_stol_as_d_star_sq(
uctbx.d_star_sq_as_two_stol(d_star_sq)), d_star_sq)
assert approx_equal(
uctbx.stol_as_d_star_sq(
uctbx.d_star_sq_as_stol(d_star_sq)), d_star_sq)
assert approx_equal(
uctbx.d_as_d_star_sq(
uctbx.d_star_sq_as_d(d_star_sq)), d_star_sq)
assert approx_equal(
uctbx.two_theta_as_d_star_sq(
uctbx.d_star_sq_as_two_theta(d_star_sq, 1.5), 1.5), d_star_sq)
assert approx_equal(
uctbx.two_theta_as_d_star_sq(two_theta, 1.5),
uctbx.two_theta_as_d_star_sq(two_theta, 1.5, False))
assert approx_equal(
uctbx.two_theta_as_d_star_sq(two_theta, 1.5),
uctbx.two_theta_as_d_star_sq(two_theta*180/pi, 1.5, True))
assert approx_equal(
uctbx.two_theta_as_d(two_theta, 1.5),
uctbx.d_star_sq_as_d(uctbx.two_theta_as_d_star_sq(two_theta, 1.5)))
assert approx_equal(
uctbx.two_theta_as_d(two_theta, 1.5, True),
uctbx.d_star_sq_as_d(uctbx.two_theta_as_d_star_sq(two_theta, 1.5, True)))
#
assert uctbx.fractional_unit_shifts(distance_frac=[0,0,0]) == (0,0,0)
assert uctbx.fractional_unit_shifts([0.6,7.4,-0.4]) == (1,7,0)
assert uctbx.fractional_unit_shifts([-6,3,-0.6]) == (-6,3,-1)
site_frac_1 = [0.3,-8.6,2.1]
for eps,expected_u2 in [(-1.e-5, 1), (1.e-5, 2)]:
site_frac_2 = [-3,5.6,0.6-eps]
assert uctbx.fractional_unit_shifts(
site_frac_1=site_frac_1,
site_frac_2=site_frac_2) == (3, -14, expected_u2)
def run(args):
def vdw_radii_callback(option, opt_str, value, parser):
# create a dict from space separated string of element types and radii
radii = {}
items = value.split()
assert len(items) % 2 == 0
for i in range(int(len(items) / 2)):
radii.setdefault(items[i*2], float(items[i*2+1]))
setattr(parser.values, option.dest, radii)
command_line = (option_parser(
usage="smtbx.masks structure reflections [options]")
.enable_symmetry_comprehensive()
.option(None, "--solvent_radius",
action="store",
type="float",
default=1.3)
.option(None, "--shrink_truncation_radius",
action="store",
type="float",
default=1.3)
.option(None, "--debug",
action="store_true")
.option(None, "--verbose",
action="store_true")
.option(None, "--resolution_factor",
action="store",
type="float",
default=1/4)
.option(None, "--grid_step",
action="store",
type="float")
.option(None, "--d_min",
action="store",
type="float")
.option(None, "--two_theta_max",
action="store",
type="float")
.option(None, "--cb_op",
action="store",
type="string")
.option(None, "--vdw_radii",
action="callback",
callback=vdw_radii_callback,
type="string",
nargs=1)
.option(None, "--use_space_group_symmetry",
action="store_true")).process(args=args)
structure_file = command_line.args[0]
ext = os.path.splitext(structure_file)[-1].lower()
if ext in ('.res', '.ins'):
xs = xray.structure.from_shelx(filename=structure_file)
elif ext == '.cif':
xs = xray.structure.from_cif(filename=structure_file)
else:
print "%s: unsupported structure file format {shelx|cif}" %ext
return
reflections_server = reflection_file_utils.reflection_file_server(
crystal_symmetry = xs.crystal_symmetry(),
reflection_files = [
reflection_file_reader.any_reflection_file(command_line.args[1])
]
)
fo_sq = reflections_server.get_miller_arrays(None)[0]
if command_line.options.cb_op is not None:
cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(command_line.options.cb_op))
fo_sq = fo_sq.change_basis(cb_op).customized_copy(
crystal_symmetry=xs)
print "structure file: %s" %command_line.args[0]
print "reflection file: %s" %command_line.args[1]
if command_line.options.debug:
print "debug: %s" %command_line.options.debug
print
xs.show_summary()
print
d_min = command_line.options.d_min
two_theta_max = command_line.options.two_theta_max
assert [d_min, two_theta_max].count(None) > 0
if two_theta_max is not None:
d_min = uctbx.two_theta_as_d(two_theta_max, wavelength=0.71073, deg=True)
exercise_masks(
xs, fo_sq,
solvent_radius=command_line.options.solvent_radius,
shrink_truncation_radius=command_line.options.shrink_truncation_radius,
resolution_factor=command_line.options.resolution_factor,
grid_step=command_line.options.grid_step,
resolution_cutoff=d_min,
atom_radii_table=command_line.options.vdw_radii,
use_space_group_symmetry=command_line.options.use_space_group_symmetry,
debug=command_line.options.debug,
verbose=command_line.options.verbose)
print "OK"
def exercise_functions():
d_star_sq_s = 1.2345
d_star_sq_a = flex.double((1.2345, 0.1234))
two_theta_s = 0.61725
two_theta_a = flex.double((0.61725, 0.65432))
# forward conversions
assert approx_equal(uctbx.d_star_sq_as_stol_sq(d_star_sq_s),
d_star_sq_s / 4)
assert approx_equal(uctbx.d_star_sq_as_stol_sq(d_star_sq_a),
[uctbx.d_star_sq_as_stol_sq(i) for i in d_star_sq_a])
assert approx_equal(
uctbx.d_star_sq_as_two_stol(d_star_sq_s)**2, d_star_sq_s)
assert approx_equal(uctbx.d_star_sq_as_two_stol(d_star_sq_a),
[uctbx.d_star_sq_as_two_stol(i) for i in d_star_sq_a])
assert approx_equal(
uctbx.d_star_sq_as_stol(d_star_sq_s)**2, d_star_sq_s / 4)
assert approx_equal(uctbx.d_star_sq_as_stol(d_star_sq_a),
[uctbx.d_star_sq_as_stol(i) for i in d_star_sq_a])
assert approx_equal(1 / (uctbx.d_star_sq_as_d(d_star_sq_s)**2),
d_star_sq_s)
assert approx_equal(uctbx.d_star_sq_as_d(d_star_sq_a),
[uctbx.d_star_sq_as_d(i) for i in d_star_sq_a])
assert approx_equal(uctbx.d_star_sq_as_two_theta(d_star_sq_s, 1.5),
2 * asin(1.5 / 2 * sqrt(d_star_sq_s)))
assert approx_equal(uctbx.d_star_sq_as_two_theta(d_star_sq_s, 1.5),
uctbx.d_star_sq_as_two_theta(d_star_sq_s, 1.5, False))
assert approx_equal(
uctbx.d_star_sq_as_two_theta(d_star_sq_a, 1.5),
[uctbx.d_star_sq_as_two_theta(i, 1.5) for i in d_star_sq_a])
assert approx_equal(
uctbx.d_star_sq_as_two_theta(d_star_sq_s, 1.5) * 180 / pi,
uctbx.d_star_sq_as_two_theta(d_star_sq_s, 1.5, True))
# reverse conversions
for d_star_sq, two_theta in zip((d_star_sq_s, d_star_sq_a),
(two_theta_s, two_theta_a)):
assert approx_equal(
uctbx.stol_sq_as_d_star_sq(uctbx.d_star_sq_as_stol_sq(d_star_sq)),
d_star_sq)
assert approx_equal(
uctbx.two_stol_as_d_star_sq(
uctbx.d_star_sq_as_two_stol(d_star_sq)), d_star_sq)
assert approx_equal(
uctbx.stol_as_d_star_sq(uctbx.d_star_sq_as_stol(d_star_sq)),
d_star_sq)
assert approx_equal(
uctbx.d_as_d_star_sq(uctbx.d_star_sq_as_d(d_star_sq)), d_star_sq)
assert approx_equal(
uctbx.two_theta_as_d_star_sq(
uctbx.d_star_sq_as_two_theta(d_star_sq, 1.5), 1.5), d_star_sq)
assert approx_equal(
uctbx.two_theta_as_d_star_sq(two_theta, 1.5),
uctbx.two_theta_as_d_star_sq(two_theta, 1.5, False))
assert approx_equal(
uctbx.two_theta_as_d_star_sq(two_theta, 1.5),
uctbx.two_theta_as_d_star_sq(two_theta * 180 / pi, 1.5, True))
assert approx_equal(
uctbx.two_theta_as_d(two_theta, 1.5),
uctbx.d_star_sq_as_d(uctbx.two_theta_as_d_star_sq(two_theta, 1.5)))
assert approx_equal(
uctbx.two_theta_as_d(two_theta, 1.5, True),
uctbx.d_star_sq_as_d(
uctbx.two_theta_as_d_star_sq(two_theta, 1.5, True)))
#
assert uctbx.fractional_unit_shifts(distance_frac=[0, 0, 0]) == (0, 0, 0)
assert uctbx.fractional_unit_shifts([0.6, 7.4, -0.4]) == (1, 7, 0)
assert uctbx.fractional_unit_shifts([-6, 3, -0.6]) == (-6, 3, -1)
site_frac_1 = [0.3, -8.6, 2.1]
for eps, expected_u2 in [(-1.e-5, 1), (1.e-5, 2)]:
site_frac_2 = [-3, 5.6, 0.6 - eps]
assert uctbx.fractional_unit_shifts(
site_frac_1=site_frac_1,
site_frac_2=site_frac_2) == (3, -14, expected_u2)
15.2671, 16.2713, 16.2628, 14.3454, 15.2642, 24.9881, 27.4904, 24.975,
15.2658, 27.2176, 14.3565, 15.2576, 15.2653, 15.2673, 14.3385, 14.355,
27.2235, 25.0048, 25.0138, 27.1408, 25.0315, 14.3464, 27.2386, 21.0258,
25.004, 14.3446, 15.2299, 15.2723, 14.3643, 14.3474, 14.3584, 15.2848,
21.0256, 21.0246, 15.261, 25.0207, 27.2373, 16.2848, 16.2854, 14.3575,
14.3636, 29.4477, 27.2583, 14.3619, 21.0374, 21.0399, 16.2755, 14.3487,
14.3618, 14.3608, 15.2829, 27.2497, 15.2715, 15.2699, 16.2646, 16.2786,
16.2821, 16.2696, 21.0368, 21.0307, 25.0431, 21.0456, 21.0224, 27.2257,
27.2486, 25.0266, 25.0252, 29.4661, 25.0415, 25.0266, 25.046, 29.4752,
27.2545, 29.4521, 37.3152, 29.4306, 29.4684, 37.3646, 28.9946, 28.9884,
29.4736, 29.4737, 30.0142]
miller_indices = flex.miller_index()
two_thetas_obs = flex.double()
for i, two_theta in enumerate(two_thetas):
d_spacing = uctbx.two_theta_as_d(two_theta, wavelength, deg=True)
for j, d in enumerate(ms.d_spacings().data()):
if abs(d - d_spacing) < 0.1:
miller_indices.append(ms.indices()[j])
two_thetas_obs.append(two_theta)
show_fit(
two_thetas_obs, miller_indices, wavelength, unit_cell_start)
refined = refinery(
two_thetas_obs, miller_indices, wavelength, unit_cell_start,
space_group=crystal_symmetry.space_group())
print
show_fit(
two_thetas_obs, miller_indices, wavelength, refined.unit_cell())