def show_literature_fits(label, n_terms, null_fit, n_points, e_other=None):
for lib in [
xray_scattering.wk1995, xray_scattering.it1992,
xray_scattering.two_gaussian_agarwal_isaacs,
xray_scattering.two_gaussian_agarwal_1978,
xray_scattering.one_gaussian_agarwal_1978
]:
if (lib == xray_scattering.wk1995):
try:
lib_gaussian = xray_scattering.wk1995(label, True).fetch()
lib_source = "WK1995"
except Exception:
lib_gaussian = None
elif (lib == xray_scattering.it1992):
try:
lib_gaussian = xray_scattering.it1992(label, True).fetch()
lib_source = "IT1992"
except Exception:
lib_gaussian = None
elif (lib.table.has_key(label)):
lib_gaussian = lib.table[label]
lib_source = lib.source_short
else:
lib_gaussian = None
if (lib_gaussian is not None):
gaussian_fit = scitbx.math.gaussian.fit(
null_fit.table_x()[:n_points],
null_fit.table_y()[:n_points],
null_fit.table_sigmas()[:n_points], lib_gaussian)
e = flex.max(gaussian_fit.significant_relative_errors())
show_fit_summary(lib_source, label, gaussian_fit, e, e_other,
lib_gaussian.n_terms())
def show_literature_fits(label, n_terms, null_fit, n_points, e_other=None):
for lib in [xray_scattering.wk1995,
xray_scattering.it1992,
xray_scattering.two_gaussian_agarwal_isaacs,
xray_scattering.two_gaussian_agarwal_1978,
xray_scattering.one_gaussian_agarwal_1978]:
if (lib == xray_scattering.wk1995):
try:
lib_gaussian = xray_scattering.wk1995(label, True).fetch()
lib_source = "WK1995"
except Exception:
lib_gaussian = None
elif (lib == xray_scattering.it1992):
try:
lib_gaussian = xray_scattering.it1992(label, True).fetch()
lib_source = "IT1992"
except Exception:
lib_gaussian = None
elif (lib.table.has_key(label)):
lib_gaussian = lib.table[label]
lib_source = lib.source_short
else:
lib_gaussian = None
if (lib_gaussian is not None):
gaussian_fit = scitbx.math.gaussian.fit(
null_fit.table_x()[:n_points],
null_fit.table_y()[:n_points],
null_fit.table_sigmas()[:n_points],
lib_gaussian)
e = flex.max(gaussian_fit.significant_relative_errors())
show_fit_summary(lib_source, label, gaussian_fit, e,
e_other, lib_gaussian.n_terms())
def calc_abs_Io(atom_types, at_collection, S_factor, Explicit_H=False):
ener_lib = server.ener_lib()
abs_Io = 0.0
for at in at_collection:
element = ener_lib.lib_atom[at].element
if (element is ''):
element = 'C'
print "Warning: unexpected atom found, and C element is used"
val = xray_scattering.it1992(element, True).fetch()
a = val.array_of_a()
c = val.c()
this_sf0 = c
for aa in a:
this_sf0 += aa
if (not Explicit_H):
if (S_factor.__contains__(at)):
scale = S_factor[at]
this_sf0 = this_sf0 * scale[0]
sel = flex.bool(atom_types == at)
isel = sel.iselection()
n_at = isel.size()
# print at, this_sf0
abs_Io = abs_Io + n_at * this_sf0
abs_Io = abs_Io**2.0
return abs_Io
def build_scattering_library(atom_types, q_array, radii, radius_scale,
Explicit_H, S_factor):
scat_lib = intensity.scattering_library(q_array)
ener_lib = server.ener_lib()
for at in atom_types:
element = ener_lib.lib_atom[at].element
if (element is ''):
element = 'C'
print "Warning: unexpected atom found, and C element is used"
val = xray_scattering.it1992(element, True).fetch()
a = val.array_of_a()
b = val.array_of_b()
c = val.c()
sf_result = scattering_factor(a, b, c, q_array)
# getting displaced solvent volumn
if (radii.__contains__(at)):
r = radii[at] * radius_scale
v = math.pi * 4.0 / 3.0 * r**3.0
else:
v = 16.44
dummy_sf = dummy_factor(v, q_array)
if (not Explicit_H):
if (S_factor.__contains__(at)):
scale = S_factor[at]
sf_result *= (scale[0] *
flex.exp(-scale[1] * q_array * q_array))
dummy_sf *= (flex.exp(-1.25 * q_array * q_array))
scat_lib.load_scattering_info(at, sf_result, dummy_sf)
return scat_lib
def exercise_it1992():
e = xray_scattering.it1992("c1")
assert e.table() == "IT1992"
assert e.label() == "C"
g = e.fetch()
assert g.n_terms() == 4
assert g.n_parameters() == 9
assert approx_equal(g.array_of_a(), (2.31000, 1.02000, 1.58860, 0.865000))
assert approx_equal(g.array_of_b(), (20.8439, 10.2075, 0.568700, 51.6512))
assert approx_equal(g.c(), 0.215600)
assert approx_equal(g.at_stol_sq(0), 5.99919997156)
assert approx_equal(g.at_stol_sq(1. / 9), 2.26575563201)
assert approx_equal(g.at_stol(1. / 9), 4.93537567523)
assert approx_equal(g.at_d_star_sq(1. / 9), 4.04815863088)
e = xray_scattering.it1992("yb2+", True)
assert e.label() == "Yb2+"
g = e.fetch()
assert approx_equal(g.array_of_a()[0], 28.1209)
assert approx_equal(g.array_of_b()[3], 20.3900)
assert approx_equal(g.c(), 3.70983)
e = xray_scattering.it1992(" yB3+")
assert e.label() == "Yb3+"
g = e.fetch()
assert approx_equal(g.array_of_a()[0], 27.8917)
n = 0
for e in xray_scattering.it1992_iterator():
n += 1
if (n == 213):
assert e.label() == "Cf"
else:
assert e.label() != "Cf"
d = xray_scattering.it1992(e.label(), True)
assert d.label() == e.label()
assert n == 213
i = xray_scattering.it1992_iterator()
j = iter(i)
assert i is j
def exercise_it1992():
e = xray_scattering.it1992("c1")
assert e.table() == "IT1992"
assert e.label() == "C"
g = e.fetch()
assert g.n_terms() == 4
assert g.n_parameters() == 9
assert approx_equal(g.array_of_a(), (2.31000, 1.02000, 1.58860, 0.865000))
assert approx_equal(g.array_of_b(), (20.8439, 10.2075, 0.568700, 51.6512))
assert approx_equal(g.c(), 0.215600)
assert approx_equal(g.at_stol_sq(0), 5.99919997156)
assert approx_equal(g.at_stol_sq(1./9), 2.26575563201)
assert approx_equal(g.at_stol(1./9), 4.93537567523)
assert approx_equal(g.at_d_star_sq(1./9), 4.04815863088)
e = xray_scattering.it1992("yb2+", True)
assert e.label() == "Yb2+"
g = e.fetch()
assert approx_equal(g.array_of_a()[0], 28.1209)
assert approx_equal(g.array_of_b()[3], 20.3900)
assert approx_equal(g.c(), 3.70983)
e = xray_scattering.it1992(" yB3+")
assert e.label() == "Yb3+"
g = e.fetch()
assert approx_equal(g.array_of_a()[0], 27.8917)
n = 0
for e in xray_scattering.it1992_iterator():
n += 1
if (n == 213):
assert e.label() == "Cf"
else:
assert e.label() != "Cf"
d = xray_scattering.it1992(e.label(), True)
assert d.label() == e.label()
assert n == 213
i = xray_scattering.it1992_iterator()
j = iter(i)
assert i is j
def run(args):
assert len(args) == 0
sds_it = xray_scattering.it1992("H").fetch()
sds_wk = xray_scattering.wk1995("H").fetch()
sds_ng = xray_scattering.n_gaussian_table_entry("H", 6).gaussian()
iso_it = xray_scattering.it1992("Hiso").fetch()
iso_wk = xray_scattering.wk1995("Hiso").fetch()
iso_ng = xray_scattering.n_gaussian_table_entry("Hiso", 6).gaussian()
print("@with g0")
print('@ s0 legend "SDS ITC Tab 6.1.1.2"')
for i, lbl in enumerate(
["SDS IT", "SDS WK", "SDS NG", "ISO IT", "ISO WK", "ISO NG"]):
print('@ s%d legend "%s"' % (i + 1, lbl))
print("@ s0 symbol 1")
print("@ s0 line linestyle 0")
for x, y in itc_tab_6112:
print(x, y)
print("&")
n_samples = 1000
for g in [sds_it, sds_wk, sds_ng, iso_it, iso_wk, iso_ng]:
for i_stol in range(n_samples + 1):
stol = 6 * i_stol / n_samples
print(stol, g.at_stol(stol))
print("&")
def run(args):
assert len(args) == 0
sds_it = xray_scattering.it1992("H").fetch()
sds_wk = xray_scattering.wk1995("H").fetch()
sds_ng = xray_scattering.n_gaussian_table_entry("H", 6).gaussian()
iso_it = xray_scattering.it1992("Hiso").fetch()
iso_wk = xray_scattering.wk1995("Hiso").fetch()
iso_ng = xray_scattering.n_gaussian_table_entry("Hiso", 6).gaussian()
print "@with g0"
print '@ s0 legend "SDS ITC Tab 6.1.1.2"'
for i,lbl in enumerate(["SDS IT", "SDS WK", "SDS NG",
"ISO IT", "ISO WK", "ISO NG"]):
print '@ s%d legend "%s"' % (i+1, lbl)
print "@ s0 symbol 1"
print "@ s0 line linestyle 0"
for x,y in itc_tab_6112:
print x, y
print "&"
n_samples = 1000
for g in [sds_it, sds_wk, sds_ng, iso_it, iso_wk, iso_ng]:
for i_stol in xrange(n_samples+1):
stol = 6 * i_stol / n_samples
print stol, g.at_stol(stol)
print "&"
def ensure_common_symbols():
lbl_it = []
for e in xray_scattering.it1992_iterator(): lbl_it.append(e.label())
lbl_it.sort()
lbl_wk = []
for e in xray_scattering.wk1995_iterator(): lbl_wk.append(e.label())
lbl_wk.sort()
assert lbl_wk == lbl_it
lbl_ng = []
for i_entry in xrange(xray_scattering.n_gaussian_table_size()):
lbl_ng.append(xray_scattering.n_gaussian_table_entry(i_entry, 6).label())
lbl_ng.sort()
assert lbl_ng == lbl_it
#
for label in xray_scattering.standard_labels_list():
it = xray_scattering.it1992(label, True).fetch()
wk = xray_scattering.wk1995(label, True).fetch()
ng = xray_scattering.n_gaussian_table_entry(label, 0, 0).gaussian()
assert approx_equal(wk.at_stol(0)/it.at_stol(0), 1, 5.e-3)
def ensure_common_symbols():
lbl_it = []
for e in xray_scattering.it1992_iterator():
lbl_it.append(e.label())
lbl_it.sort()
lbl_wk = []
for e in xray_scattering.wk1995_iterator():
lbl_wk.append(e.label())
lbl_wk.sort()
assert lbl_wk == lbl_it
lbl_ng = []
for i_entry in range(xray_scattering.n_gaussian_table_size()):
lbl_ng.append(
xray_scattering.n_gaussian_table_entry(i_entry, 6).label())
lbl_ng.sort()
assert lbl_ng == lbl_it
#
for label in xray_scattering.standard_labels_list():
it = xray_scattering.it1992(label, True).fetch()
wk = xray_scattering.wk1995(label, True).fetch()
ng = xray_scattering.n_gaussian_table_entry(label, 0, 0).gaussian()
assert approx_equal(wk.at_stol(0) / it.at_stol(0), 1, 5.e-3)
def examples():
# Generate space groups (in matrix/vector form) based on spacegroup number
# (names are *not* a pain)
# See also: http://cctbx.sourceforge.net/current/c_plus_plus/classcctbx_1_1sgtbx_1_1space__group__symbols.html#_details
from cctbx import sgtbx
for s in sgtbx.space_group_info(symbol="I41/amd").group():
print(s) # in "xyz" notation
print(s.r().as_rational().mathematica_form(), \
s.t().as_rational().transpose().mathematica_form())
print()
# now with a space group number
space_group_info = sgtbx.space_group_info(number=123)
space_group_info.show_summary()
print()
# Generate conditions for allowed reflections etc
from cctbx import crystal
from cctbx import miller
crystal_symmetry = crystal.symmetry(unit_cell=(10, 10, 13, 90, 90, 90),
space_group_info=space_group_info)
miller_set = miller.build_set(crystal_symmetry=crystal_symmetry,
anomalous_flag=False,
d_min=4)
# change the space group in order to get a few systematic absences
miller_set = miller_set.customized_copy(
space_group_info=sgtbx.space_group_info(symbol="I41/amd"))
sys_absent_flags = miller_set.sys_absent_flags()
for h, f in zip(sys_absent_flags.indices(), sys_absent_flags.data()):
print(h, f)
print()
# try also (from the command line): libtbx.help cctbx.miller
# Generate point group of space group in matrix form
point_group = miller_set.space_group().build_derived_point_group()
point_group_info = sgtbx.space_group_info(group=point_group)
point_group_info.show_summary()
for s in point_group:
print(s)
print()
# Generate point-group matrices for given coordinate
# first we have to define what we consider as special position
special_position_settings = crystal.special_position_settings(
crystal_symmetry=miller_set, min_distance_sym_equiv=0.5) # <<<<< here
site_symmetry = special_position_settings.site_symmetry(site=(0, 0.48, 0))
print("special position operator:", site_symmetry.special_op_simplified())
print("distance to original site:", site_symmetry.distance_moved())
print("point group of the special position:")
for s in site_symmetry.matrices():
print(s)
print()
# See also: http://cci.lbl.gov/~rwgk/my_papers/iucr/au0265_reprint.pdf
# Access database for form factors
from cctbx.eltbx import xray_scattering
si_form_factor = xray_scattering.it1992("Si")
gaussians = si_form_factor.fetch()
for stol in [0, 0.01, 0.02, 0.5]:
print(stol, gaussians.at_stol(stol))
print()
# anomalous scattering factors: Sasaki tables
from cctbx.eltbx import sasaki
si_table = sasaki.table("Si")
for wavelength in [0.5, 0.8, 0.9]:
data = si_table.at_angstrom(wavelength)
print(wavelength, data.fp(), data.fdp())
print()
# anomalous scattering factors: Henke tables
from cctbx.eltbx import henke
si_table = henke.table("Si")
for wavelength in [0.5, 0.8, 0.9]:
data = si_table.at_angstrom(wavelength)
print(wavelength, data.fp(), data.fdp())
print()
print("OK")
def examples():
# Generate space groups (in matrix/vector form) based on spacegroup number
# (names are *not* a pain)
# See also: http://cctbx.sourceforge.net/current/c_plus_plus/classcctbx_1_1sgtbx_1_1space__group__symbols.html#_details
from cctbx import sgtbx
for s in sgtbx.space_group_info(symbol="I41/amd").group():
print s # in "xyz" notation
print s.r().as_rational().mathematica_form(), \
s.t().as_rational().transpose().mathematica_form()
print
# now with a space group number
space_group_info = sgtbx.space_group_info(number=123)
space_group_info.show_summary()
print
# Generate conditions for allowed reflections etc
from cctbx import crystal
from cctbx import miller
crystal_symmetry = crystal.symmetry(
unit_cell=(10,10,13,90,90,90),
space_group_info=space_group_info)
miller_set = miller.build_set(
crystal_symmetry=crystal_symmetry,
anomalous_flag=False,
d_min=4)
# change the space group in order to get a few systematic absences
miller_set = miller_set.customized_copy(
space_group_info=sgtbx.space_group_info(symbol="I41/amd"))
sys_absent_flags = miller_set.sys_absent_flags()
for h,f in zip(sys_absent_flags.indices(), sys_absent_flags.data()):
print h, f
print
# try also (from the command line): libtbx.help cctbx.miller
# Generate point group of space group in matrix form
point_group = miller_set.space_group().build_derived_point_group()
point_group_info = sgtbx.space_group_info(group=point_group)
point_group_info.show_summary()
for s in point_group:
print s
print
# Generate point-group matrices for given coordinate
# first we have to define what we consider as special position
special_position_settings = crystal.special_position_settings(
crystal_symmetry=miller_set,
min_distance_sym_equiv=0.5) # <<<<< here
site_symmetry = special_position_settings.site_symmetry(
site=(0,0.48,0))
print "special position operator:", site_symmetry.special_op_simplified()
print "distance to original site:", site_symmetry.distance_moved()
print "point group of the special position:"
for s in site_symmetry.matrices():
print s
print
# See also: http://cci.lbl.gov/~rwgk/my_papers/iucr/au0265_reprint.pdf
# Access database for form factors
from cctbx.eltbx import xray_scattering
si_form_factor = xray_scattering.it1992("Si")
gaussians = si_form_factor.fetch()
for stol in [0, 0.01, 0.02, 0.5]:
print stol, gaussians.at_stol(stol)
print
# anomalous scattering factors: Sasaki tables
from cctbx.eltbx import sasaki
si_table = sasaki.table("Si")
for wavelength in [0.5, 0.8, 0.9]:
data = si_table.at_angstrom(wavelength)
print wavelength, data.fp(), data.fdp()
print
# anomalous scattering factors: Henke tables
from cctbx.eltbx import henke
si_table = henke.table("Si")
for wavelength in [0.5, 0.8, 0.9]:
data = si_table.at_angstrom(wavelength)
print wavelength, data.fp(), data.fdp()
print
print "OK"