def exercise():
t = henke.table("SI")
assert t.label() == "Si"
assert t.atomic_number() == 14
f = t.at_angstrom(2)
assert f.is_valid_fp()
assert f.is_valid_fdp()
assert f.is_valid()
from cctbx import factor_kev_angstrom
assert approx_equal(f.fp(), t.at_kev(factor_kev_angstrom / 2).fp())
assert approx_equal(f.fdp(), t.at_kev(factor_kev_angstrom / 2).fdp())
assert approx_equal(f.fp(), t.at_ev(1000 * factor_kev_angstrom / 2).fp())
assert approx_equal(f.fdp(), t.at_ev(1000 * factor_kev_angstrom / 2).fdp())
c = f.as_complex()
assert c.real == f.fp()
assert c.imag == f.fdp()
verify(t, 10.0, -9999.00, 4.00688)
verify(t, 29.3, 4.04139-14, 0.371742)
verify(t, 30000.0, 14.0266-14, 0.0228459)
n = 0
for t in henke.table_iterator():
n += 1
if (n == 1):
assert t.label() == "H"
elif (n == 92):
assert t.label() == "U"
u = henke.table(t.label())
assert u.label() == t.label()
assert n == 92
def exercise():
t = henke.table("SI")
assert t.label() == "Si"
assert t.atomic_number() == 14
f = t.at_angstrom(2)
assert f.is_valid_fp()
assert f.is_valid_fdp()
assert f.is_valid()
from cctbx import factor_kev_angstrom
assert approx_equal(f.fp(), t.at_kev(factor_kev_angstrom / 2).fp())
assert approx_equal(f.fdp(), t.at_kev(factor_kev_angstrom / 2).fdp())
assert approx_equal(f.fp(), t.at_ev(1000 * factor_kev_angstrom / 2).fp())
assert approx_equal(f.fdp(), t.at_ev(1000 * factor_kev_angstrom / 2).fdp())
c = f.as_complex()
assert c.real == f.fp()
assert c.imag == f.fdp()
verify(t, 10.0, -9999.00, 4.00688)
verify(t, 29.3, 4.04139 - 14, 0.371742)
verify(t, 30000.0, 14.0266 - 14, 0.0228459)
n = 0
for t in henke.table_iterator():
n += 1
if (n == 1):
assert t.label() == "H"
elif (n == 92):
assert t.label() == "U"
u = henke.table(t.label())
assert u.label() == t.label()
assert n == 92
def sfgen(wavelen_A, pdb_name, algo='fft', dmin=1.5, ano_flag=True):
"""
generate the structure factors from a pdb
for use with LD91
:param wavelen_A:
:param pdb_name:
:param algo:
:param dmin:
:param ano_flag:
:return:
"""
pdb_in = pdb.input(pdb_name)
xray_structure = pdb_in.xray_structure_simple()
scatts = xray_structure.scatterers()
Yb = Yb_scatter() # reads in values from the Hendrickson plot
for sc in scatts:
if sc.element_symbol() == "Yb":
sc.fp = Yb.fp(wavelen_A)
sc.fdp = Yb.fdp(wavelen_A)
else:
expected_henke = henke.table(
sc.element_symbol()).at_angstrom(wavelen_A)
sc.fp = expected_henke.fp()
sc.fdp = expected_henke.fdp()
fcalc = xray_structure.structure_factors(d_min=dmin,
algorithm=algo,
anomalous_flag=ano_flag)
return fcalc.f_calc()
def __init__(self, resolution, pdb_text, algorithm=None, wavelength=0.9):
from iotbx import pdb
pdb_inp = pdb.input(source_info=None, lines=pdb_text)
xray_structure = pdb_inp.xray_structure_simple()
xray_structure.show_summary(prefix="Input structure ")
#
# take a detour to insist on calculating anomalous contribution of every atom
scatterers = xray_structure.scatterers()
for sc in scatterers:
from cctbx.eltbx import sasaki, henke
#expected_sasaki = sasaki.table(sc.element_symbol()).at_angstrom(wavelength)
expected_henke = henke.table(
sc.element_symbol()).at_angstrom(wavelength)
sc.fp = expected_henke.fp()
sc.fdp = expected_henke.fdp()
import mmtbx.command_line.fmodel
phil2 = mmtbx.command_line.fmodel.fmodel_from_xray_structure_master_params
params2 = phil2.extract()
# adjust the cutoff of the generated intensities to assure that
# statistics will be reported to the desired high-resolution limit
# even if the observed unit cell differs slightly from the reference.
params2.output.type = "complex"
params2.high_resolution = resolution
params2.fmodel.k_sol = 0.35
params2.fmodel.b_sol = 46.
params2.structure_factors_accuracy.algorithm = algorithm
self.params2 = params2
self.xray_structure = xray_structure
def get_amplitudes(self, at_angstrom):
# Since we are getting amplitudes for nanoBragg, let us assure they are in P1
symbol = self.xs.space_group().info().type().lookup_symbol()
assert symbol == "P 1", "Must be in P1 to accept amplitudes for ExaFEL GPU interface"
# take a detour to insist on calculating anomalous contribution of every atom
scatterers = self.xs.scatterers()
for sc in scatterers:
from cctbx.eltbx import henke
expected_henke = henke.table(
sc.element_symbol()).at_angstrom(at_angstrom)
sc.fp = expected_henke.fp()
sc.fdp = expected_henke.fdp()
import mmtbx.command_line.fmodel
phil2 = mmtbx.command_line.fmodel.fmodel_from_xray_structure_master_params
params2 = phil2.extract()
params2.high_resolution = 1.6
params2.fmodel.k_sol = 0.35
params2.fmodel.b_sol = 46.
params2.structure_factors_accuracy.algorithm = "fft"
params2.output.type = "real"
import mmtbx
f_model = mmtbx.utils.fmodel_from_xray_structure(
xray_structure=self.xs,
f_obs=None,
add_sigmas=True,
params=params2).f_model
#f_model.show_summary()
return f_model
def fcalc_from_pdb(self, resolution=None, algorithm=None, wavelength=0.9):
''' Generate FCalc from PDB-formatted coordinates '''
with open(self.params.reference_coordinates, 'r') as pdb_file:
pdb_lines = pdb_file.readlines()
# Read in coordinates
pdb_inp = pdb.input(source_info=None, lines=pdb_lines)
xray_structure = pdb_inp.xray_structure_simple()
# take a detour to insist on calculating anomalous contribution of every atom
scatterers = xray_structure.scatterers()
for sc in scatterers:
expected_henke = henke.table(
sc.element_symbol()).at_angstrom(wavelength)
sc.fp = expected_henke.fp()
sc.fdp = expected_henke.fdp()
# how do we do bulk solvent?
primitive_xray_structure = xray_structure.primitive_setting()
P1_primitive_xray_structure = primitive_xray_structure.expand_to_p1()
fcalc = P1_primitive_xray_structure.structure_factors(
d_min=resolution, anomalous_flag=True,
algorithm=algorithm).f_calc()
return fcalc.amplitudes()
def fcalc_from_pdb(resolution,
algorithm=None,
wavelength=0.9,
anom=True,
ucell=None,
symbol=None,
as_amplitudes=True):
pdb_lines = 'HEADER TEST\nCRYST1 50.000 60.000 70.000 90.00 90.00 90.00 P 1\nATOM 1 O HOH A 1 56.829 2.920 55.702 1.00 20.00 O\nATOM 2 O HOH A 2 49.515 35.149 37.665 1.00 20.00 O\nATOM 3 O HOH A 3 52.667 17.794 69.925 1.00 20.00 O\nATOM 4 O HOH A 4 40.986 20.409 18.309 1.00 20.00 O\nATOM 5 O HOH A 5 46.896 37.790 41.629 1.00 20.00 O\nATOM 6 SED MSE A 6 1.000 2.000 3.000 1.00 20.00 SE\nEND\n'
from iotbx import pdb
pdb_inp = pdb.input(source_info=None, lines=pdb_lines)
xray_structure = pdb_inp.xray_structure_simple()
if ucell is not None:
assert symbol is not None
from cctbx.xray import structure
from cctbx import crystal
crystal_sym = crystal.symmetry(unit_cell=ucell,
space_group_symbol=symbol)
xray_structure = structure(scatterers=(xray_structure.scatterers()),
crystal_symmetry=crystal_sym)
scatterers = xray_structure.scatterers()
if anom:
from cctbx.eltbx import henke
for sc in scatterers:
expected_henke = henke.table(
sc.element_symbol()).at_angstrom(wavelength)
sc.fp = expected_henke.fp()
sc.fdp = expected_henke.fdp()
primitive_xray_structure = xray_structure.primitive_setting()
P1_primitive_xray_structure = primitive_xray_structure.expand_to_p1()
fcalc = P1_primitive_xray_structure.structure_factors(
d_min=resolution, anomalous_flag=anom, algorithm=algorithm).f_calc()
if as_amplitudes:
fcalc = fcalc.amplitudes().set_observation_type_xray_amplitude()
return fcalc
def elem_fp_fdp_at_eV(elem_symbol, energy, how="henke"):
if how == 'sasaki':
tbl = sasaki.table(elem_symbol)
else:
tbl = henke.table(elem_symbol)
keV = energy * 1e-3
factor = tbl.at_kev(keV)
return factor.fp(), factor.fdp()
def reset_wavelength(self,newvalue):
scatterers = self.xray_structure.scatterers()
for sc in scatterers:
from cctbx.eltbx import sasaki, henke
#expected_sasaki = sasaki.table(sc.element_symbol()).at_angstrom(newvalue)
expected_henke = henke.table(sc.element_symbol()).at_angstrom(newvalue)
sc.fp = expected_henke.fp()
sc.fdp = expected_henke.fdp()
def Yb_fp_fdp_at_eV(energy, how="henke"):
if how=='sasaki':
tbl = sasaki.table("Yb")
elif how=='henke':
tbl = henke.table("Yb")
keV = energy * 1e-3
factor = tbl.at_kev(keV)
return factor.fp(), factor.fdp()
def __init__(self, input_file=None):
if input_file is None:
input_file = "fp_fdp.npz"
self.input_file = input_file
if input_file is not None:
self._load()
self.hen_tbl = henke.table("Yb")
self.sas_tbl = sasaki.table("Yb")
def get_scattF(wavelen_A, pdblines, algo, dmin, ano_flag):
"""
mostly borrowed from tst_nanoBragg_basic.py
"""
pdb_in = iotbx.pdb.input(source_info=None, lines=pdblines)
xray_structure = pdb_in.xray_structure_simple()
scatts = xray_structure.scatterers()
for sc in scatts:
expected_henke = henke.table(
sc.element_symbol()).at_angstrom(wavelen_A)
sc.fp = expected_henke.fp()
sc.fdp = expected_henke.fdp()
fcalc = xray_structure.structure_factors(dmin=dmin,
algorithm=algo,
anomalous_flag=ano_flag)
return fcalc.fcalc()
def show_scatterers(self, fpp, wave):
print("""Label f" Coordinates Occupancy """
"Uiso, Ustar as Uiso")
scatterers = self.scatterers()
types_used = {}
for j, sc in enumerate(scatterers):
sc.fdp = fpp[j]
show_scatterer(sc, unit_cell=self.unit_cell())
types_used[sc.scattering_type] = None
print("Tabular values for %7.1f eV (%8.5f Angstrom):" %
(12398 / wave, wave))
from cctbx.eltbx import sasaki, henke
for tag in types_used.keys():
fpp_expected_sasaki = sasaki.table(tag).at_angstrom(wave).fdp()
fpp_expected_henke = henke.table(tag).at_angstrom(wave).fdp()
print(" %-4s" % tag, end=' ')
print("%6.3f" % (max(fpp_expected_sasaki, fpp_expected_henke)))
def hisym_fcalc_from_pdb(resolution,pdb_text,algorithm=None,wavelength=0.9):
from iotbx import pdb
pdb_inp = pdb.input(source_info=None,lines = pdb_text)
xray_structure = pdb_inp.xray_structure_simple()
xray_structure.show_summary(prefix="Input structure ")
#
# take a detour to insist on calculating anomalous contribution of every atom
scatterers = xray_structure.scatterers()
for sc in scatterers:
from cctbx.eltbx import sasaki, henke
#expected_sasaki = sasaki.table(sc.element_symbol()).at_angstrom(wavelength)
expected_henke = henke.table(sc.element_symbol()).at_angstrom(wavelength)
sc.fp = expected_henke.fp()
sc.fdp = expected_henke.fdp()
fcalc = xray_structure.structure_factors(
d_min=resolution, anomalous_flag=True, algorithm=algorithm).f_calc()
return fcalc.amplitudes()
def from_structure(cls,xray_structure,energy):
CS = cls()
wavelength = 12398.425/float(energy)
# take a detour to insist on calculating anomalous contribution of every atom
scatterers = xray_structure.scatterers()
print ("from structure",energy)
for sc in scatterers:
from cctbx.eltbx import sasaki, henke
#expected_sasaki = sasaki.table(sc.element_symbol()).at_angstrom(wavelength)
expected_henke = henke.table(sc.element_symbol()).at_angstrom(wavelength)
#print ( sc.element_symbol(), expected_henke.fp(),expected_henke.fdp())
sc.fp = expected_henke.fp()
sc.fdp = expected_henke.fdp()
CS.xray_structure = xray_structure
CS.energy = energy
return CS
def show_scatterers(self,fpp,wave):
print ("""Label f" Coordinates Occupancy """
"Uiso, Ustar as Uiso")
scatterers = self.scatterers()
types_used = {}
for j,sc in enumerate(scatterers):
sc.fdp = fpp[j]
show_scatterer(sc, unit_cell=self.unit_cell())
types_used[sc.scattering_type]=None
print "Tabular values for %7.1f eV (%8.5f Angstrom):"%(12398/wave,wave)
from cctbx.eltbx import sasaki, henke
for tag in types_used.keys():
fpp_expected_sasaki = sasaki.table(tag).at_angstrom(
wave).fdp()
fpp_expected_henke = henke.table(tag).at_angstrom(
wave).fdp()
print " %-4s"%tag,
print "%6.3f" % (max(fpp_expected_sasaki,fpp_expected_henke))
def fcalc_from_pdb(resolution,algorithm=None,wavelength=0.9):
from iotbx import pdb
pdb_inp = pdb.input(source_info=None,lines = pdb_lines)
xray_structure = pdb_inp.xray_structure_simple()
#
# take a detour to insist on calculating anomalous contribution of every atom
scatterers = xray_structure.scatterers()
for sc in scatterers:
from cctbx.eltbx import sasaki, henke
#expected_sasaki = sasaki.table(sc.element_symbol()).at_angstrom(wavelength)
expected_henke = henke.table(sc.element_symbol()).at_angstrom(wavelength)
sc.fp = expected_henke.fp()
sc.fdp = expected_henke.fdp()
# how do we do bulk solvent?
primitive_xray_structure = xray_structure.primitive_setting()
P1_primitive_xray_structure = primitive_xray_structure.expand_to_p1()
fcalc = P1_primitive_xray_structure.structure_factors(
d_min=resolution, anomalous_flag=True, algorithm=algorithm).f_calc()
return fcalc.amplitudes()
def fcalc_from_pdb(self, resolution, algorithm=None, override_fdp=None):
pdb_inp = pdb.input(source_info=None, lines=_pdb_lines)
xray_structure = pdb_inp.xray_structure_simple()
wavelength = self.beam.get_wavelength()
#
# take a detour to calculate anomalous contribution of every atom
scatterers = xray_structure.scatterers()
for sc in scatterers:
expected_henke = henke.table(sc.element_symbol()).at_angstrom(wavelength)
sc.fp = expected_henke.fp()
sc.fdp = override_fdp if override_fdp is not None else expected_henke.fdp()
# how do we do bulk solvent?
primitive_xray_structure = xray_structure.primitive_setting()
P1_primitive_xray_structure = primitive_xray_structure.expand_to_p1()
fcalc = P1_primitive_xray_structure.structure_factors(
d_min=resolution, anomalous_flag=True, algorithm=algorithm
).f_calc()
return fcalc.amplitudes()
def fmodel_from_pdb(resolution, pdb_text, algorithm=None, wavelength=0.9):
from iotbx import pdb
pdb_inp = pdb.input(source_info=None, lines=pdb_text)
xray_structure = pdb_inp.xray_structure_simple()
xray_structure.show_summary(prefix="Input structure ")
#
# take a detour to insist on calculating anomalous contribution of every atom
scatterers = xray_structure.scatterers()
for sc in scatterers:
from cctbx.eltbx import sasaki, henke
#expected_sasaki = sasaki.table(sc.element_symbol()).at_angstrom(wavelength)
expected_henke = henke.table(
sc.element_symbol()).at_angstrom(wavelength)
sc.fp = expected_henke.fp()
sc.fdp = expected_henke.fdp()
primitive_xray_structure = xray_structure.primitive_setting()
P1_primitive_xray_structure = primitive_xray_structure.expand_to_p1()
P1_primitive_xray_structure.show_summary(prefix="P1 structure ")
# how do we do bulk solvent?
import mmtbx.command_line.fmodel
phil2 = mmtbx.command_line.fmodel.fmodel_from_xray_structure_master_params
params2 = phil2.extract()
# adjust the cutoff of the generated intensities to assure that
# statistics will be reported to the desired high-resolution limit
# even if the observed unit cell differs slightly from the reference.
params2.output.type = "complex"
params2.high_resolution = resolution
params2.fmodel.k_sol = 0.435 # "Babinet" optimum, used 0.35 previously
params2.fmodel.b_sol = 46.
params2.structure_factors_accuracy.algorithm = algorithm
import mmtbx
f_model_complex = mmtbx.utils.fmodel_from_xray_structure(
xray_structure=P1_primitive_xray_structure,
f_obs=None,
add_sigmas=False,
params=params2).f_model
f_model_real = abs(f_model_complex)
f_model_real.set_observation_type_xray_amplitude()
f_model_real.show_summary(prefix="FMODEL ")
return f_model_real
def get_fp_fdp(atom_type=None,wavelength=None,out=sys.stdout):
if not atom_type or not wavelength:
raise Sorry("Please specify either f_double_prime or " +
"atom_type and wavelength")
from cctbx.eltbx import sasaki
try:
table = sasaki.table(atom_type)
fp_fdp = table.at_angstrom(wavelength)
except Exception:
return None
#
if not fp_fdp.is_valid():
from cctbx.eltbx import henke
try:
table = henke.table(atom_type)
fp_fdp = table.at_angstrom(wavelength)
except Exception:
return None
#print "Using Henke tables for scattering factors"
if fp_fdp.is_valid():
return fp_fdp
else:
return None
def fcalc_from_pdb(self, resolution):
from iotbx import pdb
pdb_inp = pdb.input(source_info=None, lines=pdb_lines)
xray_structure = pdb_inp.xray_structure_simple()
wavelength = self.beam.get_wavelength()
# Assuming X-ray scattering here - does not matter for the geometry. How
# would one use electron scattering instead?
scatterers = xray_structure.scatterers()
for sc in scatterers:
expected_henke = henke.table(
sc.element_symbol()).at_angstrom(wavelength)
sc.fp = expected_henke.fp()
sc.fdp = expected_henke.fdp()
primitive_xray_structure = xray_structure.primitive_setting()
P1_primitive_xray_structure = primitive_xray_structure.expand_to_p1()
fcalc = P1_primitive_xray_structure.structure_factors(
d_min=resolution, anomalous_flag=True,
algorithm="direct").f_calc()
return fcalc.amplitudes()
def __init__(self, resolution, pdb_text, wavelength=None, **kwargs):
from iotbx import pdb
self.d_min = resolution
self.algorithm = kwargs["algorithm"]
self.method = kwargs["sfall"]
pdb_inp = pdb.input(source_info=None, lines=pdb_text)
xray_structure = pdb_inp.xray_structure_simple()
#xray_structure.show_summary(prefix="Input structure ")
self.xray_structure = xray_structure
# take a detour to insist on calculating anomalous contribution of every atom
scatterers = xray_structure.scatterers()
for sc in scatterers:
from cctbx.eltbx import henke
expected_henke = henke.table(
sc.element_symbol()).at_angstrom(wavelength)
sc.fp = expected_henke.fp()
sc.fdp = expected_henke.fdp()
if self.method == "f_model":
import mmtbx.command_line.fmodel
phil2 = mmtbx.command_line.fmodel.fmodel_from_xray_structure_master_params
#phil2.show()
params2 = phil2.extract()
# adjust the cutoff of the generated intensities to assure that
# statistics will be reported to the desired high-resolution limit
# even if the observed unit cell differs slightly from the reference.
params2.high_resolution = self.d_min
params2.output.type = "complex"
params2.fmodel.k_sol = kwargs["k_sol"]
params2.fmodel.b_sol = kwargs["b_sol"]
params2.structure_factors_accuracy.algorithm = kwargs["algorithm"]
params2.structure_factors_accuracy.grid_resolution_factor = kwargs[
"grid_resolution_factor"]
if kwargs["k_sol"] > 0 and kwargs["b_sol"] > 0:
params2.mask.grid_step_factor = kwargs["grid_step_factor"]
self.params2 = params2
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")
def launch(self):
import shutil
#check whether ACTA was set, so the cif contains all necessary information to be copied back and forth
# Check if job folder already exists and (if needed) make the backup folders
if os.path.exists(self.full_dir):
self.backup = os.path.join(self.full_dir, "backup")
i = 1
while (os.path.exists(self.backup + "_%d"%i)):
i = i + 1
self.backup = self.backup + "_%d"%i
os.mkdir(self.backup)
try:
files = (file for file in os.listdir(self.full_dir)
if os.path.isfile(os.path.join(self.full_dir, file)))
for f in files:
f_work = os.path.join(self.full_dir,f)
f_dest = os.path.join(self.backup,f)
shutil.move(f_work,f_dest)
except:
pass
try:
os.mkdir(self.full_dir)
except:
pass
tries = 0
while not os.path.exists(self.full_dir) and tries < 5:
try:
os.mkdir(self.full_dir)
break
except:
time.sleep(0.1)
tries += 1
pass
time.sleep(0.1)
self.origin_folder = OV.FilePath()
# if not olx.Ins('ACTA'):
# olex.m('addins ACTA')
# olex.m('refine')
autogrow = olx.GetVar("settings.tonto.HAR.autogrow", None)
if olx.xf.latt.IsGrown() == 'true':
if olx.Alert("Please confirm",\
"""This is a grown structure. If you have created a cluster of molecules, make sure
that the structure you see on the screen obeys the crystallographic symmetry.
If this is not the case, the HAR will not work properly.
Make sure the cluster/moelcule is neutral and fully completed.
Continue?""", "YN", False) == 'N':
return
elif olx.xf.au.GetZprime() != '1' and autogrow == 'true':
olex.m("kill $q")
olx.Grow()
olex.m("grow -w")
elif olx.xf.au.GetZprime() < '1' and autogrow == 'false':
if olx.Alert("Attention!",\
"""This appears to be a z' < 1 structure.
Autogrow is disabled and the structure is not grown.
This is HIGHLY unrecomendet!
Please complete the molecule in a way it forms a full chemical entity.
Benzene would need to contain one complete 6-membered ring to work,
otherwise the wavefunction can not be calculated properly!
Are you sure you want to continue with this structure?""", "YN", False) == 'N':
return
autorefine = olx.GetVar("settings.tonto.HAR.autorefine", None)
if autorefine == 'true':
olex.m("refine")
model_file_name = os.path.join(self.full_dir, self.name) + ".cif"
olx.Kill("$Q")
olx.File(model_file_name)
data_file_name = os.path.join(self.full_dir, self.name) + ".hkl"
if not os.path.exists(data_file_name):
from cctbx_olex_adapter import OlexCctbxAdapter
from iotbx.shelx import hklf
cctbx_adaptor = OlexCctbxAdapter()
with open(data_file_name, "w") as out:
f_sq_obs = cctbx_adaptor.reflections.f_sq_obs_filtered
for j, h in enumerate(f_sq_obs.indices()):
s = f_sq_obs.sigmas()[j]
if s <= 0: f_sq_obs.sigmas()[j] = 0.01
i = f_sq_obs.data()[j]
if i < 0: f_sq_obs.data()[j] = 0
f_sq_obs.export_as_shelx_hklf(out, normalise_if_format_overflow=True)
self.save()
args = [self.parent.exe, self.name+".cif",
"-basis-dir", self.parent.basis_dir,
"-shelx-f2", self.name+".hkl"]
disp = olx.GetVar("settings.tonto.HAR.dispersion", None)
if 'true' == disp:
import olexex
from cctbx.eltbx import henke
olex_refinement_model = OV.GetRefinementModel(False)
sfac = olex_refinement_model.get('sfac')
fp_fdps = {}
wavelength = olex_refinement_model['exptl']['radiation']
if sfac is not None:
for element, sfac_dict in sfac.iteritems():
custom_fp_fdps.setdefault(element, sfac_dict['fpfdp'])
asu = olex_refinement_model['aunit']
for residue in asu['residues']:
for atom in residue['atoms']:
element_type = atom['type']
if element_type not in fp_fdps:
fpfdp = henke.table(str(element_type)).at_angstrom(wavelength).as_complex()
fp_fdps[element_type] = (fpfdp.real, fpfdp.imag)
disp_arg = " ".join(["%s %s %s" %(k, v[0], v[1]) for k,v in fp_fdps.iteritems()])
args.append("-dispersion")
args.append('%s' %disp_arg)
for k,v in HARp_instance.options.iteritems():
val = olx.GetVar(k, None)
if len(v) == 2:
if val is not None:
args.append('-' + v[1])
args.append(val)
elif k == 'settings.tonto.HAR.hydrogens':
if val == 'positions only':
args.append("-h-adps")
args.append("f")
elif val == 'isotropic':
args.append("-h-adps")
args.append("f")
args.append("-h-iso")
args.append("t")
elif val == "anisotropic":
args.append("-h-adps")
args.append("t")
elif val == "not":
args.append("-h-adps")
args.append("f")
args.append("-h-pos")
args.append("f")
pass
clustergrow = olx.GetVar("settings.tonto.HAR.cluster-grow", None)
if clustergrow == 'false':
args.append("-complete-mol")
args.append("f")
self.result_fn = os.path.join(self.full_dir, self.name) + ".archive.cif"
self.error_fn = os.path.join(self.full_dir, self.name) + ".err"
self.out_fn = os.path.join(self.full_dir, self.name) + ".out"
self.dump_fn = os.path.join(self.full_dir, "hart.exe.stackdump")
self.analysis_fn = os.path.join(self.full_dir, "stdout.fit_analysis")
os.environ['hart_cmd'] = '+&-'.join(args)
os.environ['hart_file'] = self.name
os.environ['hart_dir'] = self.full_dir
from subprocess import Popen
pyl = OV.getPYLPath()
if not pyl:
print("A problem with pyl is encountered, aborting.")
return
Popen([pyl,
os.path.join(p_path, "HARt-launch.py")])
CSV = csv()
wavelength = lambd[50]
from iotbx import pdb
pdb_text = open("1m2a.pdb", "r").read()
pdb_inp = pdb.input(source_info=None, lines=pdb_text)
xray_structure = pdb_inp.xray_structure_simple()
xray_structure.show_summary(prefix="Input structure ")
#
# take a detour to insist on calculating anomalous contribution of every atom
scatterers = xray_structure.scatterers()
for isc, sc in enumerate(scatterers):
from cctbx.eltbx import sasaki, henke
#expected_sasaki = sasaki.table(sc.element_symbol()).at_angstrom(wavelength)
expected_henke = henke.table(
sc.element_symbol()).at_angstrom(wavelength)
sc.fp = expected_henke.fp()
sc.fdp = expected_henke.fdp()
if sc.element_symbol() == "Fe":
ife = isc
break
fp = flex.double()
fdp = flex.double()
for wave, energy in zip(lambd, energies):
print(energy, end=' ')
sc = scatterers[ife]
expected_henke = henke.table(sc.element_symbol()).at_angstrom(wave)
sc.fp = expected_henke.fp()
sc.fdp = expected_henke.fdp()
