def exercise_miller_export_as_shelx_hklf():
s = """\
1 2 -1 23.34 4.56
2 -3 9 12.45 6.12
99999999999999999.9999999.99
-999-999-999-9999.99-9999.99
3 4 5999999.99999999.
3 4 5-99999.9-999999.
"""
ma = hklf.reader(file_object=StringIO(s)).as_miller_arrays()[0]
sio = StringIO()
ma.export_as_shelx_hklf(file_object=sio)
ma2 = hklf.reader(file_object=StringIO(sio.getvalue())).as_miller_arrays()[0]
assert approx_equal(ma.indices(), ma2.indices())
assert approx_equal(ma.data(), ma2.data())
assert approx_equal(ma.sigmas(), ma2.sigmas())
#
ma = ma.select(flex.size_t([0]))
def check(d, s, f):
if (s is not None): s = flex.double([s])
ma2 = ma.array(data=flex.double([d]), sigmas=s)
sio = StringIO()
ma2.export_as_shelx_hklf(sio, normalise_if_format_overflow=True)
assert not show_diff(sio.getvalue(), """\
1 2 -1%s
0 0 0 0.00 0.00
""" % f)
try: ma2.export_as_shelx_hklf(sio)
except RuntimeError: pass
else: raise Exception_expected
check(-12345678, 1, "-999999. 0.08")
check(-12345678, None, "-999999. 0.00")
check(2, -12345678, " 0.16-999999.")
check(123456789, 30, "9999999. 2.43")
check(123456789, None, "9999999. 0.00")
check(40, 123456789, " 3.249999999.")
check(-23456789, 123456789, "-999999.5263153.")
check(123456789, -23456789, "5263153.-999999.")
#
ma = hklf.reader(file_object=StringIO(s)).as_miller_arrays()[0]
ma = ma.select(flex.size_t([0,1]))
ma2 = ma.array(data=flex.double([123456789, -23456789]))
sio = StringIO()
ma2.export_as_shelx_hklf(sio, normalise_if_format_overflow=True)
assert not show_diff(sio.getvalue(), """\
1 2 -15263153. 0.00
2 -3 9-999999. 0.00
0 0 0 0.00 0.00
""")
ma2 = ma.array(data=flex.double([-23456789, 823456789]))
sio = StringIO()
ma2.export_as_shelx_hklf(sio, normalise_if_format_overflow=True)
assert not show_diff(sio.getvalue(), """\
1 2 -1-284858. 0.00
2 -3 99999999. 0.00
0 0 0 0.00 0.00
""")
def _set_res(self, event):
if len(self._ref_files) > 0 and len(self._in_files) > 0:
ref = self._ref_files[self._reflections.GetCurrentSelection()]
ins = self._in_files[self._structure.GetCurrentSelection()]
if os.path.exists(ref) and os.path.exists(ins):
hkl = hklf.reader(open(ref))
try:
ma = hkl.as_miller_arrays(crystal_symmetry=crystal_symmetry_from_ins.extract_from(ins))
except:
return
rr = ma[0].resolution_range()
self._res_high.SetValue(str(round(rr[1], 2)))
self._res_low.SetValue(str(round(rr[0], 2)))
ins_obj = Shelx(ins)
self._hydrogens.SetValue(ins_obj.has_hydrogen())
self._residues.Clear()
self._residue_list = []
for r in sorted(ins_obj.residue_list()):
if r not in (ShelxData._r + ['HOH', 'DOD', 'CL', 'MG']) or (r in ['ASP', 'GLU', 'HIS', 'ARG']):
self._residues.Append(r)
self._residue_list.append(r)
class any_reflection_file(object):
"""
Proxy object for reading a reflection file of unspecified format, and
extracting the Miller arrays contained therein.
Examples
--------
>>> from iotbx.reflection_file_reader import any_reflection_file
>>> hkl_file = any_reflection_file("data.mtz")
>>> print hkl_file.file_type()
'ccp4_mtz'
>>> print type(hkl_file.file_content())
<class 'iotbx_mtz_ext.object'>
>>> miller_arrays = hkl_file.as_miller_arrays()
"""
def __init__(self, file_name, ensure_read_access=True, strict=True):
# strict is no longer used
if (file_name.startswith("amplitudes=")
or file_name.startswith("hklf3=")
or file_name.startswith("intensities=")
or file_name.startswith("hklf4=")
or file_name.startswith("hklf+ins/res=")):
self._observation_type, self._file_name = file_name.split("=", 1)
elif (file_name.endswith("=amplitudes") or file_name.endswith("=hklf3")
or file_name.endswith("=intensities")
or file_name.endswith("=hklf4")
or file_name.endswith("=hklf+ins/res")):
self._file_name, self._observation_type = file_name.split("=", 1)
else:
self._file_name = file_name
self._observation_type = None
if (self._observation_type == "hklf3"):
self._observation_type = "amplitudes"
elif (self._observation_type == "hklf4"):
self._observation_type = "intensities"
self._file_type = None
file_name = self._file_name
try:
open(file_name) # test read access
except IOError, e:
if (ensure_read_access):
raise Sorry(str(e))
return
if (self._observation_type is not None):
try:
self._file_content = shelx_hklf.reader(file_name=file_name)
except KeyboardInterrupt:
raise
except Exception:
raise Sorry(
"Not a SHELX reflection file: %s\n"
" =%s can only be used for SHELX reflection files." %
(file_name, self._observation_type))
else:
self._file_type = "shelx_hklf"
else:
self._file_type, self._file_content = try_all_readers(
file_name=file_name)
def load_refinement(self, ref, stats):
hkl = hklf.reader(open(ref.replace('.dat', '.hkl')))
pdbf = pdb.input(file_name=ref.replace('.dat', '.pdb'))
pdbt = PDBTools(file_name=ref.replace('.dat', '.pdb'))
cs = crystal_symmetry_from_ins.extract_from(ref.replace('.dat', '.ins'))
ma = hkl.as_miller_arrays(crystal_symmetry=cs)
mp = pdbf.xray_structure_simple().scatterers()[0].multiplicity()
s = pdbt.get_s()
vm = cs.unit_cell().volume() / (pdbt.get_rmm() * mp)
c = ma[0].completeness(d_max=stats['res'])
dmin = stats['res']
r = stats['r']
rfree = stats['rfree']
self._mv.SetLabel('%.2f' % vm)
self._s.SetLabel('%.2f' % s)
self._dmin.SetLabel('%.2f' % dmin)
self._c.SetLabel('%.1f' % (c*100))
self._r.SetLabel('%.3f' % r)
self._rfree.SetLabel('%.3f' % rfree)
sigxr = self._sigx_r(s, vm, c, r, dmin)
self._sigxr.SetLabel('%.4f' % sigxr)
sigxrf = self._sigx_rfree(s, vm, c, rfree, dmin)
self._sigxrf.SetLabel('%.4f' % sigxrf)
x = np.linspace(dmin+0.5,dmin-0.5, 20)
ys = [[],[],[],[],[],[]]
for i in x:
sr = self._sigx_r(s, vm, c, r, i)
ys[0].append(sr)
ys[1].append(sr*1.15)
ys[2].append(sr*0.85)
sr = self._sigx_rfree(s, vm, c, rfree, i)
ys[3].append(sr)
ys[4].append(sr*1.15)
ys[5].append(sr*0.85)
self.ax1.plot(x, ys[0], 'b-', label='R')
self.ax1.fill_between(x, ys[1], ys[2], alpha=0.1, facecolor='blue')
self.ax1.plot(x, ys[3], 'g-', label='Rfree')
self.ax1.fill_between(x, ys[4], ys[5], alpha=0.1, facecolor='green')
al = self.ax1.axis()
yam = al[3]-al[2]
xam = al[1]-al[0]
self.ax1.axhline(y=0.0236, color='purple', label='3sig (ASP)')
self.ax1.axvline(x=dmin, ymin=0, ymax=(sigxr-al[2])/yam, color='0.7', label='Actual')
self.ax1.axhline(y=sigxr, xmin=0, xmax=(dmin-al[0])/xam, color='0.7')
self.ax1.legend(prop={'size':8}, numpoints=1, loc='best', fancybox=True)
def structure_factors_from_hkl(hkl_path, xs, weighting_scheme=None):
fo2 = hklf.reader(file_name=hkl_path).as_miller_arrays(
crystal_symmetry=xs)[0]
fo2.set_observation_type_xray_intensity()
merging = fo2.merge_equivalents(algorithm="shelx")
fo2 = merging.array()
xs.scattering_type_registry(table="it1992", d_min=fo2.d_min())
fc = fo2.structure_factors_from_scatterers(xs, algorithm="direct").f_calc()
scale = fo2.scale_factor(fc)
if weighting_scheme is not None:
weights = weighting_scheme(
fo2.data(), fo2.sigmas(), fc.as_intensity_array().data(), scale)
scale = fo2.scale_factor(fc, weights=weights)
return xs, fo2, fc, scale
def structure_factors_from_hkl(hkl_path, xs, weighting_scheme=None):
fo2 = hklf.reader(file_name=hkl_path).as_miller_arrays(
crystal_symmetry=xs)[0]
fo2.set_observation_type_xray_intensity()
merging = fo2.merge_equivalents(algorithm="shelx")
fo2 = merging.array()
xs.scattering_type_registry(table="it1992", d_min=fo2.d_min())
fc = fo2.structure_factors_from_scatterers(xs, algorithm="direct").f_calc()
scale = fo2.scale_factor(fc)
if weighting_scheme is not None:
weights = weighting_scheme(fo2.data(), fo2.sigmas(),
fc.as_intensity_array().data(), scale)
scale = fo2.scale_factor(fc, weights=weights)
return xs, fo2, fc, scale
def shelxd_read_hklf(fa_file, fa_ins, d_min, n_bins):
'''Normalise Fa values output by SHELX'''
fa_data = hklf.reader(file_name=fa_file)
c = crystal_symmetry_from_ins.extract_from(file_name=fa_ins)
fsigf_all = fa_data.as_miller_arrays(crystal_symmetry=c)[0]
fsigf = fsigf_all.select(fsigf_all.d_spacings().data()>d_min)
fsigf.setup_binner(n_bins=n_bins)
ea = fsigf.quasi_normalize_structure_factors()
ea.setup_binner(n_bins=n_bins)
ea_weak = ea.select((abs(ea.data())<1.5))
ea_weak.setup_binner(n_bins=n_bins)
return ea, ea_weak
def __init__(self, file_name, ensure_read_access=True, strict=True):
# strict is no longer used
if (file_name.startswith("amplitudes=")
or file_name.startswith("hklf3=")
or file_name.startswith("intensities=")
or file_name.startswith("hklf4=")
or file_name.startswith("hklf+ins/res=")):
self._observation_type, self._file_name = file_name.split("=", 1)
elif (file_name.endswith("=amplitudes") or file_name.endswith("=hklf3")
or file_name.endswith("=intensities")
or file_name.endswith("=hklf4")
or file_name.endswith("=hklf+ins/res")):
self._file_name, self._observation_type = file_name.split("=", 1)
else:
self._file_name = file_name
self._observation_type = None
if (self._observation_type == "hklf3"):
self._observation_type = "amplitudes"
elif (self._observation_type == "hklf4"):
self._observation_type = "intensities"
self._file_type = None
file_name = self._file_name
try:
with open(file_name): # test read access
pass
except IOError as e:
if (ensure_read_access):
raise Sorry(str(e))
return
if (self._observation_type is not None):
try:
self._file_content = shelx_hklf.reader(file_name=file_name)
except KeyboardInterrupt:
raise
except Exception:
raise Sorry(
"Not a SHELX reflection file: %s\n"
" =%s can only be used for SHELX reflection files." %
(file_name, self._observation_type))
else:
self._file_type = "shelx_hklf"
else:
self._file_type, self._file_content = try_all_readers(
file_name=file_name)
def try_all_readers(file_name):
try: content = mtz.object(file_name=file_name)
except RuntimeError: pass
else: return ("ccp4_mtz", content)
if (detect_binary_file.from_initial_block(file_name=file_name)):
try: content = unpickle_miller_arrays(file_name=file_name)
except KeyboardInterrupt: raise
except Exception: pass
else: return ("cctbx.miller.array", content)
return (None, None)
try: content = cns_reflection_reader.cns_reflection_file(
open(file_name))
except cns_reflection_reader.CNS_input_Error: pass
else: return ("cns_reflection_file", content)
try: content = cns_index_fobs_sigma_reader.reader(
file_name=file_name)
except RuntimeError: pass
else: return ("cns_index_fobs_sigma", content)
try: content = scalepack_merge.reader(
open(file_name))
except scalepack_merge.FormatError: pass
else: return ("scalepack_merge", content)
try: content = scalepack_no_merge.reader(file_name)
except KeyboardInterrupt: raise
except Exception: pass
else: return ("scalepack_no_merge_original_index", content)
try: content = dtrek_reflnlist_reader.reflnlist(
open(file_name))
except KeyboardInterrupt: raise
except Exception: pass
else: return ("dtrek_reflnlist", content)
try: content = shelx_hklf.reader(
file_name=file_name)
except KeyboardInterrupt: raise
except Exception: pass
else: return ("shelx_hklf", content)
try:
content = cif_reader(file_path=file_name)
looks_like_a_reflection_file = False
for block in content.model().values():
if '_refln_index_h' in block or '_refln.index_h' in block:
looks_like_a_reflection_file = True
break
if not looks_like_a_reflection_file:
raise RuntimeError
except KeyboardInterrupt: raise
except Exception: pass
else: return ("cif", content)
try: content = xds_ascii_reader(
open(file_name))
except KeyboardInterrupt: raise
except Exception: pass
else: return ("xds_ascii", content)
try:
content = xds_integrate_hkl_reader()
content.read_file(file_name)
except KeyboardInterrupt: raise
except Exception: pass
else: return ("xds_integrate_hkl", content)
try: content = solve_fpfm_reader(file_name=file_name)
except KeyboardInterrupt: raise
except Exception: pass
else: return ("solve_fpfm", content)
return (None, None)
def excersise():
s = """\
-1 -6 9624.8650 54.9190 1
-1 6 9749.5660 52.1870 -2
1 6 -9749.5660 52.1870 1
1 -6 -8695.6020 53.8100 -2
-1 -6 8695.6020 53.8100 1
-1 6 8746.7970 51.3980 -2
1 6 -8746.7970 51.3980 1
-1 -6 -12281.3590 49.5060 1
1 6 12185.9370 47.3950 1
-1 -6 -1316.0700044.01400 1
1 6 13 4.7500043.54900 1
-1 -6 -1479.6380048.66400 2
1 6 1432.7830051.51700 2
"""
sg = sgtbx.space_group("P 1")
uc = uctbx.unit_cell((11, 11, 13, 90, 90, 120))
cs = crystal.symmetry(unit_cell=uc, space_group=sg)
ma = hklf.reader(file_object=StringIO(s))\
.as_miller_arrays(crystal_symmetry=cs, merge_equivalents=False)
fo_sq = ma[0]
batch_numbers = ma[1]
obs = fo_sq.as_xray_observations(scale_indices=batch_numbers.data(),
twin_fractions=(xray.twin_fraction(
0.4, True), ))
measured_cnt = 0
measured_scale_indices = obs.measured_scale_indices
for bn in batch_numbers.data():
if bn > 0:
assert (measured_scale_indices[measured_cnt] == bn)
measured_cnt = measured_cnt + 1
assert (measured_cnt == obs.indices.size())
itr = obs.iterator(0)
assert (not itr.has_next())
itr = obs.iterator(1)
assert (itr.next().h == (-1, 6, 9))
itr = obs.iterator(2)
assert (itr.next().h == (1, -6, -8))
# this is supposed to fail for now until somebody re-implements
# mixed HKLF 5 + merohedral twinning in a meaningful way...
try:
obs = observations.customized_copy(
obs,
twin_fractions=(xray.twin_fraction(0.7, True), ),
twin_components=(xray.twin_component(
sgtbx.rot_mx((-1, 0, 0, 0, -1, 0, 0, 0, -1)), 0.25, True), ))
itr = obs.iterator(0)
assert (itr.has_next())
assert (itr.next().h == (1, 6, -9))
assert (not itr.has_next())
itr = obs.iterator(1)
assert (itr.next().h == (-1, -6, 9))
assert (itr.next().h == (-1, 6, 9))
assert (itr.next().h == (1, -6, -9))
assert (not itr.has_next())
ts = 1 - obs.ref_twin_components[0].value
ps = 1 - obs.ref_twin_fractions[0].value
itr = obs.iterator(0)
assert obs.scale(0) == ts * ps
nv = next(itr)
assert nv.scale == obs.ref_twin_components[0].value * ps
except RuntimeError as e:
pass
def try_all_readers(file_name):
try:
content = mtz.object(file_name=file_name)
except RuntimeError:
pass
else:
return ("ccp4_mtz", content)
if (detect_binary_file.from_initial_block(file_name=file_name)):
try:
content = unpickle_miller_arrays(file_name=file_name)
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("cctbx.miller.array", content)
return (None, None)
try:
content = cns_reflection_reader.cns_reflection_file(open(file_name))
except cns_reflection_reader.CNS_input_Error:
pass
else:
return ("cns_reflection_file", content)
try:
content = cns_index_fobs_sigma_reader.reader(file_name=file_name)
except RuntimeError:
pass
else:
return ("cns_index_fobs_sigma", content)
try:
content = scalepack_merge.reader(open(file_name))
except scalepack_merge.FormatError:
pass
else:
return ("scalepack_merge", content)
try:
content = scalepack_no_merge.reader(file_name)
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("scalepack_no_merge_original_index", content)
try:
content = dtrek_reflnlist_reader.reflnlist(open(file_name))
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("dtrek_reflnlist", content)
try:
content = shelx_hklf.reader(file_name=file_name)
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("shelx_hklf", content)
try:
content = cif_reader(file_path=file_name)
looks_like_a_reflection_file = False
for block in content.model().values():
if '_refln_index_h' in block or '_refln.index_h' in block:
looks_like_a_reflection_file = True
break
if not looks_like_a_reflection_file:
raise RuntimeError
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("cif", content)
try:
content = xds_ascii_reader(open(file_name))
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("xds_ascii", content)
try:
content = xds_integrate_hkl_reader()
content.read_file(file_name)
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("xds_integrate_hkl", content)
try:
content = solve_fpfm_reader(file_name=file_name)
except KeyboardInterrupt:
raise
except Exception:
pass
else:
return ("solve_fpfm", content)
return (None, None)
def exercise_hklf_reader():
s = (' 1 2 -1 -23.34 4.56 1\n'
' 2 -3 9 12.45 6.12 2\r\n'
'99999999999999999.9999999.999999\n'
'-999-999-999-9999.99-9999.99-999\r\n'
' 0 0 0 0.00 0.00 0\n')
r = hklf.reader(file_object=StringIO(s))
assert list(r.indices()) == [
(1, 2, -1), (2, -3, 9), (9999, 9999, 9999), (-999, -999, -999), ]
assert approx_equal(r.data(), [-23.34, 12.45, 99999.99, -9999.99, ])
assert approx_equal(r.sigmas(), [4.56, 6.12, 99999.99, -9999.99, ])
assert approx_equal(r.batch_numbers(), [1, 2, 9999, -999, ])
assert approx_equal(r.alphas(), [1, 2, 9999, -999, ])
for ma in r.as_miller_arrays():
assert ma.indices().all_eq(r.indices())
assert ma.anomalous_flag() is False
ma = r.as_miller_arrays()[0]
assert ma.data().all_approx_equal(r.data())
assert ma.sigmas().all_approx_equal(r.sigmas())
ma = r.as_miller_arrays()[1]
assert ma.data().all_eq(r.alphas())
assert ma.sigmas() is None
s = (' 0 2 3 1816.00 20.00\n'
' 0 2 415508.00 138.00\n'
' 0 2 5 4776.00 40.00\n')
r = hklf.reader(file_object=StringIO(s))
assert list(r.indices()) == [ (0,2,3), (0,2,4), (0,2,5) ]
assert r.batch_numbers() is None
assert r.alphas() is None
assert r.wavelengths() is None
for end_line in (True, False):
for something_after_end_line in (True, False):
s = (' 1 2 -1 23.34 4.56\n'
' 2 -3 9 12.45 6.12\r\n'
'99999999999999999.9999999.99\n'
'-999-999-999-9999.99-9999.99\n')
if end_line:
s += ' 0 0 0 0.00 0.00\n'
if something_after_end_line:
s += ' -5 1 0 123.45 66.12\n'
s = (s)
r = hklf.reader(file_object=StringIO(s))
assert approx_equal(r.sigmas(), [4.56, 6.12, 99999.99, -9999.99, ])
assert r.batch_numbers() is None
assert r.alphas() is None
assert r.wavelengths() is None
s = ''
try: r = hklf.reader(file_object=StringIO(s))
except RuntimeError: pass
else: raise Exception_expected
s = (' 1 2 -1 23.34 4.56 1\n'
' 2 -3 a9 12.45 6.12 2\n'
' 0 0 0 0.00 0.00 0\n')
try: r = hklf.reader(file_object=StringIO(s))
except Exception: pass
else: raise Exception_expected
s = (' 1 2 -1 23.34 4.56 1 45.36\n'
' 2 -3 9 -12.45 -6.12 2 54.63\n'
' 0 0 0 0.00 0.00 0 0\n')
r = hklf.reader(file_object=StringIO(s))
assert list(r.indices()) == [ (1, 2, -1), (2, -3, 9)]
assert approx_equal(r.data(), [23.34, -12.45])
assert approx_equal(r.sigmas(), [4.56, -6.12])
assert approx_equal(r.batch_numbers(), [1, 2])
assert approx_equal(r.wavelengths(), [45.36, 54.63])
s = (' 1 2 -1 23. 4. 2\n'
' -2 1 3 -1. 3. 1\n'
' 0 0 0 0. 0. 0\n')
r = hklf.reader(file_object=StringIO(s))
assert list(r.indices()) == [(1, 2, -1), (-2, 1, 3)]
assert approx_equal(r.data(), [23, -1])
assert approx_equal(r.sigmas(), [4, 3])
assert approx_equal(r.alphas(), [2, 1])
assert r.wavelengths() is None
s = (' 3 2 -1 32. 5.\n'
' 0 0 0\n')
r = hklf.reader(file_object=StringIO(s))
assert list(r.indices()) == [(3, 2, -1)]
assert approx_equal(r.data(), [32])
assert approx_equal(r.sigmas(), [5])
assert r.alphas() is None
assert r.wavelengths() is None
s = (
"""King Arthur: [after Arthur's cut off both of the Black Knight's arms]
Look, you stupid Bastard. You've got no arms left.
Black Knight: Yes I have.
King Arthur: *Look*!
Black Knight: It's just a flesh wound.""")
try: r = hklf.reader(file_object=StringIO(s))
except RuntimeError: pass
else: raise Exception_expected
def excersise():
s = """\
-1 -6 9624.8650 54.9190 1
-1 6 9749.5660 52.1870 -2
1 6 -9749.5660 52.1870 1
1 -6 -8695.6020 53.8100 -2
-1 -6 8695.6020 53.8100 1
-1 6 8746.7970 51.3980 -2
1 6 -8746.7970 51.3980 1
-1 -6 -12281.3590 49.5060 1
1 6 12185.9370 47.3950 1
-1 -6 -1316.0700044.01400 1
1 6 13 4.7500043.54900 1
-1 -6 -1479.6380048.66400 2
1 6 1432.7830051.51700 2
"""
sg = sgtbx.space_group("P 1")
uc = uctbx.unit_cell((11,11,13,90,90,120))
cs = crystal.symmetry(unit_cell=uc, space_group=sg)
ma = hklf.reader(file_object=StringIO(s))\
.as_miller_arrays(crystal_symmetry=cs, merge_equivalents=False)
fo_sq = ma[0]
batch_numbers = ma[1]
obs = fo_sq.as_xray_observations(
scale_indices=batch_numbers.data(),
twin_fractions=(xray.twin_fraction(0.4,True),))
measured_cnt = 0
measured_scale_indices = obs.measured_scale_indices
for bn in batch_numbers.data():
if bn > 0:
assert(measured_scale_indices[measured_cnt]==bn)
measured_cnt = measured_cnt+1
assert(measured_cnt == obs.indices.size())
itr = obs.iterator(0)
assert(not itr.has_next())
itr = obs.iterator(1)
assert(itr.next().h==(-1,6,9))
itr = obs.iterator(2)
assert(itr.next().h==(1,-6,-8))
obs = observations.customized_copy(obs,
twin_fractions=(xray.twin_fraction(0.7,True),),
twin_components=(xray.twin_component(
sgtbx.rot_mx((-1,0,0,0,-1,0,0,0,-1)), 0.25, True),))
itr = obs.iterator(0)
assert(itr.has_next())
assert(itr.next().h==(1,6,-9))
assert(not itr.has_next())
itr = obs.iterator(1)
assert(itr.next().h==(-1,-6,9))
assert(itr.next().h==(-1,6,9))
assert(itr.next().h==(1,-6,-9))
assert(not itr.has_next())
ts = 1-obs.ref_twin_components[0].value
ps = 1-obs.ref_twin_fractions[0].value
itr = obs.iterator(0)
assert obs.scale(0) == ts*ps
nv = itr.next()
assert nv.scale == obs.ref_twin_components[0].value*ps
def exercise_hklf_reader():
s = (' 1 2 -1 -23.34 4.56 1\n'
' 2 -3 9 12.45 6.12 2\r\n'
'99999999999999999.9999999.999999\n'
'-999-999-999-9999.99-9999.99-999\r\n'
' 0 0 0 0.00 0.00 0\n')
r = hklf.reader(file_object=StringIO(s))
assert list(r.indices()) == [
(1, 2, -1), (2, -3, 9), (9999, 9999, 9999), (-999, -999, -999), ]
assert approx_equal(r.data(), [-23.34, 12.45, 99999.99, -9999.99, ])
assert approx_equal(r.sigmas(), [4.56, 6.12, 99999.99, -9999.99, ])
assert approx_equal(r.batch_numbers(), [1, 2, 9999, -999, ])
assert approx_equal(r.alphas(), [1, 2, 9999, -999, ])
for ma in r.as_miller_arrays():
assert ma.indices().all_eq(r.indices())
ma = r.as_miller_arrays()[0]
assert ma.data().all_approx_equal(r.data())
assert ma.sigmas().all_approx_equal(r.sigmas())
ma = r.as_miller_arrays()[1]
assert ma.data().all_eq(r.alphas())
assert ma.sigmas() is None
s = (' 0 2 3 1816.00 20.00\n'
' 0 2 415508.00 138.00\n'
' 0 2 5 4776.00 40.00\n')
r = hklf.reader(file_object=StringIO(s))
assert list(r.indices()) == [ (0,2,3), (0,2,4), (0,2,5) ]
assert r.batch_numbers() is None
assert r.alphas() is None
assert r.wavelengths() is None
for end_line in (True, False):
for something_after_end_line in (True, False):
s = (' 1 2 -1 23.34 4.56\n'
' 2 -3 9 12.45 6.12\r\n'
'99999999999999999.9999999.99\n'
'-999-999-999-9999.99-9999.99\n')
if end_line:
s += ' 0 0 0 0.00 0.00\n'
if something_after_end_line:
s += ' -5 1 0 123.45 66.12\n'
s = (s)
r = hklf.reader(file_object=StringIO(s))
assert approx_equal(r.sigmas(), [4.56, 6.12, 99999.99, -9999.99, ])
assert r.batch_numbers() is None
assert r.alphas() is None
assert r.wavelengths() is None
s = ''
try: r = hklf.reader(file_object=StringIO(s))
except RuntimeError: pass
else: raise Exception_expected
s = (' 1 2 -1 23.34 4.56 1\n'
' 2 -3 a9 12.45 6.12 2\n'
' 0 0 0 0.00 0.00 0\n')
try: r = hklf.reader(file_object=StringIO(s))
except Exception: pass
else: raise Exception_expected
s = (' 1 2 -1 23.34 4.56 1 45.36\n'
' 2 -3 9 -12.45 -6.12 2 54.63\n'
' 0 0 0 0.00 0.00 0 0\n')
r = hklf.reader(file_object=StringIO(s))
assert list(r.indices()) == [ (1, 2, -1), (2, -3, 9)]
assert approx_equal(r.data(), [23.34, -12.45])
assert approx_equal(r.sigmas(), [4.56, -6.12])
assert approx_equal(r.batch_numbers(), [1, 2])
assert approx_equal(r.wavelengths(), [45.36, 54.63])
s = (' 1 2 -1 23. 4. 2\n'
' -2 1 3 -1. 3. 1\n'
' 0 0 0 0. 0. 0\n')
r = hklf.reader(file_object=StringIO(s))
assert list(r.indices()) == [(1, 2, -1), (-2, 1, 3)]
assert approx_equal(r.data(), [23, -1])
assert approx_equal(r.sigmas(), [4, 3])
assert approx_equal(r.alphas(), [2, 1])
assert r.wavelengths() is None
s = (' 3 2 -1 32. 5.\n'
' 0 0 0\n')
r = hklf.reader(file_object=StringIO(s))
assert list(r.indices()) == [(3, 2, -1)]
assert approx_equal(r.data(), [32])
assert approx_equal(r.sigmas(), [5])
assert r.alphas() is None
assert r.wavelengths() is None
s = (
"""King Arthur: [after Arthur's cut off both of the Black Knight's arms]
Look, you stupid Bastard. You've got no arms left.
Black Knight: Yes I have.
King Arthur: *Look*!
Black Knight: It's just a flesh wound.""")
try: r = hklf.reader(file_object=StringIO(s))
except RuntimeError: pass
else: raise Exception_expected
def exercise_miller_export_as_shelx_hklf():
s = """\
1 2 -1 23.34 4.56
2 -3 9 12.45 6.12
99999999999999999.9999999.99
-999-999-999-9999.99-9999.99
3 4 5999999.99999999.
3 4 5-99999.9-999999.
"""
ma = hklf.reader(file_object=StringIO(s)).as_miller_arrays()[0]
sio = StringIO()
ma.export_as_shelx_hklf(file_object=sio)
ma2 = hklf.reader(
file_object=StringIO(sio.getvalue())).as_miller_arrays()[0]
assert approx_equal(ma.indices(), ma2.indices())
assert approx_equal(ma.data(), ma2.data())
assert approx_equal(ma.sigmas(), ma2.sigmas())
assert ma.anomalous_flag() is False
assert ma2.anomalous_flag() is False
#
ma = ma.select(flex.size_t([0]))
def check(d, s, f, exception_expected=True):
if (s is not None): s = flex.double([s])
ma2 = ma.array(data=flex.double([d]), sigmas=s)
sio = StringIO()
ma2.export_as_shelx_hklf(sio, normalise_if_format_overflow=True)
assert not show_diff(
sio.getvalue(), """\
1 2 -1%s
0 0 0 0.00 0.00
""" % f)
if exception_expected:
try:
ma2.export_as_shelx_hklf(sio)
except RuntimeError:
pass
else:
raise Exception_expected
else:
try:
ma2.export_as_shelx_hklf(sio)
except RuntimeError:
raise Exception_not_expected
check(-12345678, 1, "-999999. 0.08")
check(-12345678, None, "-999999. 0.00")
check(2, -12345678,
" 0.16-999999.") # Should negative sigma be allowed?
check(123456789, 30, "9999999. 2.43")
check(123456789, None, "9999999. 0.00")
check(40, 123456789, " 3.249999999.")
check(-23456789, 123456789, "-999999.5263153.")
check(123456789, -23456789, "5263153.-999999.")
# Numbers that would be formatted as integers should end with "."
check(-123456, 1, "-123456. 1.00", exception_expected=False)
check(1234567, 10, "1234567. 10.00", exception_expected=False)
#
ma = hklf.reader(file_object=StringIO(s)).as_miller_arrays()[0]
ma = ma.select(flex.size_t([0, 1]))
ma2 = ma.array(data=flex.double([123456789, -23456789]))
sio = StringIO()
ma2.export_as_shelx_hklf(sio, normalise_if_format_overflow=True)
assert not show_diff(
sio.getvalue(), """\
1 2 -15263153. 0.00
2 -3 9-999999. 0.00
0 0 0 0.00 0.00
""")
ma2 = ma.array(data=flex.double([-23456789, 823456789]))
sio = StringIO()
ma2.export_as_shelx_hklf(sio, normalise_if_format_overflow=True)
assert not show_diff(
sio.getvalue(), """\
1 2 -1-284858. 0.00
2 -3 99999999. 0.00
0 0 0 0.00 0.00
""")
# Test that setting the scale range works.
ma2.export_as_shelx_hklf(sio,
scale_range=(-9999., 9999.),
normalise_if_format_overflow=True)
# Test that ignoring the scale range and normalising out-of-range values anyway works.
ma2.export_as_shelx_hklf(sio, full_dynamic_range=True)
