def exercise_match_bijvoet_mates():
h0 = flex.miller_index(((1,2,3), (-1,-2,-3), (2,3,4), (-2,-3,-4), (3,4,5)))
d0 = flex.double((1,2,3,4,5))
bm = miller.match_bijvoet_mates(
sgtbx.space_group_type(),
h0)
bm = miller.match_bijvoet_mates(
sgtbx.reciprocal_space_asu(sgtbx.space_group_type()),
h0)
bm = miller.match_bijvoet_mates(
h0)
assert tuple(bm.pairs()) == ((0,1), (2,3))
assert tuple(bm.singles("+")) == (4,)
assert tuple(bm.singles("-")) == ()
assert bm.n_singles() != 0
assert tuple(bm.pairs_hemisphere_selection("+")) == (0, 2)
assert tuple(bm.pairs_hemisphere_selection("-")) == (1, 3)
assert tuple(bm.singles_hemisphere_selection("+")) == (4,)
assert tuple(bm.singles_hemisphere_selection("-")) == ()
assert tuple(bm.miller_indices_in_hemisphere("+")) == ((1,2,3), (2,3,4))
assert tuple(bm.miller_indices_in_hemisphere("-")) == ((-1,-2,-3),(-2,-3,-4))
assert approx_equal(tuple(bm.minus(d0)), (-1, -1))
assert approx_equal(tuple(bm.additive_sigmas(d0)),
[math.sqrt(x*x+y*y) for x,y in ((1,2), (3,4))])
assert approx_equal(tuple(bm.average(d0)), (3/2., 7/2.))
h0.append((1,2,3))
try: miller.match_bijvoet_mates(h0)
except Exception: pass
else: raise Exception_expected
def exercise_match_bijvoet_mates():
h0 = flex.miller_index(((1,2,3), (-1,-2,-3), (2,3,4), (-2,-3,-4), (3,4,5)))
d0 = flex.double((1,2,3,4,5))
bm = miller.match_bijvoet_mates(
sgtbx.space_group_type(),
h0)
bm = miller.match_bijvoet_mates(
sgtbx.reciprocal_space_asu(sgtbx.space_group_type()),
h0)
bm = miller.match_bijvoet_mates(
h0)
assert tuple(bm.pairs()) == ((0,1), (2,3))
assert tuple(bm.singles("+")) == (4,)
assert tuple(bm.singles("-")) == ()
assert bm.n_singles() != 0
assert tuple(bm.pairs_hemisphere_selection("+")) == (0, 2)
assert tuple(bm.pairs_hemisphere_selection("-")) == (1, 3)
assert tuple(bm.singles_hemisphere_selection("+")) == (4,)
assert tuple(bm.singles_hemisphere_selection("-")) == ()
assert tuple(bm.miller_indices_in_hemisphere("+")) == ((1,2,3), (2,3,4))
assert tuple(bm.miller_indices_in_hemisphere("-")) == ((-1,-2,-3),(-2,-3,-4))
assert approx_equal(tuple(bm.minus(d0)), (-1, -1))
assert approx_equal(tuple(bm.additive_sigmas(d0)),
[math.sqrt(x*x+y*y) for x,y in ((1,2), (3,4))])
assert approx_equal(tuple(bm.average(d0)), (3/2., 7/2.))
h0.append((1,2,3))
try: miller.match_bijvoet_mates(h0)
except Exception: pass
else: raise Exception_expected
def compare_ccp4_and_sgtbx(syminfo_data):
for s in sgtbx.space_group_symbol_iterator():
sg = sgtbx.space_group(s.hall())
sg_type = sgtbx.space_group_type(sg)
asu = sgtbx.reciprocal_space_asu(sg_type)
sgtbx_hklasu = asu.reference_as_string().replace('==', '=')
ccp4_hklasu = syminfo_data[s.number()]
assert sgtbx_hklasu == ccp4_hklasu
assert sgtbx_hklasu in hklasu_strings
def exercise_asu():
sg_type = sgtbx.space_group_type("P 41")
asu = sgtbx.reciprocal_space_asu(sg_type)
miller_indices = flex.miller_index(((1, 2, 3), (3, 5, 0)))
for h in miller_indices:
h_eq = miller.sym_equiv_indices(sg_type.group(), h)
for i_eq in xrange(h_eq.multiplicity(False)):
h_i = h_eq(i_eq)
for anomalous_flag in (False, True):
a = miller.asym_index(sg_type.group(), asu, h_i.h())
assert a.h() == h
o = a.one_column(anomalous_flag)
assert o.i_column() == 0
t = a.two_column(anomalous_flag)
assert t.h() == h
assert (o.h() != h) == (t.i_column() == 1)
assert not anomalous_flag or (t.i_column() !=
0) == h_i.friedel_flag()
assert anomalous_flag or t.i_column() == 0
miller.map_to_asu(sg_type, False, miller_indices)
data = flex.double((0, 0))
miller.map_to_asu(sg_type, False, miller_indices, data)
miller.map_to_asu(sg_type, False, miller_indices, data, False)
miller.map_to_asu(sg_type, False, miller_indices, data, True)
data = flex.complex_double((0, 0))
miller.map_to_asu(sg_type, False, miller_indices, data)
data = flex.hendrickson_lattman(((1, 2, 3, 4), (2, 3, 4, 5)))
miller.map_to_asu(sg_type, False, miller_indices, data)
for sg_symbol in ("P 41", "P 31 1 2"):
exercise_map_to_asu(sg_symbol)
#
sg_type = sgtbx.space_group_type("P 2")
miller_indices = flex.miller_index(((1, 2, 3), (-1, -2, -3)))
assert not miller.is_unique_set_under_symmetry(
space_group_type=sg_type,
anomalous_flag=False,
miller_indices=miller_indices)
assert miller.is_unique_set_under_symmetry(space_group_type=sg_type,
anomalous_flag=True,
miller_indices=miller_indices)
assert list(
miller.unique_under_symmetry_selection(
space_group_type=sg_type,
anomalous_flag=False,
miller_indices=miller_indices)) == [0]
assert list(
miller.unique_under_symmetry_selection(
space_group_type=sg_type,
anomalous_flag=True,
miller_indices=miller_indices)) == [0, 1]
def exercise_asu():
sg_type = sgtbx.space_group_type("P 41")
asu = sgtbx.reciprocal_space_asu(sg_type)
miller_indices = flex.miller_index(((1,2,3), (3,5,0)))
for h in miller_indices:
h_eq = miller.sym_equiv_indices(sg_type.group(), h)
for i_eq in xrange(h_eq.multiplicity(False)):
h_i = h_eq(i_eq)
for anomalous_flag in (False,True):
a = miller.asym_index(sg_type.group(), asu, h_i.h())
assert a.h() == h
o = a.one_column(anomalous_flag)
assert o.i_column() == 0
t = a.two_column(anomalous_flag)
assert t.h() == h
assert (o.h() != h) == (t.i_column() == 1)
assert not anomalous_flag or (t.i_column() != 0) == h_i.friedel_flag()
assert anomalous_flag or t.i_column() == 0
miller.map_to_asu(sg_type, False, miller_indices)
data = flex.double((0,0))
miller.map_to_asu(sg_type, False, miller_indices, data)
miller.map_to_asu(sg_type, False, miller_indices, data, False)
miller.map_to_asu(sg_type, False, miller_indices, data, True)
data = flex.complex_double((0,0))
miller.map_to_asu(sg_type, False, miller_indices, data)
data = flex.hendrickson_lattman(((1,2,3,4),(2,3,4,5)))
miller.map_to_asu(sg_type, False, miller_indices, data)
for sg_symbol in ("P 41", "P 31 1 2"):
exercise_map_to_asu(sg_symbol)
#
sg_type = sgtbx.space_group_type("P 2")
miller_indices = flex.miller_index(((1,2,3), (-1,-2,-3)))
assert not miller.is_unique_set_under_symmetry(
space_group_type=sg_type,
anomalous_flag=False,
miller_indices=miller_indices)
assert miller.is_unique_set_under_symmetry(
space_group_type=sg_type,
anomalous_flag=True,
miller_indices=miller_indices)
assert list(miller.unique_under_symmetry_selection(
space_group_type=sg_type,
anomalous_flag=False,
miller_indices=miller_indices)) == [0]
assert list(miller.unique_under_symmetry_selection(
space_group_type=sg_type,
anomalous_flag=True,
miller_indices=miller_indices)) == [0,1]
def __init__(self, unmerged_intensities):
self._intensities_original_index = unmerged_intensities
self._observations = {}
from cctbx import miller, sgtbx
sg = self._intensities_original_index.space_group()
sg_type = sg.type()
asu = sgtbx.reciprocal_space_asu(sg_type)
anomalous_flag = self._intensities_original_index.anomalous_flag()
ma = self._intensities_original_index
original_indices = ma.indices()
unique_indices = original_indices.deep_copy()
isym = flex.int(unique_indices.size())
miller.map_to_asu_isym(sg_type, anomalous_flag, unique_indices, isym)
n_plus, n_minus = 0, 0
for iref in range(len(original_indices)):
h_orig = original_indices[iref]
h_uniq = unique_indices[iref]
h_isym = isym[iref]
h_eq = miller.sym_equiv_indices(sg, h_uniq)
if h_eq.is_centric():
flag = observation_group.CENTRIC
else:
asu_which = asu.which(h_uniq)
assert asu_which != 0
if asu_which == 1:
flag = observation_group.PLUS
else:
flag = observation_group.MINUS
h_uniq = tuple(-1*h for h in h_uniq)
group = self._observations.get(h_uniq)
if group is None:
group = observation_group(
h_uniq, is_centric=(flag == observation_group.CENTRIC))
self._observations[h_uniq] = group
if flag == observation_group.MINUS:
n_minus += 1
group.add_iminus(iref)
else:
n_plus += 1
group.add_iplus(iref)
def __init__(self, unmerged_intensities):
self._intensities_original_index = unmerged_intensities
self._observations = {}
from cctbx import miller, sgtbx
sg = self._intensities_original_index.space_group()
sg_type = sg.type()
asu = sgtbx.reciprocal_space_asu(sg_type)
anomalous_flag = self._intensities_original_index.anomalous_flag()
ma = self._intensities_original_index
original_indices = ma.indices()
unique_indices = original_indices.deep_copy()
isym = flex.int(unique_indices.size())
miller.map_to_asu_isym(sg_type, anomalous_flag, unique_indices, isym)
n_plus, n_minus = 0, 0
for iref in range(len(original_indices)):
h_orig = original_indices[iref]
h_uniq = unique_indices[iref]
h_isym = isym[iref]
h_eq = miller.sym_equiv_indices(sg, h_uniq)
if h_eq.is_centric():
flag = observation_group.CENTRIC
else:
asu_which = asu.which(h_uniq)
assert asu_which != 0
if asu_which == 1:
flag = observation_group.PLUS
else:
flag = observation_group.MINUS
h_uniq = tuple(-1*h for h in h_uniq)
group = self._observations.get(h_uniq)
if group is None:
group = observation_group(
h_uniq, is_centric=(flag == observation_group.CENTRIC))
self._observations[h_uniq] = group
if flag == observation_group.MINUS:
n_minus += 1
group.add_iminus(iref)
else:
n_plus += 1
group.add_iplus(iref)
def reference_map(sg, mi):
from cctbx import sgtbx
asu = sgtbx.reciprocal_space_asu(sg.type())
isym_ = []
mi_ = []
for hkl in mi:
found = False
for i_inv in range(sg.f_inv()):
for i_smx in range(sg.n_smx()):
rt_mx = sg(0, i_inv, i_smx)
hkl_ = intify(hkl * rt_mx.r())
if asu.is_inside(hkl_):
mi_.append(hkl_)
if i_inv:
isym_.append(-i_smx)
else:
isym_.append(i_smx)
found = True
break
if found:
continue
else:
assert (not sg.is_centric())
for i_inv in range(sg.f_inv()):
for i_smx in range(sg.n_smx()):
rt_mx = sg(0, i_inv, i_smx)
_hkl = [-h for h in hkl]
mhkl_ = intify(_hkl * rt_mx.r())
if asu.is_inside(mhkl_):
mi_.append(mhkl_)
isym_.append(-i_smx)
found = True
break
return mi_, isym_
def reference_map(sg, mi):
from cctbx import sgtbx
asu = sgtbx.reciprocal_space_asu(sg.type())
isym_ = []
mi_ = []
for hkl in mi:
found = False
for i_inv in range(sg.f_inv()):
for i_smx in range(sg.n_smx()):
rt_mx = sg(0, i_inv, i_smx)
hkl_ = intify(hkl * rt_mx.r())
if asu.is_inside(hkl_):
mi_.append(hkl_)
if i_inv:
isym_.append(- i_smx)
else:
isym_.append(i_smx)
found = True
break
if found:
continue
else:
assert(not sg.is_centric())
for i_inv in range(sg.f_inv()):
for i_smx in range(sg.n_smx()):
rt_mx = sg(0, i_inv, i_smx)
_hkl = [-h for h in hkl]
mhkl_ = intify(_hkl * rt_mx.r())
if asu.is_inside(mhkl_):
mi_.append(mhkl_)
isym_.append(- i_smx)
found = True
break
return mi_, isym_
spacegroup_number = -1
for arg in sys.argv:
if arg[-4:] == '.XDS':
data = map(float, open(arg, 'r').read().split())
spacegroup_number = int(data[26])
if spacegroup_number == -1:
raise RuntimeError, 'spacegroup number not found'
# now generate a space group from this, via hall symbol, then
# calculate the corresponding reciprocal space asymmetric unit
spacegroup = sgtbx.space_group_symbols(spacegroup_number).hall()
sg = sgtbx.space_group(spacegroup)
asu = sgtbx.reciprocal_space_asu(sg.type())
# and get the list of symmetry operations: these will be needed to
# reduce the unmerged miller index to the asymmetric unit, as I've
# not found a better way...
for hkl_file in hkl_files:
reflections = []
fileno =int(hkl_file.replace('.hkl', '').split('-')[-1])
dat_file = '%s.dat' % hkl_file[:-4]
hkls = read_hkl(hkl_file)
dats = read_dat(dat_file)
hits = sorted_hits[fileno]