def random_site(special_position_settings,
existing_sites,
min_hetero_distance=1.5,
general_position_only=False,
grid=None,
t_centre_of_inversion=None,
max_trials=100):
for trial in xrange(max_trials):
if (grid is None):
site = (random.random(), random.random(), random.random())
else:
site = [random.randrange(g) / float(g) for g in grid]
site_symmetry = special_position_settings.site_symmetry(site)
if (general_position_only and not site_symmetry.is_point_group_1()):
continue
sym_equiv_sites = sgtbx.sym_equiv_sites(site_symmetry)
if (not have_suitable_hetero_distance(
existing_sites, sym_equiv_sites, min_hetero_distance)):
continue
site = site_symmetry.exact_site()
if (t_centre_of_inversion is None):
return site
site_inv = [-x+t for x,t in zip(site, t_centre_of_inversion)]
site_symmetry_inv = special_position_settings.site_symmetry(site_inv)
if (general_position_only and not site_symmetry_inv.is_point_group_1()):
continue
sym_equiv_sites_inv = sgtbx.sym_equiv_sites(site_symmetry_inv)
if (not have_suitable_hetero_distance(
existing_sites + [site],
sym_equiv_sites_inv, min_hetero_distance)):
continue
return site, site_symmetry_inv.exact_site()
return None
def random_site(special_position_settings,
existing_sites,
min_hetero_distance=1.5,
general_position_only=False,
grid=None,
t_centre_of_inversion=None,
max_trials=100):
for trial in xrange(max_trials):
if (grid is None):
site = (random.random(), random.random(), random.random())
else:
site = [random.randrange(g) / float(g) for g in grid]
site_symmetry = special_position_settings.site_symmetry(site)
if (general_position_only and not site_symmetry.is_point_group_1()):
continue
sym_equiv_sites = sgtbx.sym_equiv_sites(site_symmetry)
if (not have_suitable_hetero_distance(existing_sites, sym_equiv_sites,
min_hetero_distance)):
continue
site = site_symmetry.exact_site()
if (t_centre_of_inversion is None):
return site
site_inv = [-x + t for x, t in zip(site, t_centre_of_inversion)]
site_symmetry_inv = special_position_settings.site_symmetry(site_inv)
if (general_position_only
and not site_symmetry_inv.is_point_group_1()):
continue
sym_equiv_sites_inv = sgtbx.sym_equiv_sites(site_symmetry_inv)
if (not have_suitable_hetero_distance(existing_sites + [site],
sym_equiv_sites_inv,
min_hetero_distance)):
continue
return site, site_symmetry_inv.exact_site()
return None
def loop(self):
for i_position in xrange(self.wyckoff_table.size()):
site_symmetry_i = self.wyckoff_table.random_site_symmetry(
special_position_settings=self.special_position_settings,
i_position=i_position)
equiv_sites_i = sgtbx.sym_equiv_sites(site_symmetry_i)
for j_position in xrange(self.wyckoff_table.size()):
for n_trial in xrange(self.max_trials_per_position):
site_j = self.wyckoff_table.random_site_symmetry(
special_position_settings=self.
special_position_settings,
i_position=j_position).exact_site()
dist_info = sgtbx.min_sym_equiv_distance_info(
equiv_sites_i, site_j)
if (dist_info.dist() > self.min_cross_distance):
structure = xray.structure(
special_position_settings=self.
special_position_settings,
scatterers=flex.xray_scatterer([
xray.scatterer(
scattering_type=self.scattering_type,
site=site) for site in
[site_symmetry_i.exact_site(), site_j]
]))
yield structure, dist_info.dist()
break
def show_patterson_peaks(self,
min_relative_peak_height=0.1,
show_at_least=3):
print("Patterson peaks for %s:" % str(self.input.info()))
reciprocal_map = self.input
if (reciprocal_map.anomalous_flag()):
reciprocal_map = reciprocal_map.average_bijvoet_mates()
patterson_map = reciprocal_map.patterson_map(
symmetry_flags=maptbx.use_space_group_symmetry)
patterson_map.apply_sigma_scaling()
peak_list = patterson_map.tags().peak_search(
map=patterson_map.real_map(),
parameters=maptbx.peak_search_parameters())
max_height = peak_list.heights()[0]
sym_equiv_origin = sgtbx.sym_equiv_sites(
unit_cell=patterson_map.unit_cell(),
space_group=patterson_map.space_group(),
original_site=(0, 0, 0))
print(" Fractional coordinates Height Distance from origin")
for i_peak in range(peak_list.size()):
height = peak_list.heights()[i_peak]
if (height < max_height * min_relative_peak_height
and i_peak > show_at_least):
break
site = peak_list.sites()[i_peak]
dist_info = sgtbx.min_sym_equiv_distance_info(
sym_equiv_origin, site)
print(" %8.4f %8.4f %8.4f" % (dist_info.sym_op() * site), end=' ')
print(" %8.3f %8.3f" % (height, dist_info.dist()))
print()
def random_symmetry_mates(self):
new_positions = []
for pos in self.positions():
equiv = sgtbx.sym_equiv_sites(self.site_symmetry(pos.site))
i = random.randrange(equiv.coordinates().size())
new_positions.append(emma.position(pos.label, equiv.coordinates()[i]))
return self.create_new_test_model(new_positions)
def random_symmetry_mates(self):
new_positions = []
for pos in self.positions():
equiv = sgtbx.sym_equiv_sites(self.site_symmetry(pos.site))
i = random.randrange(equiv.coordinates().size())
new_positions.append(emma.position(pos.label, equiv.coordinates()[i]))
return self.create_new_test_model(new_positions)
def peak_cluster_reduction(crystal_symmetry, peak_list,
min_peak_distance, max_reduced_peaks):
special_position_settings = crystal.special_position_settings(
crystal_symmetry=crystal_symmetry,
min_distance_sym_equiv=min_peak_distance)
peaks = []
for i,site in enumerate(peak_list.sites()):
peaks.append(dicts.easy(
site=special_position_settings.site_symmetry(site).exact_site(),
height=peak_list.heights()[i]))
reduced_peaks = []
for peak in peaks:
site_symmetry = special_position_settings.site_symmetry(peak.site)
equiv_sites = sgtbx.sym_equiv_sites(site_symmetry)
keep = True
for reduced_peak in reduced_peaks:
dist = sgtbx.min_sym_equiv_distance_info(
equiv_sites, reduced_peak.site).dist()
if (dist < min_peak_distance):
keep = False
break
if (keep == True):
reduced_peaks.append(peak)
if (len(reduced_peaks) == max_reduced_peaks): break
return reduced_peaks
def verify_match(model1, model2, tolerance, match_rt, pairs):
adj_tolerance = tolerance * (1 + 1.e-6)
for pair in pairs:
c1 = model1[pair[0]].site
c2 = match_rt * model2[pair[1]].site
equiv_c2 = sgtbx.sym_equiv_sites(model1.site_symmetry(c2.elems))
dist_info = sgtbx.min_sym_equiv_distance_info(equiv_c2, c1)
assert dist_info.dist() < adj_tolerance, str(model1.space_group_info())
def verify_match(model1, model2, tolerance, match_rt, pairs):
adj_tolerance = tolerance * (1 + 1.e-6)
for pair in pairs:
c1 = model1[pair[0]].site
c2 = match_rt * model2[pair[1]].site
equiv_c2 = sgtbx.sym_equiv_sites(model1.site_symmetry(c2.elems))
dist_info = sgtbx.min_sym_equiv_distance_info(equiv_c2, c1)
assert dist_info.dist() < adj_tolerance, str(model1.space_group_info())
def check_peaks(structure, peak_sites, max_min_dist):
for scatterer in structure.scatterers():
site_symmetry = structure.site_symmetry(scatterer.site)
equiv_sites = sgtbx.sym_equiv_sites(site_symmetry)
min_dist = None
for peak_site in peak_sites:
dist_info = sgtbx.min_sym_equiv_distance_info(equiv_sites, peak_site)
if (min_dist is None):
min_dist = dist_info.dist()
else:
min_dist = min(min_dist, dist_info.dist())
assert min_dist <= max_min_dist, (min_dist, max_min_dist)
def check_peaks(structure, peak_sites, max_min_dist):
for scatterer in structure.scatterers():
site_symmetry = structure.site_symmetry(scatterer.site)
equiv_sites = sgtbx.sym_equiv_sites(site_symmetry)
min_dist = None
for peak_site in peak_sites:
dist_info = sgtbx.min_sym_equiv_distance_info(
equiv_sites, peak_site)
if (min_dist is None):
min_dist = dist_info.dist()
else:
min_dist = min(min_dist, dist_info.dist())
assert min_dist <= max_min_dist, (min_dist, max_min_dist)
def expand_to_p1(self):
new_model = model(
crystal.special_position_settings(
crystal.symmetry.cell_equivalent_p1(self)))
for pos in self._positions:
site_symmetry = self.site_symmetry(pos.site)
equiv_sites = sgtbx.sym_equiv_sites(site_symmetry)
i = 0
for site in equiv_sites.coordinates():
i += 1
new_model.add_position(
position(label=pos.label + "_%03d" % i, site=site))
return new_model
def expand_to_p1(self):
new_model = model(
crystal.special_position_settings(
crystal.symmetry.cell_equivalent_p1(self)))
for pos in self._positions:
site_symmetry = self.site_symmetry(pos.site)
equiv_sites = sgtbx.sym_equiv_sites(site_symmetry)
i = 0
for site in equiv_sites.coordinates():
i += 1
new_model.add_position(position(
label=pos.label+"_%03d"%i,
site=site))
return new_model
def run():
uc = (10, 12, 14, 90, 90, 90)
cs = crystal.symmetry(unit_cell=uc, space_group_symbol="P 1")
assert harker.planes_cartesian(cs).count() == 0
assert harker.planes_cartesian(cs).min_distance((0, 0, 0)) is None
cs = crystal.symmetry(unit_cell=uc, space_group_symbol="P 2 2 2")
assert harker.planes_cartesian(cs).count() == 3
assert ae(harker.planes_cartesian(cs).min_distance((0.123, 0.234, 0)), 0)
assert ae(harker.planes_cartesian(cs).min_distance((0.123, 0, 0.234)), 0)
assert ae(harker.planes_cartesian(cs).min_distance((0, 0.123, 0.234)), 0)
assert ae(harker.planes_cartesian(cs).min_distance((0.1, 0.234, 0.345)), 1)
assert ae(
harker.planes_cartesian(cs).min_distance((0.234, 0.1, 0.345)), 1.2)
assert ae(
harker.planes_cartesian(cs).min_distance((0.234, 0.345, 0.1)), 1.4)
assert ae(harker.planes_cartesian(cs).min_distance((0.2, 0.2, 0.1)), 1.4)
assert ae(harker.planes_cartesian(cs).min_distance((0.2, 0.1, 0.1)), 1.2)
assert ae(harker.planes_cartesian(cs).min_distance((0.1, 0.2, 0.2)), 1)
assert ae(harker.planes_cartesian(cs).min_distance((-0.2, 0.1, 0.1)), 1.2)
assert ae(harker.planes_cartesian(cs).min_distance((0.2, -0.1, 0.1)), 1.2)
assert ae(harker.planes_cartesian(cs).min_distance((0.2, 0.1, -0.1)), 1.2)
assert ae(
harker.planes_cartesian(cs).min_distance((-0.2, -0.1, -0.1)), 1.2)
uc = (10, 10, 12, 90, 90, 120)
cs = crystal.symmetry(unit_cell=uc, space_group_symbol="P 3")
assert harker.planes_cartesian(cs).count() == 1
assert ae(harker.planes_cartesian(cs).min_distance((0, 0, 0)), 0)
assert ae(harker.planes_cartesian(cs).min_distance((0.1, 0.2, 1 / 3.)), 4)
assert ae(harker.planes_cartesian(cs).min_distance((0.1, 0.2, 1 / 2.)), 6)
cs = crystal.symmetry(unit_cell=uc, space_group_symbol="P 31")
assert harker.planes_cartesian(cs).count() == 1
assert ae(harker.planes_cartesian(cs).min_distance((0, 0, 0)), 4)
assert ae(harker.planes_cartesian(cs).min_distance((0.1, 0.2, 1 / 3.)), 0)
assert ae(harker.planes_cartesian(cs).min_distance((0.1, 0.2, 1 / 2.)), 2)
uc = (10, 10, 12, 90, 90, 90)
cs = crystal.symmetry(unit_cell=uc, space_group_symbol="P 4 2 2")
assert harker.planes_cartesian(cs).count() == 5
cs = crystal.symmetry(unit_cell=uc, space_group_symbol="P 41 2 2")
assert harker.planes_cartesian(cs).count() == 6
ps = crystal.symmetry(unit_cell=uc, space_group_symbol="P 4/m m m")
for x, d, t in (((0.1, 0.2, 0.3), 0.6, "1"), ((0.1, 0.2, 0.75), 0, "1"),
((0.1, 0.0, 0.3), 0, "m")):
ss = crystal.special_position_settings(ps).site_symmetry(x)
assert ss.point_group_type() == t
eq = sgtbx.sym_equiv_sites(ss)
for x in eq.coordinates():
assert ae(harker.planes_cartesian(cs).min_distance(x), d)
print("OK")
def run():
uc = (10,12,14,90,90,90)
cs = crystal.symmetry(unit_cell=uc, space_group_symbol="P 1")
assert harker.planes_cartesian(cs).count() == 0
assert harker.planes_cartesian(cs).min_distance((0,0,0)) is None
cs = crystal.symmetry(unit_cell=uc, space_group_symbol="P 2 2 2")
assert harker.planes_cartesian(cs).count() == 3
assert ae(harker.planes_cartesian(cs).min_distance((0.123,0.234,0)), 0)
assert ae(harker.planes_cartesian(cs).min_distance((0.123,0,0.234)), 0)
assert ae(harker.planes_cartesian(cs).min_distance((0,0.123,0.234)), 0)
assert ae(harker.planes_cartesian(cs).min_distance((0.1,0.234,0.345)), 1)
assert ae(harker.planes_cartesian(cs).min_distance((0.234,0.1,0.345)), 1.2)
assert ae(harker.planes_cartesian(cs).min_distance((0.234,0.345,0.1)), 1.4)
assert ae(harker.planes_cartesian(cs).min_distance((0.2,0.2,0.1)), 1.4)
assert ae(harker.planes_cartesian(cs).min_distance((0.2,0.1,0.1)), 1.2)
assert ae(harker.planes_cartesian(cs).min_distance((0.1,0.2,0.2)), 1)
assert ae(harker.planes_cartesian(cs).min_distance((-0.2,0.1,0.1)), 1.2)
assert ae(harker.planes_cartesian(cs).min_distance((0.2,-0.1,0.1)), 1.2)
assert ae(harker.planes_cartesian(cs).min_distance((0.2,0.1,-0.1)), 1.2)
assert ae(harker.planes_cartesian(cs).min_distance((-0.2,-0.1,-0.1)), 1.2)
uc = (10,10,12,90,90,120)
cs = crystal.symmetry(unit_cell=uc, space_group_symbol="P 3")
assert harker.planes_cartesian(cs).count() == 1
assert ae(harker.planes_cartesian(cs).min_distance((0,0,0)), 0)
assert ae(harker.planes_cartesian(cs).min_distance((0.1,0.2,1/3.)), 4)
assert ae(harker.planes_cartesian(cs).min_distance((0.1,0.2,1/2.)), 6)
cs = crystal.symmetry(unit_cell=uc, space_group_symbol="P 31")
assert harker.planes_cartesian(cs).count() == 1
assert ae(harker.planes_cartesian(cs).min_distance((0,0,0)), 4)
assert ae(harker.planes_cartesian(cs).min_distance((0.1,0.2,1/3.)), 0)
assert ae(harker.planes_cartesian(cs).min_distance((0.1,0.2,1/2.)), 2)
uc = (10,10,12,90,90,90)
cs = crystal.symmetry(unit_cell=uc, space_group_symbol="P 4 2 2")
assert harker.planes_cartesian(cs).count() == 5
cs = crystal.symmetry(unit_cell=uc, space_group_symbol="P 41 2 2")
assert harker.planes_cartesian(cs).count() == 6
ps = crystal.symmetry(unit_cell=uc, space_group_symbol="P 4/m m m")
for x,d,t in (((0.1,0.2,0.3),0.6,"1"),
((0.1,0.2,0.75),0,"1"),
((0.1,0.0,0.3),0,"m")):
ss = crystal.special_position_settings(ps).site_symmetry(x)
assert ss.point_group_type() == t
eq = sgtbx.sym_equiv_sites(ss)
for x in eq.coordinates():
assert ae(harker.planes_cartesian(cs).min_distance(x), d)
print "OK"
def next_with_effective_resolution(self):
while 1:
peak_list_index = self._peak_list_index
if (peak_list_index >= self._peak_list.size()): return None
self._peak_list_index += 1
if (self._is_processed is not None):
if (self._is_processed[peak_list_index]): continue
self._is_processed[peak_list_index] = True
grid_index = self._peak_list.grid_indices(peak_list_index)
grid_height = self._peak_list.grid_heights()[peak_list_index]
site = self._peak_list.sites()[peak_list_index]
height = self._peak_list.heights()[peak_list_index]
site_symmetry = self._special_position_settings.site_symmetry(site)
if ( self._general_positions_only
and not site_symmetry.is_point_group_1()):
continue
site = site_symmetry.exact_site()
equiv_sites = sgtbx.sym_equiv_sites(site_symmetry)
keep = True
if (self._sites.size() > 250):
import warnings
warnings.warn(
message="This function should not be used for"
" processing a large number of peaks.",
category=RuntimeWarning)
for s in self._sites:
dist = sgtbx.min_sym_equiv_distance_info(equiv_sites, s).dist()
if (dist < self._min_cross_distance):
keep = False
break
if (keep == True):
if ( self._effective_resolution is not None
and ( self._heights.size() == 0
or height < self._heights[0]
* self._significant_height_fraction)):
site, height = self._accumulate_significant(
site, height, site_symmetry, equiv_sites)
self._peak_list_indices.append(peak_list_index)
self._sites.append(site)
self._heights.append(height)
return cluster_site_info(
peak_list_index=peak_list_index,
grid_index=grid_index,
grid_height=grid_height,
site=site,
height=height)
def next_with_effective_resolution(self):
while 1:
peak_list_index = self._peak_list_index
if (peak_list_index >= self._peak_list.size()): return None
self._peak_list_index += 1
if (self._is_processed is not None):
if (self._is_processed[peak_list_index]): continue
self._is_processed[peak_list_index] = True
grid_index = self._peak_list.grid_indices(peak_list_index)
grid_height = self._peak_list.grid_heights()[peak_list_index]
site = self._peak_list.sites()[peak_list_index]
height = self._peak_list.heights()[peak_list_index]
site_symmetry = self._special_position_settings.site_symmetry(site)
if (self._general_positions_only
and not site_symmetry.is_point_group_1()):
continue
site = site_symmetry.exact_site()
equiv_sites = sgtbx.sym_equiv_sites(site_symmetry)
keep = True
if (self._sites.size() > 250):
import warnings
warnings.warn(message="This function should not be used for"
" processing a large number of peaks.",
category=RuntimeWarning)
for s in self._sites:
dist = sgtbx.min_sym_equiv_distance_info(equiv_sites, s).dist()
if (dist < self._min_cross_distance):
keep = False
break
if (keep == True):
if (self._effective_resolution is not None and
(self._heights.size() == 0 or height <
self._heights[0] * self._significant_height_fraction)):
site, height = self._accumulate_significant(
site, height, site_symmetry, equiv_sites)
self._peak_list_indices.append(peak_list_index)
self._sites.append(site)
self._heights.append(height)
return cluster_site_info(peak_list_index=peak_list_index,
grid_index=grid_index,
grid_height=grid_height,
site=site,
height=height)
def loop(self):
for i_position in xrange(self.wyckoff_table.size()):
site_symmetry_i = self.wyckoff_table.random_site_symmetry(
special_position_settings=self.special_position_settings,
i_position=i_position)
equiv_sites_i = sgtbx.sym_equiv_sites(site_symmetry_i)
for j_position in xrange(self.wyckoff_table.size()):
for n_trial in xrange(self.max_trials_per_position):
site_j = self.wyckoff_table.random_site_symmetry(
special_position_settings=self.special_position_settings,
i_position=j_position).exact_site()
dist_info = sgtbx.min_sym_equiv_distance_info(equiv_sites_i, site_j)
if (dist_info.dist() > self.min_cross_distance):
structure = xray.structure(
special_position_settings=self.special_position_settings,
scatterers=flex.xray_scatterer(
[xray.scatterer(scattering_type=self.scattering_type, site=site)
for site in [site_symmetry_i.exact_site(), site_j]]))
yield structure, dist_info.dist()
break
def match_sites_by_symmetry(ref_sites,
query_sites,
unit_cell,
space_group,
cutoff=5):
"""Pair sites in query_sites to sites in ref_sites, allowing for symmetry"""
pairings = numpy.zeros((len(ref_sites), len(query_sites)), dtype=numpy.int)
for i_ref, ref in enumerate(ref_sites):
ref_frac = unit_cell.fractionalize(ref)
sym_sites_ref = sgtbx.sym_equiv_sites(space_group=space_group,
unit_cell=unit_cell,
original_site=ref_frac)
for i_query, query in enumerate(query_sites):
query_frac = unit_cell.fractionalize(query)
min_dist = sgtbx.min_sym_equiv_distance_info(
sym_sites_ref, query_frac).dist()
if min_dist < cutoff:
pairings[i_ref, i_query] = 1
return pairings
def structure_factors(self, d_min):
print "WARNING: RESULTS NOT VERIFIED" # XXX
miller_set = miller.build_set(
crystal_symmetry=self,
anomalous_flag=True, # XXX always True?
d_min=d_min)
f_calc = flex.complex_double()
for h in miller_set.indices():
fc = 0j
for scatterer in self.scatterers():
site_symmetry = self.site_symmetry(scatterer.site)
equiv_sites = sgtbx.sym_equiv_sites(site_symmetry)
sum_exp_j_two_pi_hx = 0j
for i_symop,x in enumerate(equiv_sites.coordinates()):
sum_hx = 0
for i in xrange(3):
sum_hx += h[i] * x[i]
phase = 2 * math.pi * sum_hx
exp_j_two_pi_hx = complex(math.cos(phase), math.sin(phase))
if (scatterer.anisotropic_flag):
r = self.space_group()(i_symop).r()
hr = h
dw = adptbx.debye_waller_factor_u_star(hr, scatterer.u_star)
exp_j_two_pi_hx *= dw
sum_exp_j_two_pi_hx += exp_j_two_pi_hx
b_j = scatterer.scattering_info.bound_coh_scatt_length()
fc_site = scatterer.weight() * b_j * sum_exp_j_two_pi_hx
if (not scatterer.anisotropic_flag):
d_star_sq = self.unit_cell().d_star_sq(h)
dw = adptbx.debye_waller_factor_u_iso(d_star_sq/4, scatterer.u_iso)
fc_site *= dw
fc += fc_site
f_calc.append(fc)
return miller.array(
miller_set=miller_set,
data=f_calc)
def show_patterson_peaks(self, min_relative_peak_height=0.1, show_at_least=3):
print "Patterson peaks for %s:" % str(self.input.info())
reciprocal_map = self.input
if reciprocal_map.anomalous_flag():
reciprocal_map = reciprocal_map.average_bijvoet_mates()
patterson_map = reciprocal_map.patterson_map(symmetry_flags=maptbx.use_space_group_symmetry)
patterson_map.apply_sigma_scaling()
peak_list = patterson_map.tags().peak_search(
map=patterson_map.real_map(), parameters=maptbx.peak_search_parameters()
)
max_height = peak_list.heights()[0]
sym_equiv_origin = sgtbx.sym_equiv_sites(
unit_cell=patterson_map.unit_cell(), space_group=patterson_map.space_group(), original_site=(0, 0, 0)
)
print " Fractional coordinates Height Distance from origin"
for i_peak in xrange(peak_list.size()):
height = peak_list.heights()[i_peak]
if height < max_height * min_relative_peak_height and i_peak > show_at_least:
break
site = peak_list.sites()[i_peak]
dist_info = sgtbx.min_sym_equiv_distance_info(sym_equiv_origin, site)
print " %8.4f %8.4f %8.4f" % (dist_info.sym_op() * site),
print " %8.3f %8.3f" % (height, dist_info.dist())
print
def structure_factors(self, d_min):
print "WARNING: RESULTS NOT VERIFIED" # XXX
miller_set = miller.build_set(
crystal_symmetry=self,
anomalous_flag=True, # XXX always True?
d_min=d_min)
f_calc = flex.complex_double()
for h in miller_set.indices():
fc = 0j
for scatterer in self.scatterers():
site_symmetry = self.site_symmetry(scatterer.site)
equiv_sites = sgtbx.sym_equiv_sites(site_symmetry)
sum_exp_j_two_pi_hx = 0j
for i_symop, x in enumerate(equiv_sites.coordinates()):
sum_hx = 0
for i in xrange(3):
sum_hx += h[i] * x[i]
phase = 2 * math.pi * sum_hx
exp_j_two_pi_hx = complex(math.cos(phase), math.sin(phase))
if (scatterer.anisotropic_flag):
r = self.space_group()(i_symop).r()
hr = h
dw = adptbx.debye_waller_factor_u_star(
hr, scatterer.u_star)
exp_j_two_pi_hx *= dw
sum_exp_j_two_pi_hx += exp_j_two_pi_hx
b_j = scatterer.scattering_info.bound_coh_scatt_length()
fc_site = scatterer.weight() * b_j * sum_exp_j_two_pi_hx
if (not scatterer.anisotropic_flag):
d_star_sq = self.unit_cell().d_star_sq(h)
dw = adptbx.debye_waller_factor_u_iso(
d_star_sq / 4, scatterer.u_iso)
fc_site *= dw
fc += fc_site
f_calc.append(fc)
return miller.array(miller_set=miller_set, data=f_calc)
def run_call_back(flags, space_group_info):
verbose = flags.Verbose
if (flags.StaticModels):
model1 = (test_model()
.add_random_positions(2, "A")
.shuffle_positions()
.random_symmetry_mates()
.apply_random_eucl_op()
)
model2 = (test_model()
.add_random_positions(3, "B")
.shuffle_positions()
.random_symmetry_mates()
.apply_random_eucl_op()
.shake_positions()
.random_hand()
)
for i in (0,1):
m1 = model1
if (i): m1 = model1.transform_to_reference_setting().reset_cb_op()
for j in (0,1):
m2 = model2
if (j): m2 = model2.transform_to_reference_setting().reset_cb_op()
if (0 or verbose):
m1.show("Model1(%d)" % (i,))
m2.show("Model2(%d)" % (j,))
model_matches = emma.model_matches(m1, m2, rms_penalty_per_site=0)
analyze_refined_matches(m1, m2, model_matches.refined_matches, verbose)
return False
model_core = test_model(space_group_info)
model1 = (model_core
.add_random_positions(2, "A")
)
model2 = (model_core
.add_random_positions(3, "B")
.shuffle_positions()
.random_symmetry_mates()
.apply_random_eucl_op()
.shake_positions()
.random_hand()
)
if (0 or verbose):
model_core.show("Core")
model1.show("Model1")
model2.show("Model2")
model_matches = emma.model_matches(model1, model2, rms_penalty_per_site=0)
analyze_refined_matches(
model1, model2, model_matches.refined_matches, verbose)
assert model_matches.consensus_model().size() >= model1.size()-2
assert model_matches.consensus_model(i_model=2).size() >= model2.size()-3
model1.expand_to_p1()
model2.as_xray_structure()
for i1,i2,m1,m2 in [(1,2,model1,model2),(2,1,model2,model1)]:
m2_t = model_matches.transform_model(i_model=i2)
assert m1.unit_cell().is_similar_to(m2_t.unit_cell())
assert m1.space_group() == m2_t.space_group()
for pair in model_matches.refined_matches[0].pairs:
site1 = m1.positions()[pair[i1-1]].site
site2 = m2_t.positions()[pair[i2-1]].site
equiv_sites1 = sgtbx.sym_equiv_sites(m1.site_symmetry(site1))
dist_info = sgtbx.min_sym_equiv_distance_info(equiv_sites1, site2)
assert dist_info.dist() < model_matches.tolerance + 1.e-6
site2_closest = dist_info.sym_op() * site2
assert approx_equal(
m1.unit_cell().distance(site1, site2_closest),
dist_info.dist())
if (i1 == 1):
singles = model_matches.refined_matches[0].singles2
else:
singles = model_matches.refined_matches[0].singles1
for i_site2 in singles:
site2 = m2_t.positions()[i_site2].site
for i_site1 in xrange(len(model1.positions())):
site1 = m1.positions()[i_site1].site
equiv_sites1 = sgtbx.sym_equiv_sites(m1.site_symmetry(site1))
dist_info = sgtbx.min_sym_equiv_distance_info(equiv_sites1, site2)
if (dist_info.dist() < model_matches.tolerance - 1.e-6):
ok = False
for pair in model_matches.refined_matches[0].pairs:
if (pair[i1-1] == i_site1):
ok = True
assert ok
def run_call_back(flags, space_group_info):
verbose = flags.Verbose
if (flags.StaticModels):
model1 = (test_model().add_random_positions(2, "A").shuffle_positions(
).random_symmetry_mates().apply_random_eucl_op())
model2 = (test_model().add_random_positions(
3, "B").shuffle_positions().random_symmetry_mates().
apply_random_eucl_op().shake_positions().random_hand())
for i in (0, 1):
m1 = model1
if (i): m1 = model1.transform_to_reference_setting().reset_cb_op()
for j in (0, 1):
m2 = model2
if (j):
m2 = model2.transform_to_reference_setting().reset_cb_op()
if (0 or verbose):
m1.show("Model1(%d)" % (i, ))
m2.show("Model2(%d)" % (j, ))
model_matches = emma.model_matches(m1,
m2,
rms_penalty_per_site=0)
analyze_refined_matches(m1, m2, model_matches.refined_matches,
verbose)
return False
model_core = test_model(space_group_info)
model1 = (model_core.add_random_positions(2, "A"))
model2 = (model_core.add_random_positions(
3, "B").shuffle_positions().random_symmetry_mates().
apply_random_eucl_op().shake_positions().random_hand())
if (0 or verbose):
model_core.show("Core")
model1.show("Model1")
model2.show("Model2")
model_matches = emma.model_matches(model1, model2, rms_penalty_per_site=0)
analyze_refined_matches(model1, model2, model_matches.refined_matches,
verbose)
assert model_matches.consensus_model().size() >= model1.size() - 2
assert model_matches.consensus_model(i_model=2).size() >= model2.size() - 3
model1.expand_to_p1()
model2.as_xray_structure()
for i1, i2, m1, m2 in [(1, 2, model1, model2), (2, 1, model2, model1)]:
m2_t = model_matches.transform_model(i_model=i2)
assert m1.unit_cell().is_similar_to(m2_t.unit_cell())
assert m1.space_group() == m2_t.space_group()
for pair in model_matches.refined_matches[0].pairs:
site1 = m1.positions()[pair[i1 - 1]].site
site2 = m2_t.positions()[pair[i2 - 1]].site
equiv_sites1 = sgtbx.sym_equiv_sites(m1.site_symmetry(site1))
dist_info = sgtbx.min_sym_equiv_distance_info(equiv_sites1, site2)
assert dist_info.dist() < model_matches.tolerance + 1.e-6
site2_closest = dist_info.sym_op() * site2
assert approx_equal(m1.unit_cell().distance(site1, site2_closest),
dist_info.dist())
if (i1 == 1):
singles = model_matches.refined_matches[0].singles2
else:
singles = model_matches.refined_matches[0].singles1
for i_site2 in singles:
site2 = m2_t.positions()[i_site2].site
for i_site1 in range(len(model1.positions())):
site1 = m1.positions()[i_site1].site
equiv_sites1 = sgtbx.sym_equiv_sites(m1.site_symmetry(site1))
dist_info = sgtbx.min_sym_equiv_distance_info(
equiv_sites1, site2)
if (dist_info.dist() < model_matches.tolerance - 1.e-6):
ok = False
for pair in model_matches.refined_matches[0].pairs:
if (pair[i1 - 1] == i_site1):
ok = True
assert ok
def check_with_grid_tags(inp_symmetry, symmetry_flags,
sites_cart, point_distance,
strictly_inside, flag_write_pdb, verbose):
cb_op_inp_ref = inp_symmetry.change_of_basis_op_to_reference_setting()
if (verbose):
print "cb_op_inp_ref.c():", cb_op_inp_ref.c()
ref_symmetry = inp_symmetry.change_basis(cb_op_inp_ref)
search_symmetry = sgtbx.search_symmetry(
flags=symmetry_flags,
space_group_type=ref_symmetry.space_group_info().type(),
seminvariant=ref_symmetry.space_group_info().structure_seminvariants())
assert search_symmetry.continuous_shifts_are_principal()
continuous_shift_flags = search_symmetry.continuous_shift_flags()
if (flag_write_pdb):
tag_sites_frac = flex.vec3_double()
else:
tag_sites_frac = None
if (strictly_inside):
inp_tags = inp_symmetry.gridding(
step=point_distance*.7,
symmetry_flags=symmetry_flags).tags()
if (tag_sites_frac is not None):
for point in flex.nested_loop(inp_tags.n_real()):
if (inp_tags.tags().tag_array()[point] < 0):
point_frac_inp=[float(n)/d for n,d in zip(point, inp_tags.n_real())]
tag_sites_frac.append(point_frac_inp)
if (inp_tags.tags().n_independent() < sites_cart.size()):
print "FAIL:", inp_symmetry.space_group_info(), \
inp_tags.tags().n_independent(), sites_cart.size()
raise AssertionError
else:
inp_tags = inp_symmetry.gridding(
step=point_distance/2.,
symmetry_flags=symmetry_flags).tags()
sites_frac_inp = inp_symmetry.unit_cell().fractionalize(
sites_cart=sites_cart)
rt = cb_op_inp_ref.c().as_double_array()
sites_frac_ref = rt[:9] * sites_frac_inp
sites_frac_ref += rt[9:]
max_distance = 2 * ((.5 * math.sqrt(3) * point_distance) * 2/3.)
if (verbose):
print "max_distance:", max_distance
for point in flex.nested_loop(inp_tags.n_real()):
if (inp_tags.tags().tag_array()[point] < 0):
point_frac_inp = [float(n)/d for n,d in zip(point, inp_tags.n_real())]
if (tag_sites_frac is not None):
tag_sites_frac.append(point_frac_inp)
point_frac_ref = cb_op_inp_ref.c() * point_frac_inp
equiv_points = sgtbx.sym_equiv_sites(
unit_cell=ref_symmetry.unit_cell(),
space_group=search_symmetry.subgroup(),
original_site=point_frac_ref,
minimum_distance=2.e-6,
tolerance=1.e-6)
min_dist = sgtbx.min_sym_equiv_distance_info(
reference_sites=equiv_points,
others=sites_frac_ref,
principal_continuous_allowed_origin_shift_flags
=continuous_shift_flags).dist()
if (min_dist > max_distance):
print "FAIL:", inp_symmetry.space_group_info(), \
point_frac_ref, min_dist
raise AssertionError
if (inp_tags.tags().n_independent()+10 < sites_cart.size()):
print "FAIL:", inp_symmetry.space_group_info(), \
inp_tags.tags().n_independent(), sites_cart.size()
raise AssertionError
if (tag_sites_frac is not None):
dump_pdb(
file_name="tag_sites.pdb",
crystal_symmetry=inp_symmetry,
sites_cart=inp_symmetry.unit_cell().orthogonalize(
sites_frac=tag_sites_frac))
def check_with_grid_tags(inp_symmetry, symmetry_flags, sites_cart,
point_distance, strictly_inside, flag_write_pdb,
verbose):
cb_op_inp_ref = inp_symmetry.change_of_basis_op_to_reference_setting()
if (verbose):
print("cb_op_inp_ref.c():", cb_op_inp_ref.c())
ref_symmetry = inp_symmetry.change_basis(cb_op_inp_ref)
search_symmetry = sgtbx.search_symmetry(
flags=symmetry_flags,
space_group_type=ref_symmetry.space_group_info().type(),
seminvariant=ref_symmetry.space_group_info().structure_seminvariants())
assert search_symmetry.continuous_shifts_are_principal()
continuous_shift_flags = search_symmetry.continuous_shift_flags()
if (flag_write_pdb):
tag_sites_frac = flex.vec3_double()
else:
tag_sites_frac = None
if (strictly_inside):
inp_tags = inp_symmetry.gridding(step=point_distance * .7,
symmetry_flags=symmetry_flags).tags()
if (tag_sites_frac is not None):
for point in flex.nested_loop(inp_tags.n_real()):
if (inp_tags.tags().tag_array()[point] < 0):
point_frac_inp = [
float(n) / d for n, d in zip(point, inp_tags.n_real())
]
tag_sites_frac.append(point_frac_inp)
if (inp_tags.tags().n_independent() < sites_cart.size()):
print("FAIL:", inp_symmetry.space_group_info(), \
inp_tags.tags().n_independent(), sites_cart.size())
raise AssertionError
else:
inp_tags = inp_symmetry.gridding(step=point_distance / 2.,
symmetry_flags=symmetry_flags).tags()
sites_frac_inp = inp_symmetry.unit_cell().fractionalize(
sites_cart=sites_cart)
rt = cb_op_inp_ref.c().as_double_array()
sites_frac_ref = rt[:9] * sites_frac_inp
sites_frac_ref += rt[9:]
max_distance = 2 * ((.5 * math.sqrt(3) * point_distance) * 2 / 3.)
if (verbose):
print("max_distance:", max_distance)
for point in flex.nested_loop(inp_tags.n_real()):
if (inp_tags.tags().tag_array()[point] < 0):
point_frac_inp = [
float(n) / d for n, d in zip(point, inp_tags.n_real())
]
if (tag_sites_frac is not None):
tag_sites_frac.append(point_frac_inp)
point_frac_ref = cb_op_inp_ref.c() * point_frac_inp
equiv_points = sgtbx.sym_equiv_sites(
unit_cell=ref_symmetry.unit_cell(),
space_group=search_symmetry.subgroup(),
original_site=point_frac_ref,
minimum_distance=2.e-6,
tolerance=1.e-6)
min_dist = sgtbx.min_sym_equiv_distance_info(
reference_sites=equiv_points,
others=sites_frac_ref,
principal_continuous_allowed_origin_shift_flags=
continuous_shift_flags).dist()
if (min_dist > max_distance):
print("FAIL:", inp_symmetry.space_group_info(), \
point_frac_ref, min_dist)
raise AssertionError
if (inp_tags.tags().n_independent() + 10 < sites_cart.size()):
print("FAIL:", inp_symmetry.space_group_info(), \
inp_tags.tags().n_independent(), sites_cart.size())
raise AssertionError
if (tag_sites_frac is not None):
dump_pdb(file_name="tag_sites.pdb",
crystal_symmetry=inp_symmetry,
sites_cart=inp_symmetry.unit_cell().orthogonalize(
sites_frac=tag_sites_frac))
