def tst_find_best_cell():
uc_array = [
uctbx.unit_cell('40, 50, 60, 90, 90, 90'),
uctbx.unit_cell('40, 60, 50, 90, 90, 90'),
uctbx.unit_cell('50, 40, 60, 90, 90, 90'),
uctbx.unit_cell('50, 60, 40, 90, 90, 90'),
uctbx.unit_cell('60, 40, 50, 90, 90, 90'),
uctbx.unit_cell('60, 50, 40, 90, 90, 90')
]
uc_correct = [
uctbx.unit_cell('40, 50, 60, 90, 90, 90'),
uctbx.unit_cell('40, 60, 50, 90, 90, 90'),
uctbx.unit_cell('40, 50, 60, 90, 90, 90'),
uctbx.unit_cell('50, 60, 40, 90, 90, 90'),
uctbx.unit_cell('40, 60, 50, 90, 90, 90'),
uctbx.unit_cell('50, 60, 40, 90, 90, 90')
]
sg_info = sgtbx.space_group_info('P 21 21 2')
sg_info_2 = sgtbx.space_group_info('I 21 21 21')
sg = sg_info.group()
sg_2 = sg_info_2.group()
for uc, correct in zip(uc_array, uc_correct):
best_cell_finder = fbc(uc, sg)
assert approx_equal(correct.parameters(),
best_cell_finder.return_best_cell().parameters())
cb_op = best_cell_finder.return_change_of_basis_op_to_best_cell()
xs = crystal.symmetry(uc, space_group=sg)
assert approx_equal(correct.parameters(),
xs.change_basis(cb_op).unit_cell().parameters())
best_cell_finder = fbc(uc, sg_2)
assert approx_equal(uc_array[0].parameters(),
best_cell_finder.return_best_cell().parameters())
xs = crystal.symmetry(uc, space_group=sg_2)
cb_op = best_cell_finder.return_change_of_basis_op_to_best_cell()
assert approx_equal(uc_array[0].parameters(),
xs.change_basis(cb_op).unit_cell().parameters())
# test with incomming sg not in reference setting
uc = uctbx.unit_cell('60, 40, 30, 90, 90, 90')
sg_info_3 = sgtbx.space_group_info('P 1 1 21')
sg_3 = sg_info_3.group()
best_cell_finder = fbc(uc, sg_3)
xs_best = best_cell_finder.return_best_xs()
uc_correct = uctbx.unit_cell('40, 30, 60, 90, 90, 90')
sg_correct = sgtbx.space_group_info('P 1 21 1').group()
assert approx_equal(xs_best.unit_cell().parameters(),
uc_correct.parameters())
assert sg_correct == xs_best.space_group()
def tst_find_best_cell():
uc_array=[ uctbx.unit_cell( '40, 50, 60, 90, 90, 90' ),
uctbx.unit_cell( '40, 60, 50, 90, 90, 90' ),
uctbx.unit_cell( '50, 40, 60, 90, 90, 90' ),
uctbx.unit_cell( '50, 60, 40, 90, 90, 90' ),
uctbx.unit_cell( '60, 40, 50, 90, 90, 90' ),
uctbx.unit_cell( '60, 50, 40, 90, 90, 90' ) ]
uc_correct = [ uctbx.unit_cell( '40, 50, 60, 90, 90, 90' ),
uctbx.unit_cell( '40, 60, 50, 90, 90, 90' ),
uctbx.unit_cell( '40, 50, 60, 90, 90, 90' ),
uctbx.unit_cell( '50, 60, 40, 90, 90, 90' ),
uctbx.unit_cell( '40, 60, 50, 90, 90, 90' ),
uctbx.unit_cell( '50, 60, 40, 90, 90, 90' ) ]
sg_info = sgtbx.space_group_info( 'P 21 21 2' )
sg_info_2 = sgtbx.space_group_info( 'I 21 21 21' )
sg = sg_info.group()
sg_2 = sg_info_2.group()
for uc, correct in zip(uc_array,uc_correct):
best_cell_finder = fbc( uc, sg )
assert approx_equal( correct.parameters(),
best_cell_finder.return_best_cell().parameters() )
cb_op = best_cell_finder.return_change_of_basis_op_to_best_cell()
xs = crystal.symmetry( uc, space_group=sg)
assert approx_equal( correct.parameters(),
xs.change_basis(cb_op).unit_cell().parameters() )
best_cell_finder = fbc( uc, sg_2 )
assert approx_equal( uc_array[0].parameters(),
best_cell_finder.return_best_cell().parameters() )
xs = crystal.symmetry( uc, space_group=sg_2)
cb_op = best_cell_finder.return_change_of_basis_op_to_best_cell()
assert approx_equal( uc_array[0].parameters(),
xs.change_basis(cb_op).unit_cell().parameters() )
# test with incomming sg not in reference setting
uc = uctbx.unit_cell( '60, 40, 30, 90, 90, 90' )
sg_info_3 = sgtbx.space_group_info( 'P 1 1 21' )
sg_3 = sg_info_3.group()
best_cell_finder = fbc( uc, sg_3 )
xs_best = best_cell_finder.return_best_xs()
uc_correct = uctbx.unit_cell( '40, 30, 60, 90, 90, 90' )
sg_correct = sgtbx.space_group_info( 'P 1 21 1' ).group()
assert approx_equal( xs_best.unit_cell().parameters(),
uc_correct.parameters() )
assert sg_correct == xs_best.space_group()
def test_reference_setting_choices():
buffer = StringIO()
for space_group_info in sgtbx.reference_space_group_infos():
space_group = space_group_info.group()
uc = space_group_info.any_compatible_unit_cell(volume=57*57*76)
xs = crystal.symmetry(uc, space_group=space_group)
cobs = pt.reference_setting_choices(space_group)
if len(cobs)>1:
tmp_array = []
for cob in cobs:
xs_new =crystal.symmetry(xs.change_basis( cob ).unit_cell(),
space_group=xs.space_group() )
best_cell_finder = fbc(xs_new.unit_cell(),
xs_new.space_group() )
xs_new = best_cell_finder.return_best_xs()
tmp_array.append(xs_new)
count = 0
for tmp_xs1 in xrange(len(tmp_array)):
for tmp_xs2 in xrange(len(tmp_array)):
if (tmp_xs1 != tmp_xs2):
assert (tmp_array[tmp_xs1].space_group()
== tmp_array[tmp_xs2].space_group())
assert not approx_equal(
tmp_array[tmp_xs1].unit_cell().parameters(),
tmp_array[tmp_xs2].unit_cell().parameters(),
eps=0.001,
out=buffer)
def test_reference_setting_choices():
buffer = StringIO()
for space_group_info in sgtbx.reference_space_group_infos():
space_group = space_group_info.group()
uc = space_group_info.any_compatible_unit_cell(volume=57 * 57 * 76)
xs = crystal.symmetry(uc, space_group=space_group)
cobs = pt.reference_setting_choices(space_group)
if len(cobs) > 1:
tmp_array = []
for cob in cobs:
xs_new = crystal.symmetry(xs.change_basis(cob).unit_cell(),
space_group=xs.space_group())
best_cell_finder = fbc(xs_new.unit_cell(),
xs_new.space_group())
xs_new = best_cell_finder.return_best_xs()
tmp_array.append(xs_new)
count = 0
for tmp_xs1 in xrange(len(tmp_array)):
for tmp_xs2 in xrange(len(tmp_array)):
if (tmp_xs1 != tmp_xs2):
assert (tmp_array[tmp_xs1].space_group() ==
tmp_array[tmp_xs2].space_group())
assert not approx_equal(
tmp_array[tmp_xs1].unit_cell().parameters(),
tmp_array[tmp_xs2].unit_cell().parameters(),
eps=0.001,
out=buffer)
def test_extensively( this_chunk ):
n_chunks = 1
i_chunk = int(this_chunk)
assert i_chunk <= n_chunks
for i_sg, sg in enumerate(sgtbx.space_group_symbol_iterator()):
if i_sg % n_chunks != i_chunk:
continue
buffer = StringIO()
group = sgtbx.space_group(sg.hall())
#if group != sgtbx.space_group_info( symbol = 'I 21 21 21' ).group() :
# continue
unit_cell =sgtbx.space_group_info(group=group).any_compatible_unit_cell(
volume=57*57*76)
xs_in = crystal.symmetry(unit_cell=unit_cell, space_group=group)
xs_in = xs_in.best_cell()
# Just make sure we have the 'best cell' to start out with
xs_minimum = xs_in.change_basis(xs_in.change_of_basis_op_to_niggli_cell())
sg_min = xs_minimum.space_group()
sg_min_info = sgtbx.space_group_info(group = sg_min)
sg_min_to_ref = sg_min_info.change_of_basis_op_to_reference_setting()
sg_in_to_min = xs_in.change_of_basis_op_to_niggli_cell()
xs_ref = xs_minimum.change_basis(sg_min_to_ref)
best_cell_finder = fbc(xs_ref.unit_cell(),
xs_ref.space_group())
xs_ref = best_cell_finder.return_best_xs()
xs_lattice_pg = sgtbx.lattice_symmetry.group(
xs_minimum.unit_cell(),
max_delta=5.0)
sg_in_ref_setting = sg_min.change_basis(sg_min_to_ref)
# -----------
queue = []
if sg_in_ref_setting.is_chiral():
print "Testing : ",\
sgtbx.space_group_info(group=group),\
"( or ", sgtbx.space_group_info(group=sg_in_ref_setting),\
" in reference setting)"
for s in sg_min:
new_sg = sgtbx.space_group()
new_sg.expand_smx(s)
if new_sg in queue:
continue
else:
queue.append(new_sg)
xs_cheat = crystal.symmetry(xs_minimum.unit_cell(),
space_group=new_sg)
#print
#print "Using symop", s
xs_cheat_min = xs_cheat.change_basis(
xs_cheat.change_of_basis_op_to_niggli_cell() )
#print "This results in space group: ", xs_cheat.space_group_info()
sg_clues = pt.space_group_graph_from_cell_and_sg(
xs_cheat_min.unit_cell(),
xs_cheat_min.space_group() )
#sg_clues.show()
found_it = False
#print
#print " --- Spacegroups consistent with input parameters ---"
for sg_and_uc in sg_clues.return_likely_sg_and_cell():
check_sg = False
check_uc = False
xs = crystal.symmetry(sg_and_uc[1], space_group=sg_and_uc[0])
if approx_equal(
sg_and_uc[1].parameters(),
xs_ref.unit_cell().parameters(),
eps=0.001,
out=buffer):
if sg_and_uc[0] == sg_in_ref_setting:
found_it = True
#print sgtbx.space_group_info( group=sg_and_uc[0] ), \
# sg_and_uc[1].parameters()
if not found_it:
print "FAILURE: ", sg.hall()
assert found_it
def test_extensively(this_chunk):
n_chunks = 1
i_chunk = int(this_chunk)
assert i_chunk <= n_chunks
for i_sg, sg in enumerate(sgtbx.space_group_symbol_iterator()):
if i_sg % n_chunks != i_chunk:
continue
buffer = StringIO()
group = sgtbx.space_group(sg.hall())
#if group != sgtbx.space_group_info( symbol = 'I 21 21 21' ).group():
# continue
unit_cell = sgtbx.space_group_info(
group=group).any_compatible_unit_cell(volume=57 * 57 * 76)
xs_in = crystal.symmetry(unit_cell=unit_cell, space_group=group)
xs_in = xs_in.best_cell()
# Just make sure we have the 'best cell' to start out with
xs_minimum = xs_in.change_basis(
xs_in.change_of_basis_op_to_niggli_cell())
sg_min = xs_minimum.space_group()
sg_min_info = sgtbx.space_group_info(group=sg_min)
sg_min_to_ref = sg_min_info.change_of_basis_op_to_reference_setting()
sg_in_to_min = xs_in.change_of_basis_op_to_niggli_cell()
xs_ref = xs_minimum.change_basis(sg_min_to_ref)
best_cell_finder = fbc(xs_ref.unit_cell(), xs_ref.space_group())
xs_ref = best_cell_finder.return_best_xs()
xs_lattice_pg = sgtbx.lattice_symmetry.group(xs_minimum.unit_cell(),
max_delta=5.0)
sg_in_ref_setting = sg_min.change_basis(sg_min_to_ref)
# -----------
queue = []
if sg_in_ref_setting.is_chiral():
print "Testing : ",\
sgtbx.space_group_info(group=group),\
"( or ", sgtbx.space_group_info(group=sg_in_ref_setting),\
" in reference setting)"
for s in sg_min:
new_sg = sgtbx.space_group()
new_sg.expand_smx(s)
if new_sg in queue:
continue
else:
queue.append(new_sg)
xs_cheat = crystal.symmetry(xs_minimum.unit_cell(),
space_group=new_sg)
#print
#print "Using symop", s
xs_cheat_min = xs_cheat.change_basis(
xs_cheat.change_of_basis_op_to_niggli_cell())
#print "This results in space group: ", xs_cheat.space_group_info()
sg_clues = pt.space_group_graph_from_cell_and_sg(
xs_cheat_min.unit_cell(), xs_cheat_min.space_group())
#sg_clues.show()
found_it = False
#print
#print " --- Spacegroups consistent with input parameters ---"
for sg_and_uc in sg_clues.return_likely_sg_and_cell():
check_sg = False
check_uc = False
xs = crystal.symmetry(sg_and_uc[1],
space_group=sg_and_uc[0])
if approx_equal(sg_and_uc[1].parameters(),
xs_ref.unit_cell().parameters(),
eps=0.001,
out=buffer):
if sg_and_uc[0] == sg_in_ref_setting:
found_it = True
#print sgtbx.space_group_info( group=sg_and_uc[0] ), \
# sg_and_uc[1].parameters()
if not found_it:
print "FAILURE: ", sg.hall()
assert found_it
