def test_table(self):
for sg in gemmi.spacegroup_table():
if sg.ccp4 != 0:
self.assertEqual(sg.ccp4 % 1000, sg.number)
if sg.operations().is_centric():
self.assertEqual(sg.laue_str(), sg.point_group_hm())
else:
self.assertNotEqual(sg.laue_str(), sg.point_group_hm())
if sgtbx:
hall = sg.hall.encode()
cctbx_sg = sgtbx.space_group(hall)
cctbx_info = sgtbx.space_group_info(group=cctbx_sg)
self.assertEqual(sg.is_reference_setting(),
cctbx_info.is_reference_setting())
#to_ref = cctbx_info.change_of_basis_op_to_reference_setting()
#from_ref = '%s' % cob_to_ref.inverse().c()
c2p_sg = gemmi.Op(cctbx_sg.z2p_op().c().inverse().as_xyz())
self.assertEqual(sg.centred_to_primitive(), c2p_sg)
ops = gemmi.get_spacegroup_reference_setting(sg.number).operations()
ops.change_basis_forward(sg.basisop)
self.assertEqual(ops, sg.operations())
itb = gemmi.spacegroup_table_itb()
if sgtbx:
for s in sgtbx.space_group_symbol_iterator():
self.assertEqual(s.hall().strip(), next(itb).hall)
with self.assertRaises(StopIteration):
next(itb)
def wite_xml():
sp = SpaceGroups()
txt = ''
for s in gemmi.spacegroup_table():
print(s.number, s.short_name())
p = sp.to_mathml(s.xhm())
print(p)
txt = txt + '{} {}\n'.format(s.number, s.short_name())
txt = txt + p + '\n'
Path('testing_xml.html').write_text(txt)
def _general_format_out(self):
"""
Writes out a python file with a dictionary of a general format definition of all space groups.
"""
Path('testing2.py').unlink(missing_ok=True)
htxt = 'spgrps = {\n'
for space_group_obj in gemmi.spacegroup_table():
space_group_obj: gemmi.SpaceGroup
html = []
splitted_spgr = space_group_obj.xhm().split(' ')
if space_group_obj.short_name() == self._myshort(space_group_obj):
splitted_spgr = self.remove_setting(space_group_obj)
html.append(" '{}' : (\n (('{}', 'italic'),\n".format(space_group_obj.xhm(),
splitted_spgr.pop(0)))
if space_group_obj.short_name() == 'P21212(a)':
self.handle_p21212a_specially(html)
else:
for num, chars in enumerate(splitted_spgr):
if ':' in chars:
chars, append = chars.split(':')
if chars.startswith('-'):
html.append(" ({}, 'overline'),\n".format(chars[-1]))
else:
self._italize_chars_format(chars, html)
self._italize_chars_format(':' + append, html)
continue
if len(chars) == 1:
if isnumeric(chars):
html.append(" ('{}', 'regular'),\n".format(chars))
else:
html.append(" ('{}', 'italic'),\n".format(chars))
if len(chars) == 2 and self._get_screw(chars):
html.append(self._get_screw_format(chars))
if len(chars) == 2 and not self._get_screw(chars):
if chars.startswith('-'):
html.append(" ('{}', 'overline'),\n".format(chars[-1]))
else:
self._italize_chars_format(chars, html)
if len(chars) > 2:
txt = []
if self._get_screw(chars[:2]):
html.append(self._get_screw_format(chars[:2]))
chars = chars[:]
for chars in chars:
self._make_italic_format(chars, txt)
html.append("{}".format(''.join(txt)))
htxt = htxt + ''.join(html) \
+ " ), {{'itnumber': {}, 'crystal_system': '{}', " \
"'short-hm': '{}', 'is_reference': {}}},\n ),\n".format(space_group_obj.number,
space_group_obj.crystal_system_str(),
space_group_obj.short_name(),
space_group_obj.is_reference_setting(),
)
Path('testing2.py').write_text(htxt + '\n}')
def test_table(self):
for sg in gemmi.spacegroup_table():
if sg.ccp4 != 0:
self.assertEqual(sg.ccp4 % 1000, sg.number)
if sg.operations().is_centric():
self.assertEqual(sg.laue_str(), sg.point_group_hm())
else:
self.assertNotEqual(sg.laue_str(), sg.point_group_hm())
if sgtbx:
hall = sg.hall.encode()
cctbx_sg = sgtbx.space_group(hall)
cctbx_info = sgtbx.space_group_info(group=cctbx_sg)
self.assertEqual(sg.is_reference_setting(),
cctbx_info.is_reference_setting())
def test_table(self):
for sg in gemmi.spacegroup_table():
if sg.ccp4 != 0:
self.assertEqual(sg.ccp4 % 1000, sg.number)
if sg.operations().is_centric():
self.assertEqual(sg.laue_str(), sg.point_group_hm())
else:
self.assertNotEqual(sg.laue_str(), sg.point_group_hm())
if sgtbx:
hall = sg.hall.encode()
cctbx_sg = sgtbx.space_group(hall)
cctbx_info = sgtbx.space_group_info(group=cctbx_sg)
self.assertEqual(sg.is_reference_setting(),
cctbx_info.is_reference_setting())
#to_ref = cctbx_info.change_of_basis_op_to_reference_setting()
#from_ref = '%s' % cob_to_ref.inverse().c()
ops = gemmi.get_spacegroup_reference_setting(sg.number).operations()
ops.change_basis(sg.basisop)
self.assertEqual(ops, sg.operations())
def write_html():
s = SpaceGroups()
txt = ''
for sp in gemmi.spacegroup_table():
txt = txt + s.to_html(sp.xhm()) + '<br>\n'
Path('testing.html').write_text(txt)
def _general_format_out(self):
"""
Writes out a python file with a dictionary of a general format definition of all space groups.
"""
Path('testing2.py').unlink(missing_ok=True)
htxt = 'spgrps = {\n'
for s in gemmi.spacegroup_table():
s: gemmi.SpaceGroup
html = []
splitted_s = s.xhm().split(' ')
if s.short_name() == self._myshort(s):
splitted_s = [
x for x in s.xhm().split(':')[0].split(' ') if x != '1'
]
else:
pass
html.append(
" '{}' : (\n (('{}', 'italic'),\n".format(
s.xhm(), splitted_s.pop(0)))
if s.short_name() == 'P21212(a)':
# This one is differently formated as the others in gemmi:
html.append(
"('2', 'regular'),\n ('1' ,'sub'),\n ('2', 'regular'),\n ('1', 'sub'),\n ('2', 'regular'),"
"\n ('1', 'sub'),\n ('2(a)', 'regular'),\n")
else:
for num, c in enumerate(splitted_s):
if ':' in c:
c, append = c.split(':')
if c.startswith('-'):
html.append(
" ({}, 'overline'),\n".format(
c[-1]))
else:
self._italize_chars_format(c, html)
self._italize_chars_format(':' + append, html)
continue
if len(c) == 1:
if isnumeric(c):
html.append(
" ('{}', 'regular'),\n".format(c))
else:
html.append(
" ('{}', 'italic'),\n".format(c))
if len(c) == 2 and self._get_screw(c):
html.append(self._get_screw_format(c))
if len(c) == 2 and not self._get_screw(c):
if c.startswith('-'):
html.append(
" ('{}', 'overline'),\n".format(c[-1]))
else:
self._italize_chars_format(c, html)
if len(c) > 2:
txt = []
if self._get_screw(c[:2]):
html.append(self._get_screw_format(c[:2]))
c = c[:]
for char in c:
self._make_italic_format(char, txt)
html.append("{}".format(''.join(txt)))
htxt = htxt + ''.join(html) \
+ " ), {{'itnumber': {}, 'crystal_system': '{}', " \
"'short-hm': '{}', 'is_reference': {}}},\n ),\n".format(s.number,
s.crystal_system_str(),
s.short_name(),
s.is_reference_setting(),
)
Path('testing2.py').write_text(htxt + '\n}')
def test_with_sgtbx(self):
if sgtbx is None:
return
for s in gemmi.spacegroup_table():
self.compare_hall_symops_with_sgtbx(s.hall.encode())
self.compare_hall_symops_with_sgtbx('C -4 -2b', existing_group=False)
def test_table(self):
for sg in gemmi.spacegroup_table():
if sg.ccp4 != 0:
self.assertEqual(sg.ccp4 % 1000, sg.number)