def run():
settings = [0]
for i in range(1, 231):
settings.append({})
list_cb_op = []
for xyz in ("x,y,z", "z,x,y", "y,z,x"):
list_cb_op.append(sgtbx.change_of_basis_op(sgtbx.rt_mx(xyz)))
n_built = 0
for i in sgtbx.space_group_symbol_iterator():
hall_symbol = i.hall()
for z in "PABCIRHF":
hall_z = hall_symbol[0] + z + hall_symbol[2:]
for cb_op in list_cb_op:
group = sgtbx.space_group(hall_z).change_basis(cb_op)
sg_type = group.type()
settings[sg_type.number()][sg_type.lookup_symbol()] = 0
n_built += 1
print("# n_built =", n_built)
n_non_redundant = 0
print("settings = (")
for i in range(1, 231):
print("#", i)
symbols = list(settings[i].keys())
symbols.sort()
for s in symbols:
print("'" + s + "',")
n_non_redundant += 1
print(")")
print("# n_non_redundant =", n_non_redundant)
def get_and_check_file():
if ( not os.path.isfile(html_file)
or open(html_file).read().lower().find("not found") >= 0):
print "Skipping exercise(): input file not available"
return
table_lines = open(html_file).read().splitlines()[11:-4]
assert len(table_lines) == 530, "%d != 530" % len(table_lines)
space_group_symbol_iterator = sgtbx.space_group_symbol_iterator()
for line in table_lines:
flds = line.split()
assert len(flds) == 3
nc, hm, hall = flds
assert hall.lower() == hall
symbols = sgtbx.space_group_symbols(symbol=hm)
hm_sgtbx = symbols.universal_hermann_mauguin().replace(" ", "_") \
.replace("_:",":") \
.replace(":H",":h") \
.replace(":R",":r")
hall_sgtbx = symbols.hall().lower().replace(" ", "_")
if (hall_sgtbx[0] == "_"): hall_sgtbx = hall_sgtbx[1:]
assert hm_sgtbx == hm
assert hall_sgtbx == hall
symbols_i = space_group_symbol_iterator.next()
assert symbols_i.universal_hermann_mauguin() \
== symbols.universal_hermann_mauguin()
def exercise_space_group_contains():
g = sgtbx.space_group("P 2")
for s in ["x,y,z", "-x,-y,z", "-x+1,-y-2,z+3"]:
assert g.contains(sgtbx.rt_mx(s))
for s in ["x,y,-z", "x+1/2,y,z"]:
assert not g.contains(sgtbx.rt_mx(s))
for symbols in sgtbx.space_group_symbol_iterator():
g = sgtbx.space_group(symbols.hall())
for s in g:
assert g.contains(s)
rnd = flex.mersenne_twister(seed=0)
n_c = 0
n_nc = 0
for symbol in sgtbx.bravais_types.centric:
g = sgtbx.space_group_info(symbol=symbol,
space_group_t_den=144).group()
for s in g.change_basis(
sgtbx.change_of_basis_op("x+1/12,y-1/12,z+1/12")):
if (rnd.random_double() < 0.9): continue # avoid long runtime
gc = sgtbx.space_group(g)
gc.expand_smx(s)
if (gc.order_z() == g.order_z()):
assert g.contains(s)
n_c += 1
else:
assert not g.contains(s)
n_nc += 1
assert n_c == 11, n_c
assert n_nc == 53, n_nc
def run():
settings = [0]
for i in xrange(1, 231): settings.append({})
list_cb_op = []
for xyz in ("x,y,z", "z,x,y", "y,z,x"):
list_cb_op.append(sgtbx.change_of_basis_op(sgtbx.rt_mx(xyz)))
n_built = 0
for i in sgtbx.space_group_symbol_iterator():
hall_symbol = i.hall()
for z in "PABCIRHF":
hall_z = hall_symbol[0] + z + hall_symbol[2:]
for cb_op in list_cb_op:
group = sgtbx.space_group(hall_z).change_basis(cb_op)
sg_type = group.type()
settings[sg_type.number()][sg_type.lookup_symbol()] = 0
n_built += 1
print "# n_built =", n_built
n_non_redundant = 0
print "settings = ("
for i in xrange(1, 231):
print "#", i
symbols = settings[i].keys()
symbols.sort()
for s in symbols:
print "'" + s + "',"
n_non_redundant += 1
print ")"
print "# n_non_redundant =", n_non_redundant
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 get_test_space_group_symbols(flag_AllSpaceGroups,
flag_ChiralSpaceGroups,
flag_AllSettings,
flag_UnusualSettings):
if (flag_UnusualSettings):
namespace = {}
execfile(os.path.join(
libtbx.env.find_in_repositories(
"phenix_regression"), "settings.py"), namespace)
return namespace["settings"]
if (flag_AllSettings):
return [symbols.universal_hermann_mauguin()
for symbols in sgtbx.space_group_symbol_iterator()]
if (flag_AllSpaceGroups):
sg_numbers = xrange(1, 231)
elif (flag_ChiralSpaceGroups):
sg_numbers = (1, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 75,
76, 77, 78, 79, 80, 89, 90, 91, 92, 93, 94, 95, 96,
97, 98, 143, 144, 145, 146, 149, 150, 151, 152, 153,
154, 155, 168, 169, 170, 171, 172, 173, 177, 178,
179, 180, 181, 182, 195, 196, 197, 198, 199, 207,
208, 209, 210, 211, 212, 213, 214)
else:
sg_numbers = (1,2,3,15,16,74,75,76,142,143,144,157,167,168,194,195,230)
return [sgtbx.space_group_symbols(n).universal_hermann_mauguin()
for n in sg_numbers] + ["Hall: -F 4 21 (1,5,3)"]
def run(server_info, inp, status):
sg_number = 0
if (len(inp.sgsymbol.strip()) != 0):
sg_number = sgtbx.space_group_info(
symbol=inp.sgsymbol,
table_id=inp.convention).type().number()
n_settings = 0
print "<table border=2 cellpadding=2>"
print "<tr>"
print "<th>Space group<br>No."
print "<th>Schoenflies<br>symbol"
print "<th>Hermann-Mauguin<br>symbol"
print "<th>Hall<br>symbol"
for symbols in sgtbx.space_group_symbol_iterator():
if (sg_number == 0 or symbols.number() == sg_number):
print "<tr>"
print "<td>(%d)<td>%s" % (
symbols.number(), symbols.schoenflies())
query = "target_module=explore_symmetry&sgsymbol=" \
+ urllib.quote_plus(symbols.universal_hermann_mauguin())
print ("<td><a href=\"%s\">%s</a>") % (
server_info.script(query),
symbols.universal_hermann_mauguin())
print "<td>%s" % (symbols.hall(),)
n_settings += 1
print "</table>"
if (sg_number == 0):
print "<p>"
print "Number of settings listed:", n_settings
print "<p>"
def run(server_info, inp, status):
sg_number = 0
if (len(inp.sgsymbol.strip()) != 0):
sg_number = sgtbx.space_group_info(
symbol=inp.sgsymbol, table_id=inp.convention).type().number()
n_settings = 0
print "<table border=2 cellpadding=2>"
print "<tr>"
print "<th>Space group<br>No."
print "<th>Schoenflies<br>symbol"
print "<th>Hermann-Mauguin<br>symbol"
print "<th>Hall<br>symbol"
for symbols in sgtbx.space_group_symbol_iterator():
if (sg_number == 0 or symbols.number() == sg_number):
print "<tr>"
print "<td>(%d)<td>%s" % (symbols.number(), symbols.schoenflies())
query = "target_module=explore_symmetry&sgsymbol=" \
+ urllib.quote_plus(symbols.universal_hermann_mauguin())
print("<td><a href=\"%s\">%s</a>") % (
server_info.script(query), symbols.universal_hermann_mauguin())
print "<td>%s" % (symbols.hall(), )
n_settings += 1
print "</table>"
if (sg_number == 0):
print "<p>"
print "Number of settings listed:", n_settings
print "<p>"
def list(self):
for symbols in sgtbx.space_group_symbol_iterator():
sgi = sgtbx.space_group_info(group=sgtbx.space_group(
space_group_symbols=symbols))
if self.comparator(sgi):
if (self.chiral is None) or (self.chiral == sgi.group().is_chiral()):
yield sgi
def generate_enantiomorph_unique_spacegroups(pointgroup):
'''Generate an enantiomorph unique list of chiral spacegroups which
share a pointgroup with this pointgroup.'''
sg = space_group(space_group_symbols(pointgroup).hall())
pg = sg.build_derived_patterson_group()
eu_list = []
for j in space_group_symbol_iterator():
sg_test = space_group(j)
if not sg_test.is_chiral():
continue
pg_test = sg_test.build_derived_patterson_group()
if pg_test == pg:
enantiomorph = sg_test.change_basis(
sg_test.type().change_of_hand_op())
if not sg_test in eu_list and not \
enantiomorph in eu_list:
eu_list.append(sg_test)
return [
sg_test.type().lookup_symbol().replace(' ', '') \
for sg_test in eu_list]
def get_and_check_file():
if (not os.path.isfile(html_file)
or open(html_file).read().lower().find("not found") >= 0):
print "Skipping exercise(): input file not available"
return
table_lines = open(html_file).read().splitlines()[11:-4]
assert len(table_lines) == 530, "%d != 530" % len(table_lines)
space_group_symbol_iterator = sgtbx.space_group_symbol_iterator()
for line in table_lines:
flds = line.split()
assert len(flds) == 3
nc, hm, hall = flds
assert hall.lower() == hall
symbols = sgtbx.space_group_symbols(symbol=hm)
hm_sgtbx = symbols.universal_hermann_mauguin().replace(" ", "_") \
.replace("_:",":") \
.replace(":H",":h") \
.replace(":R",":r")
hall_sgtbx = symbols.hall().lower().replace(" ", "_")
if (hall_sgtbx[0] == "_"): hall_sgtbx = hall_sgtbx[1:]
assert hm_sgtbx == hm
assert hall_sgtbx == hall
symbols_i = space_group_symbol_iterator.next()
assert symbols_i.universal_hermann_mauguin() \
== symbols.universal_hermann_mauguin()
def run():
for symbols in sgtbx.space_group_symbol_iterator():
hm = html_markup(symbols.hermann_mauguin())
ext = symbols.extension()
if ext == '\0': ext = ''
uhm = html_markup(symbols.universal_hermann_mauguin())
print '%s,%s,%s,%s' % (symbols.number(), ''.join(hm), ext, ' '.join(uhm))
def get_test_space_group_symbols(flag_AllSpaceGroups,
flag_ChiralSpaceGroups,
flag_AllSettings,
flag_UnusualSettings):
if (flag_UnusualSettings):
namespace = {}
exec(open(os.path.join(
libtbx.env.find_in_repositories(
"phenix_regression"), "settings.py")).read(), namespace)
return namespace["settings"]
if (flag_AllSettings):
return [symbols.universal_hermann_mauguin()
for symbols in sgtbx.space_group_symbol_iterator()]
if (flag_AllSpaceGroups):
sg_numbers = range(1, 231)
elif (flag_ChiralSpaceGroups):
sg_numbers = (1, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 75,
76, 77, 78, 79, 80, 89, 90, 91, 92, 93, 94, 95, 96,
97, 98, 143, 144, 145, 146, 149, 150, 151, 152, 153,
154, 155, 168, 169, 170, 171, 172, 173, 177, 178,
179, 180, 181, 182, 195, 196, 197, 198, 199, 207,
208, 209, 210, 211, 212, 213, 214)
else:
sg_numbers = (1,2,3,15,16,74,75,76,142,143,144,157,167,168,194,195,230)
return [sgtbx.space_group_symbols(n).universal_hermann_mauguin()
for n in sg_numbers] + ["Hall: -F 4 21 (1,5,3)"]
def exercise_space_group_contains():
g = sgtbx.space_group("P 2")
for s in ["x,y,z", "-x,-y,z", "-x+1,-y-2,z+3"]:
assert g.contains(sgtbx.rt_mx(s))
for s in ["x,y,-z", "x+1/2,y,z"]:
assert not g.contains(sgtbx.rt_mx(s))
for symbols in sgtbx.space_group_symbol_iterator():
g = sgtbx.space_group(symbols.hall())
for s in g:
assert g.contains(s)
rnd = flex.mersenne_twister(seed=0)
n_c = 0
n_nc = 0
for symbol in sgtbx.bravais_types.centric:
g = sgtbx.space_group_info(symbol=symbol, space_group_t_den=144).group()
for s in g.change_basis(sgtbx.change_of_basis_op("x+1/12,y-1/12,z+1/12")):
if (rnd.random_double() < 0.9): continue # avoid long runtime
gc = sgtbx.space_group(g)
gc.expand_smx(s)
if (gc.order_z() == g.order_z()):
assert g.contains(s)
n_c += 1
else:
assert not g.contains(s)
n_nc += 1
assert n_c == 11, n_c
assert n_nc == 53, n_nc
def list(self):
for symbols in sgtbx.space_group_symbol_iterator():
sgi = sgtbx.space_group_info(group=sgtbx.space_group(
space_group_symbols=symbols))
if self.comparator(sgi):
if (self.chiral is None) or (self.chiral
== sgi.group().is_chiral()):
yield sgi
def findEquivalentSgtbxSpaceGroup(sgmm):
if not _equivsgtbx:
for smbls in sgtbx.space_group_symbol_iterator():
uhm = smbls.universal_hermann_mauguin()
grp = sgtbx.space_group_info(uhm).group()
hgrp = hashSgtbxGroup(grp)
_equivsgtbx.setdefault(hgrp, grp)
hgmm = hashMMSpaceGroup(sgmm)
return _equivsgtbx.get(hgmm)
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 browse(self):
for self.symbol in sgtbx.space_group_symbol_iterator():
self.sg = sgtbx.space_group(self.symbol.hall()).make_tidy()
self.z2p_op = self.sg.z2p_op()
self.sg_p = self.sg.change_basis(self.z2p_op)
self.on_new_space_group()
for self.op in self.sg_p:
self.rot_info = self.op.r().info()
self.tr_info = sgtbx.translation_part_info(self.op)
if self.tr_info.origin_shift().is_zero(): continue
self.on_new_symmetry()
def browse(self):
for self.symbol in sgtbx.space_group_symbol_iterator():
self.sg = sgtbx.space_group(self.symbol.hall()).make_tidy()
self.z2p_op = self.sg.z2p_op()
self.sg_p = self.sg.change_basis(self.z2p_op)
self.on_new_space_group()
for self.op in self.sg_p:
self.rot_info = self.op.r().info()
self.tr_info = sgtbx.translation_part_info(self.op)
if self.tr_info.origin_shift().is_zero(): continue
self.on_new_symmetry()
def run():
all_flds = set()
for symbols in sgtbx.space_group_symbol_iterator():
symbol = symbols.universal_hermann_mauguin()
print symbol
flds = symbol.split()
all_flds.update(flds)
with open('symops_530_html_markup.py', 'w') as f:
print >> f, 'html_markup = {'
for fld in sorted(all_flds):
print >> f, " '%s': '%s'," % (fld, fld)
print >> f, '}'
def exercise_inversion_centring():
cb = sgtbx.change_of_basis_op("x+1/12,y+1/12,z-1/12")
for symb in sgtbx.space_group_symbol_iterator():
sg = sgtbx.space_group(space_group_symbols=symb)
sg1 = sg.change_basis(cb)
icb = sg1.change_of_origin_realising_origin_centricity()
if sg1.is_centric():
assert not sg1.is_origin_centric()
sg2 = sg1.change_basis(icb)
assert sg2.is_origin_centric()
else:
assert str(icb) == "a,b,c"
def exercise_inversion_centring():
cb = sgtbx.change_of_basis_op("x+1/12,y+1/12,z-1/12")
for symb in sgtbx.space_group_symbol_iterator():
sg = sgtbx.space_group(space_group_symbols=symb)
sg1 = sg.change_basis(cb)
icb = sg1.change_of_origin_realising_origin_centricity()
if sg1.is_centric():
assert not sg1.is_origin_centric()
sg2 = sg1.change_basis(icb)
assert sg2.is_origin_centric()
else:
assert str(icb) == "a,b,c"
def exercise_ss_continuous_shifts_are_principal():
for i in range(1, 231):
sgi = sgtbx.space_group_info(number=i)
ss = sgi.structure_seminvariants()
assert ss.continuous_shifts_are_principal()
for symbols in sgtbx.space_group_symbol_iterator():
sgi = sgtbx.space_group_info(group=sgtbx.space_group(
space_group_symbols=symbols))
ss = sgi.structure_seminvariants()
if (not ss.continuous_shifts_are_principal()):
assert symbols.universal_hermann_mauguin() in [
"R 3 :R", "R 3 m :R", "R 3 c :R"
]
def run():
for symbols in sgtbx.space_group_symbol_iterator():
symbol = symbols.universal_hermann_mauguin()
print(symbol)
space_group_info = sgtbx.space_group_info(symbol=symbol)
for s in space_group_info.group():
print(s.as_xyz())
for s in space_group_info.group():
sr = s.as_rational()
print(sr.r.elems, sr.t.elems)
for s in space_group_info.group():
print(s.r().num(), s.r().den(), s.t().num(), s.t().den())
print()
def exercise_orthorhombic_hm_qualifier_as_cb_symbol():
cb_symbols = {
"cab": ["c,a,b", "z,x,y"],
"a-cb": ["a,-c,b", "x,-z,y"],
"-cba": ["-c,b,a", "-z,y,x"],
"bca": ["b,c,a", "y,z,x"],
"ba-c": ["b,a,-c", "y,x,-z"]
}
for sgsyms1 in sgtbx.space_group_symbol_iterator():
n = sgsyms1.number()
if (n < 16 or n > 74): continue
q = sgsyms1.qualifier()
if (len(q) == 0): continue
e = sgsyms1.extension()
if (e == "\0"): e = ""
ehm = sgtbx.space_group_symbols(
space_group_number=n, extension=e).universal_hermann_mauguin()
cabc, cxyz = cb_symbols[q]
assert sgtbx.change_of_basis_op(cxyz).as_abc() == cabc
assert sgtbx.change_of_basis_op(cabc).as_xyz() == cxyz
uhm_xyz = ehm + " (" + cxyz + ")"
sgsyms2 = sgtbx.space_group_symbols(symbol=uhm_xyz)
assert sgsyms2.change_of_basis_symbol() == cxyz
assert sgsyms2.extension() == sgsyms1.extension()
assert sgsyms2.universal_hermann_mauguin() == uhm_xyz
g1 = sgtbx.space_group(space_group_symbols=sgsyms1)
g2 = sgtbx.space_group(space_group_symbols=sgsyms2)
assert g2 == g1
g2 = sgtbx.space_group(
sgtbx.space_group_symbols(symbol=ehm)).change_basis(
sgtbx.change_of_basis_op(sgtbx.rt_mx(cxyz)))
assert g2 == g1
for c in [cxyz, cabc]:
g2 = sgtbx.space_group_info(
group=sgtbx.space_group(sgtbx.space_group_symbols(
symbol=ehm))).change_basis(c).group()
assert g2 == g1
cit = sgtbx.rt_mx(cxyz).r().inverse().transpose()
cit_xyz = cit.as_xyz()
g2 = sgtbx.space_group_info(
group=sgtbx.space_group(sgtbx.space_group_symbols(
symbol=ehm))).change_basis(cit_xyz).group()
assert g2 == g1
assert cit.as_xyz(False, "abc") == cabc
uhm_abc = ehm + " (" + cabc + ")"
sgsyms2 = sgtbx.space_group_symbols(symbol=uhm_abc)
assert sgsyms2.change_of_basis_symbol() == cxyz
assert sgsyms2.extension() == sgsyms1.extension()
assert sgsyms2.universal_hermann_mauguin() == uhm_xyz
g2 = sgtbx.space_group(space_group_symbols=sgsyms2)
assert g2 == g1
def exercise_orthorhombic_hm_qualifier_as_cb_symbol():
cb_symbols = {
"cab": ["c,a,b", "z,x,y"],
"a-cb": ["a,-c,b", "x,-z,y"],
"-cba": ["-c,b,a", "-z,y,x"],
"bca": ["b,c,a", "y,z,x"],
"ba-c": ["b,a,-c", "y,x,-z"]}
for sgsyms1 in sgtbx.space_group_symbol_iterator():
n = sgsyms1.number()
if (n < 16 or n > 74): continue
q = sgsyms1.qualifier()
if (len(q) == 0): continue
e = sgsyms1.extension()
if (e == "\0"): e = ""
ehm = sgtbx.space_group_symbols(
space_group_number=n, extension=e).universal_hermann_mauguin()
cabc, cxyz = cb_symbols[q]
assert sgtbx.change_of_basis_op(cxyz).as_abc() == cabc
assert sgtbx.change_of_basis_op(cabc).as_xyz() == cxyz
uhm_xyz = ehm + " ("+cxyz+")"
sgsyms2 = sgtbx.space_group_symbols(symbol=uhm_xyz)
assert sgsyms2.change_of_basis_symbol() == cxyz
assert sgsyms2.extension() == sgsyms1.extension()
assert sgsyms2.universal_hermann_mauguin() == uhm_xyz
g1 = sgtbx.space_group(space_group_symbols=sgsyms1)
g2 = sgtbx.space_group(space_group_symbols=sgsyms2)
assert g2 == g1
g2 = sgtbx.space_group(
sgtbx.space_group_symbols(symbol=ehm)).change_basis(
sgtbx.change_of_basis_op(sgtbx.rt_mx(cxyz)))
assert g2 == g1
for c in [cxyz, cabc]:
g2 = sgtbx.space_group_info(
group=sgtbx.space_group(
sgtbx.space_group_symbols(symbol=ehm))).change_basis(c).group()
assert g2 == g1
cit = sgtbx.rt_mx(cxyz).r().inverse().transpose()
cit_xyz = cit.as_xyz()
g2 = sgtbx.space_group_info(
group=sgtbx.space_group(
sgtbx.space_group_symbols(symbol=ehm))).change_basis(cit_xyz).group()
assert g2 == g1
assert cit.as_xyz(False, "abc") == cabc
uhm_abc = ehm + " ("+cabc+")"
sgsyms2 = sgtbx.space_group_symbols(symbol=uhm_abc)
assert sgsyms2.change_of_basis_symbol() == cxyz
assert sgsyms2.extension() == sgsyms1.extension()
assert sgsyms2.universal_hermann_mauguin() == uhm_xyz
g2 = sgtbx.space_group(space_group_symbols=sgsyms2)
assert g2 == g1
def run():
groups = []
lookup_dict = {}
for i_sg in range(1, 231):
space_group_info = sgtbx.space_group_info(number=i_sg)
space_group = space_group_info.group()
group = {"symbol": str(space_group_info), "number": i_sg, "operators": []}
for mx in space_group.smx():
group["operators"].append(str(mx))
groups.append(group)
for symbol in sgtbx.space_group_symbol_iterator():
lookup_dict[str(symbol.hermann_mauguin())] = symbol.number()
lookup_dict[str(symbol.hall())] = symbol.number()
print json.dumps({"groups": groups, "lookup": lookup_dict})
def exercise_ss_continuous_shifts_are_principal():
for i in xrange(1, 231):
sgi = sgtbx.space_group_info(number=i)
ss = sgi.structure_seminvariants()
assert ss.continuous_shifts_are_principal()
for symbols in sgtbx.space_group_symbol_iterator():
sgi = sgtbx.space_group_info(group=sgtbx.space_group(
space_group_symbols=symbols))
ss = sgi.structure_seminvariants()
if (not ss.continuous_shifts_are_principal()):
assert symbols.universal_hermann_mauguin() in [
"R 3 :R",
"R 3 m :R",
"R 3 c :R"]
def exercise_monoclinic_cell_choices(verbose=0):
done = {}
for space_group_number in xrange(3,16):
done.update(exercise_monoclinic_cell_choices_core(
space_group_number=space_group_number, verbose=verbose))
assert len(done) == 105
assert done.values().count(0) == 0
n = 0
for s in sgtbx.space_group_symbol_iterator():
if (s.number() < 3): continue
if (s.number() > 15): break
done[s.universal_hermann_mauguin()] = 0
n += 1
assert n == 105
assert done.values().count(0) == 105
def main():
duplicates = set()
for smbls in sgtbx.space_group_symbol_iterator():
uhm = smbls.universal_hermann_mauguin()
grp = sgtbx.space_group_info(uhm).group()
if findEquivalentMMSpaceGroup(grp): continue
shn = smbls.hermann_mauguin().replace(' ', '')
if IsSpaceGroupIdentifier(shn): continue
sg = mmSpaceGroupFromSymbol(uhm)
hsg = hashMMSpaceGroup(sg)
if hsg in duplicates: continue
adjustMMSpaceGroupNumber(sg)
duplicates.add(hsg)
print SGCode(sg)
return
def run () :
groups = []
lookup_dict = {}
for i_sg in range(1, 231) :
space_group_info = sgtbx.space_group_info(number=i_sg)
space_group = space_group_info.group()
group = { "symbol" : str(space_group_info),
"number" : i_sg,
"operators" : [] }
for mx in space_group.smx() :
group["operators"].append(str(mx))
groups.append(group)
for symbol in sgtbx.space_group_symbol_iterator() :
lookup_dict[str(symbol.hermann_mauguin())] = symbol.number()
lookup_dict[str(symbol.hall())] = symbol.number()
print json.dumps({"groups" : groups, "lookup" : lookup_dict })
def exercise_monoclinic_cell_choices(verbose=0):
done = {}
for space_group_number in range(3, 16):
done.update(
exercise_monoclinic_cell_choices_core(
space_group_number=space_group_number, verbose=verbose))
assert len(done) == 105
assert list(done.values()).count(0) == 0
n = 0
for s in sgtbx.space_group_symbol_iterator():
if (s.number() < 3): continue
if (s.number() > 15): break
done[s.universal_hermann_mauguin()] = 0
n += 1
assert n == 105
assert list(done.values()).count(0) == 105
def exercise_format_and_interpret_cryst1():
for symbols in sgtbx.space_group_symbol_iterator():
sgi = sgtbx.space_group_info(group=sgtbx.space_group(space_group_symbols=symbols))
cs = sgi.any_compatible_crystal_symmetry(volume=1000)
pdb_str = iotbx.pdb.format_cryst1_record(crystal_symmetry=cs)
cs2 = pdb.cryst1_interpretation.crystal_symmetry(cryst1_record=pdb_str)
assert cs2.is_similar_symmetry(other=cs)
#
for pdb_str in """]
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1
CRYST1 1.000 1.000 1.000 0.00 0.00 0.00 P 1
CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1
CRYST1 1.000 0.000 0.000 0.00 90.00 90.00 P 1
""".splitlines():
cs = pdb.cryst1_interpretation.crystal_symmetry(cryst1_record=pdb_str)
assert cs.unit_cell() is None
assert cs.space_group_info() is None
def xtestCreateSpaceGroup(self):
"""Check all sgtbx space groups for proper conversion to SpaceGroup."""
try:
from cctbx import sgtbx
except ImportError:
return
for smbls in sgtbx.space_group_symbol_iterator():
shn = smbls.hermann_mauguin()
short_name = shn.replace(' ', '')
if SpaceGroups.IsSpaceGroupIdentifier(short_name):
sg = SpaceGroups.GetSpaceGroup(shn)
sgnew = self.getObjCrystParSetSpaceGroup(sg)
# print "dbsg: " + repr(self.sgsEquivalent(sg, sgnew))
self.assertTrue(self.sgsEquivalent(sg, sgnew))
return
def exercise_format_and_interpret_cryst1():
for symbols in sgtbx.space_group_symbol_iterator():
sgi = sgtbx.space_group_info(group=sgtbx.space_group(
space_group_symbols=symbols))
cs = sgi.any_compatible_crystal_symmetry(volume=1000)
pdb_str = iotbx.pdb.format_cryst1_record(crystal_symmetry=cs)
cs2 = pdb.cryst1_interpretation.crystal_symmetry(cryst1_record=pdb_str)
assert cs2.is_similar_symmetry(other=cs)
#
for pdb_str in """]
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1
CRYST1 1.000 1.000 1.000 0.00 0.00 0.00 P 1
CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1
CRYST1 1.000 0.000 0.000 0.00 90.00 90.00 P 1
""".splitlines():
cs = pdb.cryst1_interpretation.crystal_symmetry(cryst1_record=pdb_str)
assert cs.unit_cell() is None
assert cs.space_group_info() is None
def generate_chiral_spacegroups(pointgroup):
sg = space_group(space_group_symbols(pointgroup).hall())
pg = sg.build_derived_patterson_group()
sg_list = []
for j in space_group_symbol_iterator():
sg_test = space_group(j)
if not sg_test.is_chiral():
continue
pg_test = sg_test.build_derived_patterson_group()
if pg_test == pg:
if not sg_test in sg_list:
sg_list.append(sg_test)
return [
sg_test.type().lookup_symbol().replace(' ', '') \
for sg_test in sg_list]
def exercise_combine_symops_and_symbol():
for symbols in sgtbx.space_group_symbol_iterator():
space_group = sgtbx.space_group_info(
symbol="Hall: %s" % symbols.hall()).group()
space_group_from_ops = sgtbx.space_group()
for s in list(space_group)[:space_group.order_p()]:
space_group_from_ops.expand_smx(s)
combined = combine_symops_and_symbol(
space_group_from_ops=space_group_from_ops,
space_group_symbol=symbols.universal_hermann_mauguin())
assert combined.group() == space_group
if (symbols.extension() in ["R", "H"]):
combined = combine_symops_and_symbol(
space_group_from_ops=space_group_from_ops,
space_group_symbol=symbols.hermann_mauguin())
assert combined.group() == space_group
if (symbols.extension() == "H"):
combined = combine_symops_and_symbol(
space_group_from_ops=space_group_from_ops,
space_group_symbol="H "+symbols.hermann_mauguin()[2:])
assert combined.group() == space_group
def exercise_combine_symops_and_symbol():
for symbols in sgtbx.space_group_symbol_iterator():
space_group = sgtbx.space_group_info(
symbol="Hall: %s" % symbols.hall()).group()
space_group_from_ops = sgtbx.space_group()
for s in list(space_group)[:space_group.order_p()]:
space_group_from_ops.expand_smx(s)
combined = combine_symops_and_symbol(
space_group_from_ops=space_group_from_ops,
space_group_symbol=symbols.universal_hermann_mauguin())
assert combined.group() == space_group
if (symbols.extension() in ["R", "H"]):
combined = combine_symops_and_symbol(
space_group_from_ops=space_group_from_ops,
space_group_symbol=symbols.hermann_mauguin())
assert combined.group() == space_group
if (symbols.extension() == "H"):
combined = combine_symops_and_symbol(
space_group_from_ops=space_group_from_ops,
space_group_symbol="H "+symbols.hermann_mauguin()[2:])
assert combined.group() == space_group
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 run(args):
assert args in [[], ["python"], ["c++"]]
#
sgno_list_by_index_list_by_cs = {}
from cctbx import sgtbx
from cctbx import miller
for symbols in sgtbx.space_group_symbol_iterator():
psgi = sgtbx.space_group_info(symbols.universal_hermann_mauguin()) \
.primitive_setting()
p_indices = miller.index_generator(space_group_type=psgi.type(),
anomalous_flag=False,
max_index=[4] * 3).to_array()
# 4 is the smallest value leading to correct results; any larger
# value will work, too, but will make this procedure slower
p1_indices = miller.expand_to_p1_iselection(
space_group=psgi.group(),
anomalous_flag=False,
indices=p_indices,
build_iselection=False).indices
from cctbx.array_family import flex
sort_perm = flex.sort_permutation(
data=miller.index_span(p1_indices).pack(p1_indices))
p1_indices = p1_indices.select(sort_perm)
index_list = tuple(p1_indices)
sgno = psgi.type().number()
sgno_list_by_index_list = sgno_list_by_index_list_by_cs \
.setdefault(symbols.crystal_system(), {})
sgno_list_by_index_list.setdefault(index_list, []).append(sgno)
from scitbx.graph import tardy_tree
cluster_manager = tardy_tree.cluster_manager(n_vertices=231)
for cs, sgno_list_by_index_list in sgno_list_by_index_list_by_cs.items():
for sgno_list in sgno_list_by_index_list.values():
i = sgno_list[0]
for j in sgno_list[1:]:
cluster_manager.connect_vertices(i=i, j=j, optimize=True)
cluster_manager.tidy()
#
# everything below is just to format the results
#
if (args == []):
for cluster in cluster_manager.clusters:
if (len(cluster) == 1): break
print(cluster)
else:
note = ("""\
Output of: cctbx/examples/find_sys_abs_equiv_space_groups.py %s
If you have to edit this table, please send email to: [email protected]
""" % args[0]).splitlines()
#
if (args == ["python"]):
print("space_group_numbers = [")
for line in note:
print(" #", line)
ci = cluster_manager.cluster_indices
cl = cluster_manager.clusters
for sgno in range(231):
cluster = list(cl[ci[sgno]])
cluster.remove(sgno)
if (len(cluster) == 0): s = "None"
else: s = str(tuple(cluster))
if (sgno == 230): comma = ""
else: comma = ","
print(" %s%s" % (s, comma))
print("]")
else:
print("""\
#ifndef CCTBX_SGTBX_SYS_ABS_EQUIV_H
#define CCTBX_SGTBX_SYS_ABS_EQUIV_H
namespace cctbx { namespace sgtbx { namespace sys_abs_equiv {
""")
data = []
ci = cluster_manager.cluster_indices
cl = cluster_manager.clusters
for line in note:
print(" //", line)
for sgno in range(231):
cluster = list(cl[ci[sgno]])
cluster.remove(sgno)
if (len(cluster) == 0):
data.append("0")
else:
cid = "data_%03d" % sgno
data.append(cid)
print(" static const unsigned %s[] = {%d, %s};" %
(cid, len(cluster), ", ".join(
[str(i) for i in cluster])))
print("")
print(" static const unsigned* space_group_numbers[] = {")
print(" ", ",\n ".join(data))
print("""\
};
}}}
#endif // GUARD""")
def run(args):
assert args in [[], ["python"], ["c++"]]
#
sgno_list_by_index_list_by_cs = {}
from cctbx import sgtbx
from cctbx import miller
for symbols in sgtbx.space_group_symbol_iterator():
psgi = sgtbx.space_group_info(symbols.universal_hermann_mauguin()) \
.primitive_setting()
p_indices = miller.index_generator(
space_group_type=psgi.type(),
anomalous_flag=False,
max_index=[4]*3).to_array()
# 4 is the smallest value leading to correct results; any larger
# value will work, too, but will make this procedure slower
p1_indices = miller.expand_to_p1_iselection(
space_group=psgi.group(),
anomalous_flag=False,
indices=p_indices,
build_iselection=False).indices
from cctbx.array_family import flex
sort_perm = flex.sort_permutation(
data=miller.index_span(p1_indices).pack(p1_indices))
p1_indices = p1_indices.select(sort_perm)
index_list = tuple(p1_indices)
sgno = psgi.type().number()
sgno_list_by_index_list = sgno_list_by_index_list_by_cs \
.setdefault(symbols.crystal_system(), {})
sgno_list_by_index_list.setdefault(index_list, []).append(sgno)
from scitbx.graph import tardy_tree
cluster_manager = tardy_tree.cluster_manager(n_vertices=231)
for cs,sgno_list_by_index_list in sgno_list_by_index_list_by_cs.items():
for sgno_list in sgno_list_by_index_list.values():
i = sgno_list[0]
for j in sgno_list[1:]:
cluster_manager.connect_vertices(i=i, j=j, optimize=True)
cluster_manager.tidy()
#
# everything below is just to format the results
#
if (args == []):
for cluster in cluster_manager.clusters:
if (len(cluster) == 1): break
print cluster
else:
note = ("""\
Output of: cctbx/examples/find_sys_abs_equiv_space_groups.py %s
If you have to edit this table, please send email to: [email protected]
""" % args[0]).splitlines()
#
if (args == ["python"]):
print "space_group_numbers = ["
for line in note:
print " #", line
ci = cluster_manager.cluster_indices
cl = cluster_manager.clusters
for sgno in xrange(231):
cluster = list(cl[ci[sgno]])
cluster.remove(sgno)
if (len(cluster) == 0): s = "None"
else: s = str(tuple(cluster))
if (sgno == 230): comma = ""
else: comma = ","
print " %s%s" % (s, comma)
print "]"
else:
print """\
#ifndef CCTBX_SGTBX_SYS_ABS_EQUIV_H
#define CCTBX_SGTBX_SYS_ABS_EQUIV_H
namespace cctbx { namespace sgtbx { namespace sys_abs_equiv {
"""
data = []
ci = cluster_manager.cluster_indices
cl = cluster_manager.clusters
for line in note:
print " //", line
for sgno in xrange(231):
cluster = list(cl[ci[sgno]])
cluster.remove(sgno)
if (len(cluster) == 0):
data.append("0")
else:
cid = "data_%03d" % sgno
data.append(cid)
print " static const unsigned %s[] = {%d, %s};" % (
cid, len(cluster), ", ".join([str(i) for i in cluster]))
print ""
print " static const unsigned* space_group_numbers[] = {"
print " ", ",\n ".join(data)
print """\
for info in syminfo_data:
# handle duplicates in syminfo.lib: pick the the one with ccp4 number
if info['xhm'] not in syminfo_dict or info['ccp4'] != 0:
syminfo_dict[info['xhm']] = info
print('''\
// This table was generated by tools/gen_sg_table.py.
// First 530 entries in the same order as in SgInfo, sgtbx and ITB.
// Note: spacegroup 68 has three duplicates with different H-M names.
''')
counter = 0
fmt = ' {%3d, %4d, %-12s, %s, %6s, %-16s, %-2d}, // %3d'
def quot(s):
return '"%s"' % s.replace('"', r'\"')
for s in sgtbx.space_group_symbol_iterator():
xhm = s.hermann_mauguin()
ext = ' 0'
if s.extension() != '\0':
xhm += ':%s' % s.extension()
ext = "'%c'" % s.extension()
info = syminfo_dict.pop(xhm)
assert info['number'] == s.number()
cctbx_sg = sgtbx.space_group(s.hall())
cctbx_info = sgtbx.space_group_info(group=cctbx_sg)
from_ref, basisop_idx = get_basisop(cctbx_info)
assert from_ref == info['basisop'], (from_ref, info['basisop'])
if gemmi:
assert (set(gemmi.symops_from_hall(s.hall())) ==
set(gemmi.symops_from_hall(info['hall']))), xhm
print(fmt % (s.number(), info['ccp4'], quot(s.hermann_mauguin()),
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_with_sgtbx(self):
if sgtbx is None:
return
for s in sgtbx.space_group_symbol_iterator():
self.compare_hall_symops_with_sgtbx(s.hall())
self.compare_hall_symops_with_sgtbx('C -4 -2b', existing_group=False)
def exercise_crystal_symmetry_utils():
as_rem = iotbx.cns.crystal_symmetry_utils.crystal_symmetry_as_sg_uc
as_inp = iotbx.cns.crystal_symmetry_utils.crystal_symmetry_as_cns_inp_defines
crystal_symmetry = crystal.symmetry(unit_cell=None, space_group_info=None)
sg_uc = as_rem(crystal_symmetry=crystal_symmetry)
assert sg_uc == "sg=None a=None b=None c=None alpha=None beta=None gamma=None"
sg_uc = as_inp(crystal_symmetry=crystal_symmetry)
assert not show_diff("\n".join(sg_uc), """\
{===>} sg="None";
{===>} a=None;
{===>} b=None;
{===>} c=None;
{===>} alpha=None;
{===>} beta=None;
{===>} gamma=None;""")
#
crystal_symmetry = crystal.symmetry(
unit_cell=(3,4,5,89,87,93),
space_group_info=None)
sg_uc = as_rem(crystal_symmetry=crystal_symmetry)
assert sg_uc == "sg=None a=3 b=4 c=5 alpha=89 beta=87 gamma=93"
sg_uc = as_inp(crystal_symmetry=crystal_symmetry)
assert not show_diff("\n".join(sg_uc), """\
{===>} sg="None";
{===>} a=3;
{===>} b=4;
{===>} c=5;
{===>} alpha=89;
{===>} beta=87;
{===>} gamma=93;""")
#
crystal_symmetry = crystal.symmetry(
unit_cell=None,
space_group_symbol=19)
sg_uc = as_rem(crystal_symmetry=crystal_symmetry)
assert sg_uc == \
"sg=P2(1)2(1)2(1) a=None b=None c=None alpha=None beta=None gamma=None"
sg_uc = as_inp(crystal_symmetry=crystal_symmetry)
assert not show_diff("\n".join(sg_uc), """\
{===>} sg="P2(1)2(1)2(1)";
{===>} a=None;
{===>} b=None;
{===>} c=None;
{===>} alpha=None;
{===>} beta=None;
{===>} gamma=None;""")
#
for symbols in sgtbx.space_group_symbol_iterator():
cs1 = sgtbx.space_group_info(
group=sgtbx.space_group(symbols)).any_compatible_crystal_symmetry(
volume=1000)
sg_uc = as_rem(crystal_symmetry=cs1)
m = re.match(iotbx.cns.crystal_symmetry_utils.re_sg_uc, sg_uc)
assert m is not None
cs2 = iotbx.cns.crystal_symmetry_utils.crystal_symmetry_from_re_match(m=m)
assert cs1.is_similar_symmetry(cs2)
#
sg_uc = as_inp(crystal_symmetry=cs1)
sio = StringIO()
print >> sio, "\n".join(sg_uc)
sio = StringIO(sio.getvalue())
cs2 = iotbx.cns.crystal_symmetry_from_inp.extract_from(file=sio)
assert cs1.is_similar_symmetry(cs2)
#
uc_sg = """\
a= 82.901 b= 82.901 c= 364.175 alpha= 90 beta= 90 gamma= 120 sg= P6(5)22"""
m = re.match(iotbx.cns.crystal_symmetry_utils.re_uc_sg, uc_sg)
cs = iotbx.cns.crystal_symmetry_utils.crystal_symmetry_from_re_match(
m=m, i_uc=1, i_sg=7)
assert cs is not None
assert str(cs.unit_cell()) == "(82.901, 82.901, 364.175, 90, 90, 120)"
assert str(cs.space_group().info()) == "P 65 2 2"
def exercise_crystal_symmetry_utils():
as_rem = iotbx.cns.crystal_symmetry_utils.crystal_symmetry_as_sg_uc
as_inp = iotbx.cns.crystal_symmetry_utils.crystal_symmetry_as_cns_inp_defines
crystal_symmetry = crystal.symmetry(unit_cell=None, space_group_info=None)
sg_uc = as_rem(crystal_symmetry=crystal_symmetry)
assert sg_uc == "sg=None a=None b=None c=None alpha=None beta=None gamma=None"
sg_uc = as_inp(crystal_symmetry=crystal_symmetry)
assert not show_diff(
"\n".join(sg_uc), """\
{===>} sg="None";
{===>} a=None;
{===>} b=None;
{===>} c=None;
{===>} alpha=None;
{===>} beta=None;
{===>} gamma=None;""")
#
crystal_symmetry = crystal.symmetry(unit_cell=(3, 4, 5, 89, 87, 93),
space_group_info=None)
sg_uc = as_rem(crystal_symmetry=crystal_symmetry)
assert sg_uc == "sg=None a=3 b=4 c=5 alpha=89 beta=87 gamma=93"
sg_uc = as_inp(crystal_symmetry=crystal_symmetry)
assert not show_diff(
"\n".join(sg_uc), """\
{===>} sg="None";
{===>} a=3;
{===>} b=4;
{===>} c=5;
{===>} alpha=89;
{===>} beta=87;
{===>} gamma=93;""")
#
crystal_symmetry = crystal.symmetry(unit_cell=None, space_group_symbol=19)
sg_uc = as_rem(crystal_symmetry=crystal_symmetry)
assert sg_uc == \
"sg=P2(1)2(1)2(1) a=None b=None c=None alpha=None beta=None gamma=None"
sg_uc = as_inp(crystal_symmetry=crystal_symmetry)
assert not show_diff(
"\n".join(sg_uc), """\
{===>} sg="P2(1)2(1)2(1)";
{===>} a=None;
{===>} b=None;
{===>} c=None;
{===>} alpha=None;
{===>} beta=None;
{===>} gamma=None;""")
#
for symbols in sgtbx.space_group_symbol_iterator():
cs1 = sgtbx.space_group_info(
group=sgtbx.space_group(symbols)).any_compatible_crystal_symmetry(
volume=1000)
sg_uc = as_rem(crystal_symmetry=cs1)
m = re.match(iotbx.cns.crystal_symmetry_utils.re_sg_uc, sg_uc)
assert m is not None
cs2 = iotbx.cns.crystal_symmetry_utils.crystal_symmetry_from_re_match(
m=m)
assert cs1.is_similar_symmetry(cs2)
#
sg_uc = as_inp(crystal_symmetry=cs1)
sio = StringIO()
print >> sio, "\n".join(sg_uc)
sio = StringIO(sio.getvalue())
cs2 = iotbx.cns.crystal_symmetry_from_inp.extract_from(file=sio)
assert cs1.is_similar_symmetry(cs2)
#
uc_sg = """\
a= 82.901 b= 82.901 c= 364.175 alpha= 90 beta= 90 gamma= 120 sg= P6(5)22"""
m = re.match(iotbx.cns.crystal_symmetry_utils.re_uc_sg, uc_sg)
cs = iotbx.cns.crystal_symmetry_utils.crystal_symmetry_from_re_match(
m=m, i_uc=1, i_sg=7)
assert cs is not None
assert str(cs.unit_cell()) == "(82.901, 82.901, 364.175, 90, 90, 120)"
assert str(cs.space_group().info()) == "P 65 2 2"
