def run(server_info, inp, status):
print "<pre>"
io_utils.show_input_symbol(inp.sgsymbol, inp.convention)
crystal_symmetry = crystal.symmetry(
unit_cell=uctbx.unit_cell(inp.ucparams),
space_group_info=sgtbx.space_group_info(symbol=inp.sgsymbol,
table_id=inp.convention))
crystal_symmetry.show_summary()
print
change_of_hand_op \
= crystal_symmetry.space_group_info().type().change_of_hand_op()
print "Change-of-hand matrix:", change_of_hand_op.c()
print " Inverse:", change_of_hand_op.c_inv()
print
print inp.coor_type, "coordinates:"
print
skip_columns = io_utils.interpret_skip_columns(inp.skip_columns)
for line in inp.coordinates:
skipped, coordinates = io_utils.interpret_coordinate_line(
line, skip_columns)
if (inp.coor_type != "Fractional"):
coordinates = crystal_symmetry.unit_cell().fractionalize(
coordinates)
flipped_coordinates = change_of_hand_op(coordinates)
if (inp.coor_type != "Fractional"):
flipped_coordinates \
= crystal_symmetry.unit_cell().orthogonalize(flipped_coordinates)
print skipped, "%.6g %.6g %.6g" % tuple(flipped_coordinates)
print "</pre>"
def run(server_info, inp, status):
print "<pre>"
# check input to prevent XSS
try:
unit_cell = uctbx.unit_cell(inp.ucparams)
space_group_info = sgtbx.space_group_info(symbol=inp.sgsymbol,
table_id=inp.convention)
except Exception:
print "Please check your inputs."
print "</pre>"
return
io_utils.show_input_symbol(inp.sgsymbol, inp.convention)
special_position_settings = crystal.special_position_settings(
crystal.symmetry(unit_cell=uctbx.unit_cell(inp.ucparams),
space_group_info=sgtbx.space_group_info(
symbol=inp.sgsymbol, table_id=inp.convention)),
min_distance_sym_equiv=float(inp.min_distance_sym_equiv))
special_position_settings.show_summary()
print "Minimum distance between symmetrically equivalent sites:",
print special_position_settings.min_distance_sym_equiv()
print
skip_columns = io_utils.interpret_skip_columns(inp.skip_columns)
wyckoff_table = special_position_settings.space_group_info().wyckoff_table(
)
unit_cell = special_position_settings.unit_cell()
print "</pre><table border=2 cellpadding=2>"
status.in_table = True
print "<tr>"
if (skip_columns): print "<th>"
print "<th colspan=3>" + inp.coor_type + " coordinates"
print "<th>Multiplicity"
print "<th>Wyckoff letter"
print "<th>Site symmetry<br>point group type"
print "<th>Special position operator"
print "</tr>"
for line in inp.coordinates:
skipped, coordinates = io_utils.interpret_coordinate_line(
line, skip_columns)
if (inp.coor_type != "Fractional"):
coordinates = unit_cell.fractionalize(coordinates)
site_symmetry = special_position_settings.site_symmetry(coordinates)
exact_site = site_symmetry.exact_site()
if (inp.coor_type != "Fractional"):
exact_site = unit_cell.orthogonalize(exact_site)
wyckoff_mapping = wyckoff_table.mapping(site_symmetry)
print "<tr>"
if (skip_columns): print "<td>", skipped
for x in exact_site:
print "<td><tt>%.6g</tt>" % (x, )
print "<td align=center>", wyckoff_mapping.position().multiplicity()
print "<td align=center>", wyckoff_mapping.position().letter()
print "<td align=center>", site_symmetry.point_group_type()
print "<td><tt>" + str(site_symmetry.special_op_simplified()) + "</tt>"
print "</tr>"
print "</table><pre>"
status.in_table = False
print "</pre>"
def run(server_info, inp, status):
print "<pre>"
io_utils.show_input_symbol(inp.sgsymbol, inp.convention)
crystal_symmetry = crystal.symmetry(
unit_cell=uctbx.unit_cell(inp.ucparams),
space_group_info=sgtbx.space_group_info(
symbol=inp.sgsymbol,
table_id=inp.convention))
crystal_symmetry.show_summary()
print
change_of_hand_op \
= crystal_symmetry.space_group_info().type().change_of_hand_op()
print "Change-of-hand matrix:", change_of_hand_op.c()
print " Inverse:", change_of_hand_op.c_inv()
print
print inp.coor_type, "coordinates:"
print
skip_columns = io_utils.interpret_skip_columns(inp.skip_columns)
for line in inp.coordinates:
skipped, coordinates = io_utils.interpret_coordinate_line(line,skip_columns)
if (inp.coor_type != "Fractional"):
coordinates = crystal_symmetry.unit_cell().fractionalize(coordinates)
flipped_coordinates = change_of_hand_op(coordinates)
if (inp.coor_type != "Fractional"):
flipped_coordinates \
= crystal_symmetry.unit_cell().orthogonalize(flipped_coordinates)
print skipped, "%.6g %.6g %.6g" % tuple(flipped_coordinates)
print "</pre>"
def run(server_info, inp, status):
print "<pre>"
io_utils.show_input_symbol(inp.sgsymbol, inp.convention)
symbols_inp = None
lookup_symbol = inp.sgsymbol
if (lookup_symbol == ""): lookup_symbol = "P 1"
if (inp.convention == "Hall"):
hall_symbol = lookup_symbol
else:
symbols_inp = sgtbx.space_group_symbols(lookup_symbol, inp.convention)
hall_symbol = symbols_inp.hall()
if (symbols_inp.number() == 0):
symbols_inp = None
inp.convention = "Hall"
else:
print "Result of symbol lookup:"
show_symbols(symbols_inp)
print
try:
ps = sgtbx.parse_string(hall_symbol)
sg = sgtbx.space_group(ps)
except RuntimeError, e:
print "-->" + ps.string() + "<--"
print ("-" * (ps.where() + 3)) + "^"
raise
def run(server_info, inp, status):
print "<pre>"
io_utils.show_input_symbol(inp.sgsymbol, inp.convention)
special_position_settings = crystal.special_position_settings(
crystal.symmetry(
unit_cell=uctbx.unit_cell(inp.ucparams),
space_group_info=sgtbx.space_group_info(
symbol=inp.sgsymbol,
table_id=inp.convention)),
min_distance_sym_equiv=float(inp.min_distance_sym_equiv))
special_position_settings.show_summary()
print "Minimum distance between symmetrically equivalent sites:",
print special_position_settings.min_distance_sym_equiv()
print
skip_columns = io_utils.interpret_skip_columns(inp.skip_columns)
wyckoff_table=special_position_settings.space_group_info().wyckoff_table()
unit_cell = special_position_settings.unit_cell()
print "</pre><table border=2 cellpadding=2>"
status.in_table = True
print "<tr>"
if (skip_columns): print "<th>"
print "<th colspan=3>" + inp.coor_type + " coordinates"
print "<th>Multiplicity"
print "<th>Wyckoff letter"
print "<th>Site symmetry<br>point group type"
print "<th>Special position operator"
print "</tr>"
for line in inp.coordinates:
skipped, coordinates = io_utils.interpret_coordinate_line(line,skip_columns)
if (inp.coor_type != "Fractional"):
coordinates = unit_cell.fractionalize(coordinates)
site_symmetry = special_position_settings.site_symmetry(coordinates)
exact_site = site_symmetry.exact_site()
if (inp.coor_type != "Fractional"):
exact_site = unit_cell.orthogonalize(exact_site)
wyckoff_mapping = wyckoff_table.mapping(site_symmetry)
print "<tr>"
if (skip_columns): print "<td>", skipped
for x in exact_site: print "<td><tt>%.6g</tt>" % (x,)
print "<td align=center>", wyckoff_mapping.position().multiplicity()
print "<td align=center>", wyckoff_mapping.position().letter()
print "<td align=center>", site_symmetry.point_group_type()
print "<td><tt>" + str(site_symmetry.special_op_simplified()) + "</tt>"
print "</tr>"
print "</table><pre>"
status.in_table = False
print "</pre>"
symbols_inp = None
inp.convention = "Hall"
else:
print "Result of symbol lookup:"
show_symbols(symbols_inp)
print
try:
ps = sgtbx.parse_string(hall_symbol)
sg = sgtbx.space_group(ps)
except RuntimeError, e:
print "-->" + ps.string() + "<--"
print ("-" * (ps.where() + 3)) + "^"
raise
io_utils.show_input_symbol(inp.sgsymbol, inp.convention)
if (len(inp.shelx_latt) != 0):
for n_fld in inp.shelx_latt:
expand_shelx_latt(sg, n_fld)
if (len(inp.symxyz) != 0):
print "Addition of symmetry operations:"
print "</pre><table border=2 cellpadding=2>"
status.in_table = True
rt_mx_analysis_header()
for s in inp.symxyz:
ps = sgtbx.parse_string(s)
try:
s = sgtbx.rt_mx(ps)
except RuntimeError, e:
print "</table><pre>"
def run(server_info, inp, status):
print("<pre>")
symbols_inp = None
lookup_symbol = inp.sgsymbol
if (lookup_symbol == ""): lookup_symbol = "P 1"
if (inp.convention == "Hall"):
hall_symbol = lookup_symbol
else:
symbols_inp = sgtbx.space_group_symbols(lookup_symbol, inp.convention)
hall_symbol = symbols_inp.hall()
if (symbols_inp.number() == 0):
symbols_inp = None
inp.convention = "Hall"
else:
print("Result of symbol lookup:")
show_symbols(symbols_inp)
print()
try:
ps = sgtbx.parse_string(hall_symbol)
sg = sgtbx.space_group(ps)
except RuntimeError as e:
print("-->" + ps.string() + "<--")
print(("-" * (ps.where() + 3)) + "^")
raise
io_utils.show_input_symbol(inp.sgsymbol, inp.convention)
if (len(inp.shelx_latt) != 0):
for n_fld in inp.shelx_latt:
expand_shelx_latt(sg, n_fld)
if (len(inp.symxyz) != 0):
print("Addition of symmetry operations:")
print("</pre><table border=2 cellpadding=2>")
status.in_table = True
rt_mx_analysis_header()
for s in inp.symxyz:
ps = sgtbx.parse_string(s)
try:
s = sgtbx.rt_mx(ps)
except RuntimeError as e:
print("</table><pre>")
status.in_table = False
print("-->" + ps.string() + "<--")
print(("-" * (ps.where() + 3)) + "^")
raise
rt_mx_analysis(s)
sg.expand_smx(s)
print("</table><pre>")
status.in_table = False
print()
sg_type = sg.type()
show_group_generic(sg_type, status)
if (inp.convention == "Hall" or len(inp.shelx_latt) != 0
or len(inp.symxyz) != 0):
symbols_match = sg.match_tabulated_settings()
if (symbols_match.number() != 0):
if (symbols_inp is None or symbols_inp.universal_hermann_mauguin()
!= symbols_match.universal_hermann_mauguin()):
print("Symmetry operations match:")
show_symbols(symbols_match)
print()
else:
print("Additional symmetry operations are redundant.")
print()
else:
print("Space group number:", sg_type.number())
print("Conventional Hermann-Mauguin symbol:", \
sgtbx.space_group_symbols(sg_type.number()) \
.universal_hermann_mauguin())
print("Universal Hermann-Mauguin symbol:", \
sg_type.universal_hermann_mauguin_symbol())
print("Hall symbol:", sg_type.hall_symbol())
print("Change-of-basis matrix:", sg_type.cb_op().c())
print(" Inverse:", sg_type.cb_op().c_inv())
print()
wyckoff_table = sgtbx.wyckoff_table(sg_type)
print("List of Wyckoff positions:")
print("</pre><table border=2 cellpadding=2>")
status.in_table = True
print("<tr>")
print("<th>Wyckoff letter")
print("<th>Multiplicity")
print("<th>Site symmetry<br>point group type")
print("<th>Representative special position operator")
print("</tr>")
for i_position in range(wyckoff_table.size()):
position = wyckoff_table.position(i_position)
print("<tr>")
print("<td>%s<td>%d<td>%s<td><tt>%s</tt>" %
(position.letter(), position.multiplicity(),
position.point_group_type(),
str(position.special_op_simplified())))
print("</tr>")
print("</table><pre>")
status.in_table = False
print()
print("Harker planes:")
print("</pre><table border=2 cellpadding=2>")
status.in_table = True
print("<tr>")
print("<th>Algebraic")
print("<th>Normal vector")
print("<th>A point in the plane")
print("</tr>")
planes = harker.planes_fractional(sg)
for plane in planes.list:
print("<tr>")
print("<td><tt>%s</tt><td>%s<td>%s" %
(plane.algebraic(), str_ev(plane.n), str(plane.p)))
print("</tr>")
print("</table><pre>")
status.in_table = False
print()
print("Additional generators of Euclidean normalizer:")
ss = sgtbx.structure_seminvariants(sg)
ss_vm = ss.vectors_and_moduli()
print(" Number of structure-seminvariant vectors and moduli:", len(ss_vm))
if (len(ss_vm)):
print(" Vector Modulus")
for vm in ss_vm:
print(" ", vm.v, vm.m)
k2l = sg_type.addl_generators_of_euclidean_normalizer(True, False)
l2n = sg_type.addl_generators_of_euclidean_normalizer(False, True)
if (len(k2l)):
print(" Inversion through a centre at:", end=' ')
assert len(k2l) == 1
print(sgtbx.translation_part_info(k2l[0]).origin_shift())
if (len(l2n)):
print(" Further generators:")
print("</pre><table border=2 cellpadding=2>")
status.in_table = True
rt_mx_analysis_header()
for s in l2n:
rt_mx_analysis(s)
print("</table><pre>")
status.in_table = False
print()
print("Grid factors implied by symmetries:")
grid_sg = sg.gridding()
grid_ss = ss.gridding()
eucl_sg = sg_type.expand_addl_generators_of_euclidean_normalizer(
True, True)
grid_eucl = eucl_sg.refine_gridding(grid_ss)
print(" Space group:", grid_sg)
print(" Structure-seminvariant vectors and moduli:", grid_ss)
print(" Euclidean normalizer:", grid_eucl)
print()
print(" All points of a grid over the unit cell are mapped")
print(" exactly onto other grid points only if the factors")
print(" shown above are factors of the grid.")
print()
print("</pre>")
symbols_inp = None
inp.convention = "Hall"
else:
print "Result of symbol lookup:"
show_symbols(symbols_inp)
print
try:
ps = sgtbx.parse_string(hall_symbol)
sg = sgtbx.space_group(ps)
except RuntimeError, e:
print "-->" + ps.string() + "<--"
print("-" * (ps.where() + 3)) + "^"
raise
io_utils.show_input_symbol(inp.sgsymbol, inp.convention)
if (len(inp.shelx_latt) != 0):
for n_fld in inp.shelx_latt:
expand_shelx_latt(sg, n_fld)
if (len(inp.symxyz) != 0):
print "Addition of symmetry operations:"
print "</pre><table border=2 cellpadding=2>"
status.in_table = True
rt_mx_analysis_header()
for s in inp.symxyz:
ps = sgtbx.parse_string(s)
try:
s = sgtbx.rt_mx(ps)
except RuntimeError, e:
print "</table><pre>"
