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)
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>")
unit_cell = uctbx.unit_cell(inp.ucparams)
unit_cell.show_parameters()
print()
if (inp.coor_type == "Fractional"):
print("Cartesian coordinates:")
else:
print("Fractional 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"):
c = unit_cell.orthogonalize(coordinates)
else:
c = unit_cell.fractionalize(coordinates)
print(skipped, "%.6g %.6g %.6g" % tuple(c))
print("</pre>")
def run(server_info, inp, status):
print "<pre>"
unit_cell = uctbx.unit_cell(inp.ucparams)
unit_cell.show_parameters()
print
if (inp.coor_type == "Fractional"):
print "Cartesian coordinates:"
else:
print "Fractional 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"):
c = unit_cell.orthogonalize(coordinates)
else:
c = unit_cell.fractionalize(coordinates)
print skipped, "%.6g %.6g %.6g" % tuple(c)
print "</pre>"
def run(server_info, inp, status):
print "<pre>"
unit_cell_old = uctbx.unit_cell(inp.ucparams_old)
print "Old symmetry:"
print " ",
unit_cell_old.show_parameters()
space_group_info_old = sgtbx.space_group_info(
symbol=inp.sgsymbol_old,
table_id=inp.convention_old)
print " ",
space_group_info_old.show_summary()
print
if (len(inp.sgsymbol_new.strip()) == 0):
space_group_info_new = space_group_info_old.reference_setting()
inp.convention_new = ""
else:
space_group_info_new = sgtbx.space_group_info(
symbol=inp.sgsymbol_new,
table_id=inp.convention_new)
print "New space group symbol:"
print " ",
space_group_info_new.show_summary()
print
if ( space_group_info_new.type().number()
!= space_group_info_old.type().number()):
print "Space group numbers are not equal!"
else:
c = space_group_info_new.type().cb_op().c_inv().multiply(
space_group_info_old.type().cb_op().c()).new_denominators(
sgtbx.cb_r_den, sgtbx.cb_t_den)
cb_op = sgtbx.change_of_basis_op(c)
print "Change-of-basis matrix:", cb_op.c()
print " Inverse:", cb_op.c_inv()
print
assert space_group_info_old.group().is_compatible_unit_cell(unit_cell_old)
unit_cell_new = unit_cell_old.change_basis(cb_op=cb_op)
print "New unit cell parameters:"
print " ",
unit_cell_new.show_parameters()
assert space_group_info_new.group().is_compatible_unit_cell(unit_cell_new)
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 = unit_cell_old.fractionalize(coordinates)
new_coordinates = cb_op(coordinates)
if (inp.coor_type != "Fractional"):
new_coordinates = unit_cell_new.orthogonalize(new_coordinates)
print skipped, "%.6g %.6g %.6g" % tuple(new_coordinates)
print "</pre>"
def run(server_info, inp, status):
print "<pre>"
unit_cell_old = uctbx.unit_cell(inp.ucparams_old)
print "Old symmetry:"
print " ",
unit_cell_old.show_parameters()
space_group_info_old = sgtbx.space_group_info(symbol=inp.sgsymbol_old,
table_id=inp.convention_old)
print " ",
space_group_info_old.show_summary()
print
if (len(inp.sgsymbol_new.strip()) == 0):
space_group_info_new = space_group_info_old.reference_setting()
inp.convention_new = ""
else:
space_group_info_new = sgtbx.space_group_info(
symbol=inp.sgsymbol_new, table_id=inp.convention_new)
print "New space group symbol:"
print " ",
space_group_info_new.show_summary()
print
if (space_group_info_new.type().number() !=
space_group_info_old.type().number()):
print "Space group numbers are not equal!"
else:
c = space_group_info_new.type().cb_op().c_inv().multiply(
space_group_info_old.type().cb_op().c()).new_denominators(
sgtbx.cb_r_den, sgtbx.cb_t_den)
cb_op = sgtbx.change_of_basis_op(c)
print "Change-of-basis matrix:", cb_op.c()
print " Inverse:", cb_op.c_inv()
print
assert space_group_info_old.group().is_compatible_unit_cell(
unit_cell_old)
unit_cell_new = unit_cell_old.change_basis(cb_op=cb_op)
print "New unit cell parameters:"
print " ",
unit_cell_new.show_parameters()
assert space_group_info_new.group().is_compatible_unit_cell(
unit_cell_new)
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 = unit_cell_old.fractionalize(coordinates)
new_coordinates = cb_op(coordinates)
if (inp.coor_type != "Fractional"):
new_coordinates = unit_cell_new.orthogonalize(new_coordinates)
print skipped, "%.6g %.6g %.6g" % tuple(new_coordinates)
print "</pre>"