def run(http_server_name=None, html_subdir="asu_gallery"):
parser = OptionParser(
usage="usage: python jv_asu.py [options] [numbers...]")
parser.add_option("-s",
"--server",
action="store",
type="string",
help="network name of http server",
metavar="NAME")
parser.add_option("-p", "--plane_group", action="store_true")
options, args = parser.parse_args()
if (options.server is not None):
http_server_name = options.server
if (not os.path.isdir(html_subdir)):
os.makedirs(html_subdir)
jv_index.write_html(open("%s/index.html" % html_subdir, "w"))
guide_to_notation.write_html(
open("%s/guide_to_notation.html" % html_subdir, "w"))
if (len(args) == 0):
if (options.plane_group):
args = ["1-17"]
else:
args = ["1-230"]
for arg in args:
numbers = [int(n) for n in arg.split('-')]
assert len(numbers) in (1, 2)
if (len(numbers) == 1): numbers *= 2
for group_type_number in xrange(numbers[0], numbers[1] + 1):
if (options.plane_group):
print "Plane group number:", group_type_number
from cctbx.sgtbx.direct_space_asu import plane_group_reference_table
asu = plane_group_reference_table.get_asu(group_type_number)
group_type_number *= -1
else:
print "Space group number:", group_type_number
asu = reference_table.get_asu(group_type_number)
for colored_grid_points in [None, []]:
asu_as_jvx(group_type_number=group_type_number,
asu=asu,
colored_grid_points=colored_grid_points,
http_server_name=http_server_name,
html_subdir=html_subdir)
def run(http_server_name=None, html_subdir="asu_gallery"):
parser = OptionParser(usage="usage: python jv_asu.py [options] [numbers...]")
parser.add_option(
"-s", "--server", action="store", type="string", help="network name of http server", metavar="NAME"
)
parser.add_option("-p", "--plane_group", action="store_true")
options, args = parser.parse_args()
if options.server is not None:
http_server_name = options.server
if not os.path.isdir(html_subdir):
os.makedirs(html_subdir)
jv_index.write_html(open("%s/index.html" % html_subdir, "w"))
guide_to_notation.write_html(open("%s/guide_to_notation.html" % html_subdir, "w"))
if len(args) == 0:
if options.plane_group:
args = ["1-17"]
else:
args = ["1-230"]
for arg in args:
numbers = [int(n) for n in arg.split("-")]
assert len(numbers) in (1, 2)
if len(numbers) == 1:
numbers *= 2
for group_type_number in xrange(numbers[0], numbers[1] + 1):
if options.plane_group:
print "Plane group number:", group_type_number
from cctbx.sgtbx.direct_space_asu import plane_group_reference_table
asu = plane_group_reference_table.get_asu(group_type_number)
group_type_number *= -1
else:
print "Space group number:", group_type_number
asu = reference_table.get_asu(group_type_number)
for colored_grid_points in [None, []]:
asu_as_jvx(
group_type_number=group_type_number,
asu=asu,
colored_grid_points=colored_grid_points,
http_server_name=http_server_name,
html_subdir=html_subdir,
)
for i in (76, 78, 91, 95, 92, 96, 144, 145, 151, 153, 152, 154,
169, 170, 171, 172, 178, 179, 180, 181, 212, 213)
])
if (len(flags.regular_args) > 1):
for arg in flags.regular_args[1:]:
numbers = [int(n) for n in arg.split('-')]
assert len(numbers) in (1, 2)
if (len(numbers) == 1): numbers *= 2
for group_type_number in range(numbers[0], numbers[1] + 1):
if (not flags.plane_group):
asu_original = reference_table.get_asu(group_type_number)
assert sgtbx.space_group(asu_original.hall_symbol) \
== sgtbx.space_group_info(number=group_type_number).group()
else:
from cctbx.sgtbx.direct_space_asu import plane_group_reference_table
asu_original = plane_group_reference_table.get_asu(
point_group_number=group_type_number)
print("Plane group number:", group_type_number)
group_type_number *= -1
asu = asu_original
if (flags.strip or flags.strip_polygons):
asu = asu_original.shape_only()
print("Writing asu_gallery files")
jv_asu.asu_as_jvx(group_type_number, asu)
if (flags.strip_grid):
asu = asu_original.shape_only()
if (flags.show_asu):
asu.show_comprehensive_summary()
check_asu(group_type_number=group_type_number,
asu=asu,
n=gridding,
is_stripped_asu=(flags.strip or flags.strip_grid),