def show_cpp(sg, f):
asu = reference_table.get_asu(sg)
func = "asu_%03d" % sg
print >> f, "facet_collection::pointer ", func, "() // Hall: ", asu.hall_symbol
print >> f, "{\n return facet_collection_asu("
out_cpp(asu, f)
print >> f, " );\n}\n"
return func
def direct_space_asu(self):
from cctbx.sgtbx.direct_space_asu import reference_table
cache = self._space_group_info_cache
if (not hasattr(cache, "_direct_space_asu")):
reference_asu = reference_table.get_asu(self.type().number())
cache._direct_space_asu = reference_asu.change_basis(
self.change_of_basis_op_to_reference_setting().inverse())
return cache._direct_space_asu
def direct_space_asu(self):
from cctbx.sgtbx.direct_space_asu import reference_table
cache = self._space_group_info_cache
if (not hasattr(cache, "_direct_space_asu")):
reference_asu = reference_table.get_asu(self.type().number())
cache._direct_space_asu = reference_asu.change_basis(
self.change_of_basis_op_to_reference_setting().inverse())
return cache._direct_space_asu
def show_cpp(sg, f):
asu = reference_table.get_asu(sg)
func = "asu_%03d" % sg
print >> f, "facet_collection::pointer ", func, "() // Hall: ", asu.hall_symbol
print >> f, "{\n return facet_collection_asu("
out_cpp(asu, f)
print >> f, " );\n}\n"
return func
def exercise_reference_table():
for space_group_number in xrange(1, 230 + 1):
space_group_info = sgtbx.space_group_info(number=space_group_number)
asu = reference_table.get_asu(space_group_number)
assert sgtbx.space_group(asu.hall_symbol) == space_group_info.group()
#
for space_group_number in xrange(1, 230 + 1):
asu = reference_table.get_asu(space_group_number)
n_long_cuts = 0
for cut in asu.cuts:
s = str(cut)
have_long_cut = (s.find("cut") >= 0)
if (space_group_number != 213):
assert not have_long_cut
elif (have_long_cut):
n_long_cuts += 1
if (space_group_number == 213):
assert n_long_cuts == 4 # done with change_basis
def exercise_reference_table():
for space_group_number in xrange(1,230+1):
space_group_info = sgtbx.space_group_info(number=space_group_number)
asu = reference_table.get_asu(space_group_number)
assert sgtbx.space_group(asu.hall_symbol) == space_group_info.group()
#
for space_group_number in xrange(1,230+1):
asu = reference_table.get_asu(space_group_number)
n_long_cuts = 0
for cut in asu.cuts:
s = str(cut)
have_long_cut = (s.find("cut") >= 0)
if (space_group_number != 213):
assert not have_long_cut
elif (have_long_cut):
n_long_cuts += 1
if (space_group_number == 213):
assert n_long_cuts == 4 # done with change_basis
def run():
exercise_reference_table()
for space_group_number in range(1,230+1):
asu = reference_table.get_asu(space_group_number)
exercise_shape_vertices(asu=asu, unit_cell=None)
debug_utils.parse_options_loop_space_groups(
sys.argv[1:], run_call_back, show_cpu_times=False)
exercise_is_simple_interaction()
exercise_non_crystallographic_asu_mappings()
print(format_cpu_times())
def run():
exercise_reference_table()
for space_group_number in xrange(1,230+1):
asu = reference_table.get_asu(space_group_number)
exercise_shape_vertices(asu=asu, unit_cell=None)
debug_utils.parse_options_loop_space_groups(
sys.argv[1:], run_call_back, show_cpu_times=False)
exercise_is_simple_interaction()
exercise_non_crystallographic_asu_mappings()
print format_cpu_times()
def exercise_float_asu(space_group_info, n_grid=6):
unit_cell = space_group_info.any_compatible_unit_cell(volume=1000)
ref_asu = reference_table.get_asu(space_group_info.type().number())
exercise_cut_planes(ref_asu.cuts)
inp_asu = space_group_info.direct_space_asu()
assert sgtbx.space_group(inp_asu.hall_symbol) == space_group_info.group()
exercise_cut_planes(inp_asu.cuts)
exercise_shape_vertices(inp_asu, unit_cell)
float_asu = inp_asu.add_buffer(unit_cell=unit_cell, thickness=0.001)
cb_mx_ref_inp = space_group_info.type().cb_op().c_inv().as_rational()
n = n_grid
for ref_n in flex.nested_loop((-n // 2, -n // 2, -n // 2), (n, n, n),
False):
# check correctness of space_group_info.direct_space_asu()
ref_r = matrix.col([rational.int(g, n) for g in ref_n])
inp_r = cb_mx_ref_inp * ref_r
assert ref_asu.is_inside(ref_r.elems) == inp_asu.is_inside(inp_r.elems)
# check correctness of cut_plane.add_buffer()
inp_r = inp_r.elems
inp_f = [float(r) for r in inp_r]
for cut in inp_asu.cuts:
r_cut = cut.strip()
r_inside = r_cut.is_inside(inp_r)
for buffer_thickness in [0.001, 1, -1][:1]:
f_cut = cut.as_float_cut_plane().add_buffer(
unit_cell=unit_cell, thickness=buffer_thickness)
f_inside = f_cut.is_inside(inp_f)
if (buffer_thickness < 0):
if (r_inside != f_inside):
assert r_inside
elif (buffer_thickness < 0.01):
assert r_inside == f_inside
elif (r_inside != f_inside):
assert f_inside
# check correctness of float_asu.add_buffer()
assert float_asu.is_inside(inp_f) == inp_asu.shape_only().is_inside(
inp_r)
asu_with_metric = inp_asu.define_metric(unit_cell)
assert asu_with_metric.hall_symbol is inp_asu.hall_symbol
assert len(asu_with_metric.cuts) == len(inp_asu.cuts)
assert asu_with_metric.unit_cell is unit_cell
asu_tight = asu_with_metric.as_float_asu()
asu_buffer = asu_with_metric.add_buffer(thickness=2)
asu_shrunk = asu_with_metric.add_buffer(relative_thickness=-1.e-5)
vertices = facet_analysis.shape_vertices(inp_asu)
for vertex in vertices:
assert inp_asu.shape_only().is_inside(vertex)
for vertex in vertices:
assert asu_tight.is_inside(matrix.col(vertex).as_float().elems)
for vertex in vertices:
assert asu_buffer.is_inside(matrix.col(vertex).as_float().elems)
for vertex in vertices:
assert not asu_shrunk.is_inside(matrix.col(vertex).as_float().elems)
def exercise_float_asu(space_group_info, n_grid=6):
unit_cell = space_group_info.any_compatible_unit_cell(volume=1000)
ref_asu = reference_table.get_asu(space_group_info.type().number())
exercise_cut_planes(ref_asu.cuts)
inp_asu = space_group_info.direct_space_asu()
assert sgtbx.space_group(inp_asu.hall_symbol) == space_group_info.group()
exercise_cut_planes(inp_asu.cuts)
exercise_shape_vertices(inp_asu, unit_cell)
float_asu = inp_asu.add_buffer(unit_cell=unit_cell, thickness=0.001)
cb_mx_ref_inp = space_group_info.type().cb_op().c_inv().as_rational()
n = n_grid
for ref_n in flex.nested_loop((-n//2,-n//2,-n//2),(n,n,n),False):
# check correctness of space_group_info.direct_space_asu()
ref_r = matrix.col([rational.int(g,n) for g in ref_n])
inp_r = cb_mx_ref_inp * ref_r
assert ref_asu.is_inside(ref_r.elems) == inp_asu.is_inside(inp_r.elems)
# check correctness of cut_plane.add_buffer()
inp_r = inp_r.elems
inp_f = [float(r) for r in inp_r]
for cut in inp_asu.cuts:
r_cut = cut.strip()
r_inside = r_cut.is_inside(inp_r)
for buffer_thickness in [0.001, 1, -1][:1]:
f_cut = cut.as_float_cut_plane().add_buffer(
unit_cell=unit_cell,
thickness=buffer_thickness)
f_inside = f_cut.is_inside(inp_f)
if (buffer_thickness < 0):
if (r_inside != f_inside):
assert r_inside
elif (buffer_thickness < 0.01):
assert r_inside == f_inside
elif (r_inside != f_inside):
assert f_inside
# check correctness of float_asu.add_buffer()
assert float_asu.is_inside(inp_f) == inp_asu.shape_only().is_inside(inp_r)
asu_with_metric = inp_asu.define_metric(unit_cell)
assert asu_with_metric.hall_symbol is inp_asu.hall_symbol
assert len(asu_with_metric.cuts) == len(inp_asu.cuts)
assert asu_with_metric.unit_cell is unit_cell
asu_tight = asu_with_metric.as_float_asu()
asu_buffer = asu_with_metric.add_buffer(thickness=2)
asu_shrunk = asu_with_metric.add_buffer(relative_thickness=-1.e-5)
vertices = facet_analysis.shape_vertices(inp_asu)
for vertex in vertices:
assert inp_asu.shape_only().is_inside(vertex)
for vertex in vertices:
assert asu_tight.is_inside(matrix.col(vertex).as_float().elems)
for vertex in vertices:
assert asu_buffer.is_inside(matrix.col(vertex).as_float().elems)
for vertex in vertices:
assert not asu_shrunk.is_inside(matrix.col(vertex).as_float().elems)
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,
)
if (not flags.enantiomorphic):
test_all(gridding)
else:
flags.regular_args.extend([
str(i)
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()
