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 exercise_shape_vertices(asu, unit_cell):
volume_asu = asu.shape_only()
asu_shape_vertices = asu.shape_vertices()
assert len(asu_shape_vertices) >= 4
facet_analysis_shape_vertices = facet_analysis.shape_vertices(asu)
assert len(asu_shape_vertices) == len(facet_analysis_shape_vertices)
asu_shape_vertices.sort()
facet_analysis_shape_vertices.sort()
assert asu_shape_vertices == facet_analysis_shape_vertices
for box_min, box_max in zip(
asu.box_min(shape_vertices=asu_shape_vertices),
asu.box_max(shape_vertices=asu_shape_vertices)):
assert box_min < box_max
if (unit_cell is None):
return
float_asu = asu.add_buffer(unit_cell=unit_cell, thickness=0)
asu_shrunk = float_asu.add_buffer(relative_thickness=-1.e-5)
mcs = asu.define_metric(unit_cell).minimum_covering_sphere()
center = matrix.col(mcs.center())
radius = mcs.radius()
n_near_sphere_surface = 0
for vertex in asu_shape_vertices:
assert volume_asu.is_inside(vertex)
float_vertex = [float(e) for e in vertex]
assert float_asu.is_inside(float_vertex)
assert not asu_shrunk.is_inside(float_vertex)
r = abs(matrix.col(unit_cell.orthogonalize(float_vertex)) - center)
assert r < radius + 1.e-5
if (radius - r < radius * 1.e-2):
n_near_sphere_surface += 1
assert n_near_sphere_surface >= 2
float_asu_shape_vertices = float_asu.shape_vertices()
assert len(float_asu_shape_vertices) >= len(asu_shape_vertices)
m_near_sphere_surface = 0
for vertex in float_asu_shape_vertices:
assert float_asu.is_inside(point=vertex)
assert not asu_shrunk.is_inside(vertex)
r = abs(matrix.col(unit_cell.orthogonalize(vertex)) - center)
assert r < radius + 1.e-5
if (radius - r < radius * 1.e-2):
m_near_sphere_surface += 1
assert m_near_sphere_surface >= n_near_sphere_surface
line_asu = copy.copy(asu)
line_asu.add_planes([(0, 0, 1), (1, 1, 1)], both_directions=True)
assert len(line_asu.cuts) == len(asu.cuts) + 4
assert line_asu.cuts[-2].n == (-line_asu.cuts[-1]).n
def exercise_shape_vertices(asu, unit_cell):
volume_asu = asu.shape_only()
asu_shape_vertices = asu.shape_vertices()
assert len(asu_shape_vertices) >= 4
facet_analysis_shape_vertices = facet_analysis.shape_vertices(asu)
assert len(asu_shape_vertices) == len(facet_analysis_shape_vertices)
asu_shape_vertices.sort()
facet_analysis_shape_vertices.sort()
assert asu_shape_vertices == facet_analysis_shape_vertices
for box_min,box_max in zip(asu.box_min(shape_vertices=asu_shape_vertices),
asu.box_max(shape_vertices=asu_shape_vertices)):
assert box_min < box_max
if (unit_cell is None):
return
float_asu = asu.add_buffer(unit_cell=unit_cell, thickness=0)
asu_shrunk = float_asu.add_buffer(relative_thickness=-1.e-5)
mcs = asu.define_metric(unit_cell).minimum_covering_sphere()
center = matrix.col(mcs.center())
radius = mcs.radius()
n_near_sphere_surface = 0
for vertex in asu_shape_vertices:
assert volume_asu.is_inside(vertex)
float_vertex = [float(e) for e in vertex]
assert float_asu.is_inside(float_vertex)
assert not asu_shrunk.is_inside(float_vertex)
r = abs(matrix.col(unit_cell.orthogonalize(float_vertex)) - center)
assert r < radius + 1.e-5
if (radius - r < radius * 1.e-2):
n_near_sphere_surface += 1
assert n_near_sphere_surface >= 2
float_asu_shape_vertices = float_asu.shape_vertices()
assert len(float_asu_shape_vertices) >= len(asu_shape_vertices)
m_near_sphere_surface = 0
for vertex in float_asu_shape_vertices:
assert float_asu.is_inside(point=vertex)
assert not asu_shrunk.is_inside(vertex)
r = abs(matrix.col(unit_cell.orthogonalize(vertex)) - center)
assert r < radius + 1.e-5
if (radius - r < radius * 1.e-2):
m_near_sphere_surface += 1
assert m_near_sphere_surface >= n_near_sphere_surface
line_asu = copy.copy(asu)
line_asu.add_planes([(0,0,1),(1,1,1)], both_directions=True)
assert len(line_asu.cuts) == len(asu.cuts) + 4
assert line_asu.cuts[-2].n == (-line_asu.cuts[-1]).n
def asu_as_jvx(group_type_number, asu, colored_grid_points=None,
http_server_name=None,
html_subdir="asu_gallery",
jars_url="http://%s/jv395/jars",
explore_symmetry_url=
"http://%s/cctbx/cctbx_web.cgi" \
+"?target_module=explore_symmetry&sgsymbol="):
if (http_server_name is None):
http_server_name = web_links.default_http_server_name
xy_plane_only = (group_type_number < 0)
space_group_info = sgtbx.space_group(asu.hall_symbol).info()
if (not xy_plane_only):
assert space_group_info.type().number() == group_type_number
list_of_polygons = facet_analysis.asu_polygons(asu)
all_edge_segments = facet_analysis.get_all_edge_segments(
asu, list_of_polygons)
all_vertices = facet_analysis.get_all_vertices(all_edge_segments)
unit_cell = space_group_info.any_compatible_unit_cell(volume=100)
ortho = orthogonalizer(unit_cell)
shrink_length = get_diagonal_extend(ortho, all_vertices) * 0.02
geometries = []
if (colored_grid_points is None):
for polygons in list_of_polygons:
for polygon, inclusive_flag in polygons:
def exclude():
for vertex in polygon:
if (vertex[0][2] != 0):
return True
return False
if (xy_plane_only and exclude()):
continue
vertices_cart = cartesian_polygon(ortho, polygon)
vertices_inside_cart = shrink_polygon(vertices_cart,
shrink_length)
points_int = jvx.pointSet()
g = jvx.geometry("facet",
backface=["hide", "show"][int(xy_plane_only)])
points_cart = g.points
points_cart.hide_points()
i = -1
for vertex in polygon:
i += 1
points_int.append(vertex[0])
points_cart.append(vertices_inside_cart[i])
faces = g.faces
point_indices = []
for vertex in polygon:
point_indices.append(points_int.index(vertex[0]))
faces.append(
jvx.face(point_indices, select_color(inclusive_flag)))
geometries.append(g)
geometries.append(
edge_geometry(ortho,
all_edge_segments,
shrink_length,
xy_plane_only=xy_plane_only))
geometries.append(
vertex_geometry(ortho, all_vertices, xy_plane_only=xy_plane_only))
else:
g = jvx.geometry("grid")
for frac in colored_grid_points:
if (xy_plane_only and frac.site[2] != 0): continue
g.points.append(jvx.point(ortho(frac.site), color=frac.color))
geometries.append(g)
if (colored_grid_points is None):
grid_label = ""
alternative_html_infix = "_grid"
alternative_label = "Grid view"
else:
grid_label = "_grid"
alternative_html_infix = ""
alternative_label = "Polygon view"
if (xy_plane_only): fmt = "asu_%02d%s"
else: fmt = "asu_%03d%s"
base_file_name = fmt % (abs(group_type_number), grid_label)
jvx_file_name = os.path.join(html_subdir, base_file_name + ".jvx")
jvx_in_html = base_file_name + ".jvx"
html_file_name = os.path.join(html_subdir, base_file_name + ".html")
prev_html = None
next_html = None
if (xy_plane_only):
fmt = "asu_%02d%s.html"
last_group_type_number = 17
else:
fmt = "asu_%03d%s.html"
last_group_type_number = 230
if (abs(group_type_number) > 1):
prev_html = fmt % (abs(group_type_number) - 1, grid_label)
else:
prev_html = fmt % (last_group_type_number, grid_label)
if (abs(group_type_number) < last_group_type_number):
next_html = fmt % (abs(group_type_number) + 1, grid_label)
else:
next_html = fmt % (1, grid_label)
alternative_html = fmt % (abs(group_type_number), alternative_html_infix)
if (colored_grid_points is None or len(colored_grid_points) > 0):
f = open(jvx_file_name, "w")
jvx.head(f)
unit_cell_geometry(ortho, xy_plane_only=xy_plane_only).jvx(f)
basis_vector_geometry(ortho, get_min_fractional(all_vertices)).jvx(f)
for g in geometries:
g.jvx(f)
jvx.tail(f)
f.close()
legend = []
l = legend.append
l("Surface area: green = inside the asymmetric unit, red = outside")
l("<br>")
l("Basis vectors: a = red, b = green, c = blue")
l("<p>")
shape_vertices = facet_analysis.shape_vertices(asu)
l("<table border=2 cellpadding=8>")
l("<tr valign=top>")
l("<td>")
remaining = []
for vertex in shape_vertices:
if (xy_plane_only and vertex[2] != 0): continue
remaining.append(vertex)
remaining.sort()
l("<pre>Number of vertices: %d" % len(remaining))
if (xy_plane_only):
j = -4
else:
j = -1
for vertex in remaining:
l(" " + str(vertex)[1:j])
l("</pre>")
l("</td>")
l("<td>")
remaining = []
for cut in asu.cuts:
if (xy_plane_only and cut.as_xyz() in ["z>=0", "z<1"]): continue
remaining.append(cut)
l("<pre>Number of faces: %d" % len(remaining))
for cut in remaining:
l(" " + cut.as_xyz())
l("</pre>")
l('<a href="guide_to_notation.html">[Guide to notation]</a>')
l("</td>")
l("<td>")
l("<pre>Geometric notation:")
for cut in remaining:
l(" " + str(cut))
l("</pre>")
l('<a href="http://scripts.iucr.org/cgi-bin/paper?pz5088" target="external">'
'[Acta Cryst. article]</a>')
l("</td>")
l("</tr>")
l("</table>")
if (not xy_plane_only):
title = "ASU " + str(space_group_info)
header = 'Space group: <a href="%s">%s</a> (No. %d)' % (
explore_symmetry_url % http_server_name +
urllib.quote_plus(str(space_group_info)), str(space_group_info),
group_type_number)
sub_header = None
else:
from cctbx.sgtbx import plane_groups
pg_symbol = plane_groups.hermann_mauguin_hall_table[-group_type_number
- 1][0].replace(
"_", " ")
title = "ASU " + pg_symbol
header = 'Plane group: %s (No. %d)' % (pg_symbol, -group_type_number)
sub_header = 'Corresponding space group: <a href="%s">%s</a> (No. %d)' % (
explore_symmetry_url % http_server_name +
urllib.quote_plus(str(space_group_info)), str(space_group_info),
space_group_info.type().number())
f = open(html_file_name, "w")
jvx.html_loader(jvx_in_html,
title=title,
header=header,
sub_header=sub_header,
index_html="index.html",
prev_html=prev_html,
next_html=next_html,
alternative_label=alternative_label,
alternative_html=alternative_html,
legend=legend,
jars_url=jars_url % http_server_name,
f=f)
f.close()
def asu_as_jvx(
group_type_number,
asu,
colored_grid_points=None,
http_server_name=None,
html_subdir="asu_gallery",
jars_url="http://%s/jv395/jars",
explore_symmetry_url="http://%s/cctbx/cctbx_web.cgi" + "?target_module=explore_symmetry&sgsymbol=",
):
if http_server_name is None:
http_server_name = web_links.default_http_server_name
xy_plane_only = group_type_number < 0
space_group_info = sgtbx.space_group(asu.hall_symbol).info()
if not xy_plane_only:
assert space_group_info.type().number() == group_type_number
list_of_polygons = facet_analysis.asu_polygons(asu)
all_edge_segments = facet_analysis.get_all_edge_segments(asu, list_of_polygons)
all_vertices = facet_analysis.get_all_vertices(all_edge_segments)
unit_cell = space_group_info.any_compatible_unit_cell(volume=100)
ortho = orthogonalizer(unit_cell)
shrink_length = get_diagonal_extend(ortho, all_vertices) * 0.02
geometries = []
if colored_grid_points is None:
for polygons in list_of_polygons:
for polygon, inclusive_flag in polygons:
def exclude():
for vertex in polygon:
if vertex[0][2] != 0:
return True
return False
if xy_plane_only and exclude():
continue
vertices_cart = cartesian_polygon(ortho, polygon)
vertices_inside_cart = shrink_polygon(vertices_cart, shrink_length)
points_int = jvx.pointSet()
g = jvx.geometry("facet", backface=["hide", "show"][int(xy_plane_only)])
points_cart = g.points
points_cart.hide_points()
i = -1
for vertex in polygon:
i += 1
points_int.append(vertex[0])
points_cart.append(vertices_inside_cart[i])
faces = g.faces
point_indices = []
for vertex in polygon:
point_indices.append(points_int.index(vertex[0]))
faces.append(jvx.face(point_indices, select_color(inclusive_flag)))
geometries.append(g)
geometries.append(edge_geometry(ortho, all_edge_segments, shrink_length, xy_plane_only=xy_plane_only))
geometries.append(vertex_geometry(ortho, all_vertices, xy_plane_only=xy_plane_only))
else:
g = jvx.geometry("grid")
for frac in colored_grid_points:
if xy_plane_only and frac.site[2] != 0:
continue
g.points.append(jvx.point(ortho(frac.site), color=frac.color))
geometries.append(g)
if colored_grid_points is None:
grid_label = ""
alternative_html_infix = "_grid"
alternative_label = "Grid view"
else:
grid_label = "_grid"
alternative_html_infix = ""
alternative_label = "Polygon view"
if xy_plane_only:
fmt = "asu_%02d%s"
else:
fmt = "asu_%03d%s"
base_file_name = fmt % (abs(group_type_number), grid_label)
jvx_file_name = os.path.join(html_subdir, base_file_name + ".jvx")
jvx_in_html = base_file_name + ".jvx"
html_file_name = os.path.join(html_subdir, base_file_name + ".html")
prev_html = None
next_html = None
if xy_plane_only:
fmt = "asu_%02d%s.html"
last_group_type_number = 17
else:
fmt = "asu_%03d%s.html"
last_group_type_number = 230
if abs(group_type_number) > 1:
prev_html = fmt % (abs(group_type_number) - 1, grid_label)
else:
prev_html = fmt % (last_group_type_number, grid_label)
if abs(group_type_number) < last_group_type_number:
next_html = fmt % (abs(group_type_number) + 1, grid_label)
else:
next_html = fmt % (1, grid_label)
alternative_html = fmt % (abs(group_type_number), alternative_html_infix)
if colored_grid_points is None or len(colored_grid_points) > 0:
f = open(jvx_file_name, "w")
jvx.head(f)
unit_cell_geometry(ortho, xy_plane_only=xy_plane_only).jvx(f)
basis_vector_geometry(ortho, get_min_fractional(all_vertices)).jvx(f)
for g in geometries:
g.jvx(f)
jvx.tail(f)
f.close()
legend = []
l = legend.append
l("Surface area: green = inside the asymmetric unit, red = outside")
l("<br>")
l("Basis vectors: a = red, b = green, c = blue")
l("<p>")
shape_vertices = facet_analysis.shape_vertices(asu)
l("<table border=2 cellpadding=8>")
l("<tr valign=top>")
l("<td>")
remaining = []
for vertex in shape_vertices:
if xy_plane_only and vertex[2] != 0:
continue
remaining.append(vertex)
remaining.sort()
l("<pre>Number of vertices: %d" % len(remaining))
if xy_plane_only:
j = -4
else:
j = -1
for vertex in remaining:
l(" " + str(vertex)[1:j])
l("</pre>")
l("</td>")
l("<td>")
remaining = []
for cut in asu.cuts:
if xy_plane_only and cut.as_xyz() in ["z>=0", "z<1"]:
continue
remaining.append(cut)
l("<pre>Number of faces: %d" % len(remaining))
for cut in remaining:
l(" " + cut.as_xyz())
l("</pre>")
l('<a href="guide_to_notation.html">[Guide to notation]</a>')
l("</td>")
l("<td>")
l("<pre>Geometric notation:")
for cut in remaining:
l(" " + str(cut))
l("</pre>")
l('<a href="http://scripts.iucr.org/cgi-bin/paper?pz5088" target="external">' "[Acta Cryst. article]</a>")
l("</td>")
l("</tr>")
l("</table>")
if not xy_plane_only:
title = "ASU " + str(space_group_info)
header = 'Space group: <a href="%s">%s</a> (No. %d)' % (
explore_symmetry_url % http_server_name + urllib.quote_plus(str(space_group_info)),
str(space_group_info),
group_type_number,
)
sub_header = None
else:
from cctbx.sgtbx import plane_groups
pg_symbol = plane_groups.hermann_mauguin_hall_table[-group_type_number - 1][0].replace("_", " ")
title = "ASU " + pg_symbol
header = "Plane group: %s (No. %d)" % (pg_symbol, -group_type_number)
sub_header = 'Corresponding space group: <a href="%s">%s</a> (No. %d)' % (
explore_symmetry_url % http_server_name + urllib.quote_plus(str(space_group_info)),
str(space_group_info),
space_group_info.type().number(),
)
f = open(html_file_name, "w")
jvx.html_loader(
jvx_in_html,
title=title,
header=header,
sub_header=sub_header,
index_html="index.html",
prev_html=prev_html,
next_html=next_html,
alternative_label=alternative_label,
alternative_html=alternative_html,
legend=legend,
jars_url=jars_url % http_server_name,
f=f,
)
f.close()
