def find_distances(unit_cell, space_group, sites_frac, distance_cutoff):
space_group_type = space_group.type()
# reference_asu, metric_free_asu, and asu are Python objects
reference_asu = cctbx.sgtbx.direct_space_asu.reference_table.get_asu(space_group_type.number())
metric_free_asu = reference_asu.change_basis(
space_group_type.cb_op().inverse() # change_of_basis_op_to_reference_setting
)
asu = cctbx.crystal.direct_space_asu.direct_space_asu(asu=metric_free_asu, unit_cell=unit_cell)
proto_asu = proto.direct_space_asu(space_group_type) # C++ type
# todo in C++: convert proto_asu cuts to as_float_cut_plane()
# all objects below are wrapped C++ objects
float_asu = cctbx.crystal.direct_space_asu_float_asu(
unit_cell=unit_cell, cuts=[cut.as_float_cut_plane() for cut in metric_free_asu.cuts], is_inside_epsilon=1.0e-6
)
asu_mappings = cctbx.crystal.direct_space_asu_asu_mappings(
space_group=space_group, asu=float_asu, buffer_thickness=distance_cutoff
)
asu_mappings.process_sites_frac(original_sites=sites_frac, min_distance_sym_equiv=0.5)
pair_asu_table = cctbx.crystal.pair_asu_table(asu_mappings=asu_mappings)
pair_asu_table.add_all_pairs(distance_cutoff=distance_cutoff)
pair_sym_table = pair_asu_table.extract_pair_sym_table()
for i, pair_sym_dict in enumerate(pair_sym_table):
print "i:", i
for j, sym_ops in pair_sym_dict.items():
print " j:", j
for sym_op in sym_ops:
frac_i = sites_frac[i]
frac_j = sites_frac[j]
frac_ji = sym_op * frac_j
print " %-20s %8.3f" % (str(sym_op), unit_cell.distance(frac_i, frac_ji))
def find_distances(unit_cell, space_group, sites_frac, distance_cutoff):
space_group_type = space_group.type()
# reference_asu, metric_free_asu, and asu are Python objects
reference_asu = cctbx.sgtbx.direct_space_asu.reference_table.get_asu(
space_group_type.number())
metric_free_asu = reference_asu.change_basis(
space_group_type.cb_op() # change_of_basis_op_to_reference_setting
.inverse())
asu = cctbx.crystal.direct_space_asu.direct_space_asu(asu=metric_free_asu,
unit_cell=unit_cell)
proto_asu = proto.direct_space_asu(space_group_type) # C++ type
# todo in C++: convert proto_asu cuts to as_float_cut_plane()
# all objects below are wrapped C++ objects
float_asu = cctbx.crystal.direct_space_asu_float_asu(
unit_cell=unit_cell,
cuts=[cut.as_float_cut_plane() for cut in metric_free_asu.cuts],
is_inside_epsilon=1.e-6)
asu_mappings = cctbx.crystal.direct_space_asu_asu_mappings(
space_group=space_group,
asu=float_asu,
buffer_thickness=distance_cutoff)
asu_mappings.process_sites_frac(original_sites=sites_frac,
min_distance_sym_equiv=0.5)
pair_asu_table = cctbx.crystal.pair_asu_table(asu_mappings=asu_mappings)
pair_asu_table.add_all_pairs(distance_cutoff=distance_cutoff)
pair_sym_table = pair_asu_table.extract_pair_sym_table()
for i, pair_sym_dict in enumerate(pair_sym_table):
print("i:", i)
for j, sym_ops in pair_sym_dict.items():
print(" j:", j)
for sym_op in sym_ops:
frac_i = sites_frac[i]
frac_j = sites_frac[j]
frac_ji = sym_op * frac_j
print(" %-20s %8.3f" %
(str(sym_op), unit_cell.distance(frac_i, frac_ji)))
def compare(spgr, n=NSteps, verbose=False):
if verbose:
print cout.getvalue()
cout.truncate(0)
grp = space_group_info(spgr)
print >> cout, "Comparing asus for group: ", spgr, " n-steps= ", n
asuo = grp.direct_space_asu()
print >> cout, "=== Original python asu ==="
asuo.show_comprehensive_summary(cout)
print >> cout, ":: raw facets"
as_raw_asu(asuo, cout)
mxo = tuple(asuo.box_max())
mno = tuple(asuo.box_min())
print >> cout, "box min= ", mno, " max= ", mxo
### NEW C++ ASU
asun = new_asu.direct_space_asu(grp.type())
print >> cout, "=== New C++ asu ==="
asun.show_comprehensive_summary(cout)
mnn = asun.box_min()
mxn = asun.box_max()
print >> cout, "box min= ", mnn, " max= ", mxn
assert mnn == mno
assert mxn == mxo
old_vertices = asuo.shape_vertices()
new_vertices = asun.shape_vertices() # C++ sorted list
assert len(old_vertices) == len(new_vertices)
# TODO: the following seems to use the same ordering operation
# as mine in C++
old_vertices = sorted(old_vertices)
for a, b in zip(old_vertices, new_vertices):
print >> cout, a, " == ", b
assert a == b, str(a) + " != " + str(b)
ins, v = loop_grid(asun, n, mnn, mxn, asuo)
print >>cout, "N inside = ", ins, " volume = ", v, \
" expected volume = ", rint(1,grp.group().order_z())
### SHAPE ONLY
asun.shape_only()
asuo = asuo.shape_only()
mxo2 = tuple(asuo.box_max())
mno2 = tuple(asuo.box_min())
mnn2 = asun.box_min()
mxn2 = asun.box_max()
assert mxo2 == mxo
assert mno2 == mno
assert mxn2 == mxn
assert mnn2 == mnn
loop_grid(asun, n, mnn, mxn, asuo)
unit_cell = grp.any_compatible_unit_cell(volume=5000.0)
fasun = asun.as_float_asu(unit_cell, 1.0E-6)
fasuo = cctbx.crystal.direct_space_asu_float_asu(
unit_cell=unit_cell,
cuts=[cut.as_float_cut_plane() for cut in asuo.cuts],
is_inside_epsilon=1.e-6)
# python sucks big: still (in 2.5) there is no float.epsilon/max/tiny/etc
assert approx_equal(fasun.is_inside_epsilon(), fasuo.is_inside_epsilon(),
1.0E-100)
assert len(fasun.cuts()) == len(fasuo.cuts()), \
"%d != %d"%(len(fasuo.cuts()),len(fasun.cuts()))
assert ((len(fasun.cuts()) < 200) & (len(fasun.cuts()) > 3)), \
len(fasun.cuts())
if verbose:
print cout.getvalue()
cout.truncate(0)
def compare(spgr, n=NSteps, verbose=False):
if verbose:
print cout.getvalue()
cout.truncate(0)
grp = space_group_info(spgr)
print >>cout, "Comparing asus for group: ", spgr, " n-steps= ", n
asuo = grp.direct_space_asu()
print >>cout, "=== Original python asu ==="
asuo.show_comprehensive_summary(cout)
print >>cout, ":: raw facets"
as_raw_asu(asuo, cout)
mxo = tuple( asuo.box_max() )
mno = tuple( asuo.box_min() )
print >>cout, "box min= ", mno, " max= ", mxo
### NEW C++ ASU
asun = new_asu.direct_space_asu(grp.type())
print >>cout, "=== New C++ asu ==="
asun.show_comprehensive_summary(cout)
mnn = asun.box_min()
mxn = asun.box_max()
print >>cout, "box min= ", mnn, " max= ", mxn
assert mnn == mno
assert mxn == mxo
old_vertices = asuo.shape_vertices()
new_vertices = asun.shape_vertices() # C++ sorted list
assert len(old_vertices) == len(new_vertices)
# TODO: the following seems to use the same ordering operation
# as mine in C++
old_vertices = sorted(old_vertices)
for a,b in zip(old_vertices,new_vertices):
print >>cout, a, " == ", b
assert a == b, str(a)+" != "+str(b)
ins,v = loop_grid(asun, n, mnn, mxn, asuo)
print >>cout, "N inside = ", ins, " volume = ", v, \
" expected volume = ", rint(1,grp.group().order_z())
### SHAPE ONLY
asun.shape_only()
asuo = asuo.shape_only()
mxo2 = tuple( asuo.box_max() )
mno2 = tuple( asuo.box_min() )
mnn2 = asun.box_min()
mxn2 = asun.box_max()
assert mxo2 == mxo
assert mno2 == mno
assert mxn2 == mxn
assert mnn2 == mnn
loop_grid(asun, n, mnn, mxn, asuo)
unit_cell = grp.any_compatible_unit_cell(volume=5000.0)
fasun = asun.as_float_asu( unit_cell, 1.0E-6);
fasuo = cctbx.crystal.direct_space_asu_float_asu(
unit_cell=unit_cell,
cuts=[cut.as_float_cut_plane() for cut in asuo.cuts],
is_inside_epsilon=1.e-6)
# python sucks big: still (in 2.5) there is no float.epsilon/max/tiny/etc
assert approx_equal(fasun.is_inside_epsilon(), fasuo.is_inside_epsilon(),
1.0E-100)
assert len(fasun.cuts()) == len(fasuo.cuts()), \
"%d != %d"%(len(fasuo.cuts()),len(fasun.cuts()))
assert ((len(fasun.cuts()) < 200) & (len(fasun.cuts()) > 3)), \
len(fasun.cuts())
if verbose:
print cout.getvalue()
cout.truncate(0)
