def exercise_python_code():
r = rational.int
assert rational.from_string("1") == 1
assert rational.from_string("2/4").as_tuple() == (1,2)
assert rational.vector((2,3,4), 3) == [r(d,3) for d in (2,3,4)]
assert rational.vector((2,3,4), (3,4,5)) == [
r(d,n) for d,n in zip((2,3,4), (3,4,5))]
assert rational.lcm_denominators(array=[]) == 1
assert rational.lcm_denominators(array=[r(3,4)]) == 4
assert rational.lcm_denominators(array=[r(3,4), r(5,6)]) == 12
def exercise_python_code():
r = rational.int
assert rational.from_string("1") == 1
assert rational.from_string("2/4").as_tuple() == (1, 2)
assert rational.vector((2, 3, 4), 3) == [r(d, 3) for d in (2, 3, 4)]
assert rational.vector(
(2, 3, 4),
(3, 4, 5)) == [r(d, n) for d, n in zip((2, 3, 4), (3, 4, 5))]
assert rational.lcm_denominators(array=[]) == 1
assert rational.lcm_denominators(array=[r(3, 4)]) == 4
assert rational.lcm_denominators(array=[r(3, 4), r(5, 6)]) == 12
def sample_asu(asu, n=(12, 12, 12), shape=False, is_stripped_asu=False):
n_redundancies = 0
u_grid = []
for i in xrange(n[0]):
b = []
for j in xrange(n[1]):
c = []
for k in xrange(n[2]):
c.append(0)
b.append(c)
u_grid.append(b)
r_grid = []
colored_grid_points = []
for i in xrange(-n[0] // 2, n[0] + 1):
b = []
for j in xrange(-n[1] // 2, n[1] + 1):
c = []
for k in xrange(-n[2] // 2, n[2] + 1):
frac = rational.vector((i, j, k), n)
f = asu.is_inside(frac)
fv = asu.is_inside(frac, shape_only=True)
if (len(asu.in_which_cuts(frac)) != 0 and fv):
colored_grid_points.append(
colored_grid_point(frac, jv_asu.select_color(f)))
if (shape):
if (not fv): assert not f
else:
fv = False
if (f or fv):
i_pr = i % n[0]
j_pr = j % n[1]
k_pr = k % n[2]
if (u_grid[i_pr][j_pr][k_pr] != 0):
n_redundancies += 1
if (not is_stripped_asu):
print "Redundancy at", (i, j, k), (i_pr, j_pr,
k_pr)
if (f):
u_grid[i_pr][j_pr][k_pr] = 1
c.append(1)
else:
u_grid[i_pr][j_pr][k_pr] = 2
c.append(2)
else:
c.append(0)
b.append(c)
r_grid.append(b)
return u_grid, r_grid, colored_grid_points, n_redundancies
def recolor_grid_points(gridding, colored_grid_points, redundancies, verbose):
color_srv = color_server()
processed_points = {}
for symop, pairs in redundancies:
if (verbose):
print "Coloring %d redundancies:" % len(pairs), symop
sys.stdout.flush()
colored_point_dict = {}
for colored_point in colored_grid_points:
colored_point_dict[colored_point.site] = colored_point
colors = color_srv.next()
for pair in pairs:
for point, color in zip(pair, colors):
frac = tuple(rational.vector(point, gridding))
if (not frac in processed_points):
processed_points[frac] = 1
colored_point_dict[frac].color = color
def analyze_redundancies(asu, n, redundancies, verbose=1):
if (len(redundancies) == 0): return
print("Overview:")
for symop, pairs in redundancies:
print(symop, ": number of redundancies:", len(pairs))
print(" ", rt_mx_analysis(sgtbx.rt_mx(symop)))
print("Details:")
for symop, pairs in redundancies:
print(symop, ": number of redundancies:", len(pairs))
print(" ", rt_mx_analysis(sgtbx.rt_mx(symop)))
all_cuts = dicts.with_default_factory(dict)
not_in_cuts = {}
for pair in pairs:
for point in pair:
cuts = asu.in_which_cuts(rational.vector(point, n))
if (len(cuts) == 0):
not_in_cuts[point] = 1
all_cuts[tuple(cuts)][point] = 1
print(" In cuts:")
for cuts, points in all_cuts.items():
print(" ", end=' ')
show_amp = False
for cut in cuts:
if (show_amp): print("&", end=' ')
print(cut, end=' ')
show_amp = True
print("#points: %d:" % len(points), end=' ')
# FIXME : ordering of keys in py2/3 is different
print(str(list(points.keys())[:4]).replace(" ", ""))
if (verbose):
print(" Pairs:")
for pair in pairs:
print(" ", pair)
if (len(not_in_cuts) > 0):
print(" Not in cuts:")
for point in not_in_cuts.keys():
print(" ", point)
raise AssertionError("Some redundant points not in any cuts.")
print()
def check_multiplicities(asu, n):
space_group = sgtbx.space_group(asu.hall_symbol)
all_cuts = asu.extract_all_cuts()
print "Total number of cuts:", len(all_cuts)
def get_code(point):
result = 0
bit = 1
for cut in all_cuts:
if (cut.evaluate(point) == 0):
result += bit
bit *= 2
return result
mults_by_code = {}
for i in xrange(-n[0] // 2, n[0] + 1):
for j in xrange(-n[1] // 2, n[1] + 1):
for k in xrange(-n[2] // 2, n[2] + 1):
point = rational.vector((i, j, k), n)
if (asu.is_inside(point)):
code = get_code(point)
if (code != 0):
m = space_group.multiplicity(site=point)
mults_by_code.setdefault(code, set()).add(m)
for code, mults in mults_by_code.items():
if (len(mults) != 1):
print "PROBLEM:", space_group.type().number(), mults_by_code
break
else:
print "cut intersection multiplicities unique:"
order_z = space_group.order_z()
tab_codes = []
for code in sorted(mults_by_code.keys()):
m = list(mults_by_code[code])[0]
if (m != order_z):
print code, m
tab_codes.append((code, m))
print "Number of cut intersection codes:", len(tab_codes)
def analyze_redundancies(asu, n, redundancies, verbose=1):
if (len(redundancies) == 0): return
print "Overview:"
for symop, pairs in redundancies:
print symop, ": number of redundancies:", len(pairs)
print " ", rt_mx_analysis(sgtbx.rt_mx(symop))
print "Details:"
for symop, pairs in redundancies:
print symop, ": number of redundancies:", len(pairs)
print " ", rt_mx_analysis(sgtbx.rt_mx(symop))
all_cuts = dicts.with_default_factory(dict)
not_in_cuts = {}
for pair in pairs:
for point in pair:
cuts = asu.in_which_cuts(rational.vector(point, n))
if (len(cuts) == 0):
not_in_cuts[point] = 1
all_cuts[tuple(cuts)][point] = 1
print " In cuts:"
for cuts, points in all_cuts.items():
print " ",
show_amp = False
for cut in cuts:
if (show_amp): print "&",
print cut,
show_amp = True
print "#points: %d:" % len(points),
print str(points.keys()[:4]).replace(" ", "")
if (verbose):
print " Pairs:"
for pair in pairs:
print " ", pair
if (len(not_in_cuts) > 0):
print " Not in cuts:"
for point in not_in_cuts.keys():
print " ", point
raise AssertionError, "Some redundant points not in any cuts."
print
def as_rational(self):
return matrix.sqr(rational.vector(self.num(), self.den()))
def as_rational(self): return matrix.sqr(rational.vector(self.num(), self.den()))
