def check_adp_set_b_iso(cmd,
xrsp_init,
output,
selection,
selection_str,
verbose,
tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name=output)
assert approx_equal(xrsp.occ, xrsp_init.occ, tolerance)
assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart, tolerance)
assert approx_equal(xrsp.use_u_iso, xrsp_init.use_u_iso, tolerance)
assert approx_equal(xrsp.use_u_aniso, xrsp_init.use_u_aniso, tolerance)
assert approx_equal(xrsp.u_iso_not_used, xrsp_init.u_iso_not_used,
tolerance)
assert approx_equal(xrsp.u_cart_not_used, xrsp_init.u_cart_not_used,
tolerance)
if (selection_str is None):
assert not_approx_equal(xrsp.u_iso_used, xrsp_init.u_iso_used,
tolerance)
for ucart in xrsp.u_cart:
b_iso = adptbx.u_as_b(adptbx.u_cart_as_u_iso(ucart))
if b_iso > 0: assert approx_equal(b_iso, 10, 0.005)
else: assert approx_equal(b_iso, -78.956, 0.005)
else:
arg1 = xrsp.u_iso_used.select(selection.select(xrsp.use_u_iso))
arg2 = xrsp_init.u_iso_used.select(
selection.select(xrsp_init.use_u_iso))
if (arg1.size() > 0): assert not_approx_equal(arg1, arg2, tolerance)
for ucart in xrsp.u_cart:
b_iso = adptbx.u_as_b(adptbx.u_cart_as_u_iso(ucart))
if b_iso > 0: assert approx_equal(b_iso, 10, 0.005)
else: assert approx_equal(b_iso, -78.956, 0.005)
def check_adp_set_b_iso(
cmd, xrsp_init, output, selection, selection_str, verbose,
tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name = output)
assert approx_equal(xrsp.occ, xrsp_init.occ,tolerance)
assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart,tolerance)
assert approx_equal(xrsp.use_u_iso, xrsp_init.use_u_iso,tolerance)
assert approx_equal(xrsp.use_u_aniso,xrsp_init.use_u_aniso,tolerance)
assert approx_equal(xrsp.u_iso_not_used, xrsp_init.u_iso_not_used,tolerance)
assert approx_equal(xrsp.u_cart_not_used,xrsp_init.u_cart_not_used,tolerance)
if(selection_str is None):
assert not_approx_equal(xrsp.u_iso_used, xrsp_init.u_iso_used,tolerance)
for ucart in xrsp.u_cart:
b_iso = adptbx.u_as_b(adptbx.u_cart_as_u_iso(ucart))
if b_iso > 0: assert approx_equal(b_iso, 10, 0.005)
else: assert approx_equal(b_iso, -78.956, 0.005)
else:
arg1 = xrsp.u_iso_used.select(selection.select(xrsp.use_u_iso))
arg2 = xrsp_init.u_iso_used.select(selection.select(xrsp_init.use_u_iso))
if(arg1.size() > 0): assert not_approx_equal(arg1, arg2,tolerance)
for ucart in xrsp.u_cart:
b_iso = adptbx.u_as_b(adptbx.u_cart_as_u_iso(ucart))
if b_iso > 0: assert approx_equal(b_iso, 10, 0.005)
else: assert approx_equal(b_iso, -78.956, 0.005)
def check_adp_to_iso(
cmd, xrsp_init, output, selection, selection_str, verbose,
tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name = output)
assert approx_equal(xrsp.occ, xrsp_init.occ,tolerance)
assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart,tolerance)
assert not_approx_equal(xrsp.use_u_iso, xrsp_init.use_u_iso,tolerance)
assert not_approx_equal(xrsp.use_u_aniso,xrsp_init.use_u_aniso,tolerance)
assert xrsp.u_iso_not_used.size() == 0
assert xrsp_init.u_iso_not_used.size() > 0
assert xrsp.u_cart_used.size() == 0
assert xrsp_init.u_cart_used.size() > 0
def check_adp_to_iso(cmd,
xrsp_init,
output,
selection,
selection_str,
verbose,
tolerance=1.e-3):
remove_files(output)
run_command(command=cmd, verbose=verbose)
xrsp = xray_structure_plus(file_name=output)
assert approx_equal(xrsp.occ, xrsp_init.occ, tolerance)
assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart, tolerance)
assert not_approx_equal(xrsp.use_u_iso, xrsp_init.use_u_iso, tolerance)
assert not_approx_equal(xrsp.use_u_aniso, xrsp_init.use_u_aniso, tolerance)
assert xrsp.u_iso_not_used.size() == 0
assert xrsp_init.u_iso_not_used.size() > 0
assert xrsp.u_cart_used.size() == 0
assert xrsp_init.u_cart_used.size() > 0
def exercise_nonbonded(nonbonded_type, repulsion_function):
for i_trial in xrange(5):
sites = random_sites(n_sites=2)
r = nonbonded_type(
sites=sites,
vdw_distance=1,
function=repulsion_function)
vdw_distance = r.delta
residual_obj = residual_functor(
restraint_type=nonbonded_type,
vdw_distance=vdw_distance,
function=repulsion_function)
for i_pert in xrange(5):
if (i_pert == 0):
sites_mod = sites
else:
sites_mod = []
for site in sites:
shift = col([random.uniform(-1,1)*vdw_distance*0.05
for i in xrange(3)])
sites_mod.append(site+shift)
r = nonbonded_type(
sites=sites_mod,
vdw_distance=vdw_distance,
function=repulsion_function)
if ( not hasattr(repulsion_function, "irexp")
or repulsion_function.irexp <= 2
or not_approx_equal(r.residual(), 0)):
fg = flex.vec3_double(finite_differences(sites_mod, residual_obj)) \
.as_double()
ag = flex.vec3_double(r.gradients()).as_double()
scale = max(1, flex.mean(flex.abs(fg)))
assert approx_equal(ag/scale, fg/scale, eps=1.e-2)
sites = [[0,0,0], [0,0,0]]
vdw_distance = 1.8
for i_step in xrange(1,100):
delta = i_step/50.
sites[1][0] = delta
r = nonbonded_type(
sites=[col(site) for site in sites],
vdw_distance=vdw_distance,
function=repulsion_function)
assert approx_equal(delta, r.delta)
def exercise_basic():
d = (1,1,1,90,90,90)
u = uctbx.unit_cell()
assert approx_equal(u.parameters(), d)
u = uctbx.unit_cell(d)
assert u.parameters() == d
assert approx_equal(u.parameters(), u.reciprocal_parameters())
assert approx_equal(u.volume(), 1)
assert approx_equal(u.longest_vector_sq(), 3)
assert approx_equal(u.shortest_vector_sq(), 1)
p = (2,3,4,80,100,110)
for i in xrange(7):
u = uctbx.unit_cell(p[:i])
assert u.parameters() == p[:i] + d[i:]
v = uctbx.unit_cell(p[:i])
assert v.parameters() == u.parameters()
if (i):
assert not_approx_equal(u.parameters(), u.reciprocal_parameters())
assert not u.is_similar_to(u.reciprocal())
assert not u.is_similar_to(u.reciprocal(), 1.e-3)
assert not u.is_similar_to(u.reciprocal(), 1.e-3, 1.e-3)
assert u.is_similar_to(u.reciprocal(), 1000, 180)
assert approx_equal(
u.reciprocal_parameters(), u.reciprocal().parameters())
assert approx_equal(
u.parameters(), u.reciprocal().reciprocal_parameters())
assert approx_equal(
u.reciprocal_metrical_matrix(), u.reciprocal().metrical_matrix())
assert approx_equal(
u.metrical_matrix(), u.reciprocal().reciprocal_metrical_matrix())
v = u.reciprocal().reciprocal()
assert u.is_similar_to(v, 1.e-3, 1.e-3)
assert approx_equal(u.volume(), 1/u.reciprocal().volume())
u = uctbx.unit_cell(p)
assert not u.is_degenerate()
assert not u.is_degenerate(1.e-10)
assert not u.is_degenerate(1.e-10, 1.e-5)
assert u.is_degenerate(10)
assert u.is_degenerate(1.e-10, 20)
m = u.metrical_matrix()
n = (2*2, 3*3, 4*4,
2*3*cos(110*pi/180), 2*4*cos(100*pi/180), 3*4*cos(80*pi/180))
assert approx_equal(m, n)
v = uctbx.unit_cell(metrical_matrix=m)
assert approx_equal(u.parameters(), v.parameters())
u = uctbx.unit_cell((2,3,4))
assert approx_equal(u.volume(), 2*3*4)
assert approx_equal(u.longest_vector_sq(), 2*2+3*3+4*4)
assert approx_equal(u.shortest_vector_sq(), 2*2)
u = uctbx.unit_cell(p)
assert approx_equal(u.volume(), 22.04006625)
assert approx_equal(
u.d_volume_d_params(),
(11.020033123326023, 7.3466887488840156, 5.5100165616630115,
0.051324088220620838, -0.051324088220620769, -0.13367230402431379))
for alpha in xrange(70,121,10):
for beta in xrange(70,121,10):
for gamma in xrange(70,121,10):
u = uctbx.unit_cell([7,11,13,alpha, beta, gamma])
v = uctbx.unit_cell(
orthogonalization_matrix=u.orthogonalization_matrix())
assert v.is_similar_to(u)
def exercise_box_frac_around_sites():
unit_cell = uctbx.unit_cell((10,10,10,90,90,120))
buffer = 2
sites_frac = flex.vec3_double([
(1/2., 2/3., 0.),
(1/2., 1/3., 0.)])
min_, max_ = unit_cell.box_frac_around_sites(
sites_frac=sites_frac, buffer=buffer)
assert approx_equal(min_, (0.26905989232414967, 0.10239322565748302, -0.2))
assert approx_equal(max_, (0.73094010767585038, 0.8976067743425169, 0.2))
sites_cart = unit_cell.orthogonalize(sites_frac=sites_frac)
min_, max_ = sites_cart.min(), sites_cart.max()
min_ = unit_cell.fractionalize([m-buffer for m in min_])
max_ = unit_cell.fractionalize([m+buffer for m in max_])
assert approx_equal(min_, (0.017863279495408259, 0.10239322565748302, -0.2))
assert approx_equal(max_, (0.98213672050459189, 0.8976067743425169, 0.2))
unit_cells = [uctbx.unit_cell(params) for params in [
(10, 15, 20, 90, 90, 90),
(10, 10, 20, 90, 90, 120),
(10, 10, 10, 60, 60, 60)]]
sites_cart = flex.vec3_double([
(2.23474, 8.72834, 4.70562),
(3.72656, 3.28621, 9.19121),
(-6.83519, -7.5707, 4.62386)])
c_inv_rs = [(1,0,0, 0,1,0, 0,0,1),
(0,1,0, 0,0,1, 1,0,0),
(0,0,1, 1,0,0, 0,1,0)]
for unit_cell_0 in unit_cells:
for c_inv_r in c_inv_rs:
unit_cell = unit_cell_0.change_basis(c_inv_r)
sites_frac = unit_cell.fractionalize(sites_cart=sites_cart)
min0, max0 = unit_cell.box_frac_around_sites(
sites_cart=sites_cart)
for x,y in zip(min0, max0): assert x < y
for buffer in [None, 0]:
min_, max_ = unit_cell.box_frac_around_sites(
sites_cart=sites_cart, buffer=buffer)
assert approx_equal(min_, min0)
assert approx_equal(max_, max0)
min_, max_ = unit_cell.box_frac_around_sites(
sites_frac=sites_frac, buffer=buffer)
assert approx_equal(min_, min0)
assert approx_equal(max_, max0)
for buffer in [0,3,5,7]:
min0, max0 = unit_cell.box_frac_around_sites(
sites_cart=sites_cart, buffer=buffer)
for x,y in zip(min0, max0): assert x < y
min_, max_ = unit_cell.box_frac_around_sites(
sites_frac=sites_frac, buffer=buffer)
assert approx_equal(min_, min0)
assert approx_equal(max_, max0)
min_, max_ = sites_cart.min(), sites_cart.max()
min_ = unit_cell.fractionalize([m-buffer for m in min_])
max_ = unit_cell.fractionalize([m+buffer for m in max_])
if (unit_cell_0 is unit_cells[0]):
assert approx_equal(min_, min0)
assert approx_equal(max_, max0)
elif (buffer == 0 and unit_cell_0 is unit_cells[1]):
assert approx_equal(min_, min0)
if (c_inv_r is c_inv_rs[2]):
assert approx_equal(max_, max0)
else:
assert not_approx_equal(max_, max0)
else:
assert not_approx_equal(min_, min0)
assert not_approx_equal(max_, max0)
def exercise_basic():
d = (1, 1, 1, 90, 90, 90)
u = uctbx.unit_cell()
assert approx_equal(u.parameters(), d)
u = uctbx.unit_cell(d)
assert u.parameters() == d
assert approx_equal(u.parameters(), u.reciprocal_parameters())
assert approx_equal(u.volume(), 1)
assert approx_equal(u.longest_vector_sq(), 3)
assert approx_equal(u.shortest_vector_sq(), 1)
p = (2, 3, 4, 80, 100, 110)
for i in range(7):
u = uctbx.unit_cell(p[:i])
assert u.parameters() == p[:i] + d[i:]
v = uctbx.unit_cell(p[:i])
assert v.parameters() == u.parameters()
if (i):
assert not_approx_equal(u.parameters(), u.reciprocal_parameters())
assert not u.is_similar_to(u.reciprocal())
assert not u.is_similar_to(u.reciprocal(), 1.e-3)
assert not u.is_similar_to(u.reciprocal(), 1.e-3, 1.e-3)
assert u.is_similar_to(u.reciprocal(), 1000, 180)
assert approx_equal(u.reciprocal_parameters(),
u.reciprocal().parameters())
assert approx_equal(u.parameters(),
u.reciprocal().reciprocal_parameters())
assert approx_equal(u.reciprocal_metrical_matrix(),
u.reciprocal().metrical_matrix())
assert approx_equal(u.metrical_matrix(),
u.reciprocal().reciprocal_metrical_matrix())
v = u.reciprocal().reciprocal()
assert u.is_similar_to(v, 1.e-3, 1.e-3)
assert approx_equal(u.volume(), 1 / u.reciprocal().volume())
u = uctbx.unit_cell(p)
assert not u.is_degenerate()
assert not u.is_degenerate(1.e-10)
assert not u.is_degenerate(1.e-10, 1.e-5)
assert u.is_degenerate(10)
assert u.is_degenerate(1.e-10, 20)
m = u.metrical_matrix()
n = (2 * 2, 3 * 3, 4 * 4, 2 * 3 * cos(110 * pi / 180),
2 * 4 * cos(100 * pi / 180), 3 * 4 * cos(80 * pi / 180))
assert approx_equal(m, n)
v = uctbx.unit_cell(metrical_matrix=m)
assert approx_equal(u.parameters(), v.parameters())
u = uctbx.unit_cell((2, 3, 4))
assert approx_equal(u.volume(), 2 * 3 * 4)
assert approx_equal(u.longest_vector_sq(), 2 * 2 + 3 * 3 + 4 * 4)
assert approx_equal(u.shortest_vector_sq(), 2 * 2)
u = uctbx.unit_cell(p)
assert approx_equal(u.volume(), 22.04006625)
assert approx_equal(
u.d_volume_d_params(),
(11.020033123326023, 7.3466887488840156, 5.5100165616630115,
0.051324088220620838, -0.051324088220620769, -0.13367230402431379))
for alpha in range(70, 121, 10):
for beta in range(70, 121, 10):
for gamma in range(70, 121, 10):
u = uctbx.unit_cell([7, 11, 13, alpha, beta, gamma])
v = uctbx.unit_cell(
orthogonalization_matrix=u.orthogonalization_matrix())
assert v.is_similar_to(u)
def exercise_box_frac_around_sites():
unit_cell = uctbx.unit_cell((10, 10, 10, 90, 90, 120))
buffer = 2
sites_frac = flex.vec3_double([(1 / 2., 2 / 3., 0.), (1 / 2., 1 / 3., 0.)])
min_, max_ = unit_cell.box_frac_around_sites(sites_frac=sites_frac,
buffer=buffer)
assert approx_equal(min_, (0.26905989232414967, 0.10239322565748302, -0.2))
assert approx_equal(max_, (0.73094010767585038, 0.8976067743425169, 0.2))
sites_cart = unit_cell.orthogonalize(sites_frac=sites_frac)
min_, max_ = sites_cart.min(), sites_cart.max()
min_ = unit_cell.fractionalize([m - buffer for m in min_])
max_ = unit_cell.fractionalize([m + buffer for m in max_])
assert approx_equal(min_,
(0.017863279495408259, 0.10239322565748302, -0.2))
assert approx_equal(max_, (0.98213672050459189, 0.8976067743425169, 0.2))
unit_cells = [
uctbx.unit_cell(params)
for params in [(10, 15, 20, 90, 90, 90), (10, 10, 20, 90, 90,
120), (10, 10, 10, 60, 60,
60)]
]
sites_cart = flex.vec3_double([(2.23474, 8.72834, 4.70562),
(3.72656, 3.28621, 9.19121),
(-6.83519, -7.5707, 4.62386)])
c_inv_rs = [(1, 0, 0, 0, 1, 0, 0, 0, 1), (0, 1, 0, 0, 0, 1, 1, 0, 0),
(0, 0, 1, 1, 0, 0, 0, 1, 0)]
for unit_cell_0 in unit_cells:
for c_inv_r in c_inv_rs:
unit_cell = unit_cell_0.change_basis(c_inv_r)
sites_frac = unit_cell.fractionalize(sites_cart=sites_cart)
min0, max0 = unit_cell.box_frac_around_sites(sites_cart=sites_cart)
for x, y in zip(min0, max0):
assert x < y
for buffer in [None, 0]:
min_, max_ = unit_cell.box_frac_around_sites(
sites_cart=sites_cart, buffer=buffer)
assert approx_equal(min_, min0)
assert approx_equal(max_, max0)
min_, max_ = unit_cell.box_frac_around_sites(
sites_frac=sites_frac, buffer=buffer)
assert approx_equal(min_, min0)
assert approx_equal(max_, max0)
for buffer in [0, 3, 5, 7]:
min0, max0 = unit_cell.box_frac_around_sites(
sites_cart=sites_cart, buffer=buffer)
for x, y in zip(min0, max0):
assert x < y
min_, max_ = unit_cell.box_frac_around_sites(
sites_frac=sites_frac, buffer=buffer)
assert approx_equal(min_, min0)
assert approx_equal(max_, max0)
min_, max_ = sites_cart.min(), sites_cart.max()
min_ = unit_cell.fractionalize([m - buffer for m in min_])
max_ = unit_cell.fractionalize([m + buffer for m in max_])
if (unit_cell_0 is unit_cells[0]):
assert approx_equal(min_, min0)
assert approx_equal(max_, max0)
elif (buffer == 0 and unit_cell_0 is unit_cells[1]):
assert approx_equal(min_, min0)
if (c_inv_r is c_inv_rs[2]):
assert approx_equal(max_, max0)
else:
assert not_approx_equal(max_, max0)
else:
assert not_approx_equal(min_, min0)
assert not_approx_equal(max_, max0)
def exercise_statistics():
import scitbx.math
for flex_type in flex_types():
a = flex_type(flex.grid((3,5)))
s = maptbx.statistics(a)
assert s.min() == 0
assert s.max() == 0
assert s.mean() == 0
assert s.mean_sq() == 0
assert s.sigma() == 0
a = flex_type([random.random() for i in xrange(3*5)])
a.resize(flex.grid((3,5)))
s = maptbx.statistics(a)
assert approx_equal(flex.min(a), s.min())
assert approx_equal(flex.max(a), s.max())
assert approx_equal(flex.mean(a), s.mean())
assert approx_equal(flex.mean_sq(a), s.mean_sq())
assert approx_equal(flex.mean_sq(a)-flex.mean(a)**2, s.sigma()**2)
b = flex_type(flex.grid((4,6)).set_focus((3,5)))
for i in xrange(3):
for j in xrange(5):
b[(i,j)] = a[(i,j)]
b[(3,5)] = -1
b[(2,5)] = 2
b.resize(flex.grid((-2,3), (2,9)).set_focus((1,8)))
t = maptbx.statistics(b)
assert not_approx_equal(flex.min(b), t.min())
assert not_approx_equal(flex.max(b), t.max())
assert not_approx_equal(flex.mean(b), t.mean())
assert not_approx_equal(flex.mean_sq(b), t.mean_sq())
assert not_approx_equal(flex.mean_sq(b)-flex.mean(b)**2, t.sigma()**2)
assert approx_equal(s.min(), t.min())
assert approx_equal(s.max(), t.max())
assert approx_equal(s.mean(), t.mean())
assert approx_equal(s.mean_sq(), t.mean_sq())
assert approx_equal(s.sigma(), t.sigma())
a = flex.double(flex.grid(5,3))
s = maptbx.more_statistics(a)
assert s.min() == 0
assert s.max() == 0
assert s.mean() == 0
assert s.mean_sq() == 0
assert s.sigma() == 0
assert s.skewness() == 0
assert s.kurtosis() == 0
a = flex.random_double(5*3)
reference = scitbx.math.basic_statistics(a)
a.resize(flex.grid(5,3))
s = maptbx.more_statistics(a)
assert approx_equal(s.min(), reference.min)
assert approx_equal(s.max(), reference.max)
assert approx_equal(s.mean(), reference.mean)
assert approx_equal(s.sigma(), reference.biased_standard_deviation)
assert approx_equal(s.skewness(), reference.skew)
assert approx_equal(s.kurtosis(), reference.kurtosis)
b = flex.double(flex.grid((6,4)).set_focus((5,3)))
for i in xrange(5):
for j in xrange(3):
b[(i,j)] = a[(i,j)]
b[(5,3)] = -1
b[(5,2)] = 2
b.resize(flex.grid((3,-2), (9,2)).set_focus((8,1)))
t = maptbx.statistics(b)
assert approx_equal(s.min(), reference.min)
assert approx_equal(s.max(), reference.max)
assert approx_equal(s.mean(), reference.mean)
assert approx_equal(s.sigma(), reference.biased_standard_deviation)
assert approx_equal(s.skewness(), reference.skew)
assert approx_equal(s.kurtosis(), reference.kurtosis)
m = flex.double(flex.grid((6,4,8)).set_focus((5,3,7)))