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 show_scatterer(self, f=None, unit_cell=None):
if (f is None): f = sys.stdout
from cctbx import adptbx
print >> f, "%-4s" % self.label[5:15],
print >> f, "%-4s" % self.scattering_type,
#print >> f, "%3d" % self.multiplicity(),
print >> f, "%6.3f" % (self.fdp),
print >> f, "(%7.4f %7.4f %7.4f)" % self.site,
print >> f, "%4.2f" % self.occupancy,
if self.flags.use_u_iso():
print >> f, "%6.4f" % self.u_iso,
else:
print >> f, '[ - ]',
if self.flags.use_u_aniso():
assert unit_cell is not None
u_cart = adptbx.u_star_as_u_cart(unit_cell, self.u_star)
print >> f, "%6.4f" % adptbx.u_cart_as_u_iso(u_cart)
print >> f, " u_cart =", ("%6.3f " * 5 + "%6.3f") % u_cart,
else:
print >> f, '[ - ]',
if False and (self.fp != 0 or self.fdp != 0):
print >> f, "\n fp,fdp = %6.4f,%6.4f" % (
self.fp,
self.fdp),
print >> f
def show_scatterer(self, f=None, unit_cell=None):
if (f is None): f = sys.stdout
from cctbx import adptbx
print("%-4s" % self.label[5:15], end=' ', file=f)
print("%-4s" % self.scattering_type, end=' ', file=f)
#print >> f, "%3d" % self.multiplicity(),
print("%6.3f" % (self.fdp), end=' ', file=f)
print("(%7.4f %7.4f %7.4f)" % self.site, end=' ', file=f)
print("%4.2f" % self.occupancy, end=' ', file=f)
if self.flags.use_u_iso():
print("%6.4f" % self.u_iso, end=' ', file=f)
else:
print('[ - ]', end=' ', file=f)
if self.flags.use_u_aniso():
assert unit_cell is not None
u_cart = adptbx.u_star_as_u_cart(unit_cell, self.u_star)
print("%6.4f" % adptbx.u_cart_as_u_iso(u_cart), file=f)
print(" u_cart =", ("%6.3f " * 5 + "%6.3f") % u_cart,
end=' ',
file=f)
else:
print('[ - ]', end=' ', file=f)
if False and (self.fp != 0 or self.fdp != 0):
print("\n fp,fdp = %6.4f,%6.4f" % (self.fp, self.fdp),
end=' ',
file=f)
print(file=f)
def as_pdb_file(self,
remark,
remarks,
fractional_coordinates,
resname,
connect):
if (remark is not None):
remarks.insert(0, remark)
s = StringIO()
for remark in remarks:
print >> s, "REMARK", remark
print >> s, "REMARK Number of scatterers:", self.scatterers().size()
print >> s, "REMARK At special positions:", \
self.special_position_indices().size()
if (fractional_coordinates):
print >> s, "REMARK Fractional coordinates"
else:
print >> s, "REMARK Cartesian coordinates"
print >> s, iotbx.pdb.format_cryst1_record(crystal_symmetry=self)
print >> s, iotbx.pdb.format_scale_records(unit_cell=self.unit_cell())
atom = iotbx.pdb.hierarchy.atom_with_labels()
if (resname is not None):
atom.resname = resname.upper()
serial = 0
for scatterer in self.scatterers():
serial += 1
atom.serial = iotbx.pdb.hy36encode(width=5, value=serial)
if (scatterer.flags.use_u_aniso_only()):
atom.uij = adptbx.u_star_as_u_cart(self.unit_cell(), scatterer.u_star)
atom.b = adptbx.u_as_b(adptbx.u_cart_as_u_iso(atom.uij))
else:
atom.uij_erase()
atom.b = adptbx.u_as_b(scatterer.u_iso)
if (fractional_coordinates):
atom.xyz = scatterer.site
else:
atom.xyz = self.unit_cell().orthogonalize(scatterer.site)
atom.occ = scatterer.occupancy
label = scatterer.label.upper()
atom.name = label[:4]
if (resname is None):
atom.resname = label[:3]
element_symbol = scatterer.element_symbol()
if (element_symbol is None): element_symbol = "Q"
assert len(element_symbol) in (1,2)
atom.element = element_symbol.upper()
atom.resseq = iotbx.pdb.hy36encode(width=4, value=serial)
print >> s, atom.format_atom_record_group()
if (connect is not None):
assert len(connect) == self.scatterers().size()
i = 0
for bonds in connect:
i += 1
l = "CONNECT%5d" % i
for bond in bonds:
l += "%5d" % (bond+1)
print >> s, l
print >> s, "END"
return s.getvalue()
def as_pdb_file(self, remark, remarks, fractional_coordinates, resname,
connect):
if (remark is not None):
remarks.insert(0, remark)
s = StringIO()
for remark in remarks:
print >> s, "REMARK", remark
print >> s, "REMARK Number of scatterers:", self.scatterers().size()
print >> s, "REMARK At special positions:", \
self.special_position_indices().size()
if (fractional_coordinates):
print >> s, "REMARK Fractional coordinates"
else:
print >> s, "REMARK Cartesian coordinates"
print >> s, iotbx.pdb.format_cryst1_record(crystal_symmetry=self)
print >> s, iotbx.pdb.format_scale_records(unit_cell=self.unit_cell())
atom = iotbx.pdb.hierarchy.atom_with_labels()
if (resname is not None):
atom.resname = resname.upper()
serial = 0
for scatterer in self.scatterers():
serial += 1
atom.serial = iotbx.pdb.hy36encode(width=5, value=serial)
if (scatterer.flags.use_u_aniso_only()):
atom.uij = adptbx.u_star_as_u_cart(self.unit_cell(),
scatterer.u_star)
atom.b = adptbx.u_as_b(adptbx.u_cart_as_u_iso(atom.uij))
else:
atom.uij_erase()
atom.b = adptbx.u_as_b(scatterer.u_iso)
if (fractional_coordinates):
atom.xyz = scatterer.site
else:
atom.xyz = self.unit_cell().orthogonalize(scatterer.site)
atom.occ = scatterer.occupancy
label = scatterer.label.upper()
atom.name = label[:4]
if (resname is None):
atom.resname = label[:3]
element_symbol = scatterer.element_symbol()
if (element_symbol is None): element_symbol = "Q"
assert len(element_symbol) in (1, 2)
atom.element = element_symbol.upper()
atom.resseq = iotbx.pdb.hy36encode(width=4, value=serial)
print >> s, atom.format_atom_record_group()
if (connect is not None):
assert len(connect) == self.scatterers().size()
i = 0
for bonds in connect:
i += 1
l = "CONNECT%5d" % i
for bond in bonds:
l += "%5d" % (bond + 1)
print >> s, l
print >> s, "END"
return s.getvalue()
def exercise_factor_u_star_u_iso():
for i_trial in xrange(100):
a = flex.random_double(size=9, factor=3)
a.resize(flex.grid(3,3))
u = a.matrix_transpose().matrix_multiply(a) # always positive-definite
u_cart = [u[0],u[4],u[8],u[1],u[2],u[5]]
unit_cell = uctbx.unit_cell((3,5,7,80,100,110))
u_star = adptbx.u_cart_as_u_star(unit_cell, u_cart)
airlie = u_star_minus_u_iso_airlie(unit_cell, u_star)
ralf = u_star_minus_u_iso_ralf(unit_cell, u_star)
assert approx_equal(ralf, airlie, 1.e-10)
f = adptbx.factor_u_star_u_iso(unit_cell=unit_cell, u_star=u_star)
assert approx_equal(f.u_iso, adptbx.u_cart_as_u_iso(u_cart))
assert approx_equal(f.u_star_minus_u_iso, airlie, 1.e-10)
def exercise_factor_u_star_u_iso():
for i_trial in xrange(100):
a = flex.random_double(size=9, factor=3)
a.resize(flex.grid(3, 3))
u = a.matrix_transpose().matrix_multiply(a) # always positive-definite
u_cart = [u[0], u[4], u[8], u[1], u[2], u[5]]
unit_cell = uctbx.unit_cell((3, 5, 7, 80, 100, 110))
u_star = adptbx.u_cart_as_u_star(unit_cell, u_cart)
airlie = u_star_minus_u_iso_airlie(unit_cell, u_star)
ralf = u_star_minus_u_iso_ralf(unit_cell, u_star)
assert approx_equal(ralf, airlie, 1.0e-10)
f = adptbx.factor_u_star_u_iso(unit_cell=unit_cell, u_star=u_star)
assert approx_equal(f.u_iso, adptbx.u_cart_as_u_iso(u_cart))
assert approx_equal(f.u_star_minus_u_iso, airlie, 1.0e-10)
def show(self, f=None, unit_cell=None):
if (f is None): f = sys.stdout
print >> f, "%-4s" % self.label,
print >> f, "%-4s" % self.scattering_type,
print >> f, "%3d" % self.multiplicity(),
print >> f, "(%7.4f %7.4f %7.4f)" % self.site,
print >> f, "%4.2f" % self.occupancy,
if self.flags.use_u_iso():
print >> f, "%6.4f" % self.u_iso,
else:
print >> f, '[ - ]',
if self.flags.use_u_aniso():
assert unit_cell is not None
u_cart = adptbx.u_star_as_u_cart(unit_cell, self.u_star)
print >> f, "%6.4f" % adptbx.u_cart_as_u_iso(u_cart)
print >> f, " u_cart =", ("%6.3f " * 5 + "%6.3f") % u_cart,
else:
print >> f, '[ - ]',
if (self.fp != 0 or self.fdp != 0):
print >> f, "\n fp,fdp = %6.4f,%6.4f" % (self.fp, self.fdp),
print >> f
def show(self, f=None, unit_cell=None):
if f is None:
f = sys.stdout
print >> f, "%-4s" % self.label,
print >> f, "%-4s" % self.scattering_type,
print >> f, "%3d" % self.multiplicity(),
print >> f, "(%7.4f %7.4f %7.4f)" % self.site,
print >> f, "%4.2f" % self.occupancy,
if self.flags.use_u_iso():
print >> f, "%6.4f" % self.u_iso,
else:
print >> f, "[ - ]",
if self.flags.use_u_aniso():
assert unit_cell is not None
u_cart = adptbx.u_star_as_u_cart(unit_cell, self.u_star)
print >> f, "%6.4f" % adptbx.u_cart_as_u_iso(u_cart)
print >> f, " u_cart =", ("%6.3f " * 5 + "%6.3f") % u_cart,
else:
print >> f, "[ - ]",
if self.fp != 0 or self.fdp != 0:
print >> f, "\n fp,fdp = %6.4f,%6.4f" % (self.fp, self.fdp),
print >> f
def exercise_interface():
episq = 8*(math.pi**2)
assert approx_equal(adptbx.u_as_b(2.3), 2.3*episq)
assert approx_equal(adptbx.b_as_u(adptbx.u_as_b(2.3)), 2.3)
u = (3,4,9, 2,1,7)
assert approx_equal(adptbx.u_as_b(u), [x*episq for x in u])
assert approx_equal(adptbx.b_as_u(adptbx.u_as_b(u)), u)
uc = uctbx.unit_cell((5,4,7,80,110,100))
for fw,bw in ((adptbx.u_cif_as_u_star, adptbx.u_star_as_u_cif),
(adptbx.u_cart_as_u_star, adptbx.u_star_as_u_cart),
(adptbx.u_cart_as_u_cif, adptbx.u_cif_as_u_cart),
(adptbx.u_cart_as_beta, adptbx.beta_as_u_cart),
(adptbx.u_cif_as_beta, adptbx.beta_as_u_cif)):
assert approx_equal(bw(uc, fw(uc, u)), u)
assert approx_equal(adptbx.beta_as_u_star(adptbx.u_star_as_beta(u)), u)
assert approx_equal(adptbx.u_cart_as_u_iso(adptbx.u_iso_as_u_cart(2.3)), 2.3)
for fw,bw in ((adptbx.u_iso_as_u_star, adptbx.u_star_as_u_iso),
(adptbx.u_iso_as_u_cif, adptbx.u_cif_as_u_iso),
(adptbx.u_iso_as_beta, adptbx.beta_as_u_iso)):
assert approx_equal(bw(uc, fw(uc, 2.3)), 2.3)
fc = adptbx.factor_u_cart_u_iso(u_cart=u)
assert approx_equal(fc.u_iso, adptbx.u_cart_as_u_iso(u))
assert approx_equal(
fc.u_cart_minus_u_iso,
[uii-fc.u_iso for uii in u[:3]]+list(u[3:]))
f = adptbx.factor_u_star_u_iso(
unit_cell=uc, u_star=adptbx.u_cart_as_u_star(uc, u))
assert approx_equal(f.u_iso, fc.u_iso)
assert approx_equal(
f.u_star_minus_u_iso,
adptbx.u_cart_as_u_star(uc, fc.u_cart_minus_u_iso))
f = adptbx.factor_u_cif_u_iso(
unit_cell=uc, u_cif=adptbx.u_cart_as_u_cif(uc, u))
assert approx_equal(f.u_iso, fc.u_iso)
assert approx_equal(
f.u_cif_minus_u_iso,
adptbx.u_cart_as_u_cif(uc, fc.u_cart_minus_u_iso))
f = adptbx.factor_beta_u_iso(
unit_cell=uc, beta=adptbx.u_cart_as_beta(uc, u))
assert approx_equal(f.u_iso, fc.u_iso)
assert approx_equal(
f.beta_minus_u_iso,
adptbx.u_cart_as_beta(uc, fc.u_cart_minus_u_iso))
assert approx_equal(adptbx.debye_waller_factor_b_iso(0.25,2.3),
math.exp(-2.3*0.25))
assert approx_equal(adptbx.debye_waller_factor_u_iso(0.25,2.3),
math.exp(-2.3*episq*0.25))
assert approx_equal(adptbx.debye_waller_factor_b_iso(uc, (1,2,3), 2.3),
adptbx.debye_waller_factor_u_iso(uc, (1,2,3), 2.3/episq))
u_star = adptbx.u_cart_as_u_star(uc, u)
dw = adptbx.debye_waller_factor_u_star((1,2,3), u_star)
assert approx_equal(dw, adptbx.debye_waller_factor_beta((1,2,3),
adptbx.u_star_as_beta(u_star)))
assert approx_equal(dw, adptbx.debye_waller_factor_u_cif(uc, (1,2,3),
adptbx.u_star_as_u_cif(uc, u_star)))
assert approx_equal(dw, adptbx.debye_waller_factor_u_cart(uc, (1,2,3),
adptbx.u_star_as_u_cart(uc, u_star)))
for e in adptbx.eigenvalues(u):
check_eigenvalue(u, e)
assert not adptbx.is_positive_definite(adptbx.eigenvalues(u))
assert not adptbx.is_positive_definite(adptbx.eigenvalues(u), 0)
assert adptbx.is_positive_definite(adptbx.eigenvalues(u), 1.22)
assert not adptbx.is_positive_definite(u)
assert not adptbx.is_positive_definite(u, 0)
assert adptbx.is_positive_definite(u, 1.22)
up = (0.534, 0.812, 0.613, 0.0166, 0.134, -0.0124)
s = adptbx.eigensystem(up)
assert approx_equal(s.values(), (0.813132, 0.713201, 0.432668))
for i in xrange(3):
check_eigenvector(up, s.values()[i], s.vectors(i))
c = (1,2,3, 3,-4,5, 4,5,6)
v = (198,18,1020,116,447,269)
assert approx_equal(adptbx.c_u_c_transpose(c, u), v)
assert approx_equal(adptbx.eigensystem(u).values(),
(14.279201519086316, 2.9369143826320214, -1.2161159017183376))
s = adptbx.eigensystem(up)
try: s.vectors(4)
except RuntimeError, e: assert str(e).endswith("Index out of range.")
else: raise Exception_expected
uf = adptbx.eigenvalue_filtering(u_cart=u, u_min=0)
assert approx_equal(uf, (3.0810418, 4.7950710, 9.3400030,
1.7461615, 1.1659954, 6.4800706))
uf = adptbx.eigenvalue_filtering(u_cart=u, u_min=0, u_max=3)
assert approx_equal(uf, (2.7430890, 1.0378360, 2.1559895,
0.6193215, -0.3921632, 1.2846854))
uf = adptbx.eigenvalue_filtering(u_cart=u, u_min=0, u_max=3)
assert approx_equal(scitbx.linalg.eigensystem.real_symmetric(u).values(),
(14.2792015, 2.9369144, -1.2161159))
assert approx_equal(scitbx.linalg.eigensystem.real_symmetric(uf).values(),
(3, 2.9369144, 0))
uf = adptbx.eigenvalue_filtering(up)
assert approx_equal(uf, up)
def u_star_minus_u_iso_ralf(unit_cell, u_star): u_cart = adptbx.u_star_as_u_cart(unit_cell, u_star) u_iso = adptbx.u_cart_as_u_iso(u_cart) u_cart_minus_u_iso = [a-u_iso for a in u_cart[:3]] + list(u_cart[3:]) return adptbx.u_cart_as_u_star(unit_cell, u_cart_minus_u_iso)
def exercise_interface():
episq = 8 * (math.pi**2)
assert approx_equal(adptbx.u_as_b(2.3), 2.3 * episq)
assert approx_equal(adptbx.b_as_u(adptbx.u_as_b(2.3)), 2.3)
u = (3, 4, 9, 2, 1, 7)
assert approx_equal(adptbx.u_as_b(u), [x * episq for x in u])
assert approx_equal(adptbx.b_as_u(adptbx.u_as_b(u)), u)
uc = uctbx.unit_cell((5, 4, 7, 80, 110, 100))
for fw, bw in ((adptbx.u_cif_as_u_star, adptbx.u_star_as_u_cif),
(adptbx.u_cart_as_u_star, adptbx.u_star_as_u_cart),
(adptbx.u_cart_as_u_cif, adptbx.u_cif_as_u_cart),
(adptbx.u_cart_as_beta, adptbx.beta_as_u_cart),
(adptbx.u_cif_as_beta, adptbx.beta_as_u_cif)):
assert approx_equal(bw(uc, fw(uc, u)), u)
assert approx_equal(adptbx.beta_as_u_star(adptbx.u_star_as_beta(u)), u)
assert approx_equal(adptbx.u_cart_as_u_iso(adptbx.u_iso_as_u_cart(2.3)),
2.3)
for fw, bw in ((adptbx.u_iso_as_u_star, adptbx.u_star_as_u_iso),
(adptbx.u_iso_as_u_cif, adptbx.u_cif_as_u_iso),
(adptbx.u_iso_as_beta, adptbx.beta_as_u_iso)):
assert approx_equal(bw(uc, fw(uc, 2.3)), 2.3)
fc = adptbx.factor_u_cart_u_iso(u_cart=u)
assert approx_equal(fc.u_iso, adptbx.u_cart_as_u_iso(u))
assert approx_equal(fc.u_cart_minus_u_iso,
[uii - fc.u_iso for uii in u[:3]] + list(u[3:]))
f = adptbx.factor_u_star_u_iso(unit_cell=uc,
u_star=adptbx.u_cart_as_u_star(uc, u))
assert approx_equal(f.u_iso, fc.u_iso)
assert approx_equal(f.u_star_minus_u_iso,
adptbx.u_cart_as_u_star(uc, fc.u_cart_minus_u_iso))
f = adptbx.factor_u_cif_u_iso(unit_cell=uc,
u_cif=adptbx.u_cart_as_u_cif(uc, u))
assert approx_equal(f.u_iso, fc.u_iso)
assert approx_equal(f.u_cif_minus_u_iso,
adptbx.u_cart_as_u_cif(uc, fc.u_cart_minus_u_iso))
f = adptbx.factor_beta_u_iso(unit_cell=uc,
beta=adptbx.u_cart_as_beta(uc, u))
assert approx_equal(f.u_iso, fc.u_iso)
assert approx_equal(f.beta_minus_u_iso,
adptbx.u_cart_as_beta(uc, fc.u_cart_minus_u_iso))
assert approx_equal(adptbx.debye_waller_factor_b_iso(0.25, 2.3),
math.exp(-2.3 * 0.25))
assert approx_equal(adptbx.debye_waller_factor_u_iso(0.25, 2.3),
math.exp(-2.3 * episq * 0.25))
assert approx_equal(
adptbx.debye_waller_factor_b_iso(uc, (1, 2, 3), 2.3),
adptbx.debye_waller_factor_u_iso(uc, (1, 2, 3), 2.3 / episq))
u_star = adptbx.u_cart_as_u_star(uc, u)
dw = adptbx.debye_waller_factor_u_star((1, 2, 3), u_star)
assert approx_equal(
dw,
adptbx.debye_waller_factor_beta((1, 2, 3),
adptbx.u_star_as_beta(u_star)))
assert approx_equal(
dw,
adptbx.debye_waller_factor_u_cif(uc, (1, 2, 3),
adptbx.u_star_as_u_cif(uc, u_star)))
assert approx_equal(
dw,
adptbx.debye_waller_factor_u_cart(uc, (1, 2, 3),
adptbx.u_star_as_u_cart(uc, u_star)))
for e in adptbx.eigenvalues(u):
check_eigenvalue(u, e)
assert not adptbx.is_positive_definite(adptbx.eigenvalues(u))
assert not adptbx.is_positive_definite(adptbx.eigenvalues(u), 0)
assert adptbx.is_positive_definite(adptbx.eigenvalues(u), 1.22)
assert not adptbx.is_positive_definite(u)
assert not adptbx.is_positive_definite(u, 0)
assert adptbx.is_positive_definite(u, 1.22)
up = (0.534, 0.812, 0.613, 0.0166, 0.134, -0.0124)
s = adptbx.eigensystem(up)
assert approx_equal(s.values(), (0.813132, 0.713201, 0.432668))
for i in xrange(3):
check_eigenvector(up, s.values()[i], s.vectors(i))
c = (1, 2, 3, 3, -4, 5, 4, 5, 6)
v = (198, 18, 1020, 116, 447, 269)
assert approx_equal(adptbx.c_u_c_transpose(c, u), v)
assert approx_equal(
adptbx.eigensystem(u).values(),
(14.279201519086316, 2.9369143826320214, -1.2161159017183376))
s = adptbx.eigensystem(up)
try:
s.vectors(4)
except RuntimeError, e:
assert str(e).endswith("Index out of range.")
def exercise_interface():
episq = 8 * (math.pi ** 2)
assert approx_equal(adptbx.u_as_b(2.3), 2.3 * episq)
assert approx_equal(adptbx.b_as_u(adptbx.u_as_b(2.3)), 2.3)
u = (3, 4, 9, 2, 1, 7)
assert approx_equal(adptbx.u_as_b(u), [x * episq for x in u])
assert approx_equal(adptbx.b_as_u(adptbx.u_as_b(u)), u)
uc = uctbx.unit_cell((5, 4, 7, 80, 110, 100))
for fw, bw in (
(adptbx.u_cif_as_u_star, adptbx.u_star_as_u_cif),
(adptbx.u_cart_as_u_star, adptbx.u_star_as_u_cart),
(adptbx.u_cart_as_u_cif, adptbx.u_cif_as_u_cart),
(adptbx.u_cart_as_beta, adptbx.beta_as_u_cart),
(adptbx.u_cif_as_beta, adptbx.beta_as_u_cif),
):
assert approx_equal(bw(uc, fw(uc, u)), u)
assert approx_equal(adptbx.beta_as_u_star(adptbx.u_star_as_beta(u)), u)
assert approx_equal(adptbx.u_cart_as_u_iso(adptbx.u_iso_as_u_cart(2.3)), 2.3)
for fw, bw in (
(adptbx.u_iso_as_u_star, adptbx.u_star_as_u_iso),
(adptbx.u_iso_as_u_cif, adptbx.u_cif_as_u_iso),
(adptbx.u_iso_as_beta, adptbx.beta_as_u_iso),
):
assert approx_equal(bw(uc, fw(uc, 2.3)), 2.3)
fc = adptbx.factor_u_cart_u_iso(u_cart=u)
assert approx_equal(fc.u_iso, adptbx.u_cart_as_u_iso(u))
assert approx_equal(fc.u_cart_minus_u_iso, [uii - fc.u_iso for uii in u[:3]] + list(u[3:]))
f = adptbx.factor_u_star_u_iso(unit_cell=uc, u_star=adptbx.u_cart_as_u_star(uc, u))
assert approx_equal(f.u_iso, fc.u_iso)
assert approx_equal(f.u_star_minus_u_iso, adptbx.u_cart_as_u_star(uc, fc.u_cart_minus_u_iso))
f = adptbx.factor_u_cif_u_iso(unit_cell=uc, u_cif=adptbx.u_cart_as_u_cif(uc, u))
assert approx_equal(f.u_iso, fc.u_iso)
assert approx_equal(f.u_cif_minus_u_iso, adptbx.u_cart_as_u_cif(uc, fc.u_cart_minus_u_iso))
f = adptbx.factor_beta_u_iso(unit_cell=uc, beta=adptbx.u_cart_as_beta(uc, u))
assert approx_equal(f.u_iso, fc.u_iso)
assert approx_equal(f.beta_minus_u_iso, adptbx.u_cart_as_beta(uc, fc.u_cart_minus_u_iso))
assert approx_equal(adptbx.debye_waller_factor_b_iso(0.25, 2.3), math.exp(-2.3 * 0.25))
assert approx_equal(adptbx.debye_waller_factor_u_iso(0.25, 2.3), math.exp(-2.3 * episq * 0.25))
assert approx_equal(
adptbx.debye_waller_factor_b_iso(uc, (1, 2, 3), 2.3),
adptbx.debye_waller_factor_u_iso(uc, (1, 2, 3), 2.3 / episq),
)
u_star = adptbx.u_cart_as_u_star(uc, u)
dw = adptbx.debye_waller_factor_u_star((1, 2, 3), u_star)
assert approx_equal(dw, adptbx.debye_waller_factor_beta((1, 2, 3), adptbx.u_star_as_beta(u_star)))
assert approx_equal(dw, adptbx.debye_waller_factor_u_cif(uc, (1, 2, 3), adptbx.u_star_as_u_cif(uc, u_star)))
assert approx_equal(dw, adptbx.debye_waller_factor_u_cart(uc, (1, 2, 3), adptbx.u_star_as_u_cart(uc, u_star)))
for e in adptbx.eigenvalues(u):
check_eigenvalue(u, e)
assert not adptbx.is_positive_definite(adptbx.eigenvalues(u))
assert not adptbx.is_positive_definite(adptbx.eigenvalues(u), 0)
assert adptbx.is_positive_definite(adptbx.eigenvalues(u), 1.22)
assert not adptbx.is_positive_definite(u)
assert not adptbx.is_positive_definite(u, 0)
assert adptbx.is_positive_definite(u, 1.22)
up = (0.534, 0.812, 0.613, 0.0166, 0.134, -0.0124)
s = adptbx.eigensystem(up)
assert approx_equal(s.values(), (0.813132, 0.713201, 0.432668))
for i in xrange(3):
check_eigenvector(up, s.values()[i], s.vectors(i))
c = (1, 2, 3, 3, -4, 5, 4, 5, 6)
v = (198, 18, 1020, 116, 447, 269)
assert approx_equal(adptbx.c_u_c_transpose(c, u), v)
assert approx_equal(adptbx.eigensystem(u).values(), (14.279201519086316, 2.9369143826320214, -1.2161159017183376))
s = adptbx.eigensystem(up)
try:
s.vectors(4)
except RuntimeError, e:
assert str(e).endswith("Index out of range.")
def u_star_minus_u_iso_ralf(unit_cell, u_star):
u_cart = adptbx.u_star_as_u_cart(unit_cell, u_star)
u_iso = adptbx.u_cart_as_u_iso(u_cart)
u_cart_minus_u_iso = [a - u_iso for a in u_cart[:3]] + list(u_cart[3:])
return adptbx.u_cart_as_u_star(unit_cell, u_cart_minus_u_iso)
