class angle_restraint_test_case(geometry_restraints_test_case):
manager = restraints.manager(
angle_proxies=geometry_restraints.shared_angle_proxy([
geom.angle_proxy((30, 0, 19), 115, 1),
geom.angle_proxy((21, 1, 2), 110, 1)
]))
proxies = manager.angle_proxies
restraint_t = geom.angle
class dihedral_restraint_test_case(geometry_restraints_test_case):
manager = restraints.manager(
dihedral_proxies=geometry_restraints.shared_dihedral_proxy([
geom.dihedral_proxy((21, 19, 24, 26), 180, 1),
geom.dihedral_proxy((5, 26, 28, 7), 60, 1)
]))
proxies = manager.dihedral_proxies
restraint_t = geom.dihedral
class bond_restraint_test_case(geometry_restraints_test_case):
manager = restraints.manager(
bond_proxies=geometry_restraints.shared_bond_simple_proxy([
geom.bond_simple_proxy((0, 30), 1.42, 1),
geom.bond_simple_proxy((1, 21), 1.42, 1)
]))
proxies = manager.bond_proxies
restraint_t = geom.bond
class fixed_u_eq_adp_test_case(adp_restraints_test_case):
proxies = fixed_u_eq_adp_restraints(
xray_structure=smtbx.development.sucrose(), u_eq_ideal=0.025).proxies
# no need to test all of them every time
proxies = adp.shared_fixed_u_eq_adp_proxy(
flex.select(proxies, flags=flex.random_bool(proxies.size(), 0.5)))
manager = restraints.manager(fixed_u_eq_adp_proxies=proxies)
def restraint(self, proxy, u_iso=None, u_cart=None):
if u_cart is None:
u_cart = self.xray_structure.scatterers().extract_u_cart(
self.xray_structure.unit_cell())
return adp.fixed_u_eq_adp(adp_restraint_params(u_cart=u_cart), proxy)
class rigid_bond_test_case(adp_restraints_test_case):
proxies = rigid_bond_restraints(
xray_structure=smtbx.development.sucrose()).proxies
# no need to test all of them every time
proxies = adp.shared_rigid_bond_proxy(
flex.select(proxies, flags=flex.random_bool(proxies.size(), 0.3)))
manager = restraints.manager(rigid_bond_proxies=proxies)
def restraint(self, proxy, u_iso=None, u_cart=None):
if u_cart is None:
u_cart = self.xray_structure.scatterers().extract_u_cart(
self.xray_structure.unit_cell())
sites_cart = self.xray_structure.sites_cart()
return adp.rigid_bond(
adp_restraint_params(sites_cart=sites_cart, u_cart=u_cart), proxy)
class adp_u_eq_similarity_test_case(adp_restraints_test_case):
proxies = adp_u_eq_similarity_restraints(
xray_structure=smtbx.development.sucrose()).proxies
# no need to test all of them every time
#proxies = adp.shared_adp_u_eq_similarity_proxy(
#flex.select(proxies, flags=flex.random_bool(proxies.size(), 0.5)))
manager = restraints.manager(adp_u_eq_similarity_proxies=proxies)
def restraint(self, proxy, u_iso=None, u_cart=None):
if u_cart is None:
u_cart=self.xray_structure.scatterers().extract_u_cart(
self.xray_structure.unit_cell())
if u_iso is None:
u_iso=self.xray_structure.scatterers().extract_u_iso()
use_u_aniso=self.xray_structure.use_u_aniso()
return adp.adp_u_eq_similarity(
adp_restraint_params(u_cart=u_cart, u_iso=u_iso, use_u_aniso=use_u_aniso),
proxy)
class adp_volume_similarity_test_case(adp_restraints_test_case):
proxies = adp_volume_similarity_restraints(
xray_structure=smtbx.development.sucrose()).proxies
manager = restraints.manager(adp_volume_similarity_proxies=proxies)
def __init__(self):
adp_restraints_test_case.__init__(self)
# eigen values and eigen vectors are dependent after all...
# may need to make smaller
self.tolerance = 0.2
def restraint(self, proxy, u_iso=None, u_cart=None):
if u_cart is None:
u_cart=self.xray_structure.scatterers().extract_u_cart(
self.xray_structure.unit_cell())
if u_iso is None:
u_iso=self.xray_structure.scatterers().extract_u_iso()
use_u_aniso=self.xray_structure.use_u_aniso()
return adp.adp_volume_similarity(
adp_restraint_params(u_cart=u_cart, u_iso=u_iso, use_u_aniso=use_u_aniso),
proxy)
def from_cif(cls, model, reflections):
"""
We could try to read in the weighting scheme.
As for constraints and restraints, the CIF format does not support them
yet
"""
from iotbx.reflection_file_reader import any_reflection_file
xs_dict = xray.structure.from_cif(file_path=model)
assert len(xs_dict) == 1, "CIF should contain only one xray structure"
xs = xs_dict.values()[0]
mas = any_reflection_file(reflections).as_miller_arrays(crystal_symmetry=xs)
fo_sq = None
for ma in mas:
if ma.is_xray_intensity_array() and ma.sigmas() is not None:
fo_sq = ma.as_xray_observations()
break
assert fo_sq is not None
return cls(fo_sq=fo_sq, xray_structure=xs,
constraints=[],
restraints_manager=restraints.manager(),
weighting_scheme=least_squares.sigma_weighting())
def exercise_manager(verbose=0):
xray_structure = smtbx.development.sucrose()
xray_structure.scatterers()[10].set_use_u_iso_only()
asu_mappings = xray_structure.asu_mappings(buffer_thickness=3.5)
pair_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
scattering_types = xray_structure.scatterers().extract_scattering_types()
pair_asu_table.add_covalent_pairs(
scattering_types, exclude_scattering_types=flex.std_string(("H","D")))
pair_sym_table = pair_asu_table.extract_pair_sym_table()
# setup adp restraint proxies
adp_similarity_proxies = \
adp_restraints.adp_similarity_restraints(
pair_sym_table=pair_sym_table).proxies
rigid_bond_proxies = \
adp_restraints.rigid_bond_restraints(
pair_sym_table=pair_sym_table).proxies
isotropic_adp_proxies = \
adp_restraints.isotropic_adp_restraints(
xray_structure=xray_structure,
pair_sym_table=pair_sym_table).proxies
bond_proxies = cctbx.geometry_restraints.shared_bond_simple_proxy()
bond_proxies.append(
cctbx.geometry_restraints.bond_simple_proxy(
i_seqs=(3,23), distance_ideal=1.44, weight=2))
bond_proxies.append(
cctbx.geometry_restraints.bond_simple_proxy(
i_seqs=(5,25), distance_ideal=1.44, weight=2))
bond_proxies.append(
cctbx.geometry_restraints.bond_simple_proxy(
i_seqs=(1,21), distance_ideal=1.44, weight=2))
angle_proxies = cctbx.geometry_restraints.shared_angle_proxy()
angle_proxies.append(
cctbx.geometry_restraints.angle_proxy(
i_seqs=(25,28,30),angle_ideal=110,weight=2))
angle_proxies.append(
cctbx.geometry_restraints.angle_proxy(
i_seqs=(23,25,28),angle_ideal=110,weight=2))
angle_proxies.append(
cctbx.geometry_restraints.angle_proxy(
i_seqs=(19,23,25),angle_ideal=110,weight=2))
bond_similarity_proxies=cctbx.geometry_restraints.shared_bond_similarity_proxy()
bond_similarity_proxies.append(
cctbx.geometry_restraints.bond_similarity_proxy(
i_seqs=((14,36),(12,38)),
weights=(10,10),
sym_ops=(sgtbx.rt_mx(),sgtbx.rt_mx())))
# setup restraints manager
manager = restraints.manager(
bond_proxies=bond_proxies,
angle_proxies=angle_proxies,
bond_similarity_proxies=bond_similarity_proxies,
adp_similarity_proxies=adp_similarity_proxies,
rigid_bond_proxies=rigid_bond_proxies,
isotropic_adp_proxies=isotropic_adp_proxies)
sio = StringIO()
manager.show_sorted(xray_structure, max_items=1, f=sio)
if sys.platform.startswith("win") and sys.version_info[:2] < (2,6):
# This appears to be a windows-specific bug with string formatting
# for python versions prior to 2.6, where the exponent is printed
# with 3 digits rather than 2.
pass
else:
assert not show_diff(sio.getvalue(), """\
Bond restraints: 3
Sorted by residual:
bond O3
C3
ideal model delta sigma weight residual
1.440 1.422 0.018 7.07e-01 2.00e+00 6.58e-04
... (remaining 2 not shown)
Bond angle restraints: 3
Sorted by residual:
angle C3
C4
C5
ideal model delta sigma weight residual
110.00 108.00 2.00 7.07e-01 2.00e+00 8.03e+00
... (remaining 2 not shown)
Bond similarity restraints: 1
Sorted by residual:
delta sigma weight rms_deltas residual sym.op.
bond O9-C9 -0.010 3.16e-01 1.00e+01 9.93e-03 9.87e-05
O8-C10 0.010 3.16e-01 1.00e+01
ADP similarity restraints: 24
Sorted by residual:
scatterers O7
C12
delta sigma weight rms_deltas residual
U11 -1.02e+00 8.00e-02 1.56e+02 5.93e-01 4.95e+02
U22 -1.03e+00 8.00e-02 1.56e+02
U33 -1.03e+00 8.00e-02 1.56e+02
U12 -4.23e-03 8.00e-02 1.56e+02
U13 -3.49e-03 8.00e-02 1.56e+02
U23 5.66e-03 8.00e-02 1.56e+02
... (remaining 23 not shown)
Rigid bond restraints: 60
Sorted by residual:
scatterers O7
C12
delta_z sigma weight residual
-6.42e-01 1.00e-02 1.00e+04 4.12e+03
... (remaining 59 not shown)
Isotropic ADP restraints: 22
Sorted by residual:
scatterer O3
delta sigma weight rms_deltas residual
U11 1.20e-03 2.00e-01 2.50e+01 1.34e-02 4.06e-02
U22 -2.46e-02 2.00e-01 2.50e+01
U33 2.34e-02 2.00e-01 2.50e+01
U12 -8.14e-03 2.00e-01 2.50e+01
U13 9.78e-03 2.00e-01 2.50e+01
U23 -8.63e-03 2.00e-01 2.50e+01
... (remaining 21 not shown)
""")
if (0 or verbose): print sio.getvalue()
def exercise_restrained_refinement(options):
import random
random.seed(1)
flex.set_random_seed(1)
xs0 = smtbx.development.random_xray_structure(
sgtbx.space_group_info('P1'),
n_scatterers=options.n_scatterers,
elements="random")
for sc in xs0.scatterers():
sc.flags.set_grad_site(True)
sc0 = xs0.scatterers()
uc = xs0.unit_cell()
mi = xs0.build_miller_set(anomalous_flag=False, d_min=options.resolution)
fo_sq = mi.structure_factors_from_scatterers(
xs0, algorithm="direct").f_calc().norm()
fo_sq = fo_sq.customized_copy(sigmas=flex.double(fo_sq.size(), 1))
i, j, k, l = random.sample(xrange(options.n_scatterers), 4)
bond_proxies = geometry_restraints.shared_bond_simple_proxy()
w = 1e9
d_ij = uc.distance(sc0[i].site, sc0[j].site) * 0.8
bond_proxies.append(
geom.bond_simple_proxy(i_seqs=(i, j), distance_ideal=d_ij, weight=w))
d_jk = uc.distance(sc0[j].site, sc0[k].site) * 0.85
bond_proxies.append(
geom.bond_simple_proxy(i_seqs=(j, k), distance_ideal=d_jk, weight=w))
d_ki = min(
uc.distance(sc0[k].site, sc0[i].site) * 0.9, (d_ij + d_jk) * 0.8)
bond_proxies.append(
geom.bond_simple_proxy(i_seqs=(k, i), distance_ideal=d_ki, weight=w))
d_jl = uc.distance(sc0[j].site, sc0[l].site) * 0.9
bond_proxies.append(
geom.bond_simple_proxy(i_seqs=(j, l), distance_ideal=d_jl, weight=w))
d_lk = min(
uc.distance(sc0[l].site, sc0[k].site) * 0.8, 0.75 * (d_jk + d_jl))
bond_proxies.append(
geom.bond_simple_proxy(i_seqs=(l, k), distance_ideal=d_jl, weight=w))
restraints_manager = restraints.manager(bond_proxies=bond_proxies)
xs1 = xs0.deep_copy_scatterers()
xs1.shake_sites_in_place(rms_difference=0.1)
def ls_problem():
xs = xs1.deep_copy_scatterers()
reparametrisation = constraints.reparametrisation(
structure=xs,
constraints=[],
connectivity_table=smtbx.utils.connectivity_table(xs),
temperature=20)
return least_squares.crystallographic_ls(
fo_sq.as_xray_observations(),
reparametrisation=reparametrisation,
restraints_manager=restraints_manager)
gradient_threshold, step_threshold = 1e-6, 1e-6
eps = 5e-3
ls = ls_problem()
t = wall_clock_time()
cycles = normal_eqns_solving.naive_iterations(
ls,
gradient_threshold=gradient_threshold,
step_threshold=step_threshold,
track_all=True)
if options.verbose:
print "%i %s steps in %.6f s" % (cycles.n_iterations, cycles,
t.elapsed())
sc = ls.xray_structure.scatterers()
for p in bond_proxies:
d = uc.distance(*[sc[i_pair].site for i_pair in p.i_seqs])
assert approx_equal(d, p.distance_ideal, eps)
ls = ls_problem()
t = wall_clock_time()
cycles = normal_eqns_solving.levenberg_marquardt_iterations(
ls,
gradient_threshold=gradient_threshold,
step_threshold=step_threshold,
tau=1e-3,
track_all=True)
if options.verbose:
print "%i %s steps in %.6f s" % (cycles.n_iterations, cycles,
t.elapsed())
sc = ls.xray_structure.scatterers()
sc = ls.xray_structure.scatterers()
for p in bond_proxies:
d = uc.distance(*[sc[i].site for i in p.i_seqs])
assert approx_equal(d, p.distance_ideal, eps)
def test_manager():
xray_structure = smtbx.development.sucrose()
xray_structure.scatterers()[10].set_use_u_iso_only()
asu_mappings = xray_structure.asu_mappings(buffer_thickness=3.5)
pair_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
scattering_types = xray_structure.scatterers().extract_scattering_types()
pair_asu_table.add_covalent_pairs(
scattering_types, exclude_scattering_types=flex.std_string(("H","D")))
pair_sym_table = pair_asu_table.extract_pair_sym_table()
# setup adp restraint proxies
adp_similarity_proxies = \
adp_restraints.adp_similarity_restraints(
pair_sym_table=pair_sym_table).proxies
rigid_bond_proxies = \
adp_restraints.rigid_bond_restraints(
pair_sym_table=pair_sym_table).proxies
rigu_proxies = \
adp_restraints.rigu_restraints(
pair_sym_table=pair_sym_table).proxies
isotropic_adp_proxies = \
adp_restraints.isotropic_adp_restraints(
xray_structure=xray_structure,
pair_sym_table=pair_sym_table).proxies
bond_proxies = cctbx.geometry_restraints.shared_bond_simple_proxy()
bond_proxies.append(
cctbx.geometry_restraints.bond_simple_proxy(
i_seqs=(3,23), distance_ideal=1.44, weight=2))
bond_proxies.append(
cctbx.geometry_restraints.bond_simple_proxy(
i_seqs=(5,25), distance_ideal=1.44, weight=2))
bond_proxies.append(
cctbx.geometry_restraints.bond_simple_proxy(
i_seqs=(1,21), distance_ideal=1.44, weight=2))
angle_proxies = cctbx.geometry_restraints.shared_angle_proxy()
angle_proxies.append(
cctbx.geometry_restraints.angle_proxy(
i_seqs=(25,28,30),angle_ideal=110,weight=2))
angle_proxies.append(
cctbx.geometry_restraints.angle_proxy(
i_seqs=(23,25,28),angle_ideal=110,weight=2))
angle_proxies.append(
cctbx.geometry_restraints.angle_proxy(
i_seqs=(19,23,25),angle_ideal=110,weight=2))
bond_similarity_proxies=cctbx.geometry_restraints.shared_bond_similarity_proxy()
bond_similarity_proxies.append(
cctbx.geometry_restraints.bond_similarity_proxy(
i_seqs=((14,36),(12,38)),
weights=(10,10),
sym_ops=(sgtbx.rt_mx(),sgtbx.rt_mx())))
chirality_proxies=cctbx.geometry_restraints.shared_chirality_proxy()
chirality_proxies.append(
cctbx.geometry_restraints.chirality_proxy(
i_seqs=(14,36,12,38),
weight=10**4,
volume_ideal=1.2,
both_signs=False))
# setup restraints manager
manager = restraints.manager(
bond_proxies=bond_proxies,
angle_proxies=angle_proxies,
bond_similarity_proxies=bond_similarity_proxies,
adp_similarity_proxies=adp_similarity_proxies,
rigid_bond_proxies=rigid_bond_proxies,
rigu_proxies=rigu_proxies,
isotropic_adp_proxies=isotropic_adp_proxies,
chirality_proxies=chirality_proxies)
sio = StringIO()
manager.show_sorted(xray_structure, max_items=1, f=sio)
if sys.platform.startswith("win") and sys.version_info[:2] < (2,6):
# This appears to be a windows-specific bug with string formatting
# for python versions prior to 2.6, where the exponent is printed
# with 3 digits rather than 2.
pass
else:
assert sio.getvalue() == """\
def exercise_restrained_refinement(options):
import random
random.seed(1)
flex.set_random_seed(1)
xs0 = smtbx.development.random_xray_structure(
sgtbx.space_group_info('P1'),
n_scatterers=options.n_scatterers,
elements="random")
for sc in xs0.scatterers():
sc.flags.set_grad_site(True)
sc0 = xs0.scatterers()
uc = xs0.unit_cell()
mi = xs0.build_miller_set(anomalous_flag=False, d_min=options.resolution)
fo_sq = mi.structure_factors_from_scatterers(
xs0, algorithm="direct").f_calc().norm()
fo_sq = fo_sq.customized_copy(sigmas=flex.double(fo_sq.size(), 1))
i, j, k, l = random.sample(xrange(options.n_scatterers), 4)
bond_proxies = geometry_restraints.shared_bond_simple_proxy()
w = 1e9
d_ij = uc.distance(sc0[i].site, sc0[j].site)*0.8
bond_proxies.append(geom.bond_simple_proxy(
i_seqs=(i, j),
distance_ideal=d_ij,
weight=w))
d_jk = uc.distance(sc0[j].site, sc0[k].site)*0.85
bond_proxies.append(geom.bond_simple_proxy(
i_seqs=(j, k),
distance_ideal=d_jk,
weight=w))
d_ki = min(uc.distance(sc0[k].site, sc0[i].site)*0.9, (d_ij + d_jk)*0.8)
bond_proxies.append(geom.bond_simple_proxy(
i_seqs=(k, i),
distance_ideal=d_ki,
weight=w))
d_jl = uc.distance(sc0[j].site, sc0[l].site)*0.9
bond_proxies.append(geom.bond_simple_proxy(
i_seqs=(j, l),
distance_ideal=d_jl,
weight=w))
d_lk = min(uc.distance(sc0[l].site, sc0[k].site)*0.8, 0.75*(d_jk + d_jl))
bond_proxies.append(geom.bond_simple_proxy(
i_seqs=(l, k),
distance_ideal=d_jl,
weight=w))
restraints_manager = restraints.manager(bond_proxies=bond_proxies)
xs1 = xs0.deep_copy_scatterers()
xs1.shake_sites_in_place(rms_difference=0.1)
def ls_problem():
xs = xs1.deep_copy_scatterers()
reparametrisation = constraints.reparametrisation(
structure=xs,
constraints=[],
connectivity_table=smtbx.utils.connectivity_table(xs),
temperature=20)
return least_squares.crystallographic_ls(
fo_sq.as_xray_observations(),
reparametrisation=reparametrisation,
restraints_manager=restraints_manager)
gradient_threshold, step_threshold = 1e-6, 1e-6
eps = 5e-3
ls = ls_problem()
t = wall_clock_time()
cycles = normal_eqns_solving.naive_iterations(
ls,
gradient_threshold=gradient_threshold,
step_threshold=step_threshold,
track_all=True)
if options.verbose:
print "%i %s steps in %.6f s" % (cycles.n_iterations, cycles, t.elapsed())
sc = ls.xray_structure.scatterers()
for p in bond_proxies:
d = uc.distance(*[ sc[i_pair].site for i_pair in p.i_seqs ])
assert approx_equal(d, p.distance_ideal, eps)
ls = ls_problem()
t = wall_clock_time()
cycles = normal_eqns_solving.levenberg_marquardt_iterations(
ls,
gradient_threshold=gradient_threshold,
step_threshold=step_threshold,
tau=1e-3,
track_all=True)
if options.verbose:
print "%i %s steps in %.6f s" % (cycles.n_iterations, cycles, t.elapsed())
sc = ls.xray_structure.scatterers()
sc = ls.xray_structure.scatterers()
for p in bond_proxies:
d = uc.distance(*[ sc[i].site for i in p.i_seqs ])
assert approx_equal(d, p.distance_ideal, eps)
def restraints_manager(self):
from smtbx.refinement.restraints import manager
kwds = dict([("%s_proxies" % name, value)
for name, value in self.proxies().iteritems()])
return manager(**kwds)
def exercise_manager(verbose=0):
xray_structure = smtbx.development.sucrose()
xray_structure.scatterers()[10].set_use_u_iso_only()
asu_mappings = xray_structure.asu_mappings(buffer_thickness=3.5)
pair_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
scattering_types = xray_structure.scatterers().extract_scattering_types()
pair_asu_table.add_covalent_pairs(scattering_types,
exclude_scattering_types=flex.std_string(
("H", "D")))
pair_sym_table = pair_asu_table.extract_pair_sym_table()
# setup adp restraint proxies
adp_similarity_proxies = \
adp_restraints.adp_similarity_restraints(
pair_sym_table=pair_sym_table).proxies
rigid_bond_proxies = \
adp_restraints.rigid_bond_restraints(
pair_sym_table=pair_sym_table).proxies
isotropic_adp_proxies = \
adp_restraints.isotropic_adp_restraints(
xray_structure=xray_structure,
pair_sym_table=pair_sym_table).proxies
bond_proxies = cctbx.geometry_restraints.shared_bond_simple_proxy()
bond_proxies.append(
cctbx.geometry_restraints.bond_simple_proxy(i_seqs=(3, 23),
distance_ideal=1.44,
weight=2))
bond_proxies.append(
cctbx.geometry_restraints.bond_simple_proxy(i_seqs=(5, 25),
distance_ideal=1.44,
weight=2))
bond_proxies.append(
cctbx.geometry_restraints.bond_simple_proxy(i_seqs=(1, 21),
distance_ideal=1.44,
weight=2))
angle_proxies = cctbx.geometry_restraints.shared_angle_proxy()
angle_proxies.append(
cctbx.geometry_restraints.angle_proxy(i_seqs=(25, 28, 30),
angle_ideal=110,
weight=2))
angle_proxies.append(
cctbx.geometry_restraints.angle_proxy(i_seqs=(23, 25, 28),
angle_ideal=110,
weight=2))
angle_proxies.append(
cctbx.geometry_restraints.angle_proxy(i_seqs=(19, 23, 25),
angle_ideal=110,
weight=2))
bond_similarity_proxies = cctbx.geometry_restraints.shared_bond_similarity_proxy(
)
bond_similarity_proxies.append(
cctbx.geometry_restraints.bond_similarity_proxy(
i_seqs=((14, 36), (12, 38)),
weights=(10, 10),
sym_ops=(sgtbx.rt_mx(), sgtbx.rt_mx())))
# setup restraints manager
manager = restraints.manager(
bond_proxies=bond_proxies,
angle_proxies=angle_proxies,
bond_similarity_proxies=bond_similarity_proxies,
adp_similarity_proxies=adp_similarity_proxies,
rigid_bond_proxies=rigid_bond_proxies,
isotropic_adp_proxies=isotropic_adp_proxies)
sio = StringIO()
manager.show_sorted(xray_structure, max_items=1, f=sio)
if sys.platform.startswith("win") and sys.version_info[:2] < (2, 6):
# This appears to be a windows-specific bug with string formatting
# for python versions prior to 2.6, where the exponent is printed
# with 3 digits rather than 2.
pass
else:
assert not show_diff(
sio.getvalue(), """\
Bond restraints: 3
Sorted by residual:
bond O3
C3
ideal model delta sigma weight residual
1.440 1.422 0.018 7.07e-01 2.00e+00 6.58e-04
... (remaining 2 not shown)
Bond angle restraints: 3
Sorted by residual:
angle C3
C4
C5
ideal model delta sigma weight residual
110.00 108.00 2.00 7.07e-01 2.00e+00 8.03e+00
... (remaining 2 not shown)
Bond similarity restraints: 1
Sorted by residual:
delta sigma weight rms_deltas residual sym.op.
bond O9-C9 -0.010 3.16e-01 1.00e+01 9.93e-03 9.87e-05
O8-C10 0.010 3.16e-01 1.00e+01
ADP similarity restraints: 24
Sorted by residual:
scatterers O7
C12
delta sigma weight rms_deltas residual
U11 -1.02e+00 8.00e-02 1.56e+02 5.93e-01 4.95e+02
U22 -1.03e+00 8.00e-02 1.56e+02
U33 -1.03e+00 8.00e-02 1.56e+02
U12 -4.23e-03 8.00e-02 1.56e+02
U13 -3.49e-03 8.00e-02 1.56e+02
U23 5.66e-03 8.00e-02 1.56e+02
... (remaining 23 not shown)
Rigid bond restraints: 60
Sorted by residual:
scatterers O7
C12
delta_z sigma weight residual
-6.42e-01 1.00e-02 1.00e+04 4.12e+03
... (remaining 59 not shown)
Isotropic ADP restraints: 22
Sorted by residual:
scatterer O3
delta sigma weight rms_deltas residual
U11 1.20e-03 2.00e-01 2.50e+01 1.34e-02 4.06e-02
U22 -2.46e-02 2.00e-01 2.50e+01
U33 2.34e-02 2.00e-01 2.50e+01
U12 -8.14e-03 2.00e-01 2.50e+01
U13 9.78e-03 2.00e-01 2.50e+01
U23 -8.63e-03 2.00e-01 2.50e+01
... (remaining 21 not shown)
""")
if (0 or verbose): print sio.getvalue()
def fget(self):
from smtbx.refinement.restraints import manager
kwds = dict([ ("%s_proxies" % name, value)
for name, value in self.proxies().iteritems() ])
return manager(**kwds)
