def __init__(self, *args, **kwds):
super(restrained_crystal_structure_builder,
self).__init__(*args, **kwds)
geom = geometry_restraints
adp = adp_restraints
self._proxies = {}
self._proxies = {
'bond':
geometry_restraints.shared_bond_simple_proxy(),
'angle':
geometry_restraints.shared_angle_proxy(),
'dihedral':
geometry_restraints.shared_dihedral_proxy(),
'planarity':
geometry_restraints.shared_planarity_proxy(),
'chirality':
geometry_restraints.shared_chirality_proxy(),
'bond_similarity':
geometry_restraints.shared_bond_similarity_proxy(),
'adp_similarity':
adp_restraints.shared_adp_similarity_proxy(),
'rigid_bond':
adp_restraints.shared_rigid_bond_proxy(),
'isotropic_adp':
adp_restraints.shared_isotropic_adp_proxy(),
'fixed_u_eq_adp':
adp_restraints.shared_fixed_u_eq_adp_proxy(),
'adp_u_eq_similarity':
adp_restraints.shared_adp_u_eq_similarity_proxy(),
'adp_volume_similarity':
adp_restraints.shared_adp_volume_similarity_proxy(),
}
def exercise_isotropic_adp():
i_seqs = (0,)
weight = 2
u_cart = ((1,2,3,5,2,8),)
u_iso = (0,)
use_u_aniso = (True,)
p = adp_restraints.isotropic_adp_proxy(
i_seqs=i_seqs,
weight=weight)
assert p.i_seqs == i_seqs
assert approx_equal(p.weight, weight)
i = adp_restraints.isotropic_adp(u_cart=u_cart[0], weight=weight)
expected_deltas = (-1, 0, 1, 5, 2, 8)
expected_gradients = (-4, 0, 4, 40, 16, 64)
assert approx_equal(i.weight, weight)
assert approx_equal(i.deltas(), expected_deltas)
assert approx_equal(i.rms_deltas(), 4.5704364002673632)
assert approx_equal(i.residual(), 376.0)
assert approx_equal(i.gradients(), expected_gradients)
gradients_aniso_cart = flex.sym_mat3_double(1, (0,0,0,0,0,0))
gradients_iso = flex.double(1,0)
proxies = adp_restraints.shared_isotropic_adp_proxy([p,p])
u_cart = flex.sym_mat3_double(u_cart)
u_iso = flex.double(u_iso)
use_u_aniso = flex.bool(use_u_aniso)
params = adp_restraint_params(u_cart=u_cart, u_iso=u_iso, use_u_aniso=use_u_aniso)
residuals = adp_restraints.isotropic_adp_residuals(params, proxies=proxies)
assert approx_equal(residuals, (i.residual(),i.residual()))
deltas_rms = adp_restraints.isotropic_adp_deltas_rms(params, proxies=proxies)
assert approx_equal(deltas_rms, (i.rms_deltas(),i.rms_deltas()))
residual_sum = adp_restraints.isotropic_adp_residual_sum(
params,
proxies=proxies,
gradients_aniso_cart=gradients_aniso_cart
)
assert approx_equal(residual_sum, 752.0)
fd_grads_aniso, fd_grads_iso = finite_difference_gradients(
restraint_type=adp_restraints.isotropic_adp,
proxy=p,
u_cart=u_cart,
u_iso=u_iso,
use_u_aniso=use_u_aniso
)
for g,e in zip(gradients_aniso_cart, fd_grads_aniso):
assert approx_equal(g, matrix.col(e)*2)
#
# check frame invariance of residual
#
u_cart = matrix.sym(sym_mat3=(0.1,0.2,0.05,0.03,0.02,0.01))
a = adp_restraints.isotropic_adp(
u_cart=u_cart.as_sym_mat3(), weight=1)
expected_residual = a.residual()
gen = flex.mersenne_twister()
for i in range(20):
R = matrix.rec(gen.random_double_r3_rotation_matrix(),(3,3))
u_cart_rot = R * u_cart * R.transpose()
a = adp_restraints.isotropic_adp(
u_cart=u_cart_rot.as_sym_mat3(), weight=1)
assert approx_equal(a.residual(), expected_residual)
def exercise_isotropic_adp():
i_seqs = (0,)
weight = 2
u_cart = ((1,2,3,5,2,8),)
u_iso = (0,)
use_u_aniso = (True,)
p = adp_restraints.isotropic_adp_proxy(
i_seqs=i_seqs,
weight=weight)
assert p.i_seqs == i_seqs
assert approx_equal(p.weight, weight)
i = adp_restraints.isotropic_adp(u_cart=u_cart[0], weight=weight)
expected_deltas = (-1, 0, 1, 5, 2, 8)
expected_gradients = (-4, 0, 4, 40, 16, 64)
assert approx_equal(i.weight, weight)
assert approx_equal(i.deltas(), expected_deltas)
assert approx_equal(i.rms_deltas(), 4.5704364002673632)
assert approx_equal(i.residual(), 376.0)
assert approx_equal(i.gradients(), expected_gradients)
gradients_aniso_cart = flex.sym_mat3_double(1, (0,0,0,0,0,0))
gradients_iso = flex.double(1,0)
proxies = adp_restraints.shared_isotropic_adp_proxy([p,p])
u_cart = flex.sym_mat3_double(u_cart)
u_iso = flex.double(u_iso)
use_u_aniso = flex.bool(use_u_aniso)
params = adp_restraint_params(u_cart=u_cart, u_iso=u_iso, use_u_aniso=use_u_aniso)
residuals = adp_restraints.isotropic_adp_residuals(params, proxies=proxies)
assert approx_equal(residuals, (i.residual(),i.residual()))
deltas_rms = adp_restraints.isotropic_adp_deltas_rms(params, proxies=proxies)
assert approx_equal(deltas_rms, (i.rms_deltas(),i.rms_deltas()))
residual_sum = adp_restraints.isotropic_adp_residual_sum(
params,
proxies=proxies,
gradients_aniso_cart=gradients_aniso_cart
)
assert approx_equal(residual_sum, 752.0)
fd_grads_aniso, fd_grads_iso = finite_difference_gradients(
restraint_type=adp_restraints.isotropic_adp,
proxy=p,
u_cart=u_cart,
u_iso=u_iso,
use_u_aniso=use_u_aniso
)
for g,e in zip(gradients_aniso_cart, fd_grads_aniso):
assert approx_equal(g, matrix.col(e)*2)
#
# check frame invariance of residual
#
u_cart = matrix.sym(sym_mat3=(0.1,0.2,0.05,0.03,0.02,0.01))
a = adp_restraints.isotropic_adp(
u_cart=u_cart.as_sym_mat3(), weight=1)
expected_residual = a.residual()
gen = flex.mersenne_twister()
for i in range(20):
R = matrix.rec(gen.random_double_r3_rotation_matrix(),(3,3))
u_cart_rot = R * u_cart * R.transpose()
a = adp_restraints.isotropic_adp(
u_cart=u_cart_rot.as_sym_mat3(), weight=1)
assert approx_equal(a.residual(), expected_residual)
def __init__(self, *args, **kwds):
super(restrained_crystal_structure_builder, self).__init__(*args, **kwds)
geom = geometry_restraints
adp = adp_restraints
self._proxies = {}
self._proxies = {
'bond': geometry_restraints.shared_bond_simple_proxy(),
'angle': geometry_restraints.shared_angle_proxy(),
'dihedral': geometry_restraints.shared_dihedral_proxy(),
'planarity': geometry_restraints.shared_planarity_proxy(),
'chirality': geometry_restraints.shared_chirality_proxy(),
'bond_similarity': geometry_restraints.shared_bond_similarity_proxy(),
'adp_similarity': adp_restraints.shared_adp_similarity_proxy(),
'rigid_bond': adp_restraints.shared_rigid_bond_proxy(),
'isotropic_adp': adp_restraints.shared_isotropic_adp_proxy(),
'fixed_u_eq_adp': adp_restraints.shared_fixed_u_eq_adp_proxy(),
'adp_u_eq_similarity': adp_restraints.shared_adp_u_eq_similarity_proxy(),
'adp_volume_similarity': adp_restraints.shared_adp_volume_similarity_proxy(),
}
def __init__(
self,
xray_structure,
pair_sym_table=None,
proxies=None,
i_seqs=None,
sigma=0.1,
sigma_terminal=None,
buffer_thickness=3.5,
):
if sigma_terminal is None:
sigma_terminal = 2 * sigma
if i_seqs is not None and len(i_seqs) == 0:
i_seqs = None
if proxies is None:
proxies = adp_restraints.shared_isotropic_adp_proxy()
scattering_types = xray_structure.scatterers().extract_scattering_types()
use_u_aniso = xray_structure.scatterers().extract_use_u_aniso()
if pair_sym_table is None:
asu_mappings = xray_structure.asu_mappings(buffer_thickness=buffer_thickness)
pair_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
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()
connectivity = pair_sym_table.full_simple_connectivity()
for i_seq, neighbours in enumerate(connectivity):
if i_seqs is not None and i_seq not in i_seqs:
continue
elif scattering_types[i_seq] in ("H", "D"):
continue
elif not use_u_aniso[i_seq]:
continue
if neighbours.size() <= 1:
weight = 1 / (sigma_terminal * sigma_terminal)
else:
weight = 1 / (sigma * sigma)
proxies.append(adp_restraints.isotropic_adp_proxy(i_seqs=(i_seq,), weight=weight))
self.proxies = proxies
def __init__(self,
xray_structure,
pair_sym_table=None,
proxies=None,
i_seqs=None,
sigma=0.1,
sigma_terminal=None,
buffer_thickness=3.5):
if sigma_terminal is None: sigma_terminal = 2 * sigma
if i_seqs is not None and len(i_seqs) == 0: i_seqs = None
if proxies is None:
proxies = adp_restraints.shared_isotropic_adp_proxy()
scattering_types = xray_structure.scatterers(
).extract_scattering_types()
use_u_aniso = xray_structure.scatterers().extract_use_u_aniso()
if pair_sym_table is None:
asu_mappings = xray_structure.asu_mappings(
buffer_thickness=buffer_thickness)
pair_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
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()
connectivity = pair_sym_table.full_simple_connectivity()
for i_seq, neighbours in enumerate(connectivity):
if i_seqs is not None and i_seq not in i_seqs: continue
elif scattering_types[i_seq] in ('H', 'D'): continue
elif not use_u_aniso[i_seq]: continue
if neighbours.size() <= 1:
weight = 1 / (sigma_terminal * sigma_terminal)
else:
weight = 1 / (sigma * sigma)
proxies.append(
adp_restraints.isotropic_adp_proxy(i_seqs=(i_seq, ),
weight=weight))
self.proxies = proxies
def exercise_proxy_show():
sites_cart = flex.vec3_double((
(-3.1739,10.8317,7.5653),(-2.5419,9.7567,6.6306),
(-3.3369,8.8794,4.5191),(-3.4640,9.9882,5.3896)))
site_labels = ("C1", "C2", "O16", "N8")
u_cart = flex.sym_mat3_double((
(0.0153,0.0206,0.0234,0.0035,-0.0052,-0.0051),
(0.0185,0.0109,0.0206,0.0005,-0.0010,0.0002),
(0.0295,0.0203,0.0218,-0.0010,-0.0003,-0.0044),
(0.0159,0.0154,0.0206,-0.0003,0.0004,0.0036)))
u_iso = flex.double((-1,-1,-1,-1))
use_u_aniso = flex.bool((True,True,True,True))
#
proxies = adp_restraints.shared_adp_similarity_proxy()
sio = StringIO()
proxies.show_sorted(
by_value="residual",
u_cart=flex.sym_mat3_double(),
u_iso=flex.double(),
use_u_aniso=flex.bool(),
f=sio)
assert not show_diff(sio.getvalue(), """\
ADP similarity restraints: 0
""")
proxies = adp_restraints.shared_adp_similarity_proxy([
adp_restraints.adp_similarity_proxy(i_seqs=[0,1],weight=25),
adp_restraints.adp_similarity_proxy(i_seqs=[2,3],weight=0.3)])
sio = StringIO()
proxies.show_sorted(
by_value="residual",
u_cart=u_cart,
u_iso=u_iso,
use_u_aniso=use_u_aniso,
f=sio,
prefix=":")
assert not show_diff(sio.getvalue(), """\
:ADP similarity restraints: 2
:Sorted by residual:
:scatterers 0
: 1
: delta sigma weight rms_deltas residual
: U11 -3.20e-03 2.00e-01 2.50e+01 4.96e-03 5.54e-03
: U22 9.70e-03 2.00e-01 2.50e+01
: U33 2.80e-03 2.00e-01 2.50e+01
: U12 3.00e-03 2.00e-01 2.50e+01
: U13 -4.20e-03 2.00e-01 2.50e+01
: U23 -5.30e-03 2.00e-01 2.50e+01
:scatterers 2
: 3
: delta sigma weight rms_deltas residual
: U11 1.36e-02 1.83e+00 3.00e-01 6.15e-03 1.02e-04
: U22 4.90e-03 1.83e+00 3.00e-01
: U33 1.20e-03 1.83e+00 3.00e-01
: U12 -7.00e-04 1.83e+00 3.00e-01
: U13 -7.00e-04 1.83e+00 3.00e-01
: U23 -8.00e-03 1.83e+00 3.00e-01
""")
sio = StringIO()
proxies.show_sorted(
by_value="rms_deltas",
site_labels=site_labels,
u_cart=u_cart,
u_iso=flex.double((0.024,0.031,0.021,0.028)),
use_u_aniso=flex.bool((False,False,False,False)),
f=sio,
prefix="=")
assert not show_diff(sio.getvalue(), """\
=ADP similarity restraints: 2
=Sorted by rms_deltas:
=scatterers C1
= C2
= delta sigma weight residual
= Uiso -7.00e-03 2.00e-01 2.50e+01 1.22e-03
=scatterers O16
= N8
= delta sigma weight residual
= Uiso -7.00e-03 1.83e+00 3.00e-01 1.47e-05
""")
#
proxies = adp_restraints.shared_isotropic_adp_proxy()
sio = StringIO()
proxies.show_sorted(
by_value="residual",
u_cart=flex.sym_mat3_double(),
u_iso=u_iso,
use_u_aniso=use_u_aniso,
f=sio)
assert not show_diff(sio.getvalue(), """\
Isotropic ADP restraints: 0
""")
proxies = adp_restraints.shared_isotropic_adp_proxy([
adp_restraints.isotropic_adp_proxy(i_seqs=(0,),weight=25),
adp_restraints.isotropic_adp_proxy(i_seqs=(2,),weight=0.3)])
sio = StringIO()
proxies.show_sorted(
by_value="residual",
site_labels=site_labels,
u_cart=u_cart,
u_iso=u_iso,
use_u_aniso=use_u_aniso,
f=sio,
prefix=" ")
assert not show_diff(sio.getvalue(), """\
Isotropic ADP restraints: 2
Sorted by residual:
scatterer C1
delta sigma weight rms_deltas residual
U11 -4.47e-03 2.00e-01 2.50e+01 4.27e-03 4.11e-03
U22 8.33e-04 2.00e-01 2.50e+01
U33 3.63e-03 2.00e-01 2.50e+01
U12 3.50e-03 2.00e-01 2.50e+01
U13 -5.20e-03 2.00e-01 2.50e+01
U23 -5.10e-03 2.00e-01 2.50e+01
scatterer O16
delta sigma weight rms_deltas residual
U11 5.63e-03 1.83e+00 3.00e-01 3.16e-03 2.69e-05
U22 -3.57e-03 1.83e+00 3.00e-01
U33 -2.07e-03 1.83e+00 3.00e-01
U12 -1.00e-03 1.83e+00 3.00e-01
U13 -3.00e-04 1.83e+00 3.00e-01
U23 -4.40e-03 1.83e+00 3.00e-01
""")
sio = StringIO()
proxies.show_sorted(
by_value="rms_deltas",
u_cart=u_cart,
u_iso=u_iso,
use_u_aniso=use_u_aniso,
f=sio,
prefix="$")
assert not show_diff(sio.getvalue(), """\
$Isotropic ADP restraints: 2
$Sorted by rms_deltas:
$scatterer 0
$ delta sigma weight rms_deltas residual
$ U11 -4.47e-03 2.00e-01 2.50e+01 4.27e-03 4.11e-03
$ U22 8.33e-04 2.00e-01 2.50e+01
$ U33 3.63e-03 2.00e-01 2.50e+01
$ U12 3.50e-03 2.00e-01 2.50e+01
$ U13 -5.20e-03 2.00e-01 2.50e+01
$ U23 -5.10e-03 2.00e-01 2.50e+01
$scatterer 2
$ delta sigma weight rms_deltas residual
$ U11 5.63e-03 1.83e+00 3.00e-01 3.16e-03 2.69e-05
$ U22 -3.57e-03 1.83e+00 3.00e-01
$ U33 -2.07e-03 1.83e+00 3.00e-01
$ U12 -1.00e-03 1.83e+00 3.00e-01
$ U13 -3.00e-04 1.83e+00 3.00e-01
$ U23 -4.40e-03 1.83e+00 3.00e-01
""")
#
proxies = adp_restraints.shared_rigid_bond_proxy()
sio = StringIO()
proxies.show_sorted(
by_value="residual",
sites_cart=flex.vec3_double(),
u_cart=flex.sym_mat3_double(),
f=sio)
assert not show_diff(sio.getvalue(), """\
Rigid bond restraints: 0
""")
proxies = adp_restraints.shared_rigid_bond_proxy([
adp_restraints.rigid_bond_proxy(i_seqs=(0,1),weight=25),
adp_restraints.rigid_bond_proxy(i_seqs=(0,2),weight=15),
adp_restraints.rigid_bond_proxy(i_seqs=(2,3),weight=25),
adp_restraints.rigid_bond_proxy(i_seqs=(3,1),weight=30)])
sio = StringIO()
proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
u_cart=u_cart,
f=sio,
prefix="*")
assert not show_diff(sio.getvalue(), """\
*Rigid bond restraints: 4
*Sorted by residual:
*scatterers O16
* N8
* delta_z sigma weight residual
* -3.96e-03 2.00e-01 2.50e+01 3.92e-04
*scatterers C1
* C2
* delta_z sigma weight residual
* 1.08e-03 2.00e-01 2.50e+01 2.89e-05
*scatterers C1
* O16
* delta_z sigma weight residual
* 4.03e-04 2.58e-01 1.50e+01 2.44e-06
*scatterers N8
* C2
* delta_z sigma weight residual
* -1.54e-04 1.83e-01 3.00e+01 7.16e-07
""")
sio = StringIO()
proxies.show_sorted(
by_value="delta",
sites_cart=sites_cart,
u_cart=u_cart,
f=sio,
prefix="||",
max_items=2)
assert not show_diff(sio.getvalue(), """\
||Rigid bond restraints: 4
||Sorted by delta:
||scatterers 2
|| 3
|| delta_z sigma weight residual
|| -3.96e-03 2.00e-01 2.50e+01 3.92e-04
||scatterers 0
|| 1
|| delta_z sigma weight residual
|| 1.08e-03 2.00e-01 2.50e+01 2.89e-05
||... (remaining 2 not shown)
""")
def exercise_proxy_show():
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.
print "Skipping exercise_proxy_show()"
return
sites_cart = flex.vec3_double((
(-3.1739,10.8317,7.5653),(-2.5419,9.7567,6.6306),
(-3.3369,8.8794,4.5191),(-3.4640,9.9882,5.3896)))
site_labels = ("C1", "C2", "O16", "N8")
u_cart = flex.sym_mat3_double((
(0.0153,0.0206,0.0234,0.0035,-0.0052,-0.0051),
(0.0185,0.0109,0.0206,0.0005,-0.0010,0.0002),
(0.0295,0.0203,0.0218,-0.0010,-0.0003,-0.0044),
(0.0159,0.0154,0.0206,-0.0003,0.0004,0.0036)))
u_iso = flex.double((-1,-1,-1,-1))
use_u_aniso = flex.bool((True,True,True,True))
#
proxies = adp_restraints.shared_adp_similarity_proxy()
sio = StringIO()
proxies.show_sorted(
by_value="residual",
u_cart=flex.sym_mat3_double(),
u_iso=flex.double(),
use_u_aniso=flex.bool(),
f=sio)
assert not show_diff(sio.getvalue(), """\
ADP similarity restraints: 0
""")
proxies = adp_restraints.shared_adp_similarity_proxy([
adp_restraints.adp_similarity_proxy(i_seqs=[0,1],weight=25),
adp_restraints.adp_similarity_proxy(i_seqs=[2,3],weight=0.3)])
sio = StringIO()
proxies.show_sorted(
by_value="residual",
u_cart=u_cart,
u_iso=u_iso,
use_u_aniso=use_u_aniso,
f=sio,
prefix=":")
assert not show_diff(sio.getvalue(), """\
:ADP similarity restraints: 2
:Sorted by residual:
:scatterers 0
: 1
: delta sigma weight rms_deltas residual
: U11 -3.20e-03 2.00e-01 2.50e+01 4.96e-03 5.54e-03
: U22 9.70e-03 2.00e-01 2.50e+01
: U33 2.80e-03 2.00e-01 2.50e+01
: U12 3.00e-03 2.00e-01 2.50e+01
: U13 -4.20e-03 2.00e-01 2.50e+01
: U23 -5.30e-03 2.00e-01 2.50e+01
:scatterers 2
: 3
: delta sigma weight rms_deltas residual
: U11 1.36e-02 1.83e+00 3.00e-01 6.15e-03 1.02e-04
: U22 4.90e-03 1.83e+00 3.00e-01
: U33 1.20e-03 1.83e+00 3.00e-01
: U12 -7.00e-04 1.83e+00 3.00e-01
: U13 -7.00e-04 1.83e+00 3.00e-01
: U23 -8.00e-03 1.83e+00 3.00e-01
""")
sio = StringIO()
proxies.show_sorted(
by_value="rms_deltas",
site_labels=site_labels,
u_cart=u_cart,
u_iso=flex.double((0.024,0.031,0.021,0.028)),
use_u_aniso=flex.bool((False,False,False,False)),
f=sio,
prefix="=")
assert not show_diff(sio.getvalue(), """\
=ADP similarity restraints: 2
=Sorted by rms_deltas:
=scatterers C1
= C2
= delta sigma weight residual
= Uiso -7.00e-03 2.00e-01 2.50e+01 1.22e-03
=scatterers O16
= N8
= delta sigma weight residual
= Uiso -7.00e-03 1.83e+00 3.00e-01 1.47e-05
""")
#
proxies = adp_restraints.shared_isotropic_adp_proxy()
sio = StringIO()
proxies.show_sorted(
by_value="residual",
u_cart=flex.sym_mat3_double(),
u_iso=u_iso,
use_u_aniso=use_u_aniso,
f=sio)
assert not show_diff(sio.getvalue(), """\
Isotropic ADP restraints: 0
""")
proxies = adp_restraints.shared_isotropic_adp_proxy([
adp_restraints.isotropic_adp_proxy(i_seqs=(0,),weight=25),
adp_restraints.isotropic_adp_proxy(i_seqs=(2,),weight=0.3)])
sio = StringIO()
proxies.show_sorted(
by_value="residual",
site_labels=site_labels,
u_cart=u_cart,
u_iso=u_iso,
use_u_aniso=use_u_aniso,
f=sio,
prefix=" ")
assert not show_diff(sio.getvalue(), """\
Isotropic ADP restraints: 2
Sorted by residual:
scatterer C1
delta sigma weight rms_deltas residual
U11 -4.47e-03 2.00e-01 2.50e+01 4.27e-03 4.11e-03
U22 8.33e-04 2.00e-01 2.50e+01
U33 3.63e-03 2.00e-01 2.50e+01
U12 3.50e-03 2.00e-01 2.50e+01
U13 -5.20e-03 2.00e-01 2.50e+01
U23 -5.10e-03 2.00e-01 2.50e+01
scatterer O16
delta sigma weight rms_deltas residual
U11 5.63e-03 1.83e+00 3.00e-01 3.16e-03 2.69e-05
U22 -3.57e-03 1.83e+00 3.00e-01
U33 -2.07e-03 1.83e+00 3.00e-01
U12 -1.00e-03 1.83e+00 3.00e-01
U13 -3.00e-04 1.83e+00 3.00e-01
U23 -4.40e-03 1.83e+00 3.00e-01
""")
sio = StringIO()
proxies.show_sorted(
by_value="rms_deltas",
u_cart=u_cart,
u_iso=u_iso,
use_u_aniso=use_u_aniso,
f=sio,
prefix="$")
assert not show_diff(sio.getvalue(), """\
$Isotropic ADP restraints: 2
$Sorted by rms_deltas:
$scatterer 0
$ delta sigma weight rms_deltas residual
$ U11 -4.47e-03 2.00e-01 2.50e+01 4.27e-03 4.11e-03
$ U22 8.33e-04 2.00e-01 2.50e+01
$ U33 3.63e-03 2.00e-01 2.50e+01
$ U12 3.50e-03 2.00e-01 2.50e+01
$ U13 -5.20e-03 2.00e-01 2.50e+01
$ U23 -5.10e-03 2.00e-01 2.50e+01
$scatterer 2
$ delta sigma weight rms_deltas residual
$ U11 5.63e-03 1.83e+00 3.00e-01 3.16e-03 2.69e-05
$ U22 -3.57e-03 1.83e+00 3.00e-01
$ U33 -2.07e-03 1.83e+00 3.00e-01
$ U12 -1.00e-03 1.83e+00 3.00e-01
$ U13 -3.00e-04 1.83e+00 3.00e-01
$ U23 -4.40e-03 1.83e+00 3.00e-01
""")
#
proxies = adp_restraints.shared_rigid_bond_proxy()
sio = StringIO()
proxies.show_sorted(
by_value="residual",
sites_cart=flex.vec3_double(),
u_cart=flex.sym_mat3_double(),
f=sio)
assert not show_diff(sio.getvalue(), """\
Rigid bond restraints: 0
""")
proxies = adp_restraints.shared_rigid_bond_proxy([
adp_restraints.rigid_bond_proxy(i_seqs=(0,1),weight=25),
adp_restraints.rigid_bond_proxy(i_seqs=(0,2),weight=15),
adp_restraints.rigid_bond_proxy(i_seqs=(2,3),weight=25),
adp_restraints.rigid_bond_proxy(i_seqs=(3,1),weight=30)])
sio = StringIO()
proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
site_labels=site_labels,
u_cart=u_cart,
f=sio,
prefix="*")
assert not show_diff(sio.getvalue(), """\
*Rigid bond restraints: 4
*Sorted by residual:
*scatterers O16
* N8
* delta_z sigma weight residual
* -3.96e-03 2.00e-01 2.50e+01 3.92e-04
*scatterers C1
* C2
* delta_z sigma weight residual
* 1.08e-03 2.00e-01 2.50e+01 2.89e-05
*scatterers C1
* O16
* delta_z sigma weight residual
* 4.03e-04 2.58e-01 1.50e+01 2.44e-06
*scatterers N8
* C2
* delta_z sigma weight residual
* -1.54e-04 1.83e-01 3.00e+01 7.16e-07
""")
sio = StringIO()
proxies.show_sorted(
by_value="delta",
sites_cart=sites_cart,
u_cart=u_cart,
f=sio,
prefix="||",
max_items=2)
assert not show_diff(sio.getvalue(), """\
||Rigid bond restraints: 4
||Sorted by delta:
||scatterers 2
|| 3
|| delta_z sigma weight residual
|| -3.96e-03 2.00e-01 2.50e+01 3.92e-04
||scatterers 0
|| 1
|| delta_z sigma weight residual
|| 1.08e-03 2.00e-01 2.50e+01 2.89e-05
||... (remaining 2 not shown)
""")
