def __init__(self,
xray_structure=None,
pair_sym_table=None,
proxies=None,
i_seqs=None,
sigma=0.04,
sigma_terminal=None,
buffer_thickness=3.5):
assert [xray_structure, pair_sym_table].count(None) == 1
if i_seqs is not None and len(i_seqs) == 0: i_seqs = None
if sigma_terminal is None: sigma_terminal = 2 * sigma
if proxies is None:
proxies = adp_restraints.shared_adp_similarity_proxy()
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)
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()
connectivity = pair_sym_table.full_simple_connectivity()
for i_seq, j_seq_dict in enumerate(pair_sym_table):
if i_seqs is not None and i_seq not in i_seqs: continue
for j_seq, sym_ops in j_seq_dict.items():
if i_seqs is not None and j_seq not in i_seqs: continue
for sym_op in sym_ops:
if sym_op.is_unit_mx():
i_is_terminal = (connectivity[i_seq].size() <= 1)
j_is_terminal = (connectivity[j_seq].size() <= 1)
if i_is_terminal or j_is_terminal:
weight = 1 / (sigma_terminal * sigma_terminal)
else:
weight = 1 / (sigma * sigma)
proxies.append(
adp_restraints.adp_similarity_proxy(i_seqs=(i_seq,
j_seq),
weight=weight))
break
self.proxies = proxies
def __init__(
self,
xray_structure=None,
pair_sym_table=None,
proxies=None,
i_seqs=None,
sigma=0.04,
sigma_terminal=None,
buffer_thickness=3.5,
):
assert [xray_structure, pair_sym_table].count(None) == 1
if i_seqs is not None and len(i_seqs) == 0:
i_seqs = None
if sigma_terminal is None:
sigma_terminal = 2 * sigma
if proxies is None:
proxies = adp_restraints.shared_adp_similarity_proxy()
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)
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()
connectivity = pair_sym_table.full_simple_connectivity()
for i_seq, j_seq_dict in enumerate(pair_sym_table):
if i_seqs is not None and i_seq not in i_seqs:
continue
for j_seq, sym_ops in j_seq_dict.items():
if i_seqs is not None and j_seq not in i_seqs:
continue
for sym_op in sym_ops:
if sym_op.is_unit_mx():
i_is_terminal = connectivity[i_seq].size() <= 1
j_is_terminal = connectivity[j_seq].size() <= 1
if i_is_terminal or j_is_terminal:
weight = 1 / (sigma_terminal * sigma_terminal)
else:
weight = 1 / (sigma * sigma)
proxies.append(adp_restraints.adp_similarity_proxy(i_seqs=(i_seq, j_seq), weight=weight))
break
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_adp_similarity():
u_cart = ((1,3,2,4,3,6),(2,4,2,6,5,1))
u_iso = (-1,-1)
use_u_aniso = (True, True)
weight = 1
a = adp_restraints.adp_similarity(
u_cart=u_cart,
weight=weight)
assert approx_equal(a.use_u_aniso, use_u_aniso)
assert a.weight == weight
assert approx_equal(a.residual(), 68)
assert approx_equal(a.gradients2(),
((-2.0, -2.0, 0.0, -8.0, -8.0, 20.0), (2.0, 2.0, -0.0, 8.0, 8.0, -20.0)))
assert approx_equal(a.deltas(), (-1.0, -1.0, 0.0, -2.0, -2.0, 5.0))
assert approx_equal(a.rms_deltas(), 2.7487370837451071)
#
u_cart = ((1,3,2,4,3,6),(-1,-1,-1,-1,-1,-1))
u_iso = (-1,2)
use_u_aniso = (True, False)
a = adp_restraints.adp_similarity(
u_cart[0], u_iso[1], weight=weight)
assert approx_equal(a.use_u_aniso, use_u_aniso)
assert a.weight == weight
assert approx_equal(a.residual(), 124)
assert approx_equal(a.gradients2(),
((-2, 2, 0, 16, 12, 24), (2, -2, 0, -16, -12, -24)))
assert approx_equal(a.deltas(), (-1, 1, 0, 4, 3, 6))
assert approx_equal(a.rms_deltas(), 3.711842908553348)
#
i_seqs_aa = (1,2) # () - ()
i_seqs_ai = (1,0) # () - o
i_seqs_ia = (3,2) # o - ()
i_seqs_ii = (0,3) # o - o
p_aa = adp_restraints.adp_similarity_proxy(i_seqs=i_seqs_aa,weight=weight)
p_ai = adp_restraints.adp_similarity_proxy(i_seqs=i_seqs_ai,weight=weight)
p_ia = adp_restraints.adp_similarity_proxy(i_seqs=i_seqs_ia,weight=weight)
p_ii = adp_restraints.adp_similarity_proxy(i_seqs=i_seqs_ii,weight=weight)
assert p_aa.i_seqs == i_seqs_aa
assert p_aa.weight == weight
u_cart = flex.sym_mat3_double(((-1,-1,-1,-1,-1,-1),
(1,2,2,4,3,6),
(2,4,2,6,5,1),
(-1,-1,-1,-1,-1,-1)))
u_iso = flex.double((1,-1,-1,2))
use_u_aniso = flex.bool((False, True,True,False))
for p in (p_aa,p_ai,p_ia,p_ii):
params = adp_restraint_params(u_cart=u_cart, u_iso=u_iso, use_u_aniso=use_u_aniso)
a = adp_restraints.adp_similarity(params, proxy=p)
assert approx_equal(a.weight, weight)
#
gradients_aniso_cart = flex.sym_mat3_double(u_cart.size(), (0,0,0,0,0,0))
gradients_iso = flex.double(u_cart.size(), 0)
proxies = adp_restraints.shared_adp_similarity_proxy([p,p])
residuals = adp_restraints.adp_similarity_residuals(params, proxies=proxies)
assert approx_equal(residuals, (a.residual(),a.residual()))
deltas_rms = adp_restraints.adp_similarity_deltas_rms(params, proxies=proxies)
assert approx_equal(deltas_rms, (a.rms_deltas(),a.rms_deltas()))
residual_sum = adp_restraints.adp_similarity_residual_sum(
params,
proxies=proxies,
gradients_aniso_cart=gradients_aniso_cart,
gradients_iso=gradients_iso)
assert approx_equal(residual_sum, 2 * a.residual())
fd_grads_aniso, fd_grads_iso = finite_difference_gradients(
restraint_type=adp_restraints.adp_similarity,
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)
for g,e in zip(gradients_iso, fd_grads_iso):
assert approx_equal(g, e*2)
#
# check frame invariance of residual
#
u_cart_1 = matrix.sym(sym_mat3=(0.1,0.2,0.05,0.03,0.02,0.01))
u_cart_2 = matrix.sym(sym_mat3=(0.21,0.32,0.11,0.02,0.02,0.07))
u_cart = (u_cart_1.as_sym_mat3(),u_cart_2.as_sym_mat3())
u_iso = (-1, -1)
use_u_aniso = (True, True)
a = adp_restraints.adp_similarity(u_cart, 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_1_rot = R * u_cart_1 * R.transpose()
u_cart_2_rot = R * u_cart_2 * R.transpose()
u_cart = (u_cart_1_rot.as_sym_mat3(),u_cart_2_rot.as_sym_mat3())
a = adp_restraints.adp_similarity(u_cart, weight=1)
assert approx_equal(a.residual(), expected_residual)
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)
""")
def exercise_adp_similarity():
u_cart = ((1,3,2,4,3,6),(2,4,2,6,5,1))
u_iso = (-1,-1)
use_u_aniso = (True, True)
weight = 1
a = adp_restraints.adp_similarity(
u_cart=u_cart,
weight=weight)
assert approx_equal(a.use_u_aniso, use_u_aniso)
assert a.weight == weight
assert approx_equal(a.residual(), 68)
assert approx_equal(a.gradients2(),
((-2.0, -2.0, 0.0, -8.0, -8.0, 20.0), (2.0, 2.0, -0.0, 8.0, 8.0, -20.0)))
assert approx_equal(a.deltas(), (-1.0, -1.0, 0.0, -2.0, -2.0, 5.0))
assert approx_equal(a.rms_deltas(), 2.7487370837451071)
#
u_cart = ((1,3,2,4,3,6),(-1,-1,-1,-1,-1,-1))
u_iso = (-1,2)
use_u_aniso = (True, False)
a = adp_restraints.adp_similarity(
u_cart[0], u_iso[1], weight=weight)
assert approx_equal(a.use_u_aniso, use_u_aniso)
assert a.weight == weight
assert approx_equal(a.residual(), 124)
assert approx_equal(a.gradients2(),
((-2, 2, 0, 16, 12, 24), (2, -2, 0, -16, -12, -24)))
assert approx_equal(a.deltas(), (-1, 1, 0, 4, 3, 6))
assert approx_equal(a.rms_deltas(), 3.711842908553348)
#
i_seqs_aa = (1,2) # () - ()
i_seqs_ai = (1,0) # () - o
i_seqs_ia = (3,2) # o - ()
i_seqs_ii = (0,3) # o - o
p_aa = adp_restraints.adp_similarity_proxy(i_seqs=i_seqs_aa,weight=weight)
p_ai = adp_restraints.adp_similarity_proxy(i_seqs=i_seqs_ai,weight=weight)
p_ia = adp_restraints.adp_similarity_proxy(i_seqs=i_seqs_ia,weight=weight)
p_ii = adp_restraints.adp_similarity_proxy(i_seqs=i_seqs_ii,weight=weight)
assert p_aa.i_seqs == i_seqs_aa
assert p_aa.weight == weight
u_cart = flex.sym_mat3_double(((-1,-1,-1,-1,-1,-1),
(1,2,2,4,3,6),
(2,4,2,6,5,1),
(-1,-1,-1,-1,-1,-1)))
u_iso = flex.double((1,-1,-1,2))
use_u_aniso = flex.bool((False, True,True,False))
for p in (p_aa,p_ai,p_ia,p_ii):
params = adp_restraint_params(u_cart=u_cart, u_iso=u_iso, use_u_aniso=use_u_aniso)
a = adp_restraints.adp_similarity(params, proxy=p)
assert approx_equal(a.weight, weight)
#
gradients_aniso_cart = flex.sym_mat3_double(u_cart.size(), (0,0,0,0,0,0))
gradients_iso = flex.double(u_cart.size(), 0)
proxies = adp_restraints.shared_adp_similarity_proxy([p,p])
residuals = adp_restraints.adp_similarity_residuals(params, proxies=proxies)
assert approx_equal(residuals, (a.residual(),a.residual()))
deltas_rms = adp_restraints.adp_similarity_deltas_rms(params, proxies=proxies)
assert approx_equal(deltas_rms, (a.rms_deltas(),a.rms_deltas()))
residual_sum = adp_restraints.adp_similarity_residual_sum(
params,
proxies=proxies,
gradients_aniso_cart=gradients_aniso_cart,
gradients_iso=gradients_iso)
assert approx_equal(residual_sum, 2 * a.residual())
fd_grads_aniso, fd_grads_iso = finite_difference_gradients(
restraint_type=adp_restraints.adp_similarity,
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)
for g,e in zip(gradients_iso, fd_grads_iso):
assert approx_equal(g, e*2)
#
# check frame invariance of residual
#
u_cart_1 = matrix.sym(sym_mat3=(0.1,0.2,0.05,0.03,0.02,0.01))
u_cart_2 = matrix.sym(sym_mat3=(0.21,0.32,0.11,0.02,0.02,0.07))
u_cart = (u_cart_1.as_sym_mat3(),u_cart_2.as_sym_mat3())
u_iso = (-1, -1)
use_u_aniso = (True, True)
a = adp_restraints.adp_similarity(u_cart, 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_1_rot = R * u_cart_1 * R.transpose()
u_cart_2_rot = R * u_cart_2 * R.transpose()
u_cart = (u_cart_1_rot.as_sym_mat3(),u_cart_2_rot.as_sym_mat3())
a = adp_restraints.adp_similarity(u_cart, weight=1)
assert approx_equal(a.residual(), expected_residual)
