def residual(restraint_type, proxy, sites_cart=None,
u_cart=None, u_iso=None, use_u_aniso=None):
if sites_cart is not None:
return restraint_type(
adp_restraint_params(sites_cart=sites_cart, u_cart=u_cart),
proxy=proxy).residual()
elif u_iso is None:
return restraint_type(
adp_restraint_params(u_cart=u_cart),
proxy=proxy).residual()
else:
assert use_u_aniso is not None
return restraint_type(
adp_restraint_params(u_cart=u_cart, u_iso=u_iso, use_u_aniso=use_u_aniso),
proxy=proxy).residual()
def residual(restraint_type, proxy, sites_cart=None,
u_cart=None, u_iso=None, use_u_aniso=None):
if sites_cart is not None:
return restraint_type(
adp_restraint_params(sites_cart=sites_cart, u_cart=u_cart),
proxy=proxy).residual()
elif u_iso is None:
return restraint_type(
adp_restraint_params(u_cart=u_cart),
proxy=proxy).residual()
else:
assert use_u_aniso is not None
return restraint_type(
adp_restraint_params(u_cart=u_cart, u_iso=u_iso, use_u_aniso=use_u_aniso),
proxy=proxy).residual()
def adp_volume_similarity_as_cif_loops(xray_structure, proxies):
site_labels = xray_structure.scatterers().extract_labels()
fmt = "%.4e"
loop = model.loop(header=(
"_restr_U_volume_similar_atom_site_label_1",
"_restr_U_volume_similar_diff",
"_restr_U_volume_similar_class_id",
))
class_loop = model.loop(header=(
"_restr_U_volume_similar_class_class_id",
"_restr_U_volume_similar_class_target_weight_param",
"_restr_U_volume_similar_class_average",
"_restr_U_volume_similar_class_esd",
"_restr_U_volume_similar_class_diff_max",
))
unit_cell = xray_structure.unit_cell()
params = adp_restraints.adp_restraint_params(
u_cart=xray_structure.scatterers().extract_u_cart(unit_cell),
u_iso=xray_structure.scatterers().extract_u_iso(),
use_u_aniso=xray_structure.use_u_aniso())
class_id = 0
for proxy in proxies:
restraint = adp_restraints.adp_volume_similarity(params=params,
proxy=proxy)
class_id += 1
class_loop.add_row(
(class_id, fmt % math.sqrt(1 / proxy.weight),
fmt % restraint.mean_u_volume, fmt % restraint.rms_deltas(),
fmt % flex.max_absolute(restraint.deltas())))
for i, i_seq in enumerate(proxy.i_seqs):
loop.add_row(
(site_labels[i_seq], fmt % restraint.deltas()[i], class_id))
return class_loop, loop
def rigu_as_cif_loop(xray_structure, proxies):
unit_cell = xray_structure.unit_cell()
sites_cart = xray_structure.sites_cart()
u_cart = xray_structure.scatterers().extract_u_cart(unit_cell)
site_labels = xray_structure.scatterers().extract_labels()
fmt = "%.6f"
loop = model.loop(header=(
"_restr_RIGU_atom_site_label_1",
"_restr_RIGU_atom_site_label_2",
"_restr_RIGU_target_weight_param",
"_restr_RIGU_U13_diff",
"_restr_RIGU_U23_diff",
"_restr_RIGU_U33_diff"
))
for proxy in proxies:
restraint = adp_restraints.rigu(
adp_restraint_params(sites_cart=sites_cart, u_cart=u_cart),
proxy=proxy)
loop.add_row((site_labels[proxy.i_seqs[0]],
site_labels[proxy.i_seqs[1]],
fmt % math.sqrt(1/proxy.weight),
fmt % restraint.delta_13(),
fmt % restraint.delta_23(),
fmt % restraint.delta_33()
))
return loop
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)
def fixed_u_eq_adp_as_cif_loop(xray_structure, proxies):
site_labels = xray_structure.scatterers().extract_labels()
fmt = "%.4f"
loop = model.loop(header=(
"_restr_U_Ueq_atom_site_label_1",
"_restr_U_Ueq_weight_param",
"_restr_U_Ueq_target",
"_restr_U_Ueq_diff"
))
unit_cell = xray_structure.unit_cell()
params = adp_restraints.adp_restraint_params(
u_cart=xray_structure.scatterers().extract_u_cart(unit_cell),
u_iso=xray_structure.scatterers().extract_u_iso(),
use_u_aniso=xray_structure.use_u_aniso()
)
for proxy in proxies:
restraint = adp_restraints.fixed_u_eq_adp(
params=params,
proxy=proxy)
for i, i_seq in enumerate(proxy.i_seqs):
loop.add_row((site_labels[i_seq],
fmt % math.sqrt(1/proxy.weight),
fmt % proxy.u_eq_ideal,
fmt % restraint.delta()))
return loop
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)
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)
def fixed_u_eq_adp_as_cif_loop(xray_structure, proxies):
site_labels = xray_structure.scatterers().extract_labels()
fmt = "%.4f"
loop = model.loop(header=(
"_restr_U_Ueq_atom_site_label_1",
"_restr_U_Ueq_weight_param",
"_restr_U_Ueq_target",
"_restr_U_Ueq_diff"
))
unit_cell = xray_structure.unit_cell()
params = adp_restraints.adp_restraint_params(
u_cart=xray_structure.scatterers().extract_u_cart(unit_cell),
u_iso=xray_structure.scatterers().extract_u_iso(),
use_u_aniso=xray_structure.use_u_aniso()
)
for proxy in proxies:
restraint = adp_restraints.fixed_u_eq_adp(
params=params,
proxy=proxy)
for i, i_seq in enumerate(proxy.i_seqs):
loop.add_row((site_labels[i_seq],
fmt % math.sqrt(1/proxy.weight),
fmt % proxy.u_eq_ideal,
fmt % restraint.delta()))
return loop
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 build_linearised_eqns(self, xray_structure, parameter_map):
n_restraints = 0
n_params = parameter_map.n_parameters
geometry_proxies = [
proxies for proxies in (self.bond_proxies, self.angle_proxies,
self.dihedral_proxies)
if proxies is not None
]
# count restraints, i.e. number of rows for restraint matrix
n_restraints = sum([proxies.size() for proxies in geometry_proxies])
if self.bond_similarity_proxies is not None:
for proxy in self.bond_similarity_proxies:
n_restraints += proxy.i_seqs.size()
geometry_proxies.append(self.bond_similarity_proxies)
if self.chirality_proxies is not None:
for proxy in self.chirality_proxies:
n_restraints += 1
geometry_proxies.append(self.chirality_proxies)
adp_proxies = []
if self.adp_similarity_proxies is not None:
adp_proxies.append(self.adp_similarity_proxies)
n_restraints += 6 * self.adp_similarity_proxies.size()
if self.adp_u_eq_similarity_proxies is not None:
adp_proxies.append(self.adp_u_eq_similarity_proxies)
for p in self.adp_u_eq_similarity_proxies:
n_restraints += len(p.i_seqs)
if self.adp_volume_similarity_proxies is not None:
adp_proxies.append(self.adp_volume_similarity_proxies)
for p in self.adp_volume_similarity_proxies:
n_restraints += len(p.i_seqs)
if self.isotropic_adp_proxies is not None:
adp_proxies.append(self.isotropic_adp_proxies)
n_restraints += 6 * self.isotropic_adp_proxies.size()
if self.fixed_u_eq_adp_proxies is not None:
adp_proxies.append(self.fixed_u_eq_adp_proxies)
n_restraints += self.fixed_u_eq_adp_proxies.size()
if self.rigid_bond_proxies is not None:
adp_proxies.append(self.rigid_bond_proxies)
n_restraints += self.rigid_bond_proxies.size()
if self.rigu_proxies is not None:
adp_proxies.append(self.rigu_proxies)
n_restraints += 3 * self.rigu_proxies.size()
# construct restraints matrix
linearised_eqns = linearised_eqns_of_restraint(n_restraints, n_params)
for proxies in geometry_proxies:
linearise_restraints(xray_structure.unit_cell(),
xray_structure.sites_cart(), parameter_map,
proxies, linearised_eqns)
u_cart = xray_structure.scatterers().extract_u_cart(
xray_structure.unit_cell())
params = adp_restraint_params(
sites_cart=xray_structure.sites_cart(),
u_cart=u_cart,
u_iso=xray_structure.scatterers().extract_u_iso(),
use_u_aniso=xray_structure.use_u_aniso())
for proxies in adp_proxies:
linearise_restraints(xray_structure.unit_cell(), params,
parameter_map, proxies, linearised_eqns)
return linearised_eqns
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)
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 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 exercise_rigu():
ins = """
CELL 0.71073 7.772741 8.721603 10.863736 90 102.9832 90
ZERR 2 0.000944 0.001056 0.001068 0 0.0107 0
LATT -1
SYMM -X,0.5+Y,-Z
SFAC C H O
UNIT 24 44 22
RIGU 0.0001 0.0001 O4 C C12
C12 1 -0.12812 0.06329 -0.17592 11.00000 0.01467 0.02689 0.02780 =
-0.00379 0.00441 -0.00377
O4 3 0.08910 0.02721 0.02186 11.00000 0.02001 0.03168 0.03125 =
-0.00504 0.00144 -0.00274
C 1 -0.05545 -0.04221 -0.06528 11.00000 0.01560 0.02699 0.02581 =
-0.00481 0.00597 -0.00068
HKLF 4
END
"""
sio = StringIO(ins)
import iotbx.shelx as shelx
model = shelx.parse_smtbx_refinement_model(file=sio)
sites_cart = model.structure.sites_cart()
u_cart = model.structure.scatterers().extract_u_cart(
model.structure.unit_cell())
arp = adp_restraint_params(sites_cart=sites_cart, u_cart=u_cart)
for rp in model._proxies['rigu']:
rr = adp_restraints.rigu(arp, rp)
U1 = matrix.sym(sym_mat3=u_cart[rp.i_seqs[0]])
U2 = matrix.sym(sym_mat3=u_cart[rp.i_seqs[1]])
vz = matrix.col(sites_cart[rp.i_seqs[1]]) - matrix.col(
sites_cart[rp.i_seqs[0]])
vy = vz.ortho()
vx = vy.cross(vz)
R = matrix.rec(
vx.normalize().elems + vy.normalize().elems + vz.normalize().elems,
(3, 3))
# with this matrix we can only test Z component as X and Y will differ
dU = ((R * U1) * R.transpose() -
(R * U2) * R.transpose()).as_sym_mat3()
assert approx_equal(dU[2], rr.delta_33())
#with the original matrix all components should match
R1 = matrix.rec(rr.RM(), (3, 3))
dU = ((R1 * U1) * R1.transpose() -
(R1 * U2) * R1.transpose()).as_sym_mat3()
assert approx_equal(dU[2], rr.delta_33())
assert approx_equal(dU[4], rr.delta_13())
assert approx_equal(dU[5], rr.delta_23())
# check the raw gradients against the reference implementation
for x, y in zip(rr.reference_gradients(R1), rr.raw_gradients()):
for idx in range(0, 6):
assert approx_equal(x[idx], y[idx])
for x, y in zip(rigu_finite_diff(R1, U1), rr.raw_gradients()):
for idx in range(0, 6):
assert approx_equal(x[idx], y[idx])
def build_linearised_eqns(self, xray_structure, parameter_map):
n_restraints = 0
n_params = parameter_map.n_parameters
geometry_proxies = [proxies for proxies in (
self.bond_proxies, self.angle_proxies, self.dihedral_proxies)
if proxies is not None]
# count restraints, i.e. number of rows for restraint matrix
n_restraints = sum([proxies.size() for proxies in geometry_proxies])
if self.bond_similarity_proxies is not None:
for proxy in self.bond_similarity_proxies:
n_restraints += proxy.i_seqs.size()
geometry_proxies.append(self.bond_similarity_proxies)
adp_proxies = []
if self.adp_similarity_proxies is not None:
adp_proxies.append(self.adp_similarity_proxies)
n_restraints += 6 * self.adp_similarity_proxies.size()
if self.adp_u_eq_similarity_proxies is not None:
adp_proxies.append(self.adp_u_eq_similarity_proxies)
for p in self.adp_u_eq_similarity_proxies:
n_restraints += len(p.i_seqs)
if self.adp_volume_similarity_proxies is not None:
adp_proxies.append(self.adp_volume_similarity_proxies)
for p in self.adp_volume_similarity_proxies:
n_restraints += len(p.i_seqs)
if self.isotropic_adp_proxies is not None:
adp_proxies.append(self.isotropic_adp_proxies)
n_restraints += 6 * self.isotropic_adp_proxies.size()
if self.fixed_u_eq_adp_proxies is not None:
adp_proxies.append(self.fixed_u_eq_adp_proxies)
n_restraints += self.fixed_u_eq_adp_proxies.size()
if self.rigid_bond_proxies is not None:
adp_proxies.append(self.rigid_bond_proxies)
n_restraints += self.rigid_bond_proxies.size()
# construct restraints matrix
linearised_eqns = linearised_eqns_of_restraint(
n_restraints, n_params)
for proxies in geometry_proxies:
linearise_restraints(
xray_structure.unit_cell(), xray_structure.sites_cart(),
parameter_map, proxies, linearised_eqns)
u_cart = xray_structure.scatterers().extract_u_cart(
xray_structure.unit_cell())
params = adp_restraint_params(
sites_cart=xray_structure.sites_cart(),
u_cart=u_cart,
u_iso=xray_structure.scatterers().extract_u_iso(),
use_u_aniso=xray_structure.use_u_aniso())
for proxies in adp_proxies:
linearise_restraints(
xray_structure.unit_cell(), params,
parameter_map, proxies, linearised_eqns)
return linearised_eqns
def rigid_bond_as_cif_loop(xray_structure, proxies):
unit_cell = xray_structure.unit_cell()
sites_cart = xray_structure.sites_cart()
u_cart = xray_structure.scatterers().extract_u_cart(unit_cell)
site_labels = xray_structure.scatterers().extract_labels()
fmt = "%.4f"
loop = model.loop(header=(
"_restr_U_rigid_atom_site_label_1",
"_restr_U_rigid_atom_site_label_2",
"_restr_U_rigid_target_weight_param",
"_restr_U_rigid_U_parallel",
"_restr_U_rigid_diff",
))
for proxy in proxies:
restraint = adp_restraints.rigid_bond(
adp_restraint_params(sites_cart=sites_cart, u_cart=u_cart),
proxy=proxy)
loop.add_row((site_labels[proxy.i_seqs[0]],
site_labels[proxy.i_seqs[1]],
fmt % math.sqrt(1/proxy.weight),
fmt % (0.5*(restraint.z_12()+restraint.z_21())),
fmt % restraint.delta_z()))
return loop
def rigid_bond_as_cif_loop(xray_structure, proxies):
unit_cell = xray_structure.unit_cell()
sites_cart = xray_structure.sites_cart()
u_cart = xray_structure.scatterers().extract_u_cart(unit_cell)
site_labels = xray_structure.scatterers().extract_labels()
fmt = "%.4f"
loop = model.loop(header=(
"_restr_U_rigid_atom_site_label_1",
"_restr_U_rigid_atom_site_label_2",
"_restr_U_rigid_target_weight_param",
"_restr_U_rigid_U_parallel",
"_restr_U_rigid_diff",
))
for proxy in proxies:
restraint = adp_restraints.rigid_bond(adp_restraint_params(
sites_cart=sites_cart, u_cart=u_cart),
proxy=proxy)
loop.add_row(
(site_labels[proxy.i_seqs[0]], site_labels[proxy.i_seqs[1]],
fmt % math.sqrt(1 / proxy.weight),
fmt % (0.5 * (restraint.z_12() + restraint.z_21())),
fmt % restraint.delta_z()))
return loop
def adp_volume_similarity_as_cif_loops(xray_structure, proxies):
site_labels = xray_structure.scatterers().extract_labels()
fmt = "%.4e"
loop = model.loop(header=(
"_restr_U_volume_similar_atom_site_label_1",
"_restr_U_volume_similar_diff",
"_restr_U_volume_similar_class_id",
))
class_loop = model.loop(header=(
"_restr_U_volume_similar_class_class_id",
"_restr_U_volume_similar_class_target_weight_param",
"_restr_U_volume_similar_class_average",
"_restr_U_volume_similar_class_esd",
"_restr_U_volume_similar_class_diff_max",
))
unit_cell = xray_structure.unit_cell()
params = adp_restraints.adp_restraint_params(
u_cart=xray_structure.scatterers().extract_u_cart(unit_cell),
u_iso=xray_structure.scatterers().extract_u_iso(),
use_u_aniso=xray_structure.use_u_aniso()
)
class_id = 0
for proxy in proxies:
restraint = adp_restraints.adp_volume_similarity(
params=params,
proxy=proxy)
class_id += 1
class_loop.add_row((class_id,
fmt % math.sqrt(1/proxy.weight),
fmt % restraint.mean_u_volume,
fmt % restraint.rms_deltas(),
fmt % flex.max_absolute(restraint.deltas())))
for i, i_seq in enumerate(proxy.i_seqs):
loop.add_row((site_labels[i_seq],
fmt % restraint.deltas()[i],
class_id))
return class_loop, loop
def _show_sorted_impl(self,
proxy_type,
proxy_label,
item_label,
by_value,
u_cart,
u_iso=None,
use_u_aniso=None,
sites_cart=None,
site_labels=None,
f=None,
prefix="",
max_items=None):
assert by_value in ["residual", "rms_deltas", "delta"]
assert site_labels is None or len(site_labels) == u_cart.size()
assert sites_cart is None or len(sites_cart) == u_cart.size()
assert [u_iso, use_u_aniso].count(None) in (0,2)
if (f is None): f = sys.stdout
print >> f, "%s%s restraints: %d" % (prefix, proxy_label, self.size())
if (self.size() == 0): return
if (max_items is not None and max_items <= 0): return
from cctbx.adp_restraints import adp_restraint_params
if use_u_aniso is None: use_u_aniso = []
if sites_cart is None: sites_cart = []
if u_iso is None: u_iso = []
params = adp_restraint_params(
sites_cart=sites_cart, u_cart=u_cart, u_iso=u_iso, use_u_aniso=use_u_aniso)
if (by_value == "residual"):
if proxy_type in (adp_similarity, adp_u_eq_similarity, adp_volume_similarity,\
isotropic_adp, fixed_u_eq_adp, rigid_bond):
data_to_sort = self.residuals(params=params)
else:
raise AssertionError
elif (by_value == "rms_deltas"):
if proxy_type in (adp_similarity, adp_u_eq_similarity, adp_volume_similarity,\
isotropic_adp, fixed_u_eq_adp):
data_to_sort = self.deltas_rms(params=params)
else:
raise AssertionError
elif (by_value == "delta"):
if proxy_type is rigid_bond:
data_to_sort = flex.abs(self.deltas(params=params))
else:
raise AssertionError
else:
raise AssertionError
i_proxies_sorted = flex.sort_permutation(data=data_to_sort, reverse=True)
if (max_items is not None):
i_proxies_sorted = i_proxies_sorted[:max_items]
item_label_blank = " " * len(item_label)
print >> f, "%sSorted by %s:" % (prefix, by_value)
dynamic_proxy_types = (
adp_u_eq_similarity,
adp_volume_similarity,
)
for i_proxy in i_proxies_sorted:
proxy = self[i_proxy]
s = item_label
if proxy_type in (isotropic_adp, fixed_u_eq_adp):
if (site_labels is None): l = str(proxy.i_seqs[0])
else: l = site_labels[proxy.i_seqs[0]]
print >> f, "%s%s %s" % (prefix, s, l)
s = item_label_blank
elif proxy_type in dynamic_proxy_types:
restraint = proxy_type(params=params, proxy=proxy)
restraint._show_sorted_item(f=f, prefix=prefix)
print >> f, \
"%s delta" % (prefix)
for n, i_seq in enumerate(proxy.i_seqs):
if (site_labels is None): l = str(i_seq)
else: l = site_labels[i_seq]
print >> f, "%s %s %9.2e" % (prefix, l, restraint.deltas()[n])
else:
for n, i_seq in enumerate(proxy.i_seqs):
if (site_labels is None): l = str(i_seq)
else: l = site_labels[i_seq]
print >> f, "%s%s %s" % (prefix, s, l)
s = item_label_blank
if proxy_type in (adp_similarity, isotropic_adp, fixed_u_eq_adp,\
rigid_bond):
restraint = proxy_type(params=params, proxy=proxy)
restraint._show_sorted_item(f=f, prefix=prefix)
elif proxy_type in dynamic_proxy_types:
pass
else:
raise AssertionError
n_not_shown = self.size() - i_proxies_sorted.size()
if (n_not_shown != 0):
print >> f, prefix + "... (remaining %d not shown)" % n_not_shown
def exercise_rigid_bond():
i_seqs = (1,2)
weight = 1
p = adp_restraints.rigid_bond_proxy(i_seqs=i_seqs,weight=weight)
assert p.i_seqs == i_seqs
assert p.weight == weight
sites = ((1,2,3),(2,3,4))
u_cart = ((1,2,3,4,5,6), (3,4,5,6,7,8))
expected_gradients = ((-4, -4, -4, -8, -8, -8), (4, 4, 4, 8, 8, 8))
r = adp_restraints.rigid_bond(sites=sites, u_cart=u_cart, weight=weight)
assert r.weight == weight
assert approx_equal(r.delta_z(), -6)
assert approx_equal(r.residual(), 36)
assert approx_equal(r.gradients(), expected_gradients)
sites_cart = flex.vec3_double(((1,2,3),(2,5,4),(3,4,5)))
u_cart = flex.sym_mat3_double(((1,2,3,4,5,6),
(2,3,3,5,7,7),
(3,4,5,3,7,8)))
r = adp_restraints.rigid_bond(
adp_restraint_params(sites_cart=sites_cart, u_cart=u_cart),
proxy=p)
assert approx_equal(r.weight, weight)
unit_cell = uctbx.unit_cell([15,25,30,90,90,90])
sites_frac = unit_cell.fractionalize(sites_cart=sites_cart)
u_star = flex.sym_mat3_double([
adptbx.u_cart_as_u_star(unit_cell, u_cart_i)
for u_cart_i in u_cart])
pair = adp_restraints.rigid_bond_pair(sites_frac[1],
sites_frac[2],
u_star[1],
u_star[2],
unit_cell)
assert approx_equal(pair.delta_z(), abs(r.delta_z()))
assert approx_equal(pair.z_12(), r.z_12())
assert approx_equal(pair.z_21(), r.z_21())
#
gradients_aniso_cart = flex.sym_mat3_double(sites_cart.size(), (0,0,0,0,0,0))
gradients_iso = flex.double(sites_cart.size(), 0)
proxies = adp_restraints.shared_rigid_bond_proxy([p,p])
params = adp_restraint_params(sites_cart=sites_cart, u_cart=u_cart)
residuals = adp_restraints.rigid_bond_residuals(params, proxies=proxies)
assert approx_equal(residuals, (r.residual(),r.residual()))
deltas = adp_restraints.rigid_bond_deltas(params, proxies=proxies)
assert approx_equal(deltas, (r.delta_z(),r.delta_z()))
residual_sum = adp_restraints.rigid_bond_residual_sum(
params=params,
proxies=proxies,
gradients_aniso_cart=gradients_aniso_cart)
assert approx_equal(residual_sum, 2 * r.residual())
for g,e in zip(gradients_aniso_cart[1:3], r.gradients()):
assert approx_equal(g, matrix.col(e)*2)
fd_grads_aniso, fd_grads_iso = finite_difference_gradients(
restraint_type=adp_restraints.rigid_bond,
proxy=p,
sites_cart=sites_cart,
u_cart=u_cart)
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_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())
site_cart_1 = matrix.col((1,2,3))
site_cart_2 = matrix.col((3,1,4.2))
sites = (tuple(site_cart_1),tuple(site_cart_2))
a = adp_restraints.rigid_bond(sites=sites, u_cart=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())
site_cart_1_rot = R * site_cart_1
site_cart_2_rot = R * site_cart_2
sites = (tuple(site_cart_1_rot),tuple(site_cart_2_rot))
a = adp_restraints.rigid_bond(
sites=sites, u_cart=u_cart,
weight=1)
assert approx_equal(a.residual(), expected_residual)
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 _show_sorted_impl(self,
proxy_type,
proxy_label,
item_label,
by_value,
u_cart,
u_iso=None,
use_u_aniso=None,
sites_cart=None,
site_labels=None,
f=None,
prefix="",
max_items=None):
assert by_value in ["residual", "rms_deltas", "delta"]
assert site_labels is None or len(site_labels) == u_cart.size()
assert sites_cart is None or len(sites_cart) == u_cart.size()
assert [u_iso, use_u_aniso].count(None) in (0, 2)
if (f is None): f = sys.stdout
print >> f, "%s%s restraints: %d" % (prefix, proxy_label, self.size())
if (self.size() == 0): return
if (max_items is not None and max_items <= 0): return
from cctbx.adp_restraints import adp_restraint_params
if use_u_aniso is None: use_u_aniso = []
if sites_cart is None: sites_cart = []
if u_iso is None: u_iso = []
params = adp_restraint_params(sites_cart=sites_cart,
u_cart=u_cart,
u_iso=u_iso,
use_u_aniso=use_u_aniso)
if (by_value == "residual"):
if proxy_type in (adp_similarity, adp_u_eq_similarity, adp_volume_similarity,\
isotropic_adp, fixed_u_eq_adp, rigid_bond):
data_to_sort = self.residuals(params=params)
else:
raise AssertionError
elif (by_value == "rms_deltas"):
if proxy_type in (adp_similarity, adp_u_eq_similarity, adp_volume_similarity,\
isotropic_adp, fixed_u_eq_adp):
data_to_sort = self.deltas_rms(params=params)
else:
raise AssertionError
elif (by_value == "delta"):
if proxy_type is rigid_bond:
data_to_sort = flex.abs(self.deltas(params=params))
else:
raise AssertionError
else:
raise AssertionError
i_proxies_sorted = flex.sort_permutation(data=data_to_sort, reverse=True)
if (max_items is not None):
i_proxies_sorted = i_proxies_sorted[:max_items]
item_label_blank = " " * len(item_label)
print >> f, "%sSorted by %s:" % (prefix, by_value)
dynamic_proxy_types = (
adp_u_eq_similarity,
adp_volume_similarity,
)
for i_proxy in i_proxies_sorted:
proxy = self[i_proxy]
s = item_label
if proxy_type in (isotropic_adp, fixed_u_eq_adp):
if (site_labels is None): l = str(proxy.i_seqs[0])
else: l = site_labels[proxy.i_seqs[0]]
print >> f, "%s%s %s" % (prefix, s, l)
s = item_label_blank
elif proxy_type in dynamic_proxy_types:
restraint = proxy_type(params=params, proxy=proxy)
restraint._show_sorted_item(f=f, prefix=prefix)
print >> f, \
"%s delta" % (prefix)
for n, i_seq in enumerate(proxy.i_seqs):
if (site_labels is None): l = str(i_seq)
else: l = site_labels[i_seq]
print >> f, "%s %s %9.2e" % (prefix, l, restraint.deltas()[n])
else:
for n, i_seq in enumerate(proxy.i_seqs):
if (site_labels is None): l = str(i_seq)
else: l = site_labels[i_seq]
print >> f, "%s%s %s" % (prefix, s, l)
s = item_label_blank
if proxy_type in (adp_similarity, isotropic_adp, fixed_u_eq_adp,\
rigid_bond):
restraint = proxy_type(params=params, proxy=proxy)
restraint._show_sorted_item(f=f, prefix=prefix)
elif proxy_type in dynamic_proxy_types:
pass
else:
raise AssertionError
n_not_shown = self.size() - i_proxies_sorted.size()
if (n_not_shown != 0):
print >> f, prefix + "... (remaining %d not shown)" % n_not_shown
def exercise_rigid_bond():
i_seqs = (1,2)
weight = 1
p = adp_restraints.rigid_bond_proxy(i_seqs=i_seqs,weight=weight)
assert p.i_seqs == i_seqs
assert p.weight == weight
sites = ((1,2,3),(2,3,4))
u_cart = ((1,2,3,4,5,6), (3,4,5,6,7,8))
expected_gradients = ((-4, -4, -4, -8, -8, -8), (4, 4, 4, 8, 8, 8))
r = adp_restraints.rigid_bond(sites=sites, u_cart=u_cart, weight=weight)
assert r.weight == weight
assert approx_equal(r.delta_z(), -6)
assert approx_equal(r.residual(), 36)
assert approx_equal(r.gradients(), expected_gradients)
sites_cart = flex.vec3_double(((1,2,3),(2,5,4),(3,4,5)))
u_cart = flex.sym_mat3_double(((1,2,3,4,5,6),
(2,3,3,5,7,7),
(3,4,5,3,7,8)))
r = adp_restraints.rigid_bond(
adp_restraint_params(sites_cart=sites_cart, u_cart=u_cart),
proxy=p)
assert approx_equal(r.weight, weight)
unit_cell = uctbx.unit_cell([15,25,30,90,90,90])
sites_frac = unit_cell.fractionalize(sites_cart=sites_cart)
u_star = flex.sym_mat3_double([
adptbx.u_cart_as_u_star(unit_cell, u_cart_i)
for u_cart_i in u_cart])
pair = adp_restraints.rigid_bond_pair(sites_frac[1],
sites_frac[2],
u_star[1],
u_star[2],
unit_cell)
assert approx_equal(pair.delta_z(), abs(r.delta_z()))
assert approx_equal(pair.z_12(), r.z_12())
assert approx_equal(pair.z_21(), r.z_21())
#
gradients_aniso_cart = flex.sym_mat3_double(sites_cart.size(), (0,0,0,0,0,0))
gradients_iso = flex.double(sites_cart.size(), 0)
proxies = adp_restraints.shared_rigid_bond_proxy([p,p])
params = adp_restraint_params(sites_cart=sites_cart, u_cart=u_cart)
residuals = adp_restraints.rigid_bond_residuals(params, proxies=proxies)
assert approx_equal(residuals, (r.residual(),r.residual()))
deltas = adp_restraints.rigid_bond_deltas(params, proxies=proxies)
assert approx_equal(deltas, (r.delta_z(),r.delta_z()))
residual_sum = adp_restraints.rigid_bond_residual_sum(
params=params,
proxies=proxies,
gradients_aniso_cart=gradients_aniso_cart)
assert approx_equal(residual_sum, 2 * r.residual())
for g,e in zip(gradients_aniso_cart[1:3], r.gradients()):
assert approx_equal(g, matrix.col(e)*2)
fd_grads_aniso, fd_grads_iso = finite_difference_gradients(
restraint_type=adp_restraints.rigid_bond,
proxy=p,
sites_cart=sites_cart,
u_cart=u_cart)
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_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())
site_cart_1 = matrix.col((1,2,3))
site_cart_2 = matrix.col((3,1,4.2))
sites = (tuple(site_cart_1),tuple(site_cart_2))
a = adp_restraints.rigid_bond(sites=sites, u_cart=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())
site_cart_1_rot = R * site_cart_1
site_cart_2_rot = R * site_cart_2
sites = (tuple(site_cart_1_rot),tuple(site_cart_2_rot))
a = adp_restraints.rigid_bond(
sites=sites, u_cart=u_cart,
weight=1)
assert approx_equal(a.residual(), expected_residual)
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)