def exercise_rigid_bond():
xray_structure = development.sucrose()
pair_sym_table = get_pair_sym_table(xray_structure)
for table in (None,pair_sym_table):
if table is None: xs = xray_structure
else: xs = None
restraints = \
adp_restraints.rigid_bond_restraints(
xray_structure=xs,
pair_sym_table=table)
assert restraints.proxies.size() == 60
i_seqs = (9,14,28,32,36,38)
restraints = \
adp_restraints.rigid_bond_restraints(
xray_structure=xs,
pair_sym_table=table,
i_seqs=i_seqs)
expected_i_seqs = (
(9,32),(9,36),(14,36),(14,32),(14,38),(32,36),(32,38),(36,38))
expected_weights = [10000]*len(expected_i_seqs)
proxies = restraints.proxies
assert proxies.size() == len(expected_i_seqs)
for i in range(proxies.size()):
assert approx_equal(proxies[i].i_seqs, expected_i_seqs[i])
assert approx_equal(proxies[i].weight, expected_weights[i])
# add more restraints to same shared proxy
i_seqs = (10,40,42)
restraints = \
adp_restraints.rigid_bond_restraints(
xray_structure=xs,
pair_sym_table=table,
proxies=proxies,
i_seqs=i_seqs)
expected_i_seqs = (
(9,32),(9,36),(14,36),(14,32),(14,38),(32,36),
(32,38),(36,38),(10,42),(10,40),(40,42))
expected_weights = [10000]*len(expected_i_seqs)
proxies = restraints.proxies
assert proxies.size() == len(expected_i_seqs)
for i in range(proxies.size()):
assert approx_equal(proxies[i].i_seqs, expected_i_seqs[i])
assert approx_equal(proxies[i].weight, expected_weights[i])
def exercise_adp_restraints_as_cif():
import libtbx.load_env
if not libtbx.env.has_module("smtbx"):
print "Skipping exercise_adp_restraints_as_cif(): smtbx not available"
return
from smtbx.refinement.restraints import adp_restraints as smtbx_adp_restraints
import smtbx.development
xs = smtbx.development.sucrose()
rigid_bond_proxies = smtbx_adp_restraints.rigid_bond_restraints(
xray_structure=xs).proxies[:3]
adp_similarity_proxies = smtbx_adp_restraints.adp_similarity_restraints(
xray_structure=xs).proxies[:3]
isotropic_adp_proxies = smtbx_adp_restraints.isotropic_adp_restraints(
xray_structure=xs).proxies[:3]
cif_block = iotbx.cif.model.block()
iotbx.cif.restraints.add_to_cif_block(
cif_block,
xs,
rigid_bond_proxies=rigid_bond_proxies,
adp_similarity_proxies=adp_similarity_proxies,
isotropic_adp_proxies=isotropic_adp_proxies)
s = StringIO()
cif_block.show(out=s)
assert not show_diff(
s.getvalue(), """\
loop_
_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
O1 C1 0.0100 0.0176 0.0006
O1 C2 0.0100 0.0194 -0.0053
O1 C3 0.0100 0.0177 0.0013
loop_
_restr_U_similar_atom_site_label_1
_restr_U_similar_atom_site_label_2
_restr_U_similar_weight_param
O1 C1 0.0400
O1 C6 0.0400
O2 C2 0.0800
loop_
_restr_U_iso_atom_site_label
_restr_U_iso_weight_param
O1 0.1000
O2 0.2000
O3 0.2000
""")
def exercise_adp_restraints_as_cif():
import libtbx.load_env
if not libtbx.env.has_module("smtbx"):
print "Skipping exercise_adp_restraints_as_cif(): smtbx not available"
return
from smtbx.refinement.restraints import adp_restraints as smtbx_adp_restraints
import smtbx.development
xs = smtbx.development.sucrose()
rigid_bond_proxies = smtbx_adp_restraints.rigid_bond_restraints(
xray_structure=xs).proxies[:3]
adp_similarity_proxies = smtbx_adp_restraints.adp_similarity_restraints(
xray_structure=xs).proxies[:3]
isotropic_adp_proxies = smtbx_adp_restraints.isotropic_adp_restraints(
xray_structure=xs).proxies[:3]
cif_block = iotbx.cif.model.block()
iotbx.cif.restraints.add_to_cif_block(
cif_block, xs,
rigid_bond_proxies=rigid_bond_proxies,
adp_similarity_proxies=adp_similarity_proxies,
isotropic_adp_proxies=isotropic_adp_proxies)
s = StringIO()
cif_block.show(out=s)
assert not show_diff(s.getvalue(), """\
loop_
_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
O1 C1 0.0100 0.0176 0.0006
O1 C2 0.0100 0.0194 -0.0053
O1 C3 0.0100 0.0177 0.0013
loop_
_restr_U_similar_atom_site_label_1
_restr_U_similar_atom_site_label_2
_restr_U_similar_weight_param
O1 C1 0.0400
O1 C6 0.0400
O2 C2 0.0800
loop_
_restr_U_iso_atom_site_label
_restr_U_iso_weight_param
O1 0.1000
O2 0.2000
O3 0.2000
""")
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)
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 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_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()
