def exercise():
t = covalent_radii.table("sI")
assert t.label() == "Si"
assert approx_equal(t.radius(), 1.11)
assert approx_equal(t.esd(), 0.02)
n = 0
for t in covalent_radii.table_iterator():
n += 1
if (n == 1):
assert t.label() == "H"
elif (n == 97):
assert t.label() == "Cm"
u = covalent_radii.table(t.label())
assert u.label() == t.label()
assert n == 97
def exercise():
t = covalent_radii.table("sI")
assert t.label() == "Si"
assert approx_equal(t.radius(), 1.11)
assert approx_equal(t.esd(), 0.02)
n = 0
for t in covalent_radii.table_iterator():
n += 1
if (n == 1):
assert t.label() == "H"
elif (n == 97):
assert t.label() == "Cm"
u = covalent_radii.table(t.label())
assert u.label() == t.label()
assert n == 97
def __init__(self,
structure,
**kwds):
from cctbx.eltbx import covalent_radii
self.structure = structure
libtbx.adopt_optional_init_args(self, kwds)
max_r = 0
for st in structure.scattering_type_registry().type_index_pairs_as_dict():
r = 0
if self.radii:
r = self.radii.get(st, 0)
if r == 0:
r = covalent_radii.table(st).radius()
if r > max_r: max_r = r
self.structure = structure
self.buffer_thickness = 2*max_r + self.covalent_bond_tolerance
asu_mappings = structure.asu_mappings(
buffer_thickness=self.buffer_thickness)
self._pair_asu_table = crystal.pair_asu_table(asu_mappings)
self._pair_asu_table_needs_updating = False
if self.radii is None:
self.radii = {}
self._pair_asu_table.add_covalent_pairs(
structure.scattering_types(),
conformer_indices=self.conformer_indices,
sym_excl_indices=self.sym_excl_indices,
tolerance=self.covalent_bond_tolerance,
radii=self.radii
)
self.pair_sym_table = self.pair_asu_table.extract_pair_sym_table()
def __init__(self, structure, **kwds):
from cctbx.eltbx import covalent_radii
self.structure = structure
libtbx.adopt_optional_init_args(self, kwds)
max_r = 0
for st in structure.scattering_type_registry(
).type_index_pairs_as_dict():
r = 0
if self.radii:
r = self.radii.get(st, 0)
if r == 0:
r = covalent_radii.table(st).radius()
if r > max_r: max_r = r
self.structure = structure
self.buffer_thickness = 2 * max_r + self.covalent_bond_tolerance
asu_mappings = structure.asu_mappings(
buffer_thickness=self.buffer_thickness)
self._pair_asu_table = crystal.pair_asu_table(asu_mappings)
self._pair_asu_table_needs_updating = False
if self.radii is None:
self.radii = {}
self._pair_asu_table.add_covalent_pairs(
structure.scattering_types(),
conformer_indices=self.conformer_indices,
sym_excl_indices=self.sym_excl_indices,
tolerance=self.covalent_bond_tolerance,
radii=self.radii)
self.pair_sym_table = self.pair_asu_table.extract_pair_sym_table()
def exercise_hbond_as_cif_loop():
xs = sucrose()
for sc in xs.scatterers():
sc.flags.set_grad_site(True)
radii = [
covalent_radii.table(elt).radius() for elt in
xs.scattering_type_registry().type_index_pairs_as_dict() ]
asu_mappings = xs.asu_mappings(
buffer_thickness=2*max(radii) + 0.5)
pair_asu_table = crystal.pair_asu_table(asu_mappings)
pair_asu_table.add_covalent_pairs(
xs.scattering_types(),
tolerance=0.5)
hbonds = [
geometry.hbond(1,5, sgtbx.rt_mx('-X,0.5+Y,2-Z')),
geometry.hbond(5,14, sgtbx.rt_mx('-X,-0.5+Y,1-Z')),
geometry.hbond(7,10, sgtbx.rt_mx('1+X,+Y,+Z')),
geometry.hbond(10,0),
geometry.hbond(12,14, sgtbx.rt_mx('-1-X,0.5+Y,1-Z')),
geometry.hbond(14,12, sgtbx.rt_mx('-1-X,-0.5+Y,1-Z')),
geometry.hbond(16,7)
]
loop = geometry.hbonds_as_cif_loop(
hbonds, pair_asu_table, xs.scatterers().extract_labels(),
sites_frac=xs.sites_frac()).loop
s = StringIO()
print >> s, loop
assert not show_diff(s.getvalue(), """\
loop_
_geom_hbond_atom_site_label_D
_geom_hbond_atom_site_label_H
_geom_hbond_atom_site_label_A
_geom_hbond_distance_DH
_geom_hbond_distance_HA
_geom_hbond_distance_DA
_geom_hbond_angle_DHA
_geom_hbond_site_symmetry_A
O2 H2 O4 0.8200 2.0636 2.8635 165.0 2_557
O4 H4 O9 0.8200 2.0559 2.8736 174.9 2_546
O5 H5 O7 0.8200 2.0496 2.8589 169.0 1_655
O7 H7 O1 0.8200 2.0573 2.8617 166.8 .
O8 H8 O9 0.8200 2.1407 2.8943 152.8 2_456
O9 H9 O8 0.8200 2.1031 2.8943 162.1 2_446
O10 H10 O5 0.8200 2.0167 2.7979 159.1 .
""")
# with a covariance matrix
flex.set_random_seed(1)
vcv_matrix = matrix.diag(
flex.random_double(size=xs.n_parameters(), factor=1e-5))\
.as_flex_double_matrix().matrix_symmetric_as_packed_u()
loop = geometry.hbonds_as_cif_loop(
hbonds, pair_asu_table, xs.scatterers().extract_labels(),
sites_frac=xs.sites_frac(),
covariance_matrix=vcv_matrix,
parameter_map=xs.parameter_map()).loop
s = StringIO()
print >> s, loop
assert not show_diff(s.getvalue(), """\
loop_
_geom_hbond_atom_site_label_D
_geom_hbond_atom_site_label_H
_geom_hbond_atom_site_label_A
_geom_hbond_distance_DH
_geom_hbond_distance_HA
_geom_hbond_distance_DA
_geom_hbond_angle_DHA
_geom_hbond_site_symmetry_A
O2 H2 O4 0.82(3) 2.06(3) 2.86(3) 165.0(18) 2_557
O4 H4 O9 0.82(4) 2.06(4) 2.87(4) 175(2) 2_546
O5 H5 O7 0.82(2) 2.05(2) 2.859(19) 169.0(18) 1_655
O7 H7 O1 0.82(2) 2.06(2) 2.86(2) 167(2) .
O8 H8 O9 0.82(3) 2.14(3) 2.89(3) 153(3) 2_456
O9 H9 O8 0.82(3) 2.10(3) 2.89(3) 162(2) 2_446
O10 H10 O5 0.82(3) 2.02(3) 2.80(3) 159(3) .
""")
cell_vcv = flex.pow2(matrix.diag(flex.random_double(size=6,factor=1e-1))\
.as_flex_double_matrix().matrix_symmetric_as_packed_u())
loop = geometry.hbonds_as_cif_loop(
hbonds, pair_asu_table, xs.scatterers().extract_labels(),
sites_frac=xs.sites_frac(),
covariance_matrix=vcv_matrix,
cell_covariance_matrix=cell_vcv,
parameter_map=xs.parameter_map()).loop
s = StringIO()
print >> s, loop
assert not show_diff(s.getvalue(), """\
loop_
_geom_hbond_atom_site_label_D
_geom_hbond_atom_site_label_H
_geom_hbond_atom_site_label_A
_geom_hbond_distance_DH
_geom_hbond_distance_HA
_geom_hbond_distance_DA
_geom_hbond_angle_DHA
_geom_hbond_site_symmetry_A
O2 H2 O4 0.82(3) 2.06(4) 2.86(4) 165.0(18) 2_557
O4 H4 O9 0.82(4) 2.06(4) 2.87(4) 175(2) 2_546
O5 H5 O7 0.82(2) 2.05(2) 2.86(2) 169.0(18) 1_655
O7 H7 O1 0.82(2) 2.06(3) 2.86(3) 167(2) .
O8 H8 O9 0.82(3) 2.14(4) 2.89(4) 153(3) 2_456
O9 H9 O8 0.82(3) 2.10(3) 2.89(4) 162(2) 2_446
O10 H10 O5 0.82(3) 2.02(3) 2.80(3) 159(3) .
""")
def __init__(self, xray_structure, name='??',
**kwds):
super(xray_structure_viewer, self).__init__(
unit_cell=xray_structure.unit_cell(),
orthographic=True,
light_position=(-1, 1, 1, 0),
**kwds)
assert self.bonding in ("covalent", "all")
assert self.bonding != "all" or self.distance_cutoff is not None
self.xray_structure = xs = xray_structure
self.setWindowTitle("%s in %s" % (name,
xs.space_group().type().hall_symbol()))
sites_frac = xs.sites_frac()
self.set_extent(sites_frac.min(), sites_frac.max())
self.is_unit_cell_shown = False
sites_cart = self.sites_cart = xs.sites_cart()
thermal_tensors = xs.extract_u_cart_plus_u_iso()
self.ellipsoid_to_sphere_transforms = {}
self.scatterer_indices = flex.std_string()
self.scatterer_labels = flex.std_string()
for i, (sc, site, u_cart) in enumerate(itertools.izip(xs.scatterers(),
sites_cart,
thermal_tensors)):
t = quadrics.ellipsoid_to_sphere_transform(site, u_cart)
self.ellipsoid_to_sphere_transforms.setdefault(
sc.element_symbol(),
quadrics.shared_ellipsoid_to_sphere_transforms()).append(t)
self.scatterer_indices.append("# %i" % i)
self.scatterer_labels.append(sc.label)
self.labels = None
self.label_font = QtGui.QFont("Arial Black", pointSize=18)
if self.bonding == "covalent":
radii = [
covalent_radii.table(elt).radius()
for elt in xs.scattering_type_registry().type_index_pairs_as_dict() ]
buffer_thickness = 2*max(radii) + self.covalent_bond_tolerance
asu_mappings = xs.asu_mappings(buffer_thickness=buffer_thickness)
bond_table = crystal.pair_asu_table(asu_mappings)
bond_table.add_covalent_pairs(xs.scattering_types(),
tolerance=self.covalent_bond_tolerance)
elif self.bonding == "all":
asu_mappings = xs.asu_mappings(buffer_thickness=self.distance_cutoff)
bond_table = crystal.pair_asu_table(asu_mappings)
bond_table.add_all_pairs(self.distance_cutoff)
pair_sym_table = bond_table.extract_pair_sym_table(
all_interactions_from_inside_asu=True)
self.bonds = flex.vec3_double()
self.bonds.reserve(len(xs.scatterers()))
uc = self.xray_structure.unit_cell()
frac = mat.rec(uc.fractionalization_matrix(), (3,3))
inv_frac = frac.inverse()
site_symms = xs.site_symmetry_table()
scatt = self.xray_structure.scatterers()
for i, neighbours in enumerate(pair_sym_table):
x0 = sites_cart[i]
sc0 = scatt[i]
for j, ops in neighbours.items():
sc1 = scatt[j]
if sc0.scattering_type == 'H' and sc1.scattering_type == 'H':
continue
for op in ops:
if op.is_unit_mx():
x1 = sites_cart[j]
else:
x1 = uc.orthogonalize(op*sites_frac[j])
op_cart = inv_frac*mat.rec(op.r().as_double(), (3,3))*frac
u1 = (op_cart
*mat.sym(sym_mat3=thermal_tensors[j])
*op_cart.transpose())
t = quadrics.ellipsoid_to_sphere_transform(x1, u1.as_sym_mat3())
self.ellipsoid_to_sphere_transforms[sc1.element_symbol()].append(t)
self.sites_cart.append(x1)
op_lbl = (" [%s]" % op).lower()
self.scatterer_indices.append("# %i%s" % (j, op_lbl))
self.scatterer_labels.append("%s%s" % (sc1.label, op_lbl))
self.bonds.append(x0)
self.bonds.append(x1)
def exercise_hbond_as_cif_loop():
xs = sucrose()
for sc in xs.scatterers():
sc.flags.set_grad_site(True)
radii = [
covalent_radii.table(elt).radius()
for elt in xs.scattering_type_registry().type_index_pairs_as_dict()
]
asu_mappings = xs.asu_mappings(buffer_thickness=2 * max(radii) + 0.5)
pair_asu_table = crystal.pair_asu_table(asu_mappings)
pair_asu_table.add_covalent_pairs(xs.scattering_types(), tolerance=0.5)
hbonds = [
geometry.hbond(1, 5, sgtbx.rt_mx('-X,0.5+Y,2-Z')),
geometry.hbond(5, 14, sgtbx.rt_mx('-X,-0.5+Y,1-Z')),
geometry.hbond(7, 10, sgtbx.rt_mx('1+X,+Y,+Z')),
geometry.hbond(10, 0),
geometry.hbond(12, 14, sgtbx.rt_mx('-1-X,0.5+Y,1-Z')),
geometry.hbond(14, 12, sgtbx.rt_mx('-1-X,-0.5+Y,1-Z')),
geometry.hbond(16, 7)
]
loop = geometry.hbonds_as_cif_loop(hbonds,
pair_asu_table,
xs.scatterers().extract_labels(),
sites_frac=xs.sites_frac()).loop
s = StringIO()
print >> s, loop
assert not show_diff(
s.getvalue(), """\
loop_
_geom_hbond_atom_site_label_D
_geom_hbond_atom_site_label_H
_geom_hbond_atom_site_label_A
_geom_hbond_distance_DH
_geom_hbond_distance_HA
_geom_hbond_distance_DA
_geom_hbond_angle_DHA
_geom_hbond_site_symmetry_A
O2 H2 O4 0.8200 2.0636 2.8635 165.0 2_557
O4 H4 O9 0.8200 2.0559 2.8736 174.9 2_546
O5 H5 O7 0.8200 2.0496 2.8589 169.0 1_655
O7 H7 O1 0.8200 2.0573 2.8617 166.8 .
O8 H8 O9 0.8200 2.1407 2.8943 152.8 2_456
O9 H9 O8 0.8200 2.1031 2.8943 162.1 2_446
O10 H10 O5 0.8200 2.0167 2.7979 159.1 .
""")
# with a covariance matrix
flex.set_random_seed(1)
vcv_matrix = matrix.diag(
flex.random_double(size=xs.n_parameters(), factor=1e-5))\
.as_flex_double_matrix().matrix_symmetric_as_packed_u()
loop = geometry.hbonds_as_cif_loop(hbonds,
pair_asu_table,
xs.scatterers().extract_labels(),
sites_frac=xs.sites_frac(),
covariance_matrix=vcv_matrix,
parameter_map=xs.parameter_map()).loop
s = StringIO()
print >> s, loop
assert not show_diff(
s.getvalue(), """\
loop_
_geom_hbond_atom_site_label_D
_geom_hbond_atom_site_label_H
_geom_hbond_atom_site_label_A
_geom_hbond_distance_DH
_geom_hbond_distance_HA
_geom_hbond_distance_DA
_geom_hbond_angle_DHA
_geom_hbond_site_symmetry_A
O2 H2 O4 0.82(3) 2.06(3) 2.86(3) 165.0(18) 2_557
O4 H4 O9 0.82(4) 2.06(4) 2.87(4) 175(2) 2_546
O5 H5 O7 0.82(2) 2.05(2) 2.859(19) 169.0(18) 1_655
O7 H7 O1 0.82(2) 2.06(2) 2.86(2) 167(2) .
O8 H8 O9 0.82(3) 2.14(3) 2.89(3) 153(3) 2_456
O9 H9 O8 0.82(3) 2.10(3) 2.89(3) 162(2) 2_446
O10 H10 O5 0.82(3) 2.02(3) 2.80(3) 159(3) .
""")
cell_vcv = flex.pow2(matrix.diag(flex.random_double(size=6,factor=1e-1))\
.as_flex_double_matrix().matrix_symmetric_as_packed_u())
loop = geometry.hbonds_as_cif_loop(hbonds,
pair_asu_table,
xs.scatterers().extract_labels(),
sites_frac=xs.sites_frac(),
covariance_matrix=vcv_matrix,
cell_covariance_matrix=cell_vcv,
parameter_map=xs.parameter_map()).loop
s = StringIO()
print >> s, loop
assert not show_diff(
s.getvalue(), """\
loop_
_geom_hbond_atom_site_label_D
_geom_hbond_atom_site_label_H
_geom_hbond_atom_site_label_A
_geom_hbond_distance_DH
_geom_hbond_distance_HA
_geom_hbond_distance_DA
_geom_hbond_angle_DHA
_geom_hbond_site_symmetry_A
O2 H2 O4 0.82(3) 2.06(4) 2.86(4) 165.0(18) 2_557
O4 H4 O9 0.82(4) 2.06(4) 2.87(4) 175(2) 2_546
O5 H5 O7 0.82(2) 2.05(2) 2.86(2) 169.0(18) 1_655
O7 H7 O1 0.82(2) 2.06(3) 2.86(3) 167(2) .
O8 H8 O9 0.82(3) 2.14(4) 2.89(4) 153(3) 2_456
O9 H9 O8 0.82(3) 2.10(3) 2.89(4) 162(2) 2_446
O10 H10 O5 0.82(3) 2.02(3) 2.80(3) 159(3) .
""")
def __init__(self, xray_structure, name='??', **kwds):
super(xray_structure_viewer,
self).__init__(unit_cell=xray_structure.unit_cell(),
orthographic=True,
light_position=(-1, 1, 1, 0),
**kwds)
assert self.bonding in ("covalent", "all")
assert self.bonding != "all" or self.distance_cutoff is not None
self.xray_structure = xs = xray_structure
self.setWindowTitle("%s in %s" %
(name, xs.space_group().type().hall_symbol()))
sites_frac = xs.sites_frac()
self.set_extent(sites_frac.min(), sites_frac.max())
self.is_unit_cell_shown = False
sites_cart = self.sites_cart = xs.sites_cart()
thermal_tensors = xs.extract_u_cart_plus_u_iso()
self.ellipsoid_to_sphere_transforms = {}
self.scatterer_indices = flex.std_string()
self.scatterer_labels = flex.std_string()
for i, (sc, site, u_cart) in enumerate(
zip(xs.scatterers(), sites_cart, thermal_tensors)):
t = quadrics.ellipsoid_to_sphere_transform(site, u_cart)
self.ellipsoid_to_sphere_transforms.setdefault(
sc.element_symbol(),
quadrics.shared_ellipsoid_to_sphere_transforms()).append(t)
self.scatterer_indices.append("# %i" % i)
self.scatterer_labels.append(sc.label)
self.labels = None
self.label_font = QtGui.QFont("Arial Black", pointSize=18)
if self.bonding == "covalent":
radii = [
covalent_radii.table(elt).radius() for elt in
xs.scattering_type_registry().type_index_pairs_as_dict()
]
buffer_thickness = 2 * max(radii) + self.covalent_bond_tolerance
asu_mappings = xs.asu_mappings(buffer_thickness=buffer_thickness)
bond_table = crystal.pair_asu_table(asu_mappings)
bond_table.add_covalent_pairs(
xs.scattering_types(), tolerance=self.covalent_bond_tolerance)
elif self.bonding == "all":
asu_mappings = xs.asu_mappings(
buffer_thickness=self.distance_cutoff)
bond_table = crystal.pair_asu_table(asu_mappings)
bond_table.add_all_pairs(self.distance_cutoff)
pair_sym_table = bond_table.extract_pair_sym_table(
all_interactions_from_inside_asu=True)
self.bonds = flex.vec3_double()
self.bonds.reserve(len(xs.scatterers()))
uc = self.xray_structure.unit_cell()
frac = mat.rec(uc.fractionalization_matrix(), (3, 3))
inv_frac = frac.inverse()
site_symms = xs.site_symmetry_table()
scatt = self.xray_structure.scatterers()
for i, neighbours in enumerate(pair_sym_table):
x0 = sites_cart[i]
sc0 = scatt[i]
for j, ops in neighbours.items():
sc1 = scatt[j]
if sc0.scattering_type == 'H' and sc1.scattering_type == 'H':
continue
for op in ops:
if op.is_unit_mx():
x1 = sites_cart[j]
else:
x1 = uc.orthogonalize(op * sites_frac[j])
op_cart = inv_frac * mat.rec(op.r().as_double(),
(3, 3)) * frac
u1 = (op_cart * mat.sym(sym_mat3=thermal_tensors[j]) *
op_cart.transpose())
t = quadrics.ellipsoid_to_sphere_transform(
x1, u1.as_sym_mat3())
self.ellipsoid_to_sphere_transforms[
sc1.element_symbol()].append(t)
self.sites_cart.append(x1)
op_lbl = (" [%s]" % op).lower()
self.scatterer_indices.append("# %i%s" % (j, op_lbl))
self.scatterer_labels.append("%s%s" %
(sc1.label, op_lbl))
self.bonds.append(x0)
self.bonds.append(x1)