def get_angles(atom_group, atom, verbose=False):
bad_hydrogen_count = 0
corrected_hydrogen_count = []
bonded = get_bonded(atom_group, atom)
if not bonded:
bad_hydrogen_count += 1
if verbose: print 'not bonded: %s' % atom.format_atom_record()
return bad_hydrogen_count, corrected_hydrogen_count
for ba in bonded:
angled = get_bonded(atom_group, ba, exclude=[atom])
if not angled:
bad_hydrogen_count += 1
if verbose: print 'not angled: %s' % atom.format_atom_record()
return bad_hydrogen_count, corrected_hydrogen_count
if angled[0].element.strip() in ["H", "D", "T"]:
return bad_hydrogen_count, corrected_hydrogen_count
try:
angle = geometry.angle(
(atom.xyz, ba.xyz, angled[0].xyz)).angle_model
except Exception:
print ' Bad angle "%s"' % (atom.format_atom_record()[:26])
bad_hydrogen_count += 1
return bad_hydrogen_count, corrected_hydrogen_count
if angle < 85.:
xyz = [0, 0, 0]
xyz[0] = ba.xyz[0] * 2 - atom.xyz[0]
xyz[1] = ba.xyz[1] * 2 - atom.xyz[1]
xyz[2] = ba.xyz[2] * 2 - atom.xyz[2]
angle = geometry.angle((xyz, ba.xyz, angled[0].xyz)).angle_model
if angle > 95.:
atom.xyz = tuple(xyz)
if verbose:
print ' Inverted "%s" ' % (atom.format_atom_record()[:26])
corrected_hydrogen_count.append(atom.i_seq)
return bad_hydrogen_count, corrected_hydrogen_count
def get_angles(atom_group, atom, verbose=False):
bad_hydrogen_count = 0
corrected_hydrogen_count = []
bonded = get_bonded(atom_group, atom)
if not bonded:
bad_hydrogen_count+=1
if verbose: print 'not bonded: %s' % atom.format_atom_record()
return bad_hydrogen_count, corrected_hydrogen_count
for ba in bonded:
angled = get_bonded(atom_group, ba, exclude=[atom])
if not angled:
bad_hydrogen_count+=1
if verbose: print 'not angled: %s' % atom.format_atom_record()
return bad_hydrogen_count, corrected_hydrogen_count
if angled[0].element.strip() in ["H", "D", "T"]:
return bad_hydrogen_count, corrected_hydrogen_count
try: angle = geometry.angle((atom.xyz,ba.xyz,angled[0].xyz)).angle_model
except Exception:
print ' Bad angle "%s"' % (atom.format_atom_record()[:26])
bad_hydrogen_count +=1
return bad_hydrogen_count, corrected_hydrogen_count
if angle<85.:
xyz=[0,0,0]
xyz[0] = ba.xyz[0]*2-atom.xyz[0]
xyz[1] = ba.xyz[1]*2-atom.xyz[1]
xyz[2] = ba.xyz[2]*2-atom.xyz[2]
angle = geometry.angle((xyz,ba.xyz,angled[0].xyz)).angle_model
if angle>95.:
atom.xyz = tuple(xyz)
if verbose: print ' Inverted "%s" ' % (atom.format_atom_record()[:26])
corrected_hydrogen_count.append(atom.i_seq)
return bad_hydrogen_count, corrected_hydrogen_count
def get_i_seqs_from_restraints_manager(
hierarchy,
restraints_manager,
xray_structure = None,
sites_cart = None,
):
if sites_cart is None and xray_structure:
sites_cart = xray_structure.sites_cart()
if sites_cart is None:
xray_structure = hierarchy.extract_xray_structure()
sites_cart = xray_structure.sites_cart()
i_seqs=[]
xyzs=[]
angle_proxies_simple = restraints_manager.geometry.angle_proxies
atoms = hierarchy.atoms()
for proxy in angle_proxies_simple:
i_seq, j_seq, k_seq = proxy.i_seqs
if(atoms[i_seq].element.strip() in ["H", "D"] or
atoms[k_seq].element.strip() in ["H", "D"]
):
if(atoms[i_seq].element.strip() in ["H", "D"] and
atoms[k_seq].element.strip() in ["H", "D"]
):
continue
if(atoms[i_seq].element.strip() in ["H", "D"]):
i_h = i_seq
site_i = sites_cart[i_seq]
site_k = sites_cart[k_seq]
else:
i_h = k_seq
site_i = sites_cart[k_seq]
site_k = sites_cart[i_seq]
site_j = sites_cart[j_seq]
if i_h in i_seqs: continue
angle = geometry.angle((site_i, site_j, site_k)).angle_model
if angle<85.:
xyz=[0,0,0]
xyz[0] = site_j[0]*2-site_i[0]
xyz[1] = site_j[1]*2-site_i[1]
xyz[2] = site_j[2]*2-site_i[2]
angle = geometry.angle((xyz, site_j, site_k)).angle_model
if angle>95.:
xyzs.append(tuple(xyz))
i_seqs.append(i_h)
return i_seqs, xyzs
def calc_angle(metrical_matrix=None): xs = quartz_p1(metrical_matrix=metrical_matrix) uc = xs.unit_cell() sites_cart = xs.sites_cart() sites = (sites_cart[4], sites_cart[0], sites_cart[5]) a = geometry.angle(sites) return a.angle_model*(math.pi/180)
def exercise_grad_metrical_matrix():
def calc_distance(metrical_matrix=None):
xs = quartz_p1(metrical_matrix=metrical_matrix)
uc = xs.unit_cell()
sites_cart = xs.sites_cart()
sites = (sites_cart[0], sites_cart[5])
d = geometry.distance(sites)
return d.distance_model
def calc_angle(metrical_matrix=None):
xs = quartz_p1(metrical_matrix=metrical_matrix)
uc = xs.unit_cell()
sites_cart = xs.sites_cart()
sites = (sites_cart[4], sites_cart[0], sites_cart[5])
a = geometry.angle(sites)
return a.angle_model*(math.pi/180)
xs = quartz_p1()
uc = xs.unit_cell()
sites_cart = xs.sites_cart()
# distances
sites = (sites_cart[0], sites_cart[5])
d = geometry.distance(sites)
grads = d.d_distance_d_metrical_matrix(uc)
fd_grads = finite_differences(calc_distance, xs.unit_cell())
assert approx_equal(grads, fd_grads)
# angles
sites = (sites_cart[4], sites_cart[0], sites_cart[5])
a = geometry.angle(sites)
grads = a.d_angle_d_metrical_matrix(uc)
fd_grads = finite_differences(calc_angle, xs.unit_cell())
assert approx_equal(grads, fd_grads)
def exercise_geometry():
xs = quartz()
uc = xs.unit_cell()
flags = xs.scatterer_flags()
for f in flags:
f.set_grad_site(True)
xs.set_scatterer_flags(flags)
cov = flex.double(
(1e-8, 1e-9, 2e-9, 3e-9, 4e-9, 5e-9, 2e-8, 1e-9, 2e-9, 3e-9, 4e-9,
3e-8, 1e-9, 2e-9, 3e-9, 2e-8, 1e-9, 2e-9, 3e-8, 1e-9, 4e-8))
cell_vcv = flex.double((3e-2, 3e-2, 0, 0, 0, 0, 3e-2, 0, 0, 0, 0, 4e-2, 0,
0, 0, 0, 0, 0, 0, 0, 0))
param_map = xs.parameter_map()
cov_cart = covariance.orthogonalize_covariance_matrix(cov, uc, param_map)
O = matrix.sqr(uc.orthogonalization_matrix())
F = matrix.sqr(uc.fractionalization_matrix())
sites_cart = xs.sites_cart()
sites_frac = xs.sites_frac()
# distances
rt_mx_ji = sgtbx.rt_mx('-y,x-y,z-1/3')
sites = (sites_cart[0], uc.orthogonalize(rt_mx_ji * sites_frac[1]))
d = geometry.distance(sites)
assert approx_equal(d.distance_model, 1.6159860469110217)
v = matrix.col(sites[1]) - matrix.col(sites[0])
r_inv_cart = (O * matrix.sqr(rt_mx_ji.r().inverse().as_double()) * F)
g = d.d_distance_d_sites()
g = matrix.row(g[0] + tuple(r_inv_cart * matrix.col(g[1])))
f = g * matrix.sqr(cov_cart.matrix_packed_u_as_symmetric()) * g.transpose()
assert approx_equal(d.variance(cov_cart, uc, rt_mx_ji), f[0], eps=1e-15)
assert approx_equal(0.0018054494791580823,
d.variance(cov_cart, cell_vcv, uc, rt_mx_ji))
rt_mx_ji = sgtbx.rt_mx('x+1,y,z')
sites = (sites_cart[0], uc.orthogonalize(rt_mx_ji * sites_frac[0]))
d = geometry.distance(sites)
assert approx_equal(d.distance_model, uc.parameters()[0])
assert approx_equal(cell_vcv.matrix_packed_u_diagonal()[0],
d.variance(cov_cart, cell_vcv, uc, rt_mx_ji))
# angles
rt_mx_ji = sgtbx.rt_mx('x-y,x,z-2/3')
rt_mx_ki = sgtbx.rt_mx('-y,x-y,z-1/3')
r_inv_cart_ji = (O * matrix.sqr(rt_mx_ji.r().inverse().as_double()) * F)
r_inv_cart_ki = (O * matrix.sqr(rt_mx_ki.r().inverse().as_double()) * F)
cov_a = covariance.extract_covariance_matrix_for_sites(
flex.size_t([1, 0, 1]), cov_cart, param_map)
sites = (uc.orthogonalize(rt_mx_ji * sites_frac[1]), sites_cart[0],
uc.orthogonalize(rt_mx_ki * sites_frac[1]))
a = geometry.angle(sites)
assert approx_equal(a.angle_model, 101.30738566828551)
g = a.d_angle_d_sites()
g = matrix.row(
tuple(r_inv_cart_ji * matrix.col(g[0])) + g[1] +
tuple(r_inv_cart_ki * matrix.col(g[2])))
f = g * matrix.sqr(cov_a.matrix_packed_u_as_symmetric()) * g.transpose()
assert approx_equal(a.variance(cov_a, uc,
(rt_mx_ji, sgtbx.rt_mx(), rt_mx_ki)),
f[0],
eps=1e-15)
assert approx_equal(
0.0042632511984529199,
a.variance(cov_a, cell_vcv, uc, (rt_mx_ji, sgtbx.rt_mx(), rt_mx_ki)))
def get_i_seqs_from_restraints_manager(
hierarchy,
restraints_manager,
xray_structure=None,
sites_cart=None,
):
if sites_cart is None and xray_structure:
sites_cart = xray_structure.sites_cart()
if sites_cart is None:
xray_structure = hierarchy.extract_xray_structure()
sites_cart = xray_structure.sites_cart()
i_seqs = []
xyzs = []
angle_proxies_simple = restraints_manager.geometry.angle_proxies
atoms = hierarchy.atoms()
for proxy in angle_proxies_simple:
i_seq, j_seq, k_seq = proxy.i_seqs
if (atoms[i_seq].element.strip() in ["H", "D"]
or atoms[k_seq].element.strip() in ["H", "D"]):
if (atoms[i_seq].element.strip() in ["H", "D"]
and atoms[k_seq].element.strip() in ["H", "D"]):
continue
if (atoms[i_seq].element.strip() in ["H", "D"]):
i_h = i_seq
site_i = sites_cart[i_seq]
site_k = sites_cart[k_seq]
else:
i_h = k_seq
site_i = sites_cart[k_seq]
site_k = sites_cart[i_seq]
site_j = sites_cart[j_seq]
if i_h in i_seqs: continue
angle = geometry.angle((site_i, site_j, site_k)).angle_model
if angle < 85.:
xyz = [0, 0, 0]
xyz[0] = site_j[0] * 2 - site_i[0]
xyz[1] = site_j[1] * 2 - site_i[1]
xyz[2] = site_j[2] * 2 - site_i[2]
angle = geometry.angle((xyz, site_j, site_k)).angle_model
if angle > 95.:
xyzs.append(tuple(xyz))
i_seqs.append(i_h)
return i_seqs, xyzs
def __init__(self,
hbonds,
pair_asu_table,
site_labels,
sites_frac=None,
sites_cart=None,
min_dha_angle=150, # degrees
max_da_distance=2.9, # angstrom
covariance_matrix=None,
cell_covariance_matrix=None,
parameter_map=None,
eps=2e-16):
assert [sites_frac, sites_cart].count(None) == 1
fmt_a = "%.1f"
pair_asu_table = pair_asu_table
asu_mappings = pair_asu_table.asu_mappings()
space_group_info = sgtbx.space_group_info(group=asu_mappings.space_group())
self.unit_cell = asu_mappings.unit_cell()
if sites_cart is not None:
sites_frac = self.unit_cell.fractionalize(sites_cart)
if sites_frac is not None:
sites_cart = self.unit_cell.orthogonalize(sites_frac)
if covariance_matrix is not None:
assert parameter_map is not None
self.covariance_matrix_cart = covariance.orthogonalize_covariance_matrix(
covariance_matrix, self.unit_cell, parameter_map)
else: self.covariance_matrix_cart = None
self.cell_covariance_matrix = cell_covariance_matrix
self.eps = eps
self.parameter_map = parameter_map
self.loop = model.loop(header=(
"_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",
))
for hbond in hbonds:
d_seq, a_seq = hbond.d_seq, hbond.a_seq
site_cart_d = sites_cart[d_seq]
if hbond.rt_mx is not None:
site_frac_a = sites_frac[a_seq]
site_frac_a = hbond.rt_mx * site_frac_a
site_cart_a = self.unit_cell.orthogonalize(site_frac_a)
else:
site_cart_a = sites_cart[a_seq]
distance_da = geometry.distance((site_cart_d, site_cart_a))
for h_seq, h_sym_groups in pair_asu_table.table()[hbond.d_seq].items():
if site_labels[h_seq][0] not in ('H','D'):
# XXX better to pass scattering types instead?
continue
site_cart_h = sites_cart[h_seq]
distance_dh = geometry.distance((site_cart_d, site_cart_h))
distance_ha = geometry.distance((site_cart_h, site_cart_a))
angle_dha = geometry.angle((site_cart_d, site_cart_h, site_cart_a))
if (angle_dha.angle_model < min_dha_angle or
distance_da.distance_model > max_da_distance):
continue
if hbond.rt_mx is not None:
sym_code = space_group_info.cif_symmetry_code(hbond.rt_mx)
else: sym_code = '.'
self.loop.add_row((
site_labels[d_seq],
site_labels[h_seq],
site_labels[a_seq],
self.formatted_distance(d_seq, h_seq, distance_dh, unit_mx),
self.formatted_distance(h_seq, a_seq, distance_ha, unit_mx),
self.formatted_distance(d_seq, a_seq, distance_da, hbond.rt_mx),
self.formatted_angle(d_seq, h_seq, a_seq, angle_dha, hbond.rt_mx),
sym_code
))
def predict_protonation(ag, verbose=False):
from cctbx import geometry
from mmtbx.monomer_library.linking_utils import get_distance2
from math import sqrt
# from cctbx_geometry_restraints_ext import *
# from cctbx.array_family import flex
"""
his1 = -37.35*X1 + 15.57*X2 - 0.64*X3 + 0.76*X4 + 17.30
his2 = -2.16*X1 - 6.08*X2 + 0.56*X3 + 0.42*X4 - 94.46
X1 = ND1-CE1
X2 = CE1-NE2
X3 = -ND1-
X4 = -NE2-
his1<0 ~> ND1 protonated
his1>0
his2<0 ~> NE2 protonated
his2>0 ~> doubly protonated
"""
bonds = {
("ND1", "CE1") : None,
("NE2", "CE1") : None,
}
if verbose:
for atom in ag.atoms():
print atom.quote()
for i, tmp_atom in enumerate(bonds):
atoms = []
for j in range(2):
for atom in ag.atoms():
if atom.name.strip()==tmp_atom[j]:
atoms.append(atom)
break
if len(atoms)==2:
d2=get_distance2(*atoms)
bonds[tmp_atom]=sqrt(d2)
angles = {
("CG", "ND1", "CE1") : None,
("CE1","NE2", "CD2") : None,
}
for i, tmp_atom in enumerate(angles):
atoms = []
for j in range(3):
for atom in ag.atoms():
if atom.name.strip()==tmp_atom[j]:
atoms.append(atom.xyz)
break
if len(atoms)==3:
angle=geometry.angle((atoms)).angle_model
angles[tmp_atom]=angle
if None in bonds.values() or None in angles.values(): return None
his1 = 17.30 - 0.64*angles[("CG", "ND1", "CE1")]
his1 += 0.76*angles[("CE1","NE2", "CD2")]
his1 -= 37.35*bonds[("ND1", "CE1")]
his1 += 15.57*bonds[("NE2", "CE1")]
his2 = -94.46 + 0.56*angles[("CG", "ND1", "CE1")]
his2 += 0.42*angles[("CE1","NE2", "CD2")]
his2 -= 2.61*bonds[("ND1", "CE1")]
his2 -= 6.08*bonds[("NE2", "CE1")]
if verbose:
print 'his1',his1
print 'his2',his2
return (his1, his2)
def predict_protonation(ag, verbose=False):
from cctbx import geometry
from mmtbx.monomer_library.linking_utils import get_distance2
from math import sqrt
# from cctbx_geometry_restraints_ext import *
# from cctbx.array_family import flex
"""
his1 = -37.35*X1 + 15.57*X2 - 0.64*X3 + 0.76*X4 + 17.30
his2 = -2.16*X1 - 6.08*X2 + 0.56*X3 + 0.42*X4 - 94.46
X1 = ND1-CE1
X2 = CE1-NE2
X3 = -ND1-
X4 = -NE2-
his1<0 ~> ND1 protonated
his1>0
his2<0 ~> NE2 protonated
his2>0 ~> doubly protonated
"""
bonds = {
("ND1", "CE1"): None,
("NE2", "CE1"): None,
}
if verbose:
for atom in ag.atoms():
print atom.quote()
for i, tmp_atom in enumerate(bonds):
atoms = []
for j in range(2):
for atom in ag.atoms():
if atom.name.strip() == tmp_atom[j]:
atoms.append(atom)
break
if len(atoms) == 2:
d2 = get_distance2(*atoms)
bonds[tmp_atom] = sqrt(d2)
angles = {
("CG", "ND1", "CE1"): None,
("CE1", "NE2", "CD2"): None,
}
for i, tmp_atom in enumerate(angles):
atoms = []
for j in range(3):
for atom in ag.atoms():
if atom.name.strip() == tmp_atom[j]:
atoms.append(atom.xyz)
break
if len(atoms) == 3:
angle = geometry.angle((atoms)).angle_model
angles[tmp_atom] = angle
if None in bonds.values() or None in angles.values(): return None
his1 = 17.30 - 0.64 * angles[("CG", "ND1", "CE1")]
his1 += 0.76 * angles[("CE1", "NE2", "CD2")]
his1 -= 37.35 * bonds[("ND1", "CE1")]
his1 += 15.57 * bonds[("NE2", "CE1")]
his2 = -94.46 + 0.56 * angles[("CG", "ND1", "CE1")]
his2 += 0.42 * angles[("CE1", "NE2", "CD2")]
his2 -= 2.61 * bonds[("ND1", "CE1")]
his2 -= 6.08 * bonds[("NE2", "CE1")]
if verbose:
print 'his1', his1
print 'his2', his2
return (his1, his2)
def exercise_geometry():
xs = quartz()
uc = xs.unit_cell()
flags = xs.scatterer_flags()
for f in flags:
f.set_grad_site(True)
xs.set_scatterer_flags(flags)
cov = flex.double((1e-8,1e-9,2e-9,3e-9,4e-9,5e-9,
2e-8,1e-9,2e-9,3e-9,4e-9,
3e-8,1e-9,2e-9,3e-9,
2e-8,1e-9,2e-9,
3e-8,1e-9,
4e-8))
cell_vcv = flex.double((3e-2,3e-2,0,0,0,0,
3e-2,0,0,0,0,
4e-2,0,0,0,
0,0,0,
0,0,
0))
param_map = xs.parameter_map()
cov_cart = covariance.orthogonalize_covariance_matrix(cov, uc, param_map)
O = matrix.sqr(uc.orthogonalization_matrix())
F = matrix.sqr(uc.fractionalization_matrix())
sites_cart = xs.sites_cart()
sites_frac = xs.sites_frac()
# distances
rt_mx_ji = sgtbx.rt_mx('-y,x-y,z-1/3')
sites = (sites_cart[0], uc.orthogonalize(rt_mx_ji*sites_frac[1]))
d = geometry.distance(sites)
assert approx_equal(d.distance_model, 1.6159860469110217)
v = matrix.col(sites[1]) - matrix.col(sites[0])
r_inv_cart = (O * matrix.sqr(rt_mx_ji.r().inverse().as_double()) * F)
g = d.d_distance_d_sites()
g = matrix.row(g[0] + tuple(r_inv_cart*matrix.col(g[1])))
f = g * matrix.sqr(cov_cart.matrix_packed_u_as_symmetric()) * g.transpose()
assert approx_equal(d.variance(cov_cart, uc, rt_mx_ji), f[0], eps=1e-15)
assert approx_equal(
0.0018054494791580823, d.variance(cov_cart, cell_vcv, uc, rt_mx_ji))
rt_mx_ji = sgtbx.rt_mx('x+1,y,z')
sites = (sites_cart[0], uc.orthogonalize(rt_mx_ji*sites_frac[0]))
d = geometry.distance(sites)
assert approx_equal(d.distance_model, uc.parameters()[0])
assert approx_equal(cell_vcv.matrix_packed_u_diagonal()[0],
d.variance(cov_cart, cell_vcv, uc, rt_mx_ji))
# angles
rt_mx_ji = sgtbx.rt_mx('x-y,x,z-2/3')
rt_mx_ki = sgtbx.rt_mx('-y,x-y,z-1/3')
r_inv_cart_ji = (O * matrix.sqr(rt_mx_ji.r().inverse().as_double()) * F)
r_inv_cart_ki = (O * matrix.sqr(rt_mx_ki.r().inverse().as_double()) * F)
cov_a = covariance.extract_covariance_matrix_for_sites(flex.size_t([1,0,1]), cov_cart, param_map)
sites = (uc.orthogonalize(rt_mx_ji*sites_frac[1]),
sites_cart[0],
uc.orthogonalize(rt_mx_ki*sites_frac[1]))
a = geometry.angle(sites)
assert approx_equal(a.angle_model, 101.30738566828551)
g = a.d_angle_d_sites()
g = matrix.row(tuple(r_inv_cart_ji*matrix.col(g[0])) + g[1] +
tuple(r_inv_cart_ki*matrix.col(g[2])))
f = g * matrix.sqr(cov_a.matrix_packed_u_as_symmetric()) * g.transpose()
assert approx_equal(
a.variance(cov_a, uc, (rt_mx_ji, sgtbx.rt_mx(), rt_mx_ki)), f[0], eps=1e-15)
assert approx_equal(0.0042632511984529199,
a.variance(cov_a, cell_vcv, uc, (rt_mx_ji, sgtbx.rt_mx(), rt_mx_ki)))
def exercise_high_symmetry_case():
"""
BF6 sitting on inversion centre in high symmetry space group.
The angles formed between F20, B17 and either F18 or F19 are necessarily
exactly equal to 90 degrees, and hence their variance should be exactly zero.
The angles formed by F18, B17 and F19 are free to refine, and hence should
have an associated variance.
"""
xs = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=(22.543, 22.543, 35.5167, 90, 90, 90),
space_group_symbol='hall: -I 4bd 2'),
scatterers=flex.xray_scatterer((
xray.scatterer( #24
label='F18',
site=(0.500000, 0.970584, -0.041027),
u=(0.000258, 0.000675, 0.000138, -0.000000, -0.000000, -0.000043),
fp=0.017939,
fdp=0.010330),
xray.scatterer( #25
label='F19',
site=(0.500000, 0.933678, 0.021766),
u=(0.000178, 0.001046, 0.000158, -0.000000, -0.000000, 0.000144),
fp=0.017939,
fdp=0.010330),
xray.scatterer( #26
label='F20',
site=(0.438015, 1.000000, 0.000000),
u=(0.000231, 0.000500, 0.000106, -0.000000, -0.000000, 0.000078),
fp=0.017939,
fdp=0.010330),
xray.scatterer( #27
label='B17',
site=(0.500000, 1.000000, 0.000000),
u=(0.000133, 0.000624, 0.000051, -0.000000, -0.000000, 0.000048),
fp=0.001413,
fdp=0.000674)
)))
flags = xs.scatterer_flags()
for f in flags: f.set_grad_site(True)
xs.set_scatterer_flags(flags)
sites_frac = xs.sites_frac()
unit_cell = xs.unit_cell()
cov = flex.double([
0,0,0,0,0,0,0,0,0,0,0,0,5.5895145222321514e-07,-1.7223269587621895e-08,0,
-2.0367609296594096e-07,-6.6231210988833185e-08,-2.6525243183929821e-09,0,0,
0,0,0,1.1503438451957222e-07,0,-3.5665932804823073e-08,
7.4165082206213702e-09,-6.8444182449209374e-09,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
9.0344019852871238e-07,1.2109549448751337e-07,-7.4794454124745421e-09,0,0,
0,0,0,1.5840179985755122e-07,9.1193835484941833e-09,0,0,0,0,0,
1.447679091961411e-07,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0])
cell_cov = flex.double([
2.4999999999999999e-07,2.4999999999999999e-07,0,0,0,0,
2.4999999999999999e-07,0,0,0,0,1.4399999999999998e-06,0,0,0,0,0,0,0,0,0])
param_map = xs.parameter_map()
cov_cart = covariance.orthogonalize_covariance_matrix(
cov, unit_cell, param_map)
i_seqs = flex.size_t((2,3,1))
cov_i_seqs = covariance.extract_covariance_matrix_for_sites(
i_seqs, cov_cart, param_map)
for sym_ops in (
(sgtbx.rt_mx(),sgtbx.rt_mx(),sgtbx.rt_mx()),
(sgtbx.rt_mx("1-x,2-y,-z"), sgtbx.rt_mx(), sgtbx.rt_mx()),
(sgtbx.rt_mx(), sgtbx.rt_mx(), sgtbx.rt_mx("1-x,2-y,-z")),
(sgtbx.rt_mx("1-x,2-y,-z"), sgtbx.rt_mx(), sgtbx.rt_mx("1-x,2-y,-z"))):
site_frac_ji = sym_ops[0] * sites_frac[i_seqs[0]]
site_frac_i = sym_ops[1] * sites_frac[i_seqs[1]]
site_frac_ki = sym_ops[2] * sites_frac[i_seqs[2]]
a = geometry.angle((unit_cell.orthogonalize(site_frac_ji),
unit_cell.orthogonalize(site_frac_i),
unit_cell.orthogonalize(site_frac_ki)))
var = a.variance(cov_i_seqs, cell_cov, unit_cell, sym_ops)
assert approx_equal(var, 0, eps=2e-16)
pair_asu_table = xs.pair_asu_table(distance_cutoff=2)
import libtbx.load_env
if libtbx.env.has_module('iotbx'):
import iotbx.cif
s = StringIO()
print >> s, iotbx.cif.distances_as_cif_loop(
pair_asu_table,
xs.scatterers().extract_labels(),
sites_frac=xs.sites_frac(),
covariance_matrix=cov,
cell_covariance_matrix=cell_cov,
parameter_map=param_map).loop
assert not show_diff(s.getvalue(), """\
loop_
_geom_bond_atom_site_label_1
_geom_bond_atom_site_label_2
_geom_bond_distance
_geom_bond_site_symmetry_2
F18 B17 1.601(13) 4_575
F19 B17 1.683(18) .
F20 B17 1.397(9) .
""")
s = StringIO()
print >> s, iotbx.cif.angles_as_cif_loop(
pair_asu_table,
xs.scatterers().extract_labels(),
sites_frac=xs.sites_frac(),
covariance_matrix=cov,
cell_covariance_matrix=cell_cov,
parameter_map=param_map).loop
assert not show_diff(s.getvalue(), """\
loop_
_geom_angle_atom_site_label_1
_geom_angle_atom_site_label_2
_geom_angle_atom_site_label_3
_geom_angle
_geom_angle_site_symmetry_1
_geom_angle_site_symmetry_3
F18 B17 F18 180.0 . 4_575
F19 B17 F18 87.1(7) . 4_575
F19 B17 F18 92.9(7) . .
F19 B17 F18 92.9(7) 4_575 4_575
F19 B17 F18 87.1(7) 4_575 .
F19 B17 F19 180.0 4_575 .
F20 B17 F18 90.0 . 4_575
F20 B17 F18 90.0 . .
F20 B17 F19 90.0 . .
F20 B17 F19 90.0 . 4_575
F20 B17 F18 90.0 9_675 4_575
F20 B17 F18 90.0 9_675 .
F20 B17 F19 90.0 9_675 .
F20 B17 F19 90.0 9_675 4_575
F20 B17 F20 180.0 9_675 .
""")