def exercise_remark_290_interpretation():
symmetry_operators = pdb.remark_290_interpretation.extract_symmetry_operators(
remark_290_records=pdb.remark_290_interpretation.example.splitlines()
)
assert symmetry_operators is not None
assert len(symmetry_operators) == 4
assert symmetry_operators[0] == sgtbx.rt_mx("X,Y,Z")
assert symmetry_operators[1] == sgtbx.rt_mx("1/2-X,-Y,1/2+Z")
assert symmetry_operators[2] == sgtbx.rt_mx("-X,1/2+Y,1/2-Z")
assert symmetry_operators[3] == sgtbx.rt_mx("1/2+X,1/2-Y,-Z")
for link_sym, expected_sym_op in [
("1555", "x,y,z"),
("1381", "x-2,y+3,z-4"),
("3729", "-x+2,1/2+y-3,1/2-z+4"),
(" 3_729 ", "-x+2,1/2+y-3,1/2-z+4"),
(" 3 729 ", "-x+2,1/2+y-3,1/2-z+4"),
("_3729", None),
("37_29", None),
]:
sym_op = pdb.remark_290_interpretation.get_link_symmetry_operator(
symmetry_operators=symmetry_operators, link_sym=link_sym
)
if sym_op is None:
assert expected_sym_op is None
else:
assert sym_op == sgtbx.rt_mx(expected_sym_op)
def exercise_space_group_contains():
g = sgtbx.space_group("P 2")
for s in ["x,y,z", "-x,-y,z", "-x+1,-y-2,z+3"]:
assert g.contains(sgtbx.rt_mx(s))
for s in ["x,y,-z", "x+1/2,y,z"]:
assert not g.contains(sgtbx.rt_mx(s))
for symbols in sgtbx.space_group_symbol_iterator():
g = sgtbx.space_group(symbols.hall())
for s in g:
assert g.contains(s)
rnd = flex.mersenne_twister(seed=0)
n_c = 0
n_nc = 0
for symbol in sgtbx.bravais_types.centric:
g = sgtbx.space_group_info(symbol=symbol, space_group_t_den=144).group()
for s in g.change_basis(sgtbx.change_of_basis_op("x+1/12,y-1/12,z+1/12")):
if (rnd.random_double() < 0.9): continue # avoid long runtime
gc = sgtbx.space_group(g)
gc.expand_smx(s)
if (gc.order_z() == g.order_z()):
assert g.contains(s)
n_c += 1
else:
assert not g.contains(s)
n_nc += 1
assert n_c == 11, n_c
assert n_nc == 53, n_nc
def exercise_monoclinic_cell_choices_core(space_group_number, verbose):
# transformation matrices for cell choices
# columns are basis vectors "new in terms of old"
# see Int. Tab. Vol. A, p. 22, Fig. 2.2.6.4.
b1 = (1, 0, 0,
0, 1, 0,
0, 0, 1)
b2 = (-1, 0, 1,
0, 1, 0,
-1, 0, 0)
b3 = (0, 0, -1,
0, 1, 0,
1, 0, -1)
flip = (0, 0, 1,
0, -1, 0,
1, 0, 0)
p3s = sgtbx.space_group("P 3*")
done = {}
ref = sgtbx.space_group_info(number=space_group_number)
ref_uhm = ref.type().universal_hermann_mauguin_symbol()
for i_fl,fl in enumerate([b1, flip]):
rfl = sgtbx.rot_mx(fl)
cfl = sgtbx.change_of_basis_op(sgtbx.rt_mx(rfl))
for i_rt,rt in enumerate(p3s):
rp3 = rt.r()
cp3 = sgtbx.change_of_basis_op(sgtbx.rt_mx(rp3))
for i_cs,cs in enumerate([b1,b2,b3]):
rcs = sgtbx.rot_mx(cs).inverse()
ccs = sgtbx.change_of_basis_op(sgtbx.rt_mx(rcs))
cb_all = cp3 * cfl * ccs
refcb = ref.change_basis(cb_all)
refcb2 = sgtbx.space_group_info(symbol=ref_uhm+"("+str(cb_all.c())+")")
assert refcb2.group() == refcb.group()
s = sgtbx.space_group_symbols(str(refcb))
q = s.qualifier()
hm = str(refcb)
if (0 or verbose): print hm, q, cb_all.c()
if (i_fl == 0):
assert q[0] == "bca"[i_rt]
if (len(q) == 2): assert q[1] == "123"[i_cs]
elif (q[0] == "-"):
assert q[1] == "bca"[i_rt]
if (len(q) == 3): assert q[2] == "123"[i_cs]
else:
assert q[0] == "bca"[i_rt]
if (len(q) == 2 and q[1] != "123"[i_cs]):
assert done[hm] == 1
done.setdefault(hm, 0)
done[hm] += 1
assert len(done) in [3, 9, 18]
assert done.values() == [18/len(done)]*len(done)
if (0 or verbose): print
return done
def exercise_orthorhombic_hm_qualifier_as_cb_symbol():
cb_symbols = {
"cab": ["c,a,b", "z,x,y"],
"a-cb": ["a,-c,b", "x,-z,y"],
"-cba": ["-c,b,a", "-z,y,x"],
"bca": ["b,c,a", "y,z,x"],
"ba-c": ["b,a,-c", "y,x,-z"]}
for sgsyms1 in sgtbx.space_group_symbol_iterator():
n = sgsyms1.number()
if (n < 16 or n > 74): continue
q = sgsyms1.qualifier()
if (len(q) == 0): continue
e = sgsyms1.extension()
if (e == "\0"): e = ""
ehm = sgtbx.space_group_symbols(
space_group_number=n, extension=e).universal_hermann_mauguin()
cabc, cxyz = cb_symbols[q]
assert sgtbx.change_of_basis_op(cxyz).as_abc() == cabc
assert sgtbx.change_of_basis_op(cabc).as_xyz() == cxyz
uhm_xyz = ehm + " ("+cxyz+")"
sgsyms2 = sgtbx.space_group_symbols(symbol=uhm_xyz)
assert sgsyms2.change_of_basis_symbol() == cxyz
assert sgsyms2.extension() == sgsyms1.extension()
assert sgsyms2.universal_hermann_mauguin() == uhm_xyz
g1 = sgtbx.space_group(space_group_symbols=sgsyms1)
g2 = sgtbx.space_group(space_group_symbols=sgsyms2)
assert g2 == g1
g2 = sgtbx.space_group(
sgtbx.space_group_symbols(symbol=ehm)).change_basis(
sgtbx.change_of_basis_op(sgtbx.rt_mx(cxyz)))
assert g2 == g1
for c in [cxyz, cabc]:
g2 = sgtbx.space_group_info(
group=sgtbx.space_group(
sgtbx.space_group_symbols(symbol=ehm))).change_basis(c).group()
assert g2 == g1
cit = sgtbx.rt_mx(cxyz).r().inverse().transpose()
cit_xyz = cit.as_xyz()
g2 = sgtbx.space_group_info(
group=sgtbx.space_group(
sgtbx.space_group_symbols(symbol=ehm))).change_basis(cit_xyz).group()
assert g2 == g1
assert cit.as_xyz(False, "abc") == cabc
uhm_abc = ehm + " ("+cabc+")"
sgsyms2 = sgtbx.space_group_symbols(symbol=uhm_abc)
assert sgsyms2.change_of_basis_symbol() == cxyz
assert sgsyms2.extension() == sgsyms1.extension()
assert sgsyms2.universal_hermann_mauguin() == uhm_xyz
g2 = sgtbx.space_group(space_group_symbols=sgsyms2)
assert g2 == g1
def run(args):
if "--full" in args:
to_do = range(1, 230 + 1)
elif "--special" in args:
to_do = sorted(special.keys())
else:
to_do = [75, 151]
for space_group_number in to_do:
sgi = sgtbx.space_group_info(number=space_group_number)
sgi.show_summary(prefix="")
sys.stdout.flush()
n_special = 0
for m in scitbx.math.unimodular_generator(range=1).all():
cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(sgtbx.rot_mx(m, 1), 1)).new_denominators(12, 144)
cb_sgi = sgi.change_basis(cb_op=cb_op)
cb_op_ref = cb_sgi.change_of_basis_op_to_reference_setting()
ref_sgi = cb_sgi.change_basis(cb_op=cb_op_ref)
assert ref_sgi.group() == sgi.group()
c = cb_op_ref.c()
if c.r().is_unit_mx() and c.t().num() != (0, 0, 0):
n_special += 1
cb_ref_sgi = sgi.change_basis(cb_op=cb_op_ref)
print " cb_op=%s -> %s" % (str(cb_op.c()), cb_ref_sgi.type().universal_hermann_mauguin_symbol())
sys.stdout.flush()
# verify that c.t() is not an allowed origin shift
assert cb_ref_sgi.group() != sgi.group()
assert special.get(space_group_number, 0) == n_special
print format_cpu_times()
def list_all_axes(space_group_symbol=None, space_group_info=None):
assert space_group_symbol is None or space_group_info is None
shift_range = 1 # XXX Works for the 230 reference settings; it is not
# XXX clear to me (rwgk) what value is needed in general.
if (space_group_symbol is not None):
space_group_info = sgtbx.space_group_info(symbol=space_group_symbol)
space_group_info.show_summary()
print
print "Rotation type, Axis direction, Intrinsic part, Origin shift"
axes_dict = {}
for s in space_group_info.group():
r = s.r()
t = s.t()
shift = [0,0,0]
for shift[0] in xrange(-shift_range,shift_range+1):
for shift[1] in xrange(-shift_range,shift_range+1):
for shift[2] in xrange(-shift_range,shift_range+1):
ts = t.plus(sgtbx.tr_vec(shift, 1)).new_denominator(t.den())
ss = sgtbx.rt_mx(r, ts)
axes_dict[rt_mx_analysis(ss)] = 0
axes_list = axes_dict.keys()
axes_list.sort()
for a in axes_list:
print a
print
def run():
settings = [0]
for i in xrange(1, 231): settings.append({})
list_cb_op = []
for xyz in ("x,y,z", "z,x,y", "y,z,x"):
list_cb_op.append(sgtbx.change_of_basis_op(sgtbx.rt_mx(xyz)))
n_built = 0
for i in sgtbx.space_group_symbol_iterator():
hall_symbol = i.hall()
for z in "PABCIRHF":
hall_z = hall_symbol[0] + z + hall_symbol[2:]
for cb_op in list_cb_op:
group = sgtbx.space_group(hall_z).change_basis(cb_op)
sg_type = group.type()
settings[sg_type.number()][sg_type.lookup_symbol()] = 0
n_built += 1
print "# n_built =", n_built
n_non_redundant = 0
print "settings = ("
for i in xrange(1, 231):
print "#", i
symbols = settings[i].keys()
symbols.sort()
for s in symbols:
print "'" + s + "',"
n_non_redundant += 1
print ")"
print "# n_non_redundant =", n_non_redundant
def exercise():
ma = miller.array(
miller.set(crystal.symmetry(unit_cell=(5,5,5, 90, 90, 90),
space_group=sgtbx.space_group('P 2x')),
indices=flex.miller_index(
[(1,0,0), (0,1,0), (0,0,1),
(-1,0,0), (0,-1,0), (0,0,-1),
(1,1,0), (1,0,1), (0,1,1),
(-1,-1,0), (-1,0,-1), (0,-1,-1),
(1,-1,0), (1,0,-1), (0,1,-1),
(-1,1,0), (-1,0,1), (0,-1,1),
(1,1,1), (-1,1,1), (1,-1,1), (1,1,-1),
(-1,-1,-1), (1,-1,-1), (-1,1,-1), (-1,-1,1)])),
data=flex.complex_double(flex.random_double(26), flex.random_double(26)))
f_at_h = dict(zip(ma.indices(), ma.data()))
for op in ("-x, y+1/2, -z", "x+1/2, -y, z-1/2"):
op = sgtbx.rt_mx(op)
original, transformed = ma.common_sets(
ma.change_basis(sgtbx.change_of_basis_op(op.inverse())))
for h, f in original:
assert f == f_at_h[h]
for h, op_f in transformed:
assert approx_equal(
op_f,
f_at_h[h*op.r()]*exp(1j*2*pi*row(h).dot(col(op.t().as_double()))))
def convert(file_object):
""" Examplify the direct use of the tool from shelx.lexer
In practice, one is strongly encouraged to make use of the tools
from shelx.parsers: that is to say, for the task handled here,
crystal_symmetry_parser (the code to follow just parrots
the implementation of crystal_symmetry_parser).
"""
space_group = None
for command, line in shelx.command_stream(file=file_object):
cmd, args = command[0], command[-1]
if cmd == "LATT":
assert space_group is None
assert len(args) == 1
space_group = sgtbx.space_group()
n = int(args[0])
if n > 0:
space_group.expand_inv(sgtbx.tr_vec((0,0,0)))
z = "*PIRFABC"[abs(n)]
space_group.expand_conventional_centring_type(z)
elif cmd == "SYMM":
assert space_group is not None
assert len(args) == 1
s = sgtbx.rt_mx(args[0])
space_group.expand_smx(s)
elif cmd == "SFAC":
return sgtbx.space_group_info(group=space_group)
def distances_as_cif_loop(xray_structure, proxies):
space_group_info = sgtbx.space_group_info(group=xray_structure.space_group())
unit_cell = xray_structure.unit_cell()
sites_cart = xray_structure.sites_cart()
site_labels = xray_structure.scatterers().extract_labels()
fmt = "%.4f"
loop = model.loop(header=(
"_restr_distance_atom_site_label_1",
"_restr_distance_atom_site_label_2",
"_restr_distance_site_symmetry_2",
"_restr_distance_target",
"_restr_distance_target_weight_param",
"_restr_distance_diff"
))
for proxy in proxies:
restraint = geometry_restraints.bond(
unit_cell=unit_cell,
sites_cart=sites_cart,
proxy=proxy)
i_seqs = proxy.i_seqs
sym_op = proxy.rt_mx_ji
if sym_op is None: sym_op = sgtbx.rt_mx()
loop.add_row((site_labels[i_seqs[0]],
site_labels[i_seqs[1]],
space_group_info.cif_symmetry_code(sym_op),
fmt % restraint.distance_ideal,
fmt % math.sqrt(1/restraint.weight),
fmt % restraint.delta))
return loop
def __init__(self, f_obs, ncs_pairs, reflections_per_bin):
adopt_init_args(self, locals())
# Create bins
f_obs.setup_binner(reflections_per_bin = reflections_per_bin)
self.binner = f_obs.binner()
n_bins = self.binner.n_bins_used()
self.n_bins = n_bins
self.SigmaN = None
self.update_SigmaN()
#
self.rbin = flex.int(f_obs.data().size(), -1)
for i_bin in self.binner.range_used():
for i_seq in self.binner.array_indices(i_bin):
self.rbin[i_seq] = i_bin-1 # i_bin starts with 1, not 0 !
assert flex.min(self.rbin)==0
assert flex.max(self.rbin)==n_bins-1
# Extract symmetry matrices
self.sym_matrices = []
for m_as_string in f_obs.space_group().smx():
o = sgtbx.rt_mx(symbol=str(m_as_string), t_den=f_obs.space_group().t_den())
m_as_double = o.r().as_double()
self.sym_matrices.append(m_as_double)
self.gradient_evaluator = None
self.target_and_grads = ext.tncs_eps_factor_refinery(
tncs_pairs = self.ncs_pairs,
f_obs = self.f_obs.data(),
sigma_f_obs = self.f_obs.sigmas(),
rbin = self.rbin,
SigmaN = self.SigmaN,
space_group = self.f_obs.space_group(),
miller_indices = self.f_obs.indices(),
fractionalization_matrix = self.f_obs.unit_cell().fractionalization_matrix(),
sym_matrices = self.sym_matrices)
self.update()
def __init__(self, file_name, header_only=False):
self.file_name = os.path.normpath(file_name)
f = open(file_name)
line = f.readline()
assert line[5] == " "
n_sym_ops_from_file = int(line[:5].strip())
assert n_sym_ops_from_file > 0
self.space_group_symbol = line[6:].strip()
self.space_group_from_ops = sgtbx.space_group()
for i in xrange(n_sym_ops_from_file):
line = f.readline().rstrip()
assert len(line) == 27
r = sgtbx.rot_mx([int(line[j*3:(j+1)*3]) for j in xrange(9)], 1)
line = f.readline().rstrip()
assert len(line) == 9
t = sgtbx.tr_vec([int(line[j*3:(j+1)*3]) for j in xrange(3)], 12)
self.space_group_from_ops.expand_smx(sgtbx.rt_mx(r, t))
f.close()
if (header_only):
self.original_indices = None
return
all_arrays = scalepack_ext.no_merge_original_index_arrays(
file_name, n_sym_ops_from_file*2+1)
self.original_indices = all_arrays.original_indices()
self.unique_indices = all_arrays.unique_indices()
self.batch_numbers = all_arrays.batch_numbers()
self.centric_tags = all_arrays.centric_tags()
self.spindle_flags = all_arrays.spindle_flags()
self.asymmetric_unit_indices = all_arrays.asymmetric_unit_indices()
self.i_obs = all_arrays.i_obs()
self.sigmas = all_arrays.sigmas()
def exercise_symmetry_equivalent():
xs = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=(1, 2, 3),
space_group_symbol='hall: P 2x'),
scatterers=flex.xray_scatterer((
xray.scatterer("C", site=(0.1, 0.2, 0.3)),
)))
xs.scatterers()[0].flags.set_grad_site(True)
connectivity_table = smtbx.utils.connectivity_table(xs)
reparametrisation = constraints.reparametrisation(
xs, [], connectivity_table)
site_0 = reparametrisation.add(constraints.independent_site_parameter,
scatterer=xs.scatterers()[0])
g = sgtbx.rt_mx('x,-y,-z')
symm_eq = reparametrisation.add(
constraints.symmetry_equivalent_site_parameter,
site=site_0, motion=g)
reparametrisation.finalise()
assert approx_equal(symm_eq.original.scatterers[0].site, (0.1, 0.2, 0.3),
eps=1e-15)
assert str(symm_eq.motion) == 'x,-y,-z'
assert symm_eq.is_variable
reparametrisation.linearise()
assert approx_equal(symm_eq.value, g*site_0.value, eps=1e-15)
reparametrisation.store()
assert approx_equal(symm_eq.value, (0.1, -0.2, -0.3), eps=1e-15)
assert approx_equal(site_0.value, (0.1, 0.2, 0.3), eps=1e-15)
def find_space_group(self):
decorated_symmetry_pool = []
denominator = 12**3
for i, (r, d) in enumerate(self.cross_correlation_peaks()):
t = sgtbx.tr_vec((d*denominator).as_int(), tr_den=denominator)
cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(r, t))
phi_sym = self.f_in_p1.symmetry_agreement_factor(
cb_op, assert_is_similar_symmetry=False)
if phi_sym < self.phi_sym_acceptance_cutoff:
status = possible_symmetry.accepted
elif phi_sym < self.phi_sym_rejection_cutoff:
status = possible_symmetry.unsure
else:
status = possible_symmetry.rejected
decorated_symmetry_pool.append(
(-status, i, possible_symmetry(r, d, phi_sym, status)))
decorated_symmetry_pool.sort()
self.symmetry_pool = [ item[-1] for item in decorated_symmetry_pool ]
self.origin = mat.mutable_zeros(3)
for symm in self.symmetry_pool:
if symm.status != symm.accepted: continue
symm.set_components_of_global_origin(self.origin)
if self.origin.elems.count(0) == 0: break
for symm in self.symmetry_pool:
if symm.status != symm.accepted: continue
symm.change_origin(self.origin)
self.space_group.expand_smx(symm.rt)
def exercise_connectivity_table():
xs = development.sucrose()
connectivity = utils.connectivity_table(xs)
pair_counts = [
2, 2, 1, 2, 1, 2, 1, 2, 1, 2, 2, 1, 2, 1, 2, 1, 2, 1, 2, 4, 1, 4, 1,
4, 1, 4, 1, 1, 4, 1, 4, 1, 4, 4, 1, 1, 4, 1, 4, 1, 4, 1, 4, 1, 1]
assert approx_equal(connectivity.pair_asu_table.pair_counts(), pair_counts)
connectivity.add_bond(0, 1)
assert approx_equal(
connectivity.pair_asu_table.pair_counts(),
[3, 3, 1, 2, 1, 2, 1, 2, 1, 2, 2, 1, 2, 1, 2, 1, 2, 1, 2, 4, 1, 4, 1,
4, 1, 4, 1, 1, 4, 1, 4, 1, 4, 4, 1, 1, 4, 1, 4, 1, 4, 1, 4, 1, 1])
connectivity.add_bond(5, 5, rt_mx_ji=sgtbx.rt_mx("x+1,y,z"))
assert connectivity.pair_asu_table.pair_counts()[5] == 4
connectivity.remove_bond(0, 1)
connectivity.remove_bond(5,5, rt_mx_ji=sgtbx.rt_mx("x+1,y,z"))
assert approx_equal(connectivity.pair_asu_table.pair_counts(), pair_counts)
def generate_unimodular_cells(cell):
Amat = sqr(cell.orthogonalization_matrix()).transpose()
for m in unimodular_generator(range=1).all():
c_inv = sgtbx.rt_mx(sgtbx.rot_mx(m))
orientation_similarity_cb_op = sgtbx.change_of_basis_op(c_inv).inverse()
new_cell = cell.change_basis(orientation_similarity_cb_op)
yield new_cell,orientation_similarity_cb_op
def change_origin(self, origin): o = self.raw_origin - origin t_l = self.one_minus_r*o t_l = sgtbx.tr_vec((sg_t_den*t_l).as_int(), tr_den=sg_t_den) self.rt = sgtbx.rt_mx(self.r, self.t_i.plus(t_l).new_denominator(sg_t_den)) tr_info = sgtbx.translation_part_info(self.rt) self.origin = tr_info.origin_shift() self.t_i = tr_info.intrinsic_part()
def issue_merohedral_twinning(self):
twin_law = self.instructions['twin'].get('matrix',
sgtbx.rt_mx('-x,-y,-z'))
n = self.instructions['twin'].get('n', 2)
assert n - 1 == len(self.instructions['basf'])
self.builder.make_merohedral_twinning(
fractions=self.instructions['basf'],
twin_law=twin_law)
def augm_arr(sym_op = 'x,y,z'):
"""returns augmented array corresponding to the symmetry operation sym_op"""
mtr = sgtbx.rt_mx(sym_op)
#constructing augmented matrix of the symmetry operation
augm_arr = numpy.reshape(
numpy.array(mtr.as_4x4_rational(), dtype = numpy.float),
(4,4)
)
return augm_arr
def get_all_axes(space_group_symbol=None, space_group_info=None, extension=0):
assert space_group_symbol is None or space_group_info is None
shift_range = 1 # RWGK Works for the 230 reference settings; it is not
# RWGK clear to me (rwgk) what value is needed in general.
if (space_group_symbol is not None):
space_group_info = sgtbx.space_group_info(symbol=space_group_symbol)
#space_group_info.show_summary()
axes_dict = {}
for smx in space_group_info.group():
r = smx.r()
t = smx.t()
shift = [0,0,0]
for shift[0] in range(-shift_range,shift_range+1):
for shift[1] in range(-shift_range,shift_range+1):
for shift[2] in range(-shift_range,shift_range+1):
ts = t.plus(sgtbx.tr_vec(shift, 1)).new_denominator(t.den())
m = sgtbx.rt_mx(r, ts)
#print m
rtmxanal = rlc_RTMxAnalysis(m)
#print r, t, shift, ts, m
if rtmxanal:
#print rtmxanal
axes_dict[rtmxanal] = 0
axes_list = axes_dict.keys()
axes_list.sort()
# reject nonenantiomorphic space groups
if len(axes_list) > 0 and not re.compile("[A-z]").search(space_group_symbol[1:]):
try:
sgtbx.space_group_info(space_group_symbol).show_summary(),
#print len(axes_list), space_group_symbol
except:
print space_group, space_group_symbol
print
sys.exit(1)
axes = []
for a in axes_list:
if len(a) == 3 and len(a[1]) == 3 and len(a[2]) == 3:
tmp_dict = {}
print "%4s %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f " % (a[0],a[1][0],a[1][1],a[1][2],a[2][0],a[2][1],a[2][2])
tmp_dict['symb'] = a[0]
start_array = N.asarray(a[1])
end_array = N.asarray(a[2])
start_vec = start_array - (end_array - start_array)*extension
end_vec = end_array + (end_array - start_array)*extension
tmp_dict['start'] = start_vec
tmp_dict['end'] = end_vec
#rlc# tmp_dict['start'] = a[1]
#rlc# tmp_dict['end'] = a[2]
axes.append(tmp_dict)
else:
print a
else:
return None
return axes
def __call__(self, params, options):
''' Import the integrate.hkl file. '''
from iotbx.xds import integrate_hkl
from dials.array_family import flex
from dials.util.command_line import Command
from cctbx import sgtbx
# Get the unit cell to calculate the resolution
uc = self._experiment.crystal.get_unit_cell()
# Read the INTEGRATE.HKL file
Command.start('Reading INTEGRATE.HKL')
handle = integrate_hkl.reader()
handle.read_file(self._integrate_hkl)
hkl = flex.miller_index(handle.hkl)
xyzcal = flex.vec3_double(handle.xyzcal)
xyzobs = flex.vec3_double(handle.xyzobs)
iobs = flex.double(handle.iobs)
sigma = flex.double(handle.sigma)
rlp = flex.double(handle.rlp)
peak = flex.double(handle.peak) * 0.01
Command.end('Read %d reflections from INTEGRATE.HKL file.' % len(hkl))
# Derive the reindex matrix
rdx = self.derive_reindex_matrix(handle)
print 'Reindex matrix:\n%d %d %d\n%d %d %d\n%d %d %d' % (rdx.elems)
# Reindex the reflections
Command.start('Reindexing reflections')
cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(sgtbx.rot_mx(rdx.elems)))
hkl = cb_op.apply(hkl)
Command.end('Reindexed %d reflections' % len(hkl))
# Create the reflection list
Command.start('Creating reflection table')
table = flex.reflection_table()
table['id'] = flex.int(len(hkl), 0)
table['panel'] = flex.size_t(len(hkl), 0)
table['miller_index'] = hkl
table['xyzcal.px'] = xyzcal
table['xyzobs.px.value'] = xyzobs
table['intensity.cor.value'] = iobs
table['intensity.cor.variance'] = sigma**2
table['intensity.prf.value'] = iobs * peak / rlp
table['intensity.prf.variance'] = (sigma * peak / rlp)**2
table['lp'] = 1.0 / rlp
table['d'] = flex.double(uc.d(h) for h in hkl)
Command.end('Created table with {0} reflections'.format(len(table)))
# Output the table to pickle file
if params.output.filename is None:
params.output.filename = 'integrate_hkl.pickle'
Command.start('Saving reflection table to %s' % params.output.filename)
table.as_pickle(params.output.filename)
Command.end('Saved reflection table to %s' % params.output.filename)
def combined_cb_op(self, other, cb_op):
sc = self.change_of_basis_op_to_minimum_cell
oc = other.change_of_basis_op_to_minimum_cell
cb_op = cb_op.new_denominators(sc)
best_choice = None
best_choice_as_hkl = None
for s_symop in self.minimum_cell_symmetry.space_group():
s_symop = sgtbx.change_of_basis_op(sgtbx.rt_mx(s_symop.r())).new_denominators(sc)
for o_symop in other.minimum_cell_symmetry.space_group():
o_symop = sgtbx.change_of_basis_op(sgtbx.rt_mx(o_symop.r())).new_denominators(sc)
possible_choice = sc.inverse() * s_symop * cb_op * o_symop * oc
possible_choice_as_hkl = possible_choice.as_hkl()
if (
best_choice_as_hkl is None
or sgtbx.compare_cb_op_as_hkl(best_choice_as_hkl, possible_choice_as_hkl) > 0
):
best_choice = possible_choice
best_choice_as_hkl = possible_choice_as_hkl
assert best_choice is not None
return best_choice
def _nnnmmm_operator(record, expected_nnn):
if (not record.startswith("REMARK 290 ")): return None
flds = record.split()
if (len(flds) != 4): return None
nnnmmm = flds[2]
if (len(nnnmmm) < 4): return None
nnn,mmm = nnnmmm[:-3], nnnmmm[-3:]
if (mmm != "555"): return None
try: nnn = int(nnn)
except ValueError: return None
if (nnn != expected_nnn): return None
try: return sgtbx.rt_mx(flds[3])
except RuntimeError: return None
def exercise_change_of_basis_between_arbitrary_space_groups():
from random import randint
from scitbx import matrix as mat
g = sgtbx.space_group_info('hall: P 2')
h = sgtbx.space_group_info('hall: P 2c')
assert g.change_of_basis_op_to(h) is None
g = sgtbx.space_group_info('hall: C 2c 2 (x+y,x-y,z)')
h = g.change_basis(sgtbx.change_of_basis_op(sgtbx.rt_mx('-y,x,z')))
cb_op = g.change_of_basis_op_to(h)
assert cb_op.as_xyz() == 'x,y,z+1/4'
assert g.change_basis(cb_op).group() == h.group()
g = sgtbx.space_group_info('hall: I 4 2 3')
z2p_op = g.change_of_basis_op_to_primitive_setting()
h = g.change_basis(z2p_op)
cb_op = g.change_of_basis_op_to(h)
assert cb_op.c() == z2p_op.c(), (cb_op.as_xyz(), z2p_op.as_xyz())
for i in xrange(1, 231):
s = sgtbx.space_group_symbols(space_group_number=i)
g = sgtbx.space_group_info(group=sgtbx.space_group(s, t_den=24))
o = tuple([ randint(0, 23) for j in xrange(3) ])
cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(sgtbx.tr_vec(o, 24)))
h = g.change_basis(cb_op)
cb_op_1 = g.change_of_basis_op_to(h)
assert cb_op_1.c().r().is_unit_mx()
delta = (mat.col(cb_op_1.c().t().as_double())
- mat.col(cb_op.c().t().as_double()))
assert h.is_allowed_origin_shift(delta, tolerance=1e-12)
z2p_op = g.change_of_basis_op_to_primitive_setting()
h = g.change_basis(z2p_op)
cb_op = g.change_of_basis_op_to(h)
h1 = g.change_basis(cb_op)
assert (h.as_reference_setting().group()
== h1.as_reference_setting().group())
def remove_bond(self, i_seq, j_seq, rt_mx_ji=sgtbx.rt_mx()):
space_group = self.pair_asu_table.asu_mappings().space_group()
r_den, t_den = space_group.r_den(), space_group.t_den()
if j_seq < i_seq:
i_seq, j_seq = j_seq, i_seq
if not rt_mx_ji.is_unit_mx():
rt_mx_ji = rt_mx_ji.inverse()
if j_seq not in self.pair_sym_table[i_seq]:
return
for i, rt_mx in enumerate(self.pair_sym_table[i_seq][j_seq]):
if (rt_mx.new_denominators(r_den, t_den) ==
rt_mx_ji.new_denominators(r_den, t_den)):
del self.pair_sym_table[i_seq][j_seq][i]
self._pair_asu_table_needs_updating = True
def add_bond(self, i_seq, j_seq, rt_mx_ji=sgtbx.rt_mx()):
try:
self.pair_asu_table.add_pair(i_seq, j_seq, rt_mx_ji)
except RuntimeError:
sites_frac = self.structure.sites_frac()
sites = [sites_frac[i_seq], sites_frac[j_seq]]
if not rt_mx_ji.is_unit_mx():
sites[-1] = rt_mx_ji * sites[-1]
d = self.structure.unit_cell().distance(sites[0], sites[1])
self.pair_sym_table = self.pair_asu_table.extract_pair_sym_table()
self._pair_asu_table = crystal.pair_asu_table(self.structure.asu_mappings(
buffer_thickness=max(self.buffer_thickness, d)))
self._pair_asu_table.add_pair_sym_table(self.pair_sym_table)
self.pair_asu_table.add_pair(i_seq, j_seq, rt_mx_ji)
def verify_definitions_in_paper_zwart_2007():
# Verification of definitions in Peter Zwart's paper for the
# CCP4 Study Weekend Jan 2007.
#
cb_symbol_xyz = "x-y,x+y,z"
cb_symbol_abc = "1/2*a-1/2*b,1/2*a+1/2*b,c"
#
# Verify the claim that cb_symbol_abc is the inverse transpose of
# cb_symbol_xyz.
cb_mx_xyz = sgtbx.rt_mx(cb_symbol_xyz, r_den=12, t_den=144)
assert sgtbx.rt_mx(cb_mx_xyz.r().inverse().transpose()).as_xyz(
symbol_letters="abc") == cb_symbol_abc
#
uhmx = "C 1 2 1 (%s)" % cb_symbol_xyz
uhma = "C 1 2 1 (%s)" % cb_symbol_abc
sx = sgtbx.space_group_info(symbol=uhmx)
sa = sgtbx.space_group_info(symbol=uhma)
assert sx.group() == sa.group()
#
# We trust that the cctbx is self-consistent.
structure_unconv = random_structure.xray_structure(
space_group_info=sx,
elements=["C"],
volume_per_atom=100,
general_positions_only=True)
assert str(structure_unconv.space_group_info()) == uhmx
cb_op = structure_unconv.change_of_basis_op_to_reference_setting()
structure_reference = structure_unconv.change_basis(cb_op=cb_op)
assert str(structure_reference.space_group_info()) == "C 1 2 1"
#
# Verify the definitions in the paper based on the assumption
# that the cctbx is self-consistent.
site_reference = structure_reference.scatterers()[0].site
site_unconv_direct = cb_mx_xyz * site_reference
assert approx_equal(
site_unconv_direct, structure_unconv.scatterers()[0].site)
def remove_bond(self, i_seq, j_seq, rt_mx_ji=sgtbx.rt_mx()):
space_group = self.pair_asu_table.asu_mappings().space_group()
r_den, t_den = space_group.r_den(), space_group.t_den()
if j_seq < i_seq:
i_seq, j_seq = j_seq, i_seq
if not rt_mx_ji.is_unit_mx():
rt_mx_ji = rt_mx_ji.inverse()
if j_seq not in self.pair_sym_table[i_seq]:
return
for i, rt_mx in enumerate(self.pair_sym_table[i_seq][j_seq]):
if (rt_mx.new_denominators(r_den,
t_den) == rt_mx_ji.new_denominators(
r_den, t_den)):
del self.pair_sym_table[i_seq][j_seq][i]
self._pair_asu_table_needs_updating = True
def SetSymop (self, value) :
if type(value)==type(u'abc'): value = value.encode("ascii", "ignore")
if (value is None) or (value is Auto) :
ValidatedTextCtrl.SetValue(self, "")
elif (isinstance(value, str)) :
try :
from cctbx import sgtbx
rt_mx = sgtbx.rt_mx(symbol=value)
except ValueError :
raise Sorry("Inappropriate value '%s' for %s." % (value,
self.GetName()))
else :
ValidatedTextCtrl.SetValue(self, str(value))
else :
raise TypeError("Type '%s' not allowed!" % type(value).__name__)
def add_bond(self, i_seq, j_seq, rt_mx_ji=sgtbx.rt_mx()):
try:
self.pair_asu_table.add_pair(i_seq, j_seq, rt_mx_ji)
except RuntimeError:
sites_frac = self.structure.sites_frac()
sites = [sites_frac[i_seq], sites_frac[j_seq]]
if not rt_mx_ji.is_unit_mx():
sites[-1] = rt_mx_ji * sites[-1]
d = self.structure.unit_cell().distance(sites[0], sites[1])
self.pair_sym_table = self.pair_asu_table.extract_pair_sym_table()
self._pair_asu_table = crystal.pair_asu_table(
self.structure.asu_mappings(
buffer_thickness=max(self.buffer_thickness, d)))
self._pair_asu_table.add_pair_sym_table(self.pair_sym_table)
self.pair_asu_table.add_pair(i_seq, j_seq, rt_mx_ji)
def SetSymop(self, value):
if type(value) == type(u'abc'): value = value.encode("ascii", "ignore")
if (value is None) or (value is Auto):
ValidatedTextCtrl.SetValue(self, "")
elif (isinstance(value, str)):
try:
from cctbx import sgtbx
rt_mx = sgtbx.rt_mx(symbol=value)
except ValueError:
raise Sorry("Inappropriate value '%s' for %s." %
(value, self.GetName()))
else:
ValidatedTextCtrl.SetValue(self, str(value))
else:
raise TypeError("Type '%s' not allowed!" % type(value).__name__)
def verify_definitions_in_paper_zwart_2007():
# Verification of definitions in Peter Zwart's paper for the
# CCP4 Study Weekend Jan 2007.
#
cb_symbol_xyz = "x-y,x+y,z"
cb_symbol_abc = "1/2*a-1/2*b,1/2*a+1/2*b,c"
#
# Verify the claim that cb_symbol_abc is the inverse transpose of
# cb_symbol_xyz.
cb_mx_xyz = sgtbx.rt_mx(cb_symbol_xyz, r_den=12, t_den=144)
assert sgtbx.rt_mx(cb_mx_xyz.r().inverse().transpose()).as_xyz(
symbol_letters="abc") == cb_symbol_abc
#
uhmx = "C 1 2 1 (%s)" % cb_symbol_xyz
uhma = "C 1 2 1 (%s)" % cb_symbol_abc
sx = sgtbx.space_group_info(symbol=uhmx)
sa = sgtbx.space_group_info(symbol=uhma)
assert sx.group() == sa.group()
#
# We trust that the cctbx is self-consistent.
structure_unconv = random_structure.xray_structure(
space_group_info=sx,
elements=["C"],
volume_per_atom=100,
general_positions_only=True)
assert str(structure_unconv.space_group_info()) == uhmx
cb_op = structure_unconv.change_of_basis_op_to_reference_setting()
structure_reference = structure_unconv.change_basis(cb_op=cb_op)
assert str(structure_reference.space_group_info()) == "C 1 2 1"
#
# Verify the definitions in the paper based on the assumption
# that the cctbx is self-consistent.
site_reference = structure_reference.scatterers()[0].site
site_unconv_direct = cb_mx_xyz * site_reference
assert approx_equal(site_unconv_direct,
structure_unconv.scatterers()[0].site)
def run():
while 1:
line = sys.stdin.readline()[:-1]
flds = line.split(None, 2)
if (len(flds) == 0): break
nspgrp = int(flds[0]) # read spacegroup number
nsym = int(flds[1]) # read nsym
print nspgrp, nsym, flds[2] # print it all
group = sgtbx.space_group() # now interpret the symops
for i in xrange(nsym):
line = sys.stdin.readline()[:-1] # get the i'th symop
# print line
group.expand_smx(sgtbx.rt_mx(line)) # and interpret
info = sgtbx.space_group_info(group=group)
print info.type().hall_symbol() # now produce the sg symbol
print info
def run():
while 1:
line = sys.stdin.readline()[:-1]
flds = line.split(None, 2)
if (len(flds) == 0): break
nspgrp = int(flds[0]) # read spacegroup number
nsym = int(flds[1]) # read nsym
print(nspgrp, nsym, flds[2]) # print it all
group = sgtbx.space_group() # now interpret the symops
for i in range(nsym):
line = sys.stdin.readline()[:-1] # get the i'th symop
# print line
group.expand_smx(sgtbx.rt_mx(line)) # and interpret
info = sgtbx.space_group_info(group=group)
print(info.type().hall_symbol()) # now produce the sg symbol
print(info)
def exercise_double_coset_decomposition(crystal_symmetry_ri, lattice_group,
miller_array_subs, miller_array_sub_as,
miller_array_sub_bs,
coset_decompositions, i, j, verbose):
group_a = miller_array_subs[i].space_group_info().group()
group_b = miller_array_subs[j].space_group_info().group()
miller_array_sub_a = miller_array_sub_as[i]
miller_array_sub_b = miller_array_sub_bs[j]
single_coset_ccs = {}
for partition in coset_decompositions[i].partitions:
cb_op = sgtbx.change_of_basis_op(partition[0])
cb = miller_array_sub_a.change_basis(cb_op).map_to_asu()
cc = cb.correlation(other=miller_array_sub_b).coefficient()
key = "%.6f" % cc
single_coset_ccs.setdefault(key, []).append(str(partition[0]))
double_coset_ccs = {}
for c in sgtbx.cosets.double_unique(lattice_group, group_a, group_b):
cb_op = sgtbx.change_of_basis_op(c)
cb = miller_array_sub_b.change_basis(cb_op).map_to_asu()
cc = cb.correlation(other=miller_array_sub_a).coefficient()
key = "%.6f" % cc
double_coset_ccs.setdefault(key, []).append(str(c))
double_coset_repetitions = [len(v) for v in double_coset_ccs.values()]
failure = (max(double_coset_repetitions) > 1)
if (failure or verbose):
print(
[str(sgtbx.space_group_info(group=g)) for g in (group_a, group_b)])
print("single_coset ops:", list(single_coset_ccs.values()))
print("double_coset ops:", list(double_coset_ccs.values()))
if (failure):
for cc, ops in double_coset_ccs.items():
if (len(ops) > 1):
print(cc, ops)
for op in ops:
ri = sgtbx.rt_mx(op).r().info()
print(" ", ri.type(), ri.sense(), ri.ev())
raise RuntimeError("max(double_coset_repetitions) > 1")
single_coset_ccs = list(single_coset_ccs.keys())
double_coset_ccs = list(double_coset_ccs.keys())
single_coset_ccs.sort()
double_coset_ccs.sort()
failure = (double_coset_ccs != single_coset_ccs)
if (failure or verbose):
print("single_coset_ccs:", single_coset_ccs)
print("double_coset_ccs:", double_coset_ccs)
if (failure):
raise RuntimeError("double_coset_ccs != single_coset_ccs")
def _nnnmmm_operator(record, expected_nnn):
if (not record.startswith("REMARK 290 ")): return None
flds = record.split()
if (len(flds) != 4): return None
nnnmmm = flds[2]
if (len(nnnmmm) < 4): return None
nnn, mmm = nnnmmm[:-3], nnnmmm[-3:]
if (mmm != "555"): return None
try:
nnn = int(nnn)
except ValueError:
return None
if (nnn != expected_nnn): return None
try:
return sgtbx.rt_mx(flds[3])
except RuntimeError:
return None
def space_group_from_remark_symop(self):
from cctbx import sgtbx
result = None
for remark in self.remarks:
remark = remark.lstrip()[6:].strip().replace(" ", "").lower()
if ( remark.startswith("symop(")
and remark.endswith(")")):
s = remark[6:-1]
try:
s = sgtbx.rt_mx(s)
except RuntimeError:
pass
else:
if (result is None):
result = sgtbx.space_group()
result.expand_smx(s)
return result
def algebraic(self):
op = self.operation()
# eliminate minus signs to make the expression look more like
# what people are used to see
r = op.r().num()
d = op.r().den()
signs = [None, None, None]
for j in xrange(3):
for i in xrange(3):
rij = r[i * 3 + j]
if (signs[i] is None and rij != 0):
if (rij < 0): signs[i] = -1
else: signs[i] = 1
m = list(sgtbx.rot_mx(d, d).num())
for i in xrange(3):
if (signs[i] == -1): m[i * 4] *= -1
return str(sgtbx.rt_mx(op.r().multiply(sgtbx.rot_mx(m, d)), op.t()))
def space_group_from_remark_symop(self):
from cctbx import sgtbx
result = None
for remark in self.remarks:
remark = remark.lstrip()[6:].strip().replace(" ", "").lower()
if ( remark.startswith("symop(")
and remark.endswith(")")):
s = remark[6:-1]
try:
s = sgtbx.rt_mx(s)
except RuntimeError:
pass
else:
if (result is None):
result = sgtbx.space_group()
result.expand_smx(s)
return result
def exercise_comprehensive(args):
if ("--verbose" in args):
out = sys.stdout
else:
out = StringIO()
if ("--paranoid" in args):
cb_range = 2
else:
cb_range = 1
for symbol in bravais_types.acentric:
print("bravais type:", symbol)
sym = sgtbx.space_group_info(symbol=symbol) \
.any_compatible_crystal_symmetry(volume=1000) \
.niggli_cell()
abc = list(sym.unit_cell().parameters()[:3])
abc.sort()
for cb_elements in flex.nested_loop([-cb_range] * 9,
[cb_range + 1] * 9):
r = sgtbx.rot_mx(cb_elements)
if (r.determinant() != 1): continue
cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(r))
sym_cb = sym.change_basis(cb_op)
abc_cb = list(sym_cb.unit_cell().parameters()[:3])
abc_cb.sort()
for x, y in zip(abc, abc_cb):
assert y - x > -1.e-6
if (y - x > 1.e-4): break
else:
print("cb_ob:", cb_op.c(), cb_elements, file=out)
assert min(cb_elements) >= -1
assert max(cb_elements) <= 1
for s in sym_cb.space_group():
assert s.r().den() == 1
r_num = s.r().num()
print("r:", r_num, file=out)
assert min(r_num) >= -1
assert max(r_num) <= 1
for enforce in [False, True]:
lattice_group = sgtbx.lattice_symmetry.group(
reduced_cell=sym_cb.unit_cell(),
max_delta=1.4,
enforce_max_delta_for_generated_two_folds=enforce)
assert lattice_group == sym_cb.space_group()
sys.stdout.flush()
print(file=out)
def bond_similarity_as_cif_loops(xray_structure, proxies):
space_group_info = sgtbx.space_group_info(
group=xray_structure.space_group())
unit_cell = xray_structure.unit_cell()
sites_cart = xray_structure.sites_cart()
site_labels = xray_structure.scatterers().extract_labels()
fmt = "%.4f"
loop = model.loop(header=(
"_restr_equal_distance_atom_site_label_1",
"_restr_equal_distance_atom_site_label_2",
"_restr_equal_distance_site_symmetry_2",
"_restr_equal_distance_class_id",
))
class_loop = model.loop(header=(
"_restr_equal_distance_class_class_id",
"_restr_equal_distance_class_target_weight_param",
"_restr_equal_distance_class_average",
"_restr_equal_distance_class_esd",
"_restr_equal_distance_class_diff_max",
))
class_id = 0
for proxy in proxies:
restraint = geometry_restraints.bond_similarity(unit_cell=unit_cell,
sites_cart=sites_cart,
proxy=proxy)
class_id += 1
esd = math.sqrt(
flex.sum(flex.pow2(restraint.deltas())) *
(1. / proxy.i_seqs.size()))
class_loop.add_row((
class_id,
fmt % math.sqrt(1 / proxy.weights[0]), # assume equal weights
fmt % restraint.mean_distance(),
fmt % esd,
fmt % flex.max_absolute(restraint.deltas())))
for i in range(proxy.i_seqs.size()):
i_seq, j_seq = proxy.i_seqs[i]
if proxy.sym_ops is None:
sym_op = sgtbx.rt_mx()
else:
sym_op = proxy.sym_ops[i]
loop.add_row(
(site_labels[i_seq], site_labels[j_seq],
space_group_info.cif_symmetry_code(sym_op), class_id))
return class_loop, loop
def derive_change_of_basis_op(from_hkl, to_hkl):
# exclude those reflections that we couldn't index
sel = (to_hkl != (0, 0, 0)) & (from_hkl != (0, 0, 0))
assert sel.count(True) >= 3 # need minimum of 3 equations ?
to_hkl = to_hkl.select(sel)
from_hkl = from_hkl.select(sel)
# for each miller index, solve a system of linear equations to find the
# change of basis operator
h, k, l = to_hkl.as_vec3_double().parts()
r = []
from scitbx.lstbx import normal_eqns
for i in range(3):
eqns = normal_eqns.linear_ls(3)
for index, hkl in zip((h, k, l)[i], from_hkl):
eqns.add_equation(
right_hand_side=index, design_matrix_row=flex.double(hkl), weight=1
)
eqns.solve()
r.extend(eqns.solution())
from scitbx import matrix
from scitbx.math import continued_fraction
denom = 12
r = [
int(denom * continued_fraction.from_real(r_, eps=1e-2).as_rational())
for r_ in r
]
r = matrix.sqr(r).transpose()
# print (1/denom)*r
# now convert into a cctbx change_of_basis_op object
change_of_basis_op = sgtbx.change_of_basis_op(
sgtbx.rt_mx(sgtbx.rot_mx(r, denominator=denom))
).inverse()
print("discovered change_of_basis_op=%s" % (str(change_of_basis_op)))
# sanity check that this is the right cb_op
assert (change_of_basis_op.apply(from_hkl) == to_hkl).count(False) == 0
return change_of_basis_op
def create_shelx_reflection_data_source(self,
format,
indices_transform=None,
change_of_basis_op=None,
data_scale=1):
""" format is one of 3, 4, 5, etc.
data_scale scales the data and their standard deviations
"""
assert [indices_transform, change_of_basis_op].count(None) == 1
if change_of_basis_op is None:
if indices_transform.is_unit_mx():
change_of_basis_op = sgtbx.change_of_basis_op()
else:
r = sgtbx.rt_mx(indices_transform.new_denominator(24).transpose())
change_of_basis_op = sgtbx.change_of_basis_op(r).inverse()
self.reflection_file_format = "hklf%i" % format
self.data_change_of_basis_op = change_of_basis_op
self.data_scale = data_scale
def compatible_symmetries(point_group):
""" Primitive setting assumed """
for op in point_group:
r = op.r()
order = r.order()
if r.info().type() == 1: continue
yield op
invariants = [matrix.col(u) for u in r.info().basis_of_invariant()]
if len(invariants) == 2:
t1, t2 = invariants
invariants.extend((t1 + t2, t1 - t2))
translations = []
for t in invariants:
t = sgtbx.tr_vec(t, order).mod_short()
if not t.is_zero() and t not in translations:
translations.append(t)
for t in translations:
yield sgtbx.rt_mx(r, t.new_denominator(sgtbx.sg_t_den))
def _analyse_symmetry(self):
sym_ops = [sgtbx.rt_mx(s).new_denominators(1, 12) for s in self.target.sym_ops]
if not self.input_space_group:
self._symmetry_analysis = SymmetryAnalysis(
self.coords, sym_ops, self.subgroups, self.cb_op_inp_min
)
logger.info(str(self._symmetry_analysis))
self.best_solution = self._symmetry_analysis.best_solution
self.best_subgroup = self.best_solution.subgroup
else:
self.best_solution = None
self._symmetry_analysis = None
cosets = sgtbx.cosets.left_decomposition(
self.target._lattice_group,
self.best_subgroup["subsym"].space_group().build_derived_acentric_group(),
)
self.reindexing_ops = self._reindexing_ops(self.coords, sym_ops, cosets)
def _analyse_symmetry(self):
if self.input_space_group is not None:
self.best_solution = None
self._symmetry_analysis = None
return
sym_ops = [
sgtbx.rt_mx(s).new_denominators(1, 12) for s in self.target.get_sym_ops()
]
self._symmetry_analysis = SymmetryAnalysis(
self.coords, sym_ops, self.subgroups, self.cb_op_inp_min
)
logger.info(str(self._symmetry_analysis))
self.best_solution = self._symmetry_analysis.best_solution
self.best_subgroup = self.best_solution.subgroup
cosets = sgtbx.cosets.left_decomposition(
self.lattice_group, self.best_solution.subgroup["subsym"].space_group()
)
self.params.cluster.n_clusters = len(cosets.partitions)
def simple_and_slow(pair_asu_table, max_shell=10):
asu_mappings = pair_asu_table.asu_mappings()
term_table = []
for i_seq_pivot, pair_asu_dict_pivot in enumerate(pair_asu_table.table()):
rt_mx_pivot = asu_mappings.get_rt_mx(i_seq=i_seq_pivot, i_sym=0)
if (pair_asu_dict_pivot.size() == 0):
term_table.append([])
continue
nodes_middle = []
nodes_next = [
node(asu_mappings=asu_mappings,
i_seq=i_seq_pivot,
rt_mx=sgtbx.rt_mx())
]
terms = [1]
for i_shell_minus_1 in range(max_shell):
nodes_prev = nodes_middle
nodes_middle = nodes_next
nodes_next = []
for node_m in nodes_middle:
rt_mx_i = asu_mappings.get_rt_mx(i_seq=node_m.i_seq, i_sym=0)
rt_mx_ni = node_m.rt_mx.multiply(rt_mx_i.inverse())
for j_seq, j_sym_groups in pair_asu_table.table()[
node_m.i_seq].items():
for j_sym_group in j_sym_groups:
for j_sym in j_sym_group:
rt_mx_j = asu_mappings.get_rt_mx(i_seq=j_seq,
i_sym=j_sym)
new_node = node(asu_mappings=asu_mappings,
i_seq=j_seq,
rt_mx=rt_mx_ni.multiply(rt_mx_j))
if (not find_node(test_node=new_node,
node_list=nodes_prev)
and not find_node(test_node=new_node,
node_list=nodes_middle)
and not find_node(test_node=new_node,
node_list=nodes_next)):
nodes_next.append(new_node)
terms.append(len(nodes_next))
term_table.append(terms)
return term_table
def chirality_as_cif_loop(xray_structure, proxies):
space_group_info = sgtbx.space_group_info(group=xray_structure.space_group())
unit_cell = xray_structure.unit_cell()
sites_cart = xray_structure.sites_cart()
site_labels = xray_structure.scatterers().extract_labels()
fmt = "%.4f"
loop = model.loop(header=(
"_restr_chirality_atom_site_label_1",
"_restr_chirality_atom_site_label_2",
"_restr_chirality_atom_site_label_3",
"_restr_chirality_atom_site_label_4",
"_restr_chirality_site_symmetry_1",
"_restr_chirality_site_symmetry_2",
"_restr_chirality_site_symmetry_3",
"_restr_chirality_site_symmetry_4",
"_restr_chirality_volume_target",
"_restr_chirality_weight_param",
"_restr_chirality_diff",
))
unit_mxs = [sgtbx.rt_mx()]*4
for proxy in proxies:
restraint = geometry_restraints.chirality(
unit_cell=unit_cell,
sites_cart=sites_cart,
proxy=proxy)
sym_ops = proxy.sym_ops
if sym_ops is None: sym_ops = unit_mxs
i_seqs = proxy.i_seqs
loop.add_row((site_labels[i_seqs[0]],
site_labels[i_seqs[1]],
site_labels[i_seqs[2]],
site_labels[i_seqs[3]],
space_group_info.cif_symmetry_code(sym_ops[0]),
space_group_info.cif_symmetry_code(sym_ops[1]),
space_group_info.cif_symmetry_code(sym_ops[2]),
space_group_info.cif_symmetry_code(sym_ops[3]),
fmt % restraint.volume_ideal,
fmt % math.sqrt(1/restraint.weight),
fmt % restraint.delta))
return loop
def run(args):
assert len(args) == 1
lines = open(args[0]).read().splitlines()
title = lines[0]
unit_cell = uctbx.unit_cell(lines[1])
n_symops = int(lines[2].split()[0])
space_group = sgtbx.space_group()
for line in lines[3:3+n_symops]:
coeffs = [float(field) for field in line.split()]
space_group.expand_smx(sgtbx.rt_mx(coeffs[:9], coeffs[9:]))
crystal_symmetry = crystal.symmetry(
unit_cell=unit_cell,
space_group=space_group)
miller_indices = flex.miller_index()
data = flex.double()
sigmas = flex.double()
for i_line in xrange(3+n_symops,len(lines)):
fields = lines[i_line].split()
assert len(fields) == 5
miller_indices.append([int(value) for value in fields[:3]])
data.append(float(fields[3]))
sigmas.append(float(fields[4]))
miller_set=miller.set(
crystal_symmetry=crystal_symmetry,
indices=miller_indices,
anomalous_flag=False)
miller_array = miller_set.array(
data=data,
sigmas=sigmas).set_observation_type_xray_intensity()
print "Before merging:"
miller_array.show_summary()
print
merged = miller_array.merge_equivalents()
merged.show_summary()
print
merged_array = merged.array()
print "After merging:"
merged_array.show_comprehensive_summary()
print
def sample(two_folds, fudge_factor, deltas, perturbations):
for two_fold in two_folds:
group = sgtbx.space_group()
group.expand_smx(sgtbx.rt_mx(two_fold))
assert group.order_z() == 2
sym = sgtbx.space_group_info(
group=group).any_compatible_crystal_symmetry(volume=1000)
for i_trial in xrange(30):
while True:
uc_fudge = list(sym.unit_cell().parameters())
for i in xrange(6):
uc_fudge[i] *= 1 + (random.random() * 2 - 1) * fudge_factor
try:
uc_fudge = uctbx.unit_cell(uc_fudge)
except ValueError:
pass
else:
break
deltas.append(
two_fold.le_page_1982_delta(reduced_cell=uc_fudge, deg=True))
perturbations.append(
two_fold.lebedev_2005_perturbation(reduced_cell=uc_fudge))
def __init__(self, cif_block, strict=False):
# The order of priority for determining space group is:
# sym_ops, hall symbol, H-M symbol, space group number
self.cif_block = cif_block
sym_ops = self.get_cif_item('_space_group_symop_operation_xyz')
sym_op_ids = self.get_cif_item('_space_group_symop_id')
space_group = None
if sym_ops is not None:
if isinstance(sym_ops, basestring):
sym_ops = flex.std_string([sym_ops])
if sym_op_ids is not None:
if isinstance(sym_op_ids, basestring):
sym_op_ids = flex.std_string([sym_op_ids])
assert len(sym_op_ids) == len(sym_ops)
self.sym_ops = {}
space_group = sgtbx.space_group()
if isinstance(sym_ops, basestring): sym_ops = [sym_ops]
for i, op in enumerate(sym_ops):
try:
s = sgtbx.rt_mx(op)
except RuntimeError, e:
str_e = str(e)
if "Parse error: " in str_e:
raise CifBuilderError(
"Error interpreting symmetry operator: %s" %
(str_e.split("Parse error: ")[-1]))
else:
raise
if sym_op_ids is None:
sym_op_id = i + 1
else:
try:
sym_op_id = int(sym_op_ids[i])
except ValueError, e:
raise CifBuilderError(
"Error interpreting symmetry operator id: %s" %
(str(e)))
self.sym_ops[sym_op_id] = s
space_group.expand_smx(s)
def __init__(self, lf):
self.symbol = None
l = lf.next()
print l.strip()
if (lf.eof): return
no, number, symbol, m = l.split()
assert no == "NO."
number = int(number)
assert int(float(m)) == float(m)
m = int(float(m))
space_group = sgtbx.space_group()
if (m < 0):
space_group.expand_inv(sgtbx.tr_vec((0, 0, 0)))
space_group.expand_conventional_centring_type(symbol[0])
t_den = space_group.t_den()
matrices = []
for i in xrange(abs(m)):
l = lf.next()
assert not lf.eof
flds = l.split()
assert len(flds) == 12
r = [int(e) for e in flds[1:4] + flds[5:8] + flds[9:12]]
t = [
int(round(float(e) * t_den))
for e in (flds[0], flds[4], flds[8])
]
try:
s = sgtbx.rt_mx(sgtbx.rot_mx(r), sgtbx.tr_vec(t))
except RuntimeError, e:
print e
print l
else:
try:
matrices.append(s)
space_group.expand_smx(s)
except RuntimeError, e:
print e
print l
print s
def _residue_groups_rt_mx_ij(self, atom1, atom2, unit_cell, symop_str, symop):
"""
Get atoms object and residue group object for H and heavy atom
"""
xyzs1 = atom1.parent().parent().atoms().extract_xyz()
xyzs2 = atom2.parent().parent().atoms().extract_xyz()
rg1 = atom1.parent().parent().detached_copy()
rg2 = atom2.parent().parent().detached_copy()
if symop_str:
rt_mx_ji = sgtbx.rt_mx(str(symop))
xyzs2 = unit_cell.fractionalize(xyzs2)
m3 = rt_mx_ji.r().as_double()
m3 = scitbx.matrix.sqr(m3)
t = rt_mx_ji.t().as_double()
t = scitbx.matrix.col((t[0],t[1],t[2]))
xyzs2 = unit_cell.orthogonalize(m3.elems*xyzs2+t)
rg2.atoms().set_xyz(xyzs2)
for atom in rg2.atoms():
if atom.name==atom2.name:
atom2=atom
break
return rg1, rg2, atom1, atom2
def filtered_commands(self):
""" Yields those command in self.command_stream
that this parser is not concerned with. On the contrary,
LATT, SYMM are swallowed (CELL is yielded because it carries
the wavelength too).
"""
unit_cell = None
unit_cell_param_sigmas = None
space_group = sgtbx.space_group()
for command, line in self.command_stream:
cmd, args = command[0], command[-1]
if cmd == 'CELL':
assert unit_cell is None
unit_cell = uctbx.unit_cell(args[1:])
yield command, line
elif cmd == 'ZERR':
assert unit_cell_param_sigmas is None
unit_cell_param_sigmas = args[1:]
yield command, line
elif cmd == 'LATT':
assert len(args) == 1
n = int(args[0])
if n > 0:
space_group.expand_inv(sgtbx.tr_vec((0, 0, 0)))
z = "*PIRFABC"[abs(n)]
space_group.expand_conventional_centring_type(z)
elif cmd == 'SYMM':
assert len(args) == 1
s = sgtbx.rt_mx(args[0])
space_group.expand_smx(s)
else:
if cmd == 'SFAC':
assert unit_cell is not None
self.builder.make_crystal_symmetry(unit_cell=unit_cell,
space_group=space_group)
self.builder.set_unit_cell_parameter_sigmas(
unit_cell_param_sigmas)
yield command, line
def __init__(self, si_structure, si_si_sym_table):
self.structure = si_structure.deep_copy_scatterers()
bond_sym_table = crystal.pair_sym_table(si_si_sym_table.size())
sites_frac = si_structure.sites_frac()
i_oxygen = count(1)
for i_seq,pair_sym_dict in enumerate(si_si_sym_table):
site_frac_i = mx.col(sites_frac[i_seq])
for j_seq,sym_ops in pair_sym_dict.items():
assert j_seq >= i_seq
for rt_mx_ji in sym_ops:
site_frac_ji = mx.col(rt_mx_ji * sites_frac[j_seq])
bond_center = (site_frac_i + site_frac_ji) / 2
i_seq_o = self.structure.scatterers().size()
self.structure.add_scatterer(xray.scatterer(
label="O%d"%i_oxygen.next(),
site=bond_center))
bond_sym_table[i_seq].setdefault(i_seq_o).append(
sgtbx.rt_mx(1,1))
bond_sym_table[j_seq].setdefault(i_seq_o).append(
rt_mx_ji.inverse_cancel())
bond_sym_table.append(crystal.pair_sym_dict())
self.bond_sym_table = bond_sym_table.tidy(
site_symmetry_table=self.structure.site_symmetry_table())
def add_user_vector(self):
uc = self.viewer.miller_array.unit_cell()
ln = len(self.viewer.all_vectors)
label = self.params.viewer.user_label
order = 0
try:
hklvec = ""
abcvec = ""
hklop = ""
if self.params.viewer.add_user_vector_hkl not in [None, "", "()"]:
hklvec = eval(self.params.viewer.add_user_vector_hkl.replace(" ",""))
# convert into cartesian space
cartvec = list( self.viewer.scene.renderscale*(hklvec * matrix.sqr(uc.fractionalization_matrix()).transpose()) )
elif self.params.viewer.add_user_vector_abc not in [None, "", "()"]:
abcvec = eval(self.params.viewer.add_user_vector_abc.replace(" ",""))
# convert into cartesian space
cartvec = list(abcvec * matrix.sqr(uc.orthogonalization_matrix()))
elif self.params.viewer.add_user_vector_hkl_op not in [None, ""]:
hklop = self.params.viewer.add_user_vector_hkl_op.replace(" ","")
rt = sgtbx.rt_mx(symbol=hklop, r_den=12, t_den=144)
rt.r().as_double()
self.viewer.symops.append( rt ) #
(cartvec, a, label, order) = self.viewer.GetVectorAndAngleFromRotationMx( rt.r() )
if label:
label = "%s-fold_%s" %(str(int(roundoff(2*math.pi/a, 0))), self.params.viewer.user_label)
self.mprint("Rotation axis, %s, added" %label)
if (self.params.viewer.add_user_vector_hkl in [None, "", "()"] \
and self.params.viewer.add_user_vector_abc in [None, "", "()"] \
and self.params.viewer.add_user_vector_hkl_op) in [None, ""]:
self.mprint("No vector was specified")
self.uservectors.append( (ln, label, order, cartvec, hklop, str(hklvec), str(abcvec) ))
self.list_vectors()
except Exception as e:
raise Sorry( str(e))
self.params.viewer.add_user_vector_hkl_op = ""
self.params.viewer.add_user_vector_hkl = ""
self.params.viewer.add_user_vector_abc = ""
def __init__(self, f_obs, ncs_pairs, reflections_per_bin):
adopt_init_args(self, locals())
# Create bins
f_obs.setup_binner(reflections_per_bin=reflections_per_bin)
self.binner = f_obs.binner()
n_bins = self.binner.n_bins_used()
self.n_bins = n_bins
self.SigmaN = None
self.update_SigmaN()
#
self.rbin = flex.int(f_obs.data().size(), -1)
for i_bin in self.binner.range_used():
for i_seq in self.binner.array_indices(i_bin):
self.rbin[i_seq] = i_bin - 1 # i_bin starts with 1, not 0 !
assert flex.min(self.rbin) == 0
assert flex.max(self.rbin) == n_bins - 1
# Extract symmetry matrices
self.sym_matrices = []
for m_as_string in f_obs.space_group().smx():
o = sgtbx.rt_mx(symbol=str(m_as_string),
t_den=f_obs.space_group().t_den())
m_as_double = o.r().as_double()
self.sym_matrices.append(m_as_double)
self.gradient_evaluator = None
self.target_and_grads = ext.tncs_eps_factor_refinery(
tncs_pairs=self.ncs_pairs,
f_obs=self.f_obs.data(),
sigma_f_obs=self.f_obs.sigmas(),
rbin=self.rbin,
SigmaN=self.SigmaN,
space_group=self.f_obs.space_group(),
miller_indices=self.f_obs.indices(),
fractionalization_matrix=self.f_obs.unit_cell(
).fractionalization_matrix(),
sym_matrices=self.sym_matrices)
self.update()
def process_nonbonded_for_links(
self,
bond_params_table,
bond_asu_table,
geometry_proxy_registries,
link_metals=True,
link_residues=True,
link_carbohydrates=True,
link_amino_acid_rna_dna=False,
link_ligands=False,
link_small_molecules=False,
max_bonded_cutoff=None,
metal_coordination_cutoff=3.,
amino_acid_bond_cutoff=2.,
inter_residue_bond_cutoff=2.,
second_row_buffer=0.5,
carbohydrate_bond_cutoff=2.,
ligand_bond_cutoff=2.,
small_molecule_bond_cutoff=2.,
include_selections=None,
exclude_selections=None,
log=None,
verbose=False,
):
assert hasattr(self, "_cif")
if max_bonded_cutoff is None:
max_bonded_cutoff = max(
metal_coordination_cutoff,
amino_acid_bond_cutoff,
carbohydrate_bond_cutoff,
ligand_bond_cutoff,
small_molecule_bond_cutoff,
inter_residue_bond_cutoff + second_row_buffer,
)
max_bonded_cutoff_standard = max_bonded_cutoff
if include_selections:
for selection_1, selection_2, cutoff in include_selections:
max_bonded_cutoff = max(max_bonded_cutoff, cutoff)
# check that linking required
## has_checks = []
## for i, link_boolean in enumerate([link_carbohydrates,
## ]
## ):
## if i==0: ct = "common_saccharide"
## rc = False
## if link_boolean:
## rc = check_all_classes(self.pdb_hierarchy, ct)
## has_checks.append(rc)
## has_checks.append(link_amino_acid_rna_dna)
## if not filter(None, has_checks): return
#
if max_bonded_cutoff > 15:
raise Sorry(
"One of the following parameters: \nmetal_coordination_" +
"cutoff, amino_acid_bond_cutoff," +
"inter_residue_bond_cutoff, \ncarbohydrate_bond_cutoff,"
"bonds.bond_distance_cutoff \nis greater than 15A. Please check and"
+ " correct these parameters.")
if verbose and log is not None:
print("""
metal_coordination_cutoff %s
amino_acid_bond_cutoff %s
carbohydrate_bond_cutoff %s
inter_residue_bond_cutoff %s
second_row_buffer %s
""" % (
metal_coordination_cutoff,
amino_acid_bond_cutoff,
carbohydrate_bond_cutoff,
inter_residue_bond_cutoff,
second_row_buffer,
),
file=log)
from cctbx import crystal
from cctbx.array_family import flex
#
def _nonbonded_pair_objects(
max_bonded_cutoff=3.,
i_seqs=None,
):
if i_seqs is None:
atoms = self.pdb_hierarchy.atoms()
i_seqs = flex.size_t()
for atom in atoms:
i_seqs.append(atom.i_seq)
if (self.model_indices is not None):
model_indices = self.model_indices.select(i_seqs)
conformer_indices = self.conformer_indices.select(i_seqs)
sym_excl_indices = self.sym_excl_indices.select(i_seqs)
donor_acceptor_excl_groups = self.donor_acceptor_excl_groups.select(
i_seqs)
asu_mappings = self.special_position_settings.asu_mappings(
buffer_thickness=max_bonded_cutoff)
sites_cart = self.sites_cart.select(i_seqs)
asu_mappings.process_sites_cart(
original_sites=sites_cart,
site_symmetry_table=self.site_symmetry_table().select(i_seqs))
pair_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
nonbonded_proxies = geometry_restraints.nonbonded_sorted_asu_proxies(
model_indices=model_indices,
conformer_indices=conformer_indices,
sym_excl_indices=sym_excl_indices,
donor_acceptor_excl_groups=donor_acceptor_excl_groups,
nonbonded_params=geometry_restraints.nonbonded_params(
default_distance=1),
nonbonded_types=flex.std_string(conformer_indices.size()),
nonbonded_charges=flex.int(conformer_indices.size(), 0),
nonbonded_distance_cutoff_plus_buffer=max_bonded_cutoff,
min_cubicle_edge=5,
shell_asu_tables=[pair_asu_table])
return nonbonded_proxies, sites_cart, pair_asu_table, asu_mappings, i_seqs
#
def _nonbonded_pair_generator_geometry_restraints_sort(
nonbonded_proxies, max_bonded_cutoff=3.):
rc = nonbonded_proxies.get_sorted(
by_value="delta",
sites_cart=sites_cart,
include_proxy=True,
)
if rc is None: return
rc, junk = rc
for item in rc:
yield item
#
if (log is not None):
print("""
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : %-5s - %0.2f
Amimo acid : %-5s - %0.2f
Carbohydrate : %-5s - %0.2f
Ligands : %-5s - %0.2f
Small molecules : %-5s - %0.2f
Amino acid - RNA/DNA : %-5s
""" % (
link_metals,
metal_coordination_cutoff,
link_residues,
amino_acid_bond_cutoff,
link_carbohydrates,
carbohydrate_bond_cutoff,
link_ligands,
ligand_bond_cutoff,
link_small_molecules,
small_molecule_bond_cutoff,
link_amino_acid_rna_dna,
),
file=log)
t0 = time.time()
atoms = self.pdb_hierarchy.atoms()
bond_data = []
bond_data_i_seqs = {}
simple_bonds = 0
sym_bonds = 0
link_data = []
simple_links = 0
sym_links = 0
done = ResidueLinkClass()
links = {}
custom_links = {}
exclude_out_lines = {}
# main loop
nonbonded_proxies, sites_cart, pair_asu_table, asu_mappings, nonbonded_i_seqs = \
_nonbonded_pair_objects(max_bonded_cutoff=max_bonded_cutoff,
)
initial_pair_asu_table_table = bond_asu_table.table().deep_copy()
for ii, item in enumerate(
_nonbonded_pair_generator_geometry_restraints_sort(
nonbonded_proxies=nonbonded_proxies,
max_bonded_cutoff=max_bonded_cutoff,
)):
labels, i_seq, j_seq, distance, vdw_distance, sym_op, rt_mx_ji, proxy = item
#
# include & exclude selection
#
origin_id = None
if (include_selections and distance >= max_bonded_cutoff_standard):
for selection_1, selection_2, bond_cutoff in include_selections:
if ((i_seq in selection_1 and j_seq in selection_2) or
(i_seq in selection_2 and j_seq in selection_1)):
metal_coordination_cutoff = bond_cutoff
amino_acid_bond_cutoff = bond_cutoff
carbohydrate_bond_cutoff = bond_cutoff
ligand_bond_cutoff = bond_cutoff
small_molecule_bond_cutoff = bond_cutoff
inter_residue_bond_cutoff = bond_cutoff
saccharide_bond_cutoff = bond_cutoff
link_residues = True
break
else:
continue # exclude this nonbond from consideration
exclude_this_nonbonded = False
if exclude_selections:
for selection_1, selection_2 in exclude_selections:
if selection_2: # check both
if ((i_seq in selection_1 and j_seq in selection_2) or
(i_seq in selection_2 and j_seq in selection_1)):
exclude_this_nonbonded = True
break
else:
if i_seq in selection_1 or j_seq in selection_1:
exclude_this_nonbonded = True
# XXX this is a poor job!!!
if bond_asu_table.contains(i_seq, j_seq, 0): continue
if bond_asu_table.contains(i_seq, j_seq, 1): continue
atom1 = atoms[i_seq]
atom2 = atoms[j_seq]
if exclude_this_nonbonded:
key = (selection_1, selection_2)
if key not in exclude_out_lines:
exclude_out_lines[key] = \
' bond %s\n%s%s\n%smodel %.2f' % (
atom1.id_str(),
' '*9,
atom2.id_str(),
' '*6,
distance)
continue
#
# moving sections of this to outside the loop
# - SF4
#
if link_metals:
moved = ['SF4', 'F3S']
if (atom1.parent().resname in moved
or atom2.parent().resname in moved):
continue
if verbose:
print(i_seq, j_seq, atom1.quote(), end=' ')
print(atom2.quote(), end=' ')
print("Distance: %0.2f" % distance, rt_mx_ji, sym_op)
# don't link atoms not in the same conformer (works for models also)...
if not atom1.is_in_same_conformer_as(atom2):
assert 0
continue
# don't link atoms in same residue group
if atom1.parent().parent() == atom2.parent().parent(): continue
atom_group1 = atom1.parent()
atom_group2 = atom2.parent()
# dont't like atom groups in different altloc expect " "
if atom_group1.altloc.strip() == atom_group2.altloc.strip(): pass
elif atom_group1.altloc.strip() == "": pass
elif atom_group2.altloc.strip() == "": pass
else: continue
# don't link some classes
classes1 = linking_utils.get_classes(atom1)
classes2 = linking_utils.get_classes(atom2)
use_only_bond_cutoff = False
if verbose:
print("""
Residue classes
%s
%s """ % (classes1, classes2))
# why was this commented out???
if not link_ligands and (classes1.other or classes2.other):
continue
if (not link_small_molecules
and (classes1.common_small_molecule
or classes2.common_small_molecule)):
continue
# is_proxy_set between any of the atoms ????????
if classes1.common_amino_acid and classes2.common_amino_acid:
if not link_residues:
continue
# special amino acid linking
# - cyclic
# - beta, delta ???
if possible_cyclic_peptide(atom1,
atom2): # first & last peptide
use_only_bond_cutoff = True
if sym_op:
if classes1.common_amino_acid and classes2.common_saccharide:
continue
if classes2.common_amino_acid and classes1.common_saccharide:
continue
#
# bonded atoms can't link to same atom, eg MG-PG and MG-O1P
#
if bond_data:
bonded = False
if i_seq in bond_data_i_seqs:
for t_i in bond_data_i_seqs[i_seq]:
if bond_asu_table.contains(j_seq, t_i, 0):
bonded = True
if j_seq in bond_data_i_seqs:
for t_i in bond_data_i_seqs[j_seq]:
if bond_asu_table.contains(i_seq, t_i, 0):
bonded = True
if bonded: continue
#
key = [
atom1.id_str()[9:-1],
atom2.id_str()[9:-1],
]
key.sort()
if sym_op:
key.append(str(rt_mx_ji))
key = tuple(key)
# hydrogens
if atom1.element.strip() in hydrogens:
done[atom2.id_str()] = atom1.id_str()
if atom2.element.strip() in hydrogens:
done[atom1.id_str()] = atom2.id_str()
# bond length cutoff & some logic
if not linking_utils.is_atom_pair_linked(
atom1,
atom2,
distance=distance,
max_bonded_cutoff=max_bonded_cutoff,
amino_acid_bond_cutoff=amino_acid_bond_cutoff,
inter_residue_bond_cutoff=inter_residue_bond_cutoff,
second_row_buffer=second_row_buffer,
saccharide_bond_cutoff=carbohydrate_bond_cutoff,
metal_coordination_cutoff=metal_coordination_cutoff,
use_only_bond_cutoff=use_only_bond_cutoff,
link_metals=link_metals,
verbose=verbose,
):
if verbose:
print("is not linked", atom1.quote(), atom2.quote(), key)
print('link_metals', link_metals)
if (atom1.element.strip().upper() in hydrogens
or atom2.element.strip().upper() in hydrogens):
pass
else:
done.setdefault(key, [])
done[key].append([atom1.name, atom2.name])
continue
# check some valences...
if not (classes1.common_element or classes2.common_element):
if not linking_utils.check_valence(self.pdb_hierarchy, atom1):
print(
" Atom %s rejected from bonding due to valence issues."
% atom1.quote(),
file=log)
continue
if not linking_utils.check_valence(self.pdb_hierarchy, atom2):
print(
" Atom %s rejected from bonding due to valence issues."
% atom2.quote(),
file=log)
continue
# got a link....
class1 = linking_utils.get_classes(
atom1, #_group1.resname,
important_only=True,
)
class2 = linking_utils.get_classes(
atom2, #_group2.resname,
important_only=True,
)
class_key = [class1, class2]
class_key.sort()
class_key = tuple(class_key)
if verbose: print('class_key', class_key)
#
if not link_metals and "metal" in class_key: continue
#atoms_must_be = {}
if not link_residues:
if class_key in [
("common_amino_acid", "common_amino_acid"),
#("common_amino_acid", "other"),
]:
continue
#else:
# atoms_must_be.setdefault(("common_amino_acid",
# "common_amino_acid"),["C", "N"])
# atoms_must_be.setdefault(("common_amino_acid", "other"),["C", "N"])
if not link_carbohydrates and "common_saccharide" in class_key:
continue
if not link_amino_acid_rna_dna:
if "common_amino_acid" in class_key and "common_rna_dna" in class_key:
continue
#
names = [atom1.name, atom2.name]
if verbose: print('names', names)
names.sort()
atom1_key = None
atom2_key = None
if class1 in linking_setup.maximum_per_atom_links: # is one
atom1_key = atom1.id_str()
if class2 in linking_setup.maximum_per_atom_links: # is one
atom2_key = atom2.id_str()
if verbose:
print('-' * 80)
print('class_key', class_key)
print('done')
for k, item in done.items():
print("> %s : %s" % (k, item))
print('key', key)
print('atom keys', atom1_key, atom2_key)
# exclude duplicate symmetry op.
if key in done:
if names in done[key]: continue
if atom1.parent().altloc == atom2.parent().altloc:
if atom1_key:
if atom1_key in done: continue
done[atom1_key] = key
if atom2_key:
if atom2_key in done: continue
done[atom2_key] = key
#
current_number_of_links = len(done.setdefault(key, []))
if (current_number_of_links >=
linking_setup.maximum_inter_residue_links.get(
class_key, 1)):
if verbose:
print(
"too many links:", current_number_of_links,
linking_setup.maximum_inter_residue_links.get(
class_key, 1), class_key)
continue
#
done[key].append(names)
done_key = key
# get all possible links
i_seqs = []
for atom in atom_group1.atoms():
i_seqs.append(atom.i_seq)
j_seqs = []
for atom in atom_group2.atoms():
j_seqs.append(atom.i_seq)
ij_seqs = []
for i in i_seqs:
for j in j_seqs:
tmp = [i, j]
tmp.sort()
ij_seqs.append(tuple(tmp))
# check that a link not already made
link_found = False
if verbose:
print('len simple bond proxies',
len(geometry_proxy_registries.bond_simple.proxies))
# Consistency check - debugging only
# for bsp in geometry_proxy_registries.bond_simple.proxies:
# if bsp.i_seqs[1] not in initial_pair_asu_table_table[bsp.i_seqs[0]].keys():
# print "ERROR!!!", bsp.i_seqs
# STOP()
# Proposed fast loop: Time building additional restraints for
# ribosome went from 5272 to 204 seconds.
for p in ij_seqs:
if p[1] in initial_pair_asu_table_table[p[0]].keys():
link_found = True
break
# VERY SLOW !!! - original loop
# for bond_simple_proxy in geometry_proxy_registries.bond_simple.proxies:
# if bond_simple_proxy.i_seqs in ij_seqs:
# link_found = True
# break
if link_found: continue
# check for any link between atom groups based on residue name, eg ASN-NAG
# get predefined link
link, swap, key = linking_utils.is_atom_group_pair_linked(
atom_group1,
atom_group2,
self.mon_lib_srv,
)
if verbose:
print('link', link)
print('swap', swap)
print('key', key)
if swap:
tmp = atom_group2
atom_group2 = atom_group1
atom_group1 = tmp
space_group = self.special_position_settings.space_group()
#
if len(done_key) == 2:
link_rt_mx_ji = sgtbx.rt_mx(symbol="x,y,z",
t_den=space_group.t_den())
else:
link_rt_mx_ji = sgtbx.rt_mx(symbol=done_key[2],
t_den=space_group.t_den())
#
if link:
# apply a standard link
origin_id = origin_ids.get_origin_id(
'link_%s' % key,
return_none_if_absent=True,
)
if origin_id is None:
# user defined links should not be applied here
continue
count, bond_i_seqs = _apply_link_using_proxies(
link,
atom_group1,
atom_group2,
bond_params_table,
bond_asu_table,
geometry_proxy_registries,
rt_mx_ji=link_rt_mx_ji,
origin_id=origin_id,
)
origin_id = None
if len(bond_i_seqs) == 0:
if verbose:
print('failed to link using %s' % key)
continue
links.setdefault(key, [])
links[key].append([atom_group1, atom_group2])
links[key][-1] += bond_i_seqs[0] # odd?
if verbose: print("predefined residue named link", key)
continue
#
#if atoms_must_be:
# # this could be fancier...
# # link_residues is peptide and SG links
# atoms_must_be_key = [atom1.element.strip(), atom2.element.strip()]
# #atoms_must_be_key = [atom1.name.strip(), atom2.name.strip()]
# atoms_must_be_key.sort()
# if class_key in atoms_must_be and "S" not in atoms_must_be_key:
# if atoms_must_be[class_key]!=atoms_must_be_key:
# continue
rc = linking_utils.process_atom_groups_for_linking_single_link(
self.pdb_hierarchy,
atom1,
atom2,
verbose=verbose,
)
if not rc:
done.remove_link(done_key, names)
continue
pdbres, link_key, link_atoms = rc
assert len(link_key) == 1
key = link_key[0]
link = self.mon_lib_srv.link_link_id_dict.get(key, None)
if verbose:
print('pdbres', pdbres)
print('link', link)
print('link_key', link_key)
print('link_atoms', link_atoms)
if key.find("ALPHA1") > -1 or key.find(
"BETA1") > -1: # is handled in elif
key, cif, bond_i_seqs = \
glyco_utils.apply_glyco_link_using_proxies_and_atoms(
atom_group2,
atom_group1,
bond_params_table,
bond_asu_table,
geometry_proxy_registries,
rt_mx_ji=link_rt_mx_ji,
link_carbon_dist=carbohydrate_bond_cutoff,
origin_id=origin_ids['glycosidic custom'],
)
links.setdefault(key, [])
links[key].append([atom_group1, atom_group2])
links[key][-1] += bond_i_seqs
continue
elif link:
origin_id = origin_ids['link_%s' % key]
count, bond_i_seqs = _apply_link_using_proxies(
link,
atom_group1,
atom_group2,
bond_params_table,
bond_asu_table,
geometry_proxy_registries,
rt_mx_ji=link_rt_mx_ji,
origin_id=origin_id,
)
origin_id = None
links.setdefault(key, [])
links[key].append([atom_group1, atom_group2])
links[key][-1] += bond_i_seqs[0]
continue
else:
# possible peptide or rna/dna link
rc = check_for_peptide_links(atom1, atom2)
# no peptide links across symmetry
if len(done_key) == 3:
rc = None
if rc:
key, swap = rc
link = self.mon_lib_srv.link_link_id_dict.get(key)
if swap:
tmp = atom_group2
atom_group2 = atom_group1
atom_group1 = tmp
origin_id = origin_ids['link_%s' % key]
rc = _apply_link_using_proxies(
link,
atom_group1,
atom_group2,
bond_params_table,
bond_asu_table,
geometry_proxy_registries,
rt_mx_ji=link_rt_mx_ji,
origin_id=origin_id,
)
if not rc:
tmp = atom_group2
atom_group2 = atom_group1
atom_group1 = tmp
rc = _apply_link_using_proxies(
link,
atom_group1,
atom_group2,
bond_params_table,
bond_asu_table,
geometry_proxy_registries,
rt_mx_ji=link_rt_mx_ji,
origin_id=origin_id,
)
origin_id = None
# not added to links so not LINK record
if sym_op:
sym_links += 1
link_data.append((
atoms[i_seq].id_str(),
atoms[j_seq].id_str(),
rt_mx_ji,
key,
))
else:
simple_links += 1
link_data.append((
atoms[i_seq].id_str(),
atoms[j_seq].id_str(),
None, #rt_mx_ji,
key,
))
continue
#
custom_links.setdefault(ii, [])
custom_links[ii].append([atom_group1, atom_group2, atom1, atom2])
# simple
origin_id = origin_ids['Misc. bond']
if ((classes1.common_rna_dna or classes1.ccp4_mon_lib_rna_dna) and
(classes2.common_rna_dna or classes2.ccp4_mon_lib_rna_dna)):
bond_name = "h-dna"
assert 0
elif (linking_utils.get_classes(atom1, important_only=True)
== "metal" or linking_utils.get_classes(
atom2, important_only=True) == "metal"):
origin_id = origin_ids['metal coordination']
if sym_op:
sym_bonds += 1
bond_data.append((
atoms[i_seq].id_str(),
atoms[j_seq].id_str(),
rt_mx_ji,
origin_id,
))
bond_data_i_seqs.setdefault(i_seq, [])
bond_data_i_seqs.setdefault(j_seq, [])
bond_data_i_seqs[i_seq].append(j_seq)
bond_data_i_seqs[j_seq].append(i_seq)
pair_asu_table.add_pair(proxy)
else:
simple_bonds += 1
bond_data.append((
atoms[i_seq].id_str(),
atoms[j_seq].id_str(),
None, #rt_mx,
origin_id,
))
bond_data_i_seqs.setdefault(i_seq, [])
bond_data_i_seqs.setdefault(j_seq, [])
bond_data_i_seqs[i_seq].append(j_seq)
bond_data_i_seqs[j_seq].append(i_seq)
pair_asu_table.add_pair(proxy.i_seqs)
# END MAIN LOOP for ii, item in enumerate(nonbonded?)
#
#
if verbose:
for key in sorted(custom_links):
print('-' * 80)
print(key)
for pair in custom_links[key]:
for atom in pair:
try:
print(atom.quote())
except Exception:
print(atom)
pair_sym_table = pair_asu_table.extract_pair_sym_table()
n_simple, n_symmetry = 0, 0
self.pdb_link_records.setdefault("LINK", [])
retain = []
for ijk, sym_pair in enumerate(pair_sym_table.iterator()):
i_seq, j_seq = sym_pair.i_seqs()
origin_id = bond_data[ijk][-1]
assert i_seq == nonbonded_i_seqs[i_seq]
assert j_seq == nonbonded_i_seqs[j_seq]
atom1 = atoms[i_seq]
atom2 = atoms[j_seq]
# check for NA linkage
classes1 = linking_utils.get_classes(atom1)
classes2 = linking_utils.get_classes(atom2)
ans = bondlength_defaults.run(atom1, atom2)
equil = 2.3
weight = 0.02
slack = 0.
if len(ans) > 0:
equil = ans[0]
if len(ans) > 1:
weight = ans[1]
if len(ans) > 2:
slack = ans[2]
if equil is None:
equil = 2.3
added_to_asu_table = False
try:
#bond_asu_table.add_pair([i_seq, j_seq])
bond_asu_table.add_pair(i_seq=i_seq,
j_seq=j_seq,
rt_mx_ji=sym_pair.rt_mx_ji)
added_to_asu_table = True
except RuntimeError as e:
error = """
Difficulties linking atoms
%s
%s
Suggestions include providing restraints for any unknown residues.
""" % (atom1.quote(), atom2.quote())
print(error, file=log)
if added_to_asu_table:
retain.append(ijk)
if (sym_pair.rt_mx_ji.is_unit_mx()): n_simple += 1
else: n_symmetry += 1
assert origin_id
bond_params_table.update(
i_seq=i_seq,
j_seq=j_seq,
params=geometry_restraints.bond_params(
distance_ideal=equil,
weight=1.0 / weight**2,
slack=slack,
origin_id=origin_id,
))
# adding link to PDB
self.pdb_link_records["LINK"].append([
self.pdb_atoms[i_seq], self.pdb_atoms[j_seq],
sym_pair.rt_mx_ji
])
# output
if link_data:
print(" Number of additional links: simple=%d, symmetry=%d" % (
simple_links,
sym_bonds,
),
file=log)
for label1, label2, sym_op, link_name in sorted(link_data):
if sym_op is None:
print(" Simple link: %s - %s" % (label1, label2),
file=log)
for label1, label2, sym_op, bond_type in sorted(bond_data):
if sym_op:
print(" Symmetry link: %s - %s sym. op: %s" % (
label1,
label2,
sym_op,
),
file=log)
if (log is not None):
print(" Number of custom bonds: simple=%d, symmetry=%d" %
(n_simple, n_symmetry),
file=log)
if (n_symmetry == 0):
blanks = ""
else:
blanks = " "
#
def _sort_on_id(ag1, ag2):
ag1 = ag1[0]
ag2 = ag2[0]
if ag1.id_str()[4:] == ag2.id_str()[4:]:
if ag1.altloc < ag2.altloc:
return -1
return 1
elif ag1.id_str()[4:] < ag2.id_str()[4:]:
return -1
return 1
#
if exclude_out_lines:
print(
" Excluded links - shortest distance candidate listed for each exclusion",
file=log)
for key, item in exclude_out_lines.items():
print(item, file=log)
if links:
explained = []
print(" Links applied", file=log)
for key in sorted(links):
print(" %s" % key, file=log)
links[key].sort(key=cmp_to_key(_sort_on_id))
for ag1, ag2, i_seq, j_seq in links[key]:
self.pdb_link_records["LINK"].append([
self.pdb_atoms[i_seq],
self.pdb_atoms[j_seq],
"x,y,z", #link_rt_mx_ji,
])
if ag1.altloc or ag2.altloc:
print(' "%s" - "%s" : altloc "%s" - "%s"' % (
ag1.id_str(),
ag2.id_str(),
ag1.altloc,
ag2.altloc,
),
file=log)
else:
print(' "%s" - "%s"' % (
ag1.id_str(),
ag2.id_str(),
),
file=log)
explain = ""
if key.find("ALPHA") == 0 or key.find("BETA") == 0:
true_alpha_beta = glyco_utils.get_alpha_beta(
ag2.resname,
fake=False,
)
if true_alpha_beta and key.find(
true_alpha_beta.upper()) == -1:
one = "a beta"
two = "an alpha"
if true_alpha_beta == "alpha":
one = "an alpha"
two = "a beta"
explain = "%s~> Even though %s is %s isomer," % (
' ' * 7, ag2.resname, one)
explain += " %s linkage is required..." % (two)
if explain not in explained:
print(explain, file=log)
explained.append(explain)
if bond_data:
print(" Number of additional bonds: simple=%d, symmetry=%d" % (
simple_bonds,
sym_bonds,
),
file=log)
for caption, bond_type in [
("Coordination", 'metal coordination'),
("Other bonds", 'bond'),
]:
print(" %s:" % caption, file=log)
for ijk, (label1, label2, sym_op,
bt) in enumerate(sorted(bond_data)):
if sym_op is None and bt == bond_type and ijk in retain:
print(" Simple bond: %s - %s" % (label1, label2),
file=log)
for ijk, (label1, label2, sym_op,
bt) in enumerate(sorted(bond_data)):
if sym_op and bt == bond_type and ijk in retain:
print(" Symmetry bond: %s - %s sym. op: %s" % (
label1,
label2,
sym_op,
),
file=log)
if (log is not None):
print(' Time building additional restraints: %0.2f' %
(time.time() - t0),
file=log)
def CheckFormat(self, value):
if type(value) == type(u'abc'): value = value.encode("ascii", "ignore")
from cctbx import sgtbx
rt_mx = sgtbx.rt_mx(symbol=value)
return value
def mat_to_symop(mat):
return sgtbx.change_of_basis_op(
sgtbx.rt_mx(matrix.sqr(mat), (0, 0, 0), r_den=12, t_den=144)).as_hkl()
