def find_symmetry_from_crystal_structure(crystal_structure):
work_f_calc = crystal_structure.structure_factors(d_min=1).f_calc().expand_to_p1()
sg_dict = {}
state = False
try:
sf_symm = symmetry_search.structure_factor_symmetry(f_in_p1=work_f_calc)
sgi = sf_symm.space_group_info
sg_dict = _space_group_info_to_dict(sgi)
state = True
except Exception as e:
sg_dict = dict(hall='P 1', hermann_mauguin='P 1', number=1, crystal_system='Triclinic', cctbx_name='P 1')
#return both the space group and a flag to specify that the assignment was successful
return (sg_dict, state)
def run(args):
import iotbx.phil
pcl = iotbx.phil.process_command_line(args=args, master_string="""\
symmetry_search {
structure_factor_d_min = 2
.type = float
}
""")
if (len(pcl.remaining_args) != 1):
from libtbx.utils import Usage
import libtbx.load_env
print
pcl.master.show()
print
raise Usage(
"%s pdb_file|poscar_file [parameters]" % libtbx.env.dispatcher_name)
inp_file = pcl.remaining_args[0]
from libtbx.str_utils import show_string
import iotbx.pdb
if (iotbx.pdb.is_pdb_file(inp_file)):
print "PDB file:", show_string(inp_file)
pdb_inp = iotbx.pdb.input(file_name=inp_file)
xs = pdb_inp.xray_structure_simple()
else:
print "POSCAR file:", show_string(inp_file)
import iotbx.poscar
poscar = iotbx.poscar.reader(lines=open(inp_file).read().splitlines())
poscar.make_up_types_if_necessary()
xs = poscar.xray_structure()
print
pcl.work.show()
print
params = pcl.work.extract().symmetry_search
print "Unit cell:", xs.unit_cell()
print
fc_p1 = xs.structure_factors(
d_min=params.structure_factor_d_min).f_calc().expand_to_p1()
from cctbx import symmetry_search
sf_symm = symmetry_search.structure_factor_symmetry(f_in_p1=fc_p1)
print sf_symm
print
print sf_symm.space_group_info
print
def find_symmetry_from_crystal_structure(crystal_structure):
work_f_calc = crystal_structure.structure_factors(
d_min=1).f_calc().expand_to_p1()
sg_dict = {}
state = False
try:
sf_symm = symmetry_search.structure_factor_symmetry(
f_in_p1=work_f_calc)
sgi = sf_symm.space_group_info
sg_dict = _space_group_info_to_dict(sgi)
state = True
except Exception as e:
sg_dict = dict(hall='P 1',
hermann_mauguin='P 1',
number=1,
crystal_system='Triclinic',
cctbx_name='P 1')
#return both the space group and a flag to specify that the assignment was successful
return (sg_dict, state)
def exercise(space_group_info,
fixed_random_seed=True,
shifted_origin=None,
elements=None,
d_min=0.8,
grid_resolution_factor=1/3.,
verbose=False,
**kwds):
if elements is None:
n_C = 5
n_O = 1
n_N = 1
elements = ["C"]*n_C + ["O"]*n_O + ["N"]*n_N
if verbose:
print elements
target_space_group_type = space_group_info.type()
hall = sgtbx.space_group_symbols(
target_space_group_type.lookup_symbol()).hall()
print hall
if fixed_random_seed:
random.seed(1)
flex.set_random_seed(1)
# Generate a random structure in real space,
# compute its structure factors,
# that we will try to recover the symmetry of
target_structure = random_structure.xray_structure(
space_group_info=space_group_info,
elements=elements,
use_u_iso=True,
random_u_iso=True,
random_u_iso_scale=0.04,
use_u_aniso=False,
)
if shifted_origin is None:
shifted_origin = flex.random_double(3)
shifted_origin = mat.col(shifted_origin)
if verbose:
print "new origin = (%.3f, %.3f, %.3f)" % shifted_origin.elems
print
target_structure_in_p1 = target_structure\
.expand_to_p1().apply_shift(shifted_origin)
target_f_in_p1 = miller.build_set(
crystal_symmetry=target_structure_in_p1,
anomalous_flag=False,
d_min=d_min
).structure_factors_from_scatterers(
xray_structure=target_structure_in_p1,
algorithm="direct").f_calc()
# Recover space group?
sf_symm = symmetry_search.structure_factor_symmetry(target_f_in_p1)
if verbose:
print sf_symm
solution_hall, target_hall = [
sgi.as_reference_setting().type().hall_symbol()
for sgi in (sf_symm.space_group_info,
target_structure.space_group_info()) ]
assert solution_hall == target_hall, (solution_hall, target_hall)
# Shift maximises goodness of symmetry?
gos, solution_f = sf_symm.symmetrised_structure_factors()
if space_group_info.type().hall_symbol() != ' P 1':
assert gos.correlation > 0.99
assert gos.gradient == (0, 0, 0)
gos_away_from_max = sf_symm.symmetrised_structure_factors(
delta=mat.col((0.1, 0.1, 0.1)))[0]
assert gos_away_from_max.correlation < 0.9, gos_away_from_max.correlation
# Recovered origin
"""The sequence of transform read:
----->target structure
^ V
^ V (1, shifted_origin=sigma)
^ V
^ shifted target
^ V
^ V sf_symm.cb_op_to_primitive = (P, 0)
^ V
^ shifted target in primitive cell = shifted solution in primitive cell
^ V
^ V (1, -sf_symm.origin=-s)
^ V
^ solution in primitive cell
^ V
^ V solution_to_target_cb_op = (Q, q)
^ V
^------------
The total transfrom from the target structure back to it reads
(QP, q') with q' = (Q,q)(-s + P sigma) = (Q,q)delta_o
with
delta_o = sf_symm.cb_op_to_primitive(shifted_origin) - sf_symm.origin
(Q, q') must leave the target structure space group invariant.
Most of the time Q is the unit matrix and the test boils down to check
whether delta is an allowed origin shift after changing to the input cell
but it does not hurt to do the more general test all the time.
"""
solution_to_target_cb_op = (
target_structure.space_group_info()
.change_of_basis_op_to_reference_setting().inverse()
*
sf_symm.space_group_info
.change_of_basis_op_to_reference_setting())
if verbose:
print
print "solution -> target: %s" % solution_to_target_cb_op.as_xyz()
delta_o = (mat.col(sf_symm.cb_op_to_primitive(shifted_origin))
- sf_symm.origin)
delta = mat.col(solution_to_target_cb_op(delta_o))
stabilising_cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(
(solution_to_target_cb_op*sf_symm.cb_op_to_primitive).c().r(),
sgtbx.tr_vec((delta*72).as_int()*2, tr_den=144)))
# guarding against rounding errors on some platforms (e.g. FC8)
# meaning that (delta*144).as_int() would not work.
target_sg = target_structure.space_group()
assert target_sg == target_sg.change_basis(stabilising_cb_op)
def exercise(space_group_info,
fixed_random_seed=True,
shifted_origin=None,
elements=None,
d_min=0.8,
grid_resolution_factor=1/3.,
verbose=False,
**kwds):
if elements is None:
n_C = 5
n_O = 1
n_N = 1
elements = ["C"]*n_C + ["O"]*n_O + ["N"]*n_N
if verbose:
print(elements)
target_space_group_type = space_group_info.type()
hall = sgtbx.space_group_symbols(
target_space_group_type.lookup_symbol()).hall()
print(hall)
if fixed_random_seed:
random.seed(1)
flex.set_random_seed(1)
# Generate a random structure in real space,
# compute its structure factors,
# that we will try to recover the symmetry of
target_structure = random_structure.xray_structure(
space_group_info=space_group_info,
elements=elements,
use_u_iso=True,
random_u_iso=True,
random_u_iso_scale=0.04,
use_u_aniso=False,
)
if shifted_origin is None:
shifted_origin = flex.random_double(3)
shifted_origin = mat.col(shifted_origin)
if verbose:
print("new origin = (%.3f, %.3f, %.3f)" % shifted_origin.elems)
print()
target_structure_in_p1 = target_structure\
.expand_to_p1().apply_shift(shifted_origin)
target_f_in_p1 = miller.build_set(
crystal_symmetry=target_structure_in_p1,
anomalous_flag=False,
d_min=d_min
).structure_factors_from_scatterers(
xray_structure=target_structure_in_p1,
algorithm="direct").f_calc()
# Recover space group?
sf_symm = symmetry_search.structure_factor_symmetry(target_f_in_p1)
if verbose:
print(sf_symm)
solution_hall, target_hall = [
sgi.as_reference_setting().type().hall_symbol()
for sgi in (sf_symm.space_group_info,
target_structure.space_group_info()) ]
assert solution_hall == target_hall, (solution_hall, target_hall)
# Shift maximises goodness of symmetry?
gos, solution_f = sf_symm.symmetrised_structure_factors()
if space_group_info.type().hall_symbol() != ' P 1':
assert gos.correlation > 0.99
assert gos.gradient == (0, 0, 0)
gos_away_from_max = sf_symm.symmetrised_structure_factors(
delta=mat.col((0.1, 0.1, 0.1)))[0]
assert gos_away_from_max.correlation < 0.9, gos_away_from_max.correlation
# Recovered origin
"""The sequence of transform read:
----->target structure
^ V
^ V (1, shifted_origin=sigma)
^ V
^ shifted target
^ V
^ V sf_symm.cb_op_to_primitive = (P, 0)
^ V
^ shifted target in primitive cell = shifted solution in primitive cell
^ V
^ V (1, -sf_symm.origin=-s)
^ V
^ solution in primitive cell
^ V
^ V solution_to_target_cb_op = (Q, q)
^ V
^------------
The total transfrom from the target structure back to it reads
(QP, q') with q' = (Q,q)(-s + P sigma) = (Q,q)delta_o
with
delta_o = sf_symm.cb_op_to_primitive(shifted_origin) - sf_symm.origin
(Q, q') must leave the target structure space group invariant.
Most of the time Q is the unit matrix and the test boils down to check
whether delta is an allowed origin shift after changing to the input cell
but it does not hurt to do the more general test all the time.
"""
solution_to_target_cb_op = (
target_structure.space_group_info()
.change_of_basis_op_to_reference_setting().inverse()
*
sf_symm.space_group_info
.change_of_basis_op_to_reference_setting())
if verbose:
print()
print("solution -> target: %s" % solution_to_target_cb_op.as_xyz())
delta_o = (mat.col(sf_symm.cb_op_to_primitive(shifted_origin))
- sf_symm.origin)
delta = mat.col(solution_to_target_cb_op(delta_o))
stabilising_cb_op = sgtbx.change_of_basis_op(sgtbx.rt_mx(
(solution_to_target_cb_op*sf_symm.cb_op_to_primitive).c().r(),
sgtbx.tr_vec((delta*72).as_int()*2, tr_den=144)))
# guarding against rounding errors on some platforms (e.g. FC8)
# meaning that (delta*144).as_int() would not work.
target_sg = target_structure.space_group()
assert target_sg == target_sg.change_basis(stabilising_cb_op)
