def test_grid_step(n_sites=50, volume_per_atom=50, d_min=2.0):
grid_step = (0.2, 0.4, 0.6, 0.7, 0.9, 1.0)
for step in grid_step:
symmetry = crystal.symmetry(space_group_symbol="P1")
structure = random_structure.xray_structure(
space_group_info=symmetry.space_group_info(),
elements=["C"] * n_sites,
volume_per_atom=volume_per_atom,
random_u_iso=False)
fc = structure.structure_factors(d_min=d_min,
anomalous_flag=False,
algorithm="fft").f_calc()
manager = max_like_non_uniform.ordered_solvent_distribution(
structure=structure, fo=fc, grid_step=step)
f_water_dist = manager.fcalc_from_distribution()
### check phase compatibility with the symmetry:
centrics = f_water_dist.select_centric()
if (centrics.indices().size() > 0):
ideal = centrics.phase_transfer(centrics)
assert flex.max(flex.abs(ideal.data() - centrics.data())) < 1.e-6
###
#print "max = ", flex.max( flex.abs( f_water_dist.data() ) )
#print "min = ", flex.min( flex.abs( f_water_dist.data() ) )
#print "ave = ", flex.mean( flex.abs( f_water_dist.data() ) )
assert flex.max(flex.abs(f_water_dist.data())) < 1.0
def test_less_one(space_group_info, volume_per_atom=100, d_min=1.8):
#symmetry = crystal.symmetry(space_group_symbol="p212121")
#space_group_info = symmetry.space_group_info()
#n_sym = space_group_info.type().group().n_smx()
for n_atoms in (1, 10):
if (n_atoms == 1):
denom = 16.0
else:
denom = 4.0
for element in ("C", "O", "N"):
structure = random_structure.xray_structure(
space_group_info=space_group_info,
elements=[element] * n_atoms,
volume_per_atom=volume_per_atom,
random_u_iso=False)
fc = structure.structure_factors(d_min=d_min,
anomalous_flag=False,
algorithm="fft").f_calc()
manager = max_like_non_uniform.ordered_solvent_distribution(
structure=structure, fo=fc, grid_step=fc.d_min() / denom)
f_water_dist = manager.fcalc_from_distribution()
### check phase compatibility with the symmetry:
centrics = f_water_dist.select_centric()
if (centrics.indices().size() > 0):
ideal = centrics.phase_transfer(centrics)
assert flex.max(
flex.abs(ideal.data() - centrics.data())) < 1.e-6
###
#print "max = ", flex.max( flex.abs( f_water_dist.data() ) )
#print "min = ", flex.min( flex.abs( f_water_dist.data() ) )
#print "ave = ", flex.mean( flex.abs( f_water_dist.data() ) )
assert flex.max(flex.abs(f_water_dist.data())) < 1.0
def test_grid_step(n_sites = 50,
volume_per_atom = 50,
d_min = 2.0):
grid_step = (0.2,0.4,0.6,0.7,0.9,1.0)
for step in grid_step:
symmetry = crystal.symmetry(space_group_symbol="P1")
structure = random_structure.xray_structure(space_group_info = symmetry.space_group_info(),
elements=["C"]*n_sites,
volume_per_atom=volume_per_atom,
random_u_iso=False)
fc = structure.structure_factors(d_min = d_min,
anomalous_flag=False,
algorithm="fft").f_calc()
manager = max_like_non_uniform.ordered_solvent_distribution(
structure = structure,
fo = fc,
grid_step = step)
f_water_dist = manager.fcalc_from_distribution()
### check phase compatibility with the symmetry:
centrics = f_water_dist.select_centric()
if(centrics.indices().size() > 0):
ideal = centrics.phase_transfer(centrics)
assert flex.max(flex.abs(ideal.data() - centrics.data())) < 1.e-6
###
#print "max = ", flex.max( flex.abs( f_water_dist.data() ) )
#print "min = ", flex.min( flex.abs( f_water_dist.data() ) )
#print "ave = ", flex.mean( flex.abs( f_water_dist.data() ) )
assert flex.max( flex.abs( f_water_dist.data() ) ) < 1.0
def test_r(space_group_info,
step = 0.6,
d_min = 4.0):
r = (-1.05,-0.1,0.0,1.05,0.1)
n_sym = space_group_info.type().group().n_smx()
if(n_sym != 8):
for x in r:
for y in r:
for z in r:
symmetry = crystal.symmetry(unit_cell = space_group_info.any_compatible_unit_cell(volume= 2000),
space_group_info = space_group_info)
#symmetry = crystal.symmetry(unit_cell=(11., 12., 13., 75., 85., 95.),
# space_group_symbol="P1")
#symmetry = crystal.symmetry(unit_cell=(11., 12., 13., 90., 90., 90.),
# space_group_symbol="p212121")
structure = xray.structure(crystal_symmetry=symmetry)
scatterer = xray.scatterer(
site = (x,y,z),
u = 0.1,
occupancy = 1.0,
scattering_type = "O")
structure.add_scatterer(scatterer)
fc = structure.structure_factors(d_min = d_min,
anomalous_flag=False,
algorithm="fft").f_calc()
manager = max_like_non_uniform.ordered_solvent_distribution(
structure = structure,
fo = fc,
grid_step = step)
f_water_dist = manager.fcalc_from_distribution()
### check phase compatibility with the symmetry:
centrics = f_water_dist.select_centric()
if(centrics.indices().size() > 0):
ideal = centrics.phase_transfer(centrics)
assert flex.max(flex.abs(ideal.data() - centrics.data())) < 1.e-6
###
#print "max = ", flex.max( flex.abs( f_water_dist.data() ) )
#print "min = ", flex.min( flex.abs( f_water_dist.data() ) )
#print "ave = ", flex.mean( flex.abs( f_water_dist.data() ) )
assert flex.max( flex.abs( f_water_dist.data() ) ) < 1.0
def test_r(space_group_info, step=0.6, d_min=4.0):
r = (-1.05, -0.1, 0.0, 1.05, 0.1)
n_sym = space_group_info.type().group().n_smx()
if (n_sym != 8):
for x in r:
for y in r:
for z in r:
symmetry = crystal.symmetry(
unit_cell=space_group_info.any_compatible_unit_cell(
volume=2000),
space_group_info=space_group_info)
#symmetry = crystal.symmetry(unit_cell=(11., 12., 13., 75., 85., 95.),
# space_group_symbol="P1")
#symmetry = crystal.symmetry(unit_cell=(11., 12., 13., 90., 90., 90.),
# space_group_symbol="p212121")
structure = xray.structure(crystal_symmetry=symmetry)
scatterer = xray.scatterer(site=(x, y, z),
u=0.1,
occupancy=1.0,
scattering_type="O")
structure.add_scatterer(scatterer)
fc = structure.structure_factors(d_min=d_min,
anomalous_flag=False,
algorithm="fft").f_calc()
manager = max_like_non_uniform.ordered_solvent_distribution(
structure=structure, fo=fc, grid_step=step)
f_water_dist = manager.fcalc_from_distribution()
### check phase compatibility with the symmetry:
centrics = f_water_dist.select_centric()
if (centrics.indices().size() > 0):
ideal = centrics.phase_transfer(centrics)
assert flex.max(
flex.abs(ideal.data() - centrics.data())) < 1.e-6
###
#print "max = ", flex.max( flex.abs( f_water_dist.data() ) )
#print "min = ", flex.min( flex.abs( f_water_dist.data() ) )
#print "ave = ", flex.mean( flex.abs( f_water_dist.data() ) )
assert flex.max(flex.abs(f_water_dist.data())) < 1.0
def test_less_one(space_group_info,
volume_per_atom = 100,
d_min = 1.8):
#symmetry = crystal.symmetry(space_group_symbol="p212121")
#space_group_info = symmetry.space_group_info()
#n_sym = space_group_info.type().group().n_smx()
for n_atoms in (1,10):
if(n_atoms == 1):
denom = 16.0
else:
denom = 4.0
for element in ("C","O","N"):
structure = random_structure.xray_structure(
space_group_info=space_group_info,
elements=[element]*n_atoms,
volume_per_atom=volume_per_atom,
random_u_iso=False)
fc = structure.structure_factors(d_min = d_min,
anomalous_flag = False,
algorithm = "fft").f_calc()
manager = max_like_non_uniform.ordered_solvent_distribution(
structure = structure,
fo = fc,
grid_step = fc.d_min()/denom)
f_water_dist = manager.fcalc_from_distribution()
### check phase compatibility with the symmetry:
centrics = f_water_dist.select_centric()
if(centrics.indices().size() > 0):
ideal = centrics.phase_transfer(centrics)
assert flex.max(flex.abs(ideal.data() - centrics.data())) < 1.e-6
###
#print "max = ", flex.max( flex.abs( f_water_dist.data() ) )
#print "min = ", flex.min( flex.abs( f_water_dist.data() ) )
#print "ave = ", flex.mean( flex.abs( f_water_dist.data() ) )
assert flex.max( flex.abs( f_water_dist.data() ) ) < 1.0
