def exercise_trigonometric_ff():
from math import cos, sin, pi
sgi = sgtbx.space_group_info("P1")
cs = sgi.any_compatible_crystal_symmetry(volume=1000)
miller_set = miller.build_set(cs, anomalous_flag=False, d_min=1)
miller_set = miller_set.select(flex.random_double(miller_set.size()) < 0.2)
for i in xrange(5):
sites = flex.random_double(9)
x1, x2, x3 = (matrix.col(sites[:3]), matrix.col(sites[3:6]), matrix.col(sites[6:]))
xs = xray.structure(crystal.special_position_settings(cs))
for x in (x1, x2, x3):
sc = xray.scatterer(site=x, scattering_type="const")
sc.flags.set_grad_site(True)
xs.add_scatterer(sc)
f_sq = structure_factors.f_calc_modulus_squared(xs)
for h in miller_set.indices():
h = matrix.col(h)
phi1, phi2, phi3 = 2 * pi * h.dot(x1), 2 * pi * h.dot(x2), 2 * pi * h.dot(x3)
fc_mod_sq = 3 + 2 * (cos(phi1 - phi2) + cos(phi2 - phi3) + cos(phi3 - phi1))
g = []
g.extend(-2 * (sin(phi1 - phi2) - sin(phi3 - phi1)) * 2 * pi * h)
g.extend(-2 * (sin(phi2 - phi3) - sin(phi1 - phi2)) * 2 * pi * h)
g.extend(-2 * (sin(phi3 - phi1) - sin(phi2 - phi3)) * 2 * pi * h)
grad_fc_mod_sq = g
f_sq.linearise(h)
assert approx_equal(f_sq.observable, fc_mod_sq)
assert approx_equal(f_sq.grad_observable, grad_fc_mod_sq)
def iass_as_xray_structure(self, iass):
ias_xray_structure = xray.structure(
crystal_symmetry = self.xray_structure.crystal_symmetry())
for ias in iass:
assert ias.status is not None
if(ias.status):
if(self.params.use_map):
site_cart = ias.peak_position_cart
b_iso = ias.b_iso
q = ias.q
else:
site_cart = ias.site_cart_predicted
b_iso = (ias.atom_1.b_iso + ias.atom_2.b_iso)*0.5
q = self.params.initial_ias_occupancy
if(b_iso is None):
b_iso = (ias.atom_1.b_iso + ias.atom_2.b_iso)*0.5
if(q is None):
q = self.params.initial_ias_occupancy
if(site_cart is None):
site_cart = ias.site_cart_predicted
assert [b_iso, q].count(None) == 0
if(site_cart is not None):
ias_scatterer = xray.scatterer(
label = ias.name,
scattering_type = ias.name,
site = self.xray_structure.unit_cell().fractionalize(site_cart),
u = adptbx.b_as_u(b_iso),
occupancy = q)
ias_xray_structure.add_scatterer(ias_scatterer)
ias_xray_structure.scattering_type_registry(
custom_dict = ias_scattering_dict)
return ias_xray_structure
def xray_structure(O, u_iso=0):
from cctbx import xray
from cctbx import crystal
return xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=O.unit_cell(), space_group_symbol="P1"),
scatterers=O.scatterers(u_iso=u_iso))
def move_sites_if_necessary_for_shelx_fvar_encoding(xray_structure):
from cctbx import xray
from scitbx import matrix
xs = xray_structure
scs = xs.scatterers().deep_copy()
sstab = xs.site_symmetry_table()
for i_sc in xs.special_position_indices():
site = scs[i_sc].site
ss = sstab.get(i_sc)
sos = sos_orig = ss.special_op_simplified()
fvars = [None]
coded_variables = sos.shelx_fvar_encoding(site=site, fvars=fvars)
if coded_variables is None:
site_0 = matrix.col(site).each_mod_short()
for u in unit_shifts_prioritized:
site = site_0 + matrix.col(u)
ss = xs.site_symmetry(site)
sos = ss.special_op_simplified()
coded_variables = sos.shelx_fvar_encoding(site=site, fvars=fvars)
if coded_variables is not None:
scs[i_sc].site = site
break
else:
raise_special_position_constraints_cannot_be_encoded(sos_orig)
result = xray.structure(
special_position_settings=xs,
scatterers=scs,
non_unit_occupancy_implies_min_distance_sym_equiv_zero=xs.non_unit_occupancy_implies_min_distance_sym_equiv_zero(),
scattering_type_registry=xs.scattering_type_registry(),
)
assert result.special_position_indices().all_eq(xs.special_position_indices())
return result
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 exercise_is_simple_interaction():
for space_group_symbol in ["P1", "P41"]:
for shifts in flex.nested_loop((-2, -2, -2), (2, 2, 2), False):
shifts = matrix.col(shifts)
structure = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=(10, 10, 20, 90, 90, 90),
space_group_symbol=space_group_symbol),
scatterers=flex.xray_scatterer([
xray.scatterer(label="O",
site=shifts + matrix.col((0, 0, 0))),
xray.scatterer(label="N",
site=shifts + matrix.col((0.5, 0.5, 0))),
xray.scatterer(label="C",
site=shifts + matrix.col((0.25, 0.25, 0)))
]))
asu_mappings = structure.asu_mappings(buffer_thickness=7)
pair_generator = crystal.neighbors_simple_pair_generator(
asu_mappings=asu_mappings, distance_cutoff=7)
simple_interactions = {}
for i_pair, pair in enumerate(pair_generator):
if (asu_mappings.is_simple_interaction(pair)):
assert asu_mappings_is_simple_interaction_emulation(
asu_mappings, pair)
key = (pair.i_seq, pair.j_seq)
assert simple_interactions.get(key, None) is None
simple_interactions[key] = 1
else:
assert not asu_mappings_is_simple_interaction_emulation(
asu_mappings, pair)
assert len(simple_interactions) == 2
assert simple_interactions[(0, 2)] == 1
assert simple_interactions[(1, 2)] == 1
def quartz():
return xray.structure(
crystal_symmetry=crystal.symmetry(
(5.01,5.01,5.47,90,90,120), "P6222"),
scatterers=flex.xray_scatterer([
xray.scatterer("Si", (1/2.,1/2.,1/3.)),
xray.scatterer("O", (0.197,-0.197,0.83333))]))
def demo():
"""
Result of ICSD query:
N * -Cr2O3-[R3-CH] Baster, M.;Bouree, F.;Kowalska, A.;Latacz, Z(2000)
C 4.961950 4.961950 13.597400 90.000000 90.000000 120.000000
S GRUP R -3 C
A Cr1 0.000000 0.000000 0.347570 0.000000
A O1 0.305830 0.000000 0.250000
"""
crystal_symmetry = crystal.symmetry(
unit_cell="4.961950 4.961950 13.597400 90.000000 90.000000 120.000000",
space_group_symbol="R -3 C")
scatterers = flex.xray_scatterer()
scatterers.append(xray.scatterer(
label="Cr1", site=(0.000000,0.000000,0.347570)))
scatterers.append(xray.scatterer(
label="O1", site=(0.305830,0.000000,0.250000)))
icsd_structure = xray.structure(
crystal_symmetry=crystal_symmetry,
scatterers=scatterers)
icsd_structure.show_summary().show_scatterers()
print
icsd_structure.show_distances(distance_cutoff=2.5)
print
primitive_structure = icsd_structure.primitive_setting()
primitive_structure.show_summary().show_scatterers()
print
p1_structure = primitive_structure.expand_to_p1()
p1_structure.show_summary().show_scatterers()
print
print "OK"
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 extract_structure(self, phase_nr=1):
"""This method tries to extract the crystal structure from the parsed pcrfile.
:returns: the extracted structure
:rtype: cctbx.xray.structure
"""
from cctbx import xray
from cctbx import crystal
from cctbx.array_family import flex
p = self.cfg['phases'][str(phase_nr)]
atoms = p['atoms']
unit_cell = [ p['a'], p['b'], p['c'], p['alpha'], p['beta'], p['gamma'] ]
special_position_settings=crystal.special_position_settings(
crystal_symmetry=crystal.symmetry(
unit_cell=unit_cell,
space_group_symbol=p['SYMB']))
scatterers = []
for k, a in atoms.iteritems():
scatterers.append(xray.scatterer(label=a['LABEL'],
scattering_type=a['NTYP'],
site=(a['X'], a['Y'], a['Z']),
b=a['B']))
scatterers_flex=flex.xray_scatterer(scatterers)
structure = xray.structure(special_position_settings=special_position_settings,
scatterers=scatterers_flex)
return structure.as_py_code()
def mg_structure_dict_to_cctbx_crystal_structure(d):
"""
Compatible with pymatgen Structure.to_dict() format
to a cctbx crystal structure object
"""
params = " ".join([
str(o) for o in [
d['lattice']['a'], d['lattice']['b'], d['lattice']['c'],
d['lattice']['alpha'], d['lattice']['beta'], d['lattice']['gamma']
]
])
unit_cell = uctbx.unit_cell(params)
symbol = 'P 1'
crystal_symmetry = crystal.symmetry(unit_cell=unit_cell,
space_group_symbol=symbol)
"""
site = tuple([0.0, 0.20, 0.3])
scatterers.append(xray.scatterer(label=lable, site=site, occupancy=occupancy)
crystal_structure = xray.structure(crystal_symmetry=crystal_symmetry, scatterers=scatterers)
"""
scatterers = flex.xray_scatterer()
for site in d['sites']:
abc = tuple(site['abc'])
for specie in site['species']:
label = specie['element'].encode('utf8')
occupancy = float(specie['occu'])
scatterers.append(
xray.scatterer(label=label, site=abc, occupancy=occupancy))
crystal_structure = xray.structure(crystal_symmetry=crystal_symmetry,
scatterers=scatterers)
return crystal_structure
def __init__(self,unitcell,spacegroup,scatterers):
self.sg=sgtbx.space_group_info(spacegroup)
self.uc=uctbx.unit_cell(unitcell)
self.scatt=scatterers
self.cctbx_scatterers=flex.xray_scatterer()
for s in self.scatt:
self.cctbx_scatterers.append(xray.scatterer(label=s.label,site=s.site,occupancy=s.occupancy,u=s.u_iso))
try:
#old cctbx version
xray.add_scatterers_ext(unit_cell=self.uc,
space_group=self.sg.group(),
scatterers=self.cctbx_scatterers,
site_symmetry_table=sgtbx.site_symmetry_table(),
site_symmetry_table_for_new=sgtbx.site_symmetry_table(),
min_distance_sym_equiv=0.5,
u_star_tolerance=0,
assert_min_distance_sym_equiv=True)
except:
# cctbx version >= 2011_04_06_0217
#print "Whoops, cctbx version 2011"
xray.add_scatterers_ext(unit_cell=self.uc,
space_group=self.sg.group(),
scatterers=self.cctbx_scatterers,
site_symmetry_table=sgtbx.site_symmetry_table(),
site_symmetry_table_for_new=sgtbx.site_symmetry_table(),
min_distance_sym_equiv=0.5,
u_star_tolerance=0,
assert_min_distance_sym_equiv=True,
non_unit_occupancy_implies_min_distance_sym_equiv_zero=False)
cs=crystal.symmetry(self.uc,spacegroup)
sp=crystal.special_position_settings(cs)
self.structure=xray.structure(sp,self.cctbx_scatterers)
self.structure_as_P1=self.structure.expand_to_p1()
def move_sites_if_necessary_for_shelx_fvar_encoding(xray_structure):
from cctbx import xray
from scitbx import matrix
xs = xray_structure
scs = xs.scatterers().deep_copy()
sstab = xs.site_symmetry_table()
for i_sc in xs.special_position_indices():
site = scs[i_sc].site
ss = sstab.get(i_sc)
sos = sos_orig = ss.special_op_simplified()
fvars = [None]
coded_variables = sos.shelx_fvar_encoding(site=site, fvars=fvars)
if (coded_variables is None):
site_0 = matrix.col(site).each_mod_short()
for u in unit_shifts_prioritized:
site = site_0 + matrix.col(u)
ss = xs.site_symmetry(site)
sos = ss.special_op_simplified()
coded_variables = sos.shelx_fvar_encoding(site=site,
fvars=fvars)
if (coded_variables is not None):
scs[i_sc].site = site
break
else:
raise_special_position_constraints_cannot_be_encoded(sos_orig)
result = xray.structure(
special_position_settings=xs,
scatterers=scs,
non_unit_occupancy_implies_min_distance_sym_equiv_zero=xs.
non_unit_occupancy_implies_min_distance_sym_equiv_zero(),
scattering_type_registry=xs.scattering_type_registry())
assert result.special_position_indices().all_eq(
xs.special_position_indices())
return result
def iass_as_xray_structure(self, iass):
ias_xray_structure = xray.structure(
crystal_symmetry = self.xray_structure.crystal_symmetry())
for ias in iass:
assert ias.status is not None
if(ias.status):
if(self.params.use_map):
site_cart = ias.peak_position_cart
b_iso = ias.b_iso
q = ias.q
else:
site_cart = ias.site_cart_predicted
b_iso = (ias.atom_1.b_iso + ias.atom_2.b_iso)*0.5
q = self.params.initial_ias_occupancy
if(b_iso is None):
b_iso = (ias.atom_1.b_iso + ias.atom_2.b_iso)*0.5
if(q is None):
q = self.params.initial_ias_occupancy
if(site_cart is None):
site_cart = ias.site_cart_predicted
assert [b_iso, q].count(None) == 0
if(site_cart is not None):
ias_scatterer = xray.scatterer(
label = ias.name,
scattering_type = ias.name,
site = self.xray_structure.unit_cell().fractionalize(site_cart),
u = adptbx.b_as_u(b_iso),
occupancy = q)
ias_xray_structure.add_scatterer(ias_scatterer)
ias_xray_structure.scattering_type_registry(
custom_dict = ias_scattering_dict)
return ias_xray_structure
def add_new_solvent(self):
b_solv = self.params.b_iso
new_scatterers = flex.xray_scatterer(
self.sites.size(),
xray.scatterer(occupancy = self.params.occupancy,
b = b_solv,
scattering_type = self.params.scattering_type,
label = 'HOH'))
new_scatterers.set_sites(self.sites)
solvent_xray_structure = xray.structure(
special_position_settings = self.model.xray_structure,
scatterers = new_scatterers)
xrs_sol = self.model.xray_structure.select(self.model.solvent_selection())
xrs_mac = self.model.xray_structure.select(~self.model.solvent_selection())
xrs_sol = xrs_sol.concatenate(other = solvent_xray_structure)
sol_sel = flex.bool(xrs_mac.scatterers().size(), False)
sol_sel.extend( flex.bool(xrs_sol.scatterers().size(), True) )
self.model.add_solvent(
solvent_xray_structure = solvent_xray_structure,
residue_name = self.params.output_residue_name,
atom_name = self.params.output_atom_name,
chain_id = self.params.output_chain_id,
refine_occupancies = self.params.refine_occupancies,
refine_adp = self.params.new_solvent)
self.fmodel.update_xray_structure(
xray_structure = self.model.xray_structure,
update_f_calc = False)
def exercise_intersection():
sites_frac = flex.vec3_double([
(0.02,0.10,0.02),
(0.10,0.02,0.40),
(0.98,0.10,0.60),
(0.10,0.98,0.80),
(0.20,0.50,0.98)])
from cctbx import xray
xray_structure = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=(30,30,50,90,90,120),
space_group_symbol="P1"),
scatterers=flex.xray_scatterer([
xray.scatterer(label=str(i), scattering_type="Si", site=site_frac)
for i,site_frac in enumerate(sites_frac)]))
d_min = 0.7
f_calc = xray_structure.structure_factors(d_min=d_min).f_calc()
fft_map = f_calc.fft_map(resolution_factor=1/6.)
fft_map.apply_sigma_scaling()
density_map = fft_map.real_map_unpadded()
#
cm1 = xray_structure.center_of_mass()
cm2 = maptbx.center_of_mass(map_data=density_map, unit_cell=xray_structure.unit_cell(),
cutoff=20) #large cutoff to make map look like point scattereres
assert approx_equal(cm1, cm2, 0.1)
def __init__(self, n_runs, **kwds):
libtbx.adopt_optional_init_args(self, kwds)
self.n_runs = n_runs
self.crystal_symmetry = crystal.symmetry(
unit_cell=uctbx.unit_cell((5.1534, 5.1534, 8.6522, 90, 90, 120)),
space_group_symbol='Hall: P 6c')
self.structure = xray.structure(
self.crystal_symmetry.special_position_settings(),
flex.xray_scatterer((
xray.scatterer('K1',
site=(0, 0, -0.00195),
u=self.u_cif_as_u_star((0.02427, 0.02427, 0.02379,
0.01214, 0.00000, 0.00000))),
xray.scatterer('S1',
site=(1/3, 2/3, 0.204215),
u=self.u_cif_as_u_star((0.01423, 0.01423, 0.01496,
0.00712, 0.00000, 0.00000 ))),
xray.scatterer('Li1',
site=(1/3, 2/3, 0.815681),
u=self.u_cif_as_u_star((0.02132, 0.02132, 0.02256,
0.01066, 0.00000, 0.00000 ))),
xray.scatterer('O1',
site=(1/3, 2/3, 0.035931),
u=self.u_cif_as_u_star((0.06532, 0.06532, 0.01669,
0.03266, 0.00000, 0.00000 ))),
xray.scatterer('O2',
site=(0.343810, 0.941658, 0.258405),
u=self.u_cif_as_u_star((0.02639, 0.02079, 0.05284,
0.01194, -0.00053,-0.01180 )))
)))
mi = self.crystal_symmetry.build_miller_set(anomalous_flag=False,
d_min=0.5)
fo_sq = mi.structure_factors_from_scatterers(
self.structure, algorithm="direct").f_calc().norm()
self.fo_sq = fo_sq.customized_copy(sigmas=flex.double(fo_sq.size(), 1))
def add_new_solvent(self):
b_solv = self.params.b_iso
new_scatterers = flex.xray_scatterer(
self.sites.size(),
xray.scatterer(occupancy=self.params.occupancy,
b=b_solv,
scattering_type=self.params.scattering_type,
label='HOH'))
new_scatterers.set_sites(self.sites)
solvent_xray_structure = xray.structure(
special_position_settings=self.model.xray_structure,
scatterers=new_scatterers)
xrs_sol = self.model.xray_structure.select(
self.model.solvent_selection())
xrs_mac = self.model.xray_structure.select(
~self.model.solvent_selection())
xrs_sol = xrs_sol.concatenate(other=solvent_xray_structure)
sol_sel = flex.bool(xrs_mac.scatterers().size(), False)
sol_sel.extend(flex.bool(xrs_sol.scatterers().size(), True))
self.model.add_solvent(
solvent_xray_structure=solvent_xray_structure,
residue_name=self.params.output_residue_name,
atom_name=self.params.output_atom_name,
chain_id=self.params.output_chain_id,
refine_occupancies=self.params.refine_occupancies,
refine_adp=self.params.new_solvent)
self.fmodel.update_xray_structure(
xray_structure=self.model.xray_structure, update_f_calc=False)
def test_spacegroup_tidy_pickling():
quartz_structure = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=(5.01,5.01,5.47,90,90,120),
space_group_symbol="P6222"),
scatterers=flex.xray_scatterer(
[
xray.scatterer(label="Si", site=(1/2.,1/2.,1/3.), u=0.2),
xray.scatterer(label="O", site=(0.197,-0.197,0.83333), u=0)
])
)
asu_mappings = quartz_structure.asu_mappings(buffer_thickness=2)
pair_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
pair_asu_table.add_all_pairs(distance_cutoff=1.7)
pair_sym_table = pair_asu_table.extract_pair_sym_table()
new_asu_mappings = quartz_structure.asu_mappings(buffer_thickness=5)
new_pair_asu_table = crystal.pair_asu_table(asu_mappings=new_asu_mappings)
new_pair_asu_table.add_pair_sym_table(sym_table=pair_sym_table)
spg = new_pair_asu_table.asu_mappings().space_group()
pspg = pickle.loads(pickle.dumps(spg))
mstr = ""
pmstr = ""
for rt in spg.all_ops():
mstr += rt.r().as_xyz() + "\n"
for rt in pspg.all_ops():
pmstr += rt.r().as_xyz() + "\n"
assert mstr == pmstr
def extract_structure(self, phase_nr=1):
"""This method tries to extract the crystal structure from the parsed pcrfile.
:returns: the extracted structure
:rtype: cctbx.xray.structure
"""
from cctbx import xray
from cctbx import crystal
from cctbx.array_family import flex
p = self.cfg['phases'][str(phase_nr)]
atoms = p['atoms']
unit_cell = [p['a'], p['b'], p['c'], p['alpha'], p['beta'], p['gamma']]
special_position_settings = crystal.special_position_settings(
crystal_symmetry=crystal.symmetry(unit_cell=unit_cell,
space_group_symbol=p['SYMB']))
scatterers = []
for k, a in atoms.iteritems():
scatterers.append(
xray.scatterer(label=a['LABEL'],
scattering_type=a['NTYP'],
site=(a['X'], a['Y'], a['Z']),
b=a['B']))
scatterers_flex = flex.xray_scatterer(scatterers)
structure = xray.structure(
special_position_settings=special_position_settings,
scatterers=scatterers_flex)
return structure.as_py_code()
def exercise_trigonometric_ff():
from math import cos, sin, pi
sgi = sgtbx.space_group_info("P1")
cs = sgi.any_compatible_crystal_symmetry(volume=1000)
miller_set = miller.build_set(cs, anomalous_flag=False, d_min=1)
miller_set = miller_set.select(flex.random_double(miller_set.size()) < 0.2)
for i in range(5):
sites = flex.random_double(9)
x1, x2, x3 = (matrix.col(sites[:3]), matrix.col(sites[3:6]),
matrix.col(sites[6:]))
xs = xray.structure(crystal.special_position_settings(cs))
for x in (x1, x2, x3):
sc = xray.scatterer(site=x, scattering_type="const")
sc.flags.set_grad_site(True)
xs.add_scatterer(sc)
f_sq = structure_factors.f_calc_modulus_squared(xs)
for h in miller_set.indices():
h = matrix.col(h)
phi1, phi2, phi3 = 2 * pi * h.dot(x1), 2 * pi * h.dot(
x2), 2 * pi * h.dot(x3)
fc_mod_sq = 3 + 2 * (cos(phi1 - phi2) + cos(phi2 - phi3) +
cos(phi3 - phi1))
g = []
g.extend(-2 * (sin(phi1 - phi2) - sin(phi3 - phi1)) * 2 * pi * h)
g.extend(-2 * (sin(phi2 - phi3) - sin(phi1 - phi2)) * 2 * pi * h)
g.extend(-2 * (sin(phi3 - phi1) - sin(phi2 - phi3)) * 2 * pi * h)
grad_fc_mod_sq = g
f_sq.linearise(h)
assert approx_equal(f_sq.observable, fc_mod_sq)
assert approx_equal(f_sq.grad_observable, grad_fc_mod_sq)
def _append_to_model(self):
mean_b = flex.mean(self.model.get_hierarchy().atoms().extract_b())
self.ma.add(" new water B factors will be set to mean B: %8.3f" %
mean_b)
sp = crystal.special_position_settings(self.model.crystal_symmetry())
scatterers = flex.xray_scatterer()
for site_frac in self.sites_frac_water:
sc = xray.scatterer(label="O",
site=site_frac,
u=adptbx.b_as_u(mean_b),
occupancy=1.0)
scatterers.append(sc)
xrs_water = xray.structure(sp, scatterers)
#
chain_ids_taken = []
for chain in self.model.get_hierarchy().chains():
chain_ids_taken.append(chain.id)
unique_taken = list(set(chain_ids_taken))
if (len(unique_taken) == 1):
solvent_chain = unique_taken[0]
else:
for solvent_chain in all_chain_ids():
if (not solvent_chain in chain_ids_taken):
break
self.ma.add(" new water will have chain ID: '%s'" % solvent_chain)
#
self.model.add_solvent(solvent_xray_structure=xrs_water,
atom_name="O",
residue_name="HOH",
chain_id=solvent_chain,
refine_adp="isotropic")
def compare_with_cctbx_structure_factors(n_scatt, n_refl, output_lines):
from cctbx import xray
from cctbx import miller
from cctbx import crystal
from cctbx.array_family import flex
crystal_symmetry = crystal.symmetry(unit_cell=(11, 12, 13, 90, 90, 90),
space_group_symbol="P1")
scatterers = flex.xray_scatterer()
miller_indices = flex.miller_index()
f_calc = flex.complex_double()
for line in output_lines:
flds = line.split()
assert len(flds) in [4, 5]
if (len(flds) == 4):
x, y, z, b_iso = [float(s) for s in flds]
scatterers.append(
xray.scatterer(site=(x, y, z),
b=b_iso,
scattering_type="const"))
else:
miller_indices.append([int(s) for s in flds[:3]])
f_calc.append(complex(float(flds[3]), float(flds[4])))
assert scatterers.size() == n_scatt
assert miller_indices.size() == n_refl
xs = xray.structure(crystal_symmetry=crystal_symmetry,
scatterers=scatterers)
fc = miller_array = miller.set(crystal_symmetry=crystal_symmetry,
indices=miller_indices,
anomalous_flag=False).array(data=f_calc)
fc2 = fc.structure_factors_from_scatterers(xray_structure=xs,
algorithm="direct",
cos_sin_table=False).f_calc()
for f1, f2 in zip(fc.data(), fc2.data()):
assert approx_equal(f1, f2, eps=1e-5)
def iucr_structure(self):
#self._fragments = [Fragment(self._scatterers)] #?
self._iucr_structure = xray.structure(
special_position_settings = self._special_position_settings,
scatterers = self._scatterers
)
return self._iucr_structure
def loop(self):
for i_position in xrange(self.wyckoff_table.size()):
site_symmetry_i = self.wyckoff_table.random_site_symmetry(
special_position_settings=self.special_position_settings,
i_position=i_position)
equiv_sites_i = sgtbx.sym_equiv_sites(site_symmetry_i)
for j_position in xrange(self.wyckoff_table.size()):
for n_trial in xrange(self.max_trials_per_position):
site_j = self.wyckoff_table.random_site_symmetry(
special_position_settings=self.
special_position_settings,
i_position=j_position).exact_site()
dist_info = sgtbx.min_sym_equiv_distance_info(
equiv_sites_i, site_j)
if (dist_info.dist() > self.min_cross_distance):
structure = xray.structure(
special_position_settings=self.
special_position_settings,
scatterers=flex.xray_scatterer([
xray.scatterer(
scattering_type=self.scattering_type,
site=site) for site in
[site_symmetry_i.exact_site(), site_j]
]))
yield structure, dist_info.dist()
break
def fcalc_from_pdb(resolution,
algorithm=None,
wavelength=0.9,
anom=True,
ucell=None,
symbol=None,
as_amplitudes=True):
pdb_lines = 'HEADER TEST\nCRYST1 50.000 60.000 70.000 90.00 90.00 90.00 P 1\nATOM 1 O HOH A 1 56.829 2.920 55.702 1.00 20.00 O\nATOM 2 O HOH A 2 49.515 35.149 37.665 1.00 20.00 O\nATOM 3 O HOH A 3 52.667 17.794 69.925 1.00 20.00 O\nATOM 4 O HOH A 4 40.986 20.409 18.309 1.00 20.00 O\nATOM 5 O HOH A 5 46.896 37.790 41.629 1.00 20.00 O\nATOM 6 SED MSE A 6 1.000 2.000 3.000 1.00 20.00 SE\nEND\n'
from iotbx import pdb
pdb_inp = pdb.input(source_info=None, lines=pdb_lines)
xray_structure = pdb_inp.xray_structure_simple()
if ucell is not None:
assert symbol is not None
from cctbx.xray import structure
from cctbx import crystal
crystal_sym = crystal.symmetry(unit_cell=ucell,
space_group_symbol=symbol)
xray_structure = structure(scatterers=(xray_structure.scatterers()),
crystal_symmetry=crystal_sym)
scatterers = xray_structure.scatterers()
if anom:
from cctbx.eltbx import henke
for sc in scatterers:
expected_henke = henke.table(
sc.element_symbol()).at_angstrom(wavelength)
sc.fp = expected_henke.fp()
sc.fdp = expected_henke.fdp()
primitive_xray_structure = xray_structure.primitive_setting()
P1_primitive_xray_structure = primitive_xray_structure.expand_to_p1()
fcalc = P1_primitive_xray_structure.structure_factors(
d_min=resolution, anomalous_flag=anom, algorithm=algorithm).f_calc()
if as_amplitudes:
fcalc = fcalc.amplitudes().set_observation_type_xray_amplitude()
return fcalc
def __init__(self, n_runs, **kwds):
libtbx.adopt_optional_init_args(self, kwds)
self.n_runs = n_runs
self.crystal_symmetry = crystal.symmetry(
unit_cell=uctbx.unit_cell((5.1534, 5.1534, 8.6522, 90, 90, 120)),
space_group_symbol='Hall: P 6c')
self.structure = xray.structure(
self.crystal_symmetry.special_position_settings(),
flex.xray_scatterer((
xray.scatterer('K1',
site=(0, 0, -0.00195),
u=self.u_cif_as_u_star((0.02427, 0.02427, 0.02379,
0.01214, 0.00000, 0.00000))),
xray.scatterer('S1',
site=(1/3, 2/3, 0.204215),
u=self.u_cif_as_u_star((0.01423, 0.01423, 0.01496,
0.00712, 0.00000, 0.00000 ))),
xray.scatterer('Li1',
site=(1/3, 2/3, 0.815681),
u=self.u_cif_as_u_star((0.02132, 0.02132, 0.02256,
0.01066, 0.00000, 0.00000 ))),
xray.scatterer('O1',
site=(1/3, 2/3, 0.035931),
u=self.u_cif_as_u_star((0.06532, 0.06532, 0.01669,
0.03266, 0.00000, 0.00000 ))),
xray.scatterer('O2',
site=(0.343810, 0.941658, 0.258405),
u=self.u_cif_as_u_star((0.02639, 0.02079, 0.05284,
0.01194, -0.00053,-0.01180 )))
)))
mi = self.crystal_symmetry.build_miller_set(anomalous_flag=False,
d_min=0.5)
fo_sq = mi.structure_factors_from_scatterers(
self.structure, algorithm="direct").f_calc().norm()
self.fo_sq = fo_sq.customized_copy(sigmas=flex.double(fo_sq.size(), 1))
def _find_peaks(self, min_peak_peak_distance=1.5):
cg = maptbx.crystal_gridding(
space_group_info=self.model.crystal_symmetry().space_group_info(),
symmetry_flags=maptbx.use_space_group_symmetry,
unit_cell=self.unit_cell,
pre_determined_n_real=self.map_data.accessor().all())
cgt = maptbx.crystal_gridding_tags(gridding=cg)
peak_search_parameters = maptbx.peak_search_parameters(
peak_search_level=3,
max_peaks=0,
peak_cutoff=self.cutoff,
interpolate=True,
min_distance_sym_equiv=0,
general_positions_only=False, # ???????XXXXXXXXXXXXXX
min_cross_distance=min_peak_peak_distance,
min_cubicle_edge=5)
psr = cgt.peak_search(parameters=peak_search_parameters,
map=self.map_data).all(max_clusters=99999999)
# Convert peaks into water xray.structure
mean_b = flex.mean(self.model.get_hierarchy().atoms().extract_b())
sp = crystal.special_position_settings(self.model.crystal_symmetry())
scatterers = flex.xray_scatterer()
for site_frac in psr.sites():
sc = xray.scatterer(label="O",
site=site_frac,
u=adptbx.b_as_u(mean_b),
occupancy=1.0)
scatterers.append(sc)
self.xrs_water = xray.structure(sp, scatterers)
#
self.ma.add(" total peaks found: %d" %
self.xrs_water.scatterers().size())
self.ma.add(" B factors set to : %8.3f" % mean_b)
if (self.debug): self._write_pdb_file(file_name_prefix="hoh_all_peaks")
def exercise_is_simple_interaction():
for space_group_symbol in ["P1", "P41"]:
for shifts in flex.nested_loop((-2,-2,-2),(2,2,2),False):
shifts = matrix.col(shifts)
structure = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=(10,10,20,90,90,90),
space_group_symbol=space_group_symbol),
scatterers=flex.xray_scatterer([
xray.scatterer(label="O", site=shifts+matrix.col((0,0,0))),
xray.scatterer(label="N", site=shifts+matrix.col((0.5,0.5,0))),
xray.scatterer(label="C", site=shifts+matrix.col((0.25,0.25,0)))]))
asu_mappings = structure.asu_mappings(buffer_thickness=7)
pair_generator = crystal.neighbors_simple_pair_generator(
asu_mappings=asu_mappings,
distance_cutoff=7)
simple_interactions = {}
for i_pair,pair in enumerate(pair_generator):
if (asu_mappings.is_simple_interaction(pair)):
assert asu_mappings_is_simple_interaction_emulation(
asu_mappings, pair)
key = (pair.i_seq,pair.j_seq)
assert simple_interactions.get(key, None) is None
simple_interactions[key] = 1
else:
assert not asu_mappings_is_simple_interaction_emulation(
asu_mappings, pair)
assert len(simple_interactions) == 2
assert simple_interactions[(0,2)] == 1
assert simple_interactions[(1,2)] == 1
def exercise_rigid_pivoted_rotatable():
uc = uctbx.unit_cell((1, 1, 1))
xs = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=uc,
space_group_symbol='hall: P 2x 2y'),
scatterers=flex.xray_scatterer(( #triangle
xray.scatterer('C0', site=(0,0,0)),
xray.scatterer('C1', site=(0,2,0)),
xray.scatterer('C2', site=(1,1,0)),
)))
r = constraints.ext.reparametrisation(xs.unit_cell())
sc = xs.scatterers()
pivot = r.add(constraints.independent_site_parameter, sc[0])
pivot_neighbour = r.add(constraints.independent_site_parameter, sc[1])
azimuth = r.add(constraints.independent_scalar_parameter,
value=pi/2, variable=True)
size = r.add(constraints.independent_scalar_parameter,
value=1, variable=False)
rg = r.add(constraints.rigid_pivoted_rotatable_group,
pivot=pivot,
pivot_neighbour=pivot_neighbour,
azimuth=azimuth,
size=size,
scatterers=(sc[1], sc[2]))
site_proxy = r.add(constraints.rigid_site_proxy, rg, 1)
r.finalise()
r.linearise()
r.store()
#check that proxy and the final results are the same...
assert approx_equal(
uc.distance(col(site_proxy.value), col(sc[2].site)), 0, eps=1e-15)
#rotation happens around the center of gravity
assert approx_equal(
uc.distance(col((0,1,1)), col(sc[2].site)), 0, eps=1e-15)
def xray_structure(O, u_iso=0):
from cctbx import xray
from cctbx import crystal
return xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=O.unit_cell(), space_group_symbol="P1"),
scatterers=O.scatterers(u_iso=u_iso))
def test_addition_scatterers():
'''
Test overlaps when adding and moving scatterers
Test water scatterers with and without labels
'''
clashes = get_clashes_result(raw_records=raw_records_3)
results = clashes.get_results()
assert(results.n_clashes == 3)
assert approx_equal(results.clashscore, 1000, eps=0.1)
# Add water scatterers
model = clashes.model
xrs = model.get_xray_structure()
new_scatterers = flex.xray_scatterer(
xrs.scatterers().size(),
xray.scatterer(occupancy = 1, b = 10, scattering_type = "O"))
new_sites_frac = xrs.unit_cell().fractionalize(xrs.sites_cart()+[0.5,0,0])
new_scatterers.set_sites(new_sites_frac)
new_xrs = xray.structure(
special_position_settings = xrs,
scatterers = new_scatterers)
model.add_solvent(
solvent_xray_structure = new_xrs,
refine_occupancies = False,
refine_adp = "isotropic")
pnps = pnp.manager(model = model)
clashes = pnps.get_clashes()
results = clashes.get_results()
assert(results.n_clashes == 15)
assert approx_equal(results.clashscore, 2500, eps=5)
def exercise_SFweight_spline_core(structure, d_min, verbose=0):
structure.scattering_type_registry(d_min=d_min)
f_obs = abs(structure.structure_factors(
d_min=d_min, anomalous_flag=False).f_calc())
if (0 or verbose):
f_obs.show_summary()
f_obs = miller.array(
miller_set=f_obs,
data=f_obs.data(),
sigmas=flex.sqrt(f_obs.data()))
partial_structure = xray.structure(
crystal_symmetry=structure,
scatterers=structure.scatterers()[:-2])
f_calc = f_obs.structure_factors_from_scatterers(
xray_structure=partial_structure).f_calc()
test_set_flags = (flex.random_double(size=f_obs.indices().size()) < 0.1)
sfweight = clipper.SFweight_spline_interface(
unit_cell=f_obs.unit_cell(),
space_group=f_obs.space_group(),
miller_indices=f_obs.indices(),
anomalous_flag=f_obs.anomalous_flag(),
f_obs_data=f_obs.data(),
f_obs_sigmas=f_obs.sigmas(),
f_calc=f_calc.data(),
test_set_flags=test_set_flags,
n_refln=f_obs.indices().size()//10,
n_param=20)
if (0 or verbose):
print "number_of_spline_parameters:",sfweight.number_of_spline_parameters()
print "mean fb: %.8g" % flex.mean(flex.abs(sfweight.fb()))
print "mean fd: %.8g" % flex.mean(flex.abs(sfweight.fd()))
print "mean phi: %.8g" % flex.mean(sfweight.centroid_phases())
print "mean fom: %.8g" % flex.mean(sfweight.figures_of_merit())
return sfweight
def __init__(self,
space_group=SpaceGroup('P 1'),
lattice=Lattice(1.0, 1.0, 1.0, 90.0, 90.0, 90.0),
sites=[]):
"""
Crystal object.
Functions as a wrapper to a cctbx xray.structure object,
but adds additional variables and functionality.
Core object of this package.
Input:
SpaceGroup space_group space group for the current crystal
List of Site objects sites List of Site objects.
Warning:
'crystal_structure' must be given,
or 'space_group', 'lattice', and 'sites' must be given,
or creation of the crystal will fail.
"""
try:
crystal_symmetry = crystal.symmetry(
unit_cell=str(lattice),
space_group_symbol=space_group.cctbx_name)
except Exception as e:
raise SymmetryError(
"SpaceGroup {s} is incompatible with Lattice -> {l} cctbx error {e}"
.format(l=str(lattice), s=SpaceGroup.cctbx_name, e=e))
scatterers = flex.xray_scatterer()
for i, site in enumerate(sites):
# the element name can be pulled from scatterer via the s.element_symbol() method (if it's an element!!!)
# example: 'atom-b-12',or 'vacancy-c-3'
# we need to set the scattering_type so we can freely use the label to store metadata
#scattering_type = something
#scatterers.append(xray.scatterer(label=atom.name, site=tuple(atom.abc), occupancy=atom.occupancy), scattering_type=atom.name)
#Method #2
# explicitly add metadata to _meta
st_temp, dash, num = site.label.partition("-")
if dash == "-":
k = site.label
else:
k = "-".join([site.label, str(i)])
# problems here not sure what's up
k = str(k)
# print "label = ", k, ' type of label = ', type(k)
# print "site = ", tuple(site.abc)
# print "occupancy = ", site.occupancy
scatterers.append(
xray.scatterer(label=k,
site=tuple(site.abc),
occupancy=site.occupancy))
# Test for coherency of Lattice and SpaceGroup
self.crystal_structure = xray.structure(
crystal_symmetry=crystal_symmetry, scatterers=scatterers)
def as_xray_structure(self, min_distance_sym_equiv=0.5):
result = xray.structure(
special_position_settings=crystal.special_position_settings(
crystal_symmetry=self.crystal_symmetry(),
min_distance_sym_equiv=min_distance_sym_equiv))
for atm in self.atoms:
result.add_scatterer(atm.as_xray_scatterer())
return result
def get_xrs():
crystal_symmetry = crystal.symmetry(
unit_cell=(10,10,10,90,90,90),
space_group_symbol="P 1")
return xray.structure(
crystal_symmetry=crystal_symmetry,
scatterers=flex.xray_scatterer([
xray.scatterer(label="C", site=(0,0,0))]))
def as_xray_structure(self, min_distance_sym_equiv=0.5):
result = xray.structure(
special_position_settings=crystal.special_position_settings(
crystal_symmetry=self.crystal_symmetry(),
min_distance_sym_equiv=min_distance_sym_equiv))
for atm in self.atoms:
result.add_scatterer(atm.as_xray_scatterer())
return result
def exercise_2():
symmetry = crystal.symmetry(
unit_cell=(5.67, 10.37, 10.37, 90, 135.49, 90),
space_group_symbol="C2")
structure = xray.structure(crystal_symmetry=symmetry)
atmrad = flex.double()
xyzf = flex.vec3_double()
for k in xrange(100):
scatterer = xray.scatterer(
site = ((1.+k*abs(math.sin(k)))/1000.0,
(1.+k*abs(math.cos(k)))/1000.0,
(1.+ k)/1000.0),
scattering_type = "C")
structure.add_scatterer(scatterer)
atmrad.append(van_der_waals_radii.vdw.table[scatterer.element_symbol()])
xyzf.append(scatterer.site)
miller_set = miller.build_set(
crystal_symmetry=structure,
d_min=1.0,
anomalous_flag=False)
step = 0.5
crystal_gridding = maptbx.crystal_gridding(
unit_cell=structure.unit_cell(),
step=step)
nxyz = crystal_gridding.n_real()
shrink_truncation_radius = 1.0
solvent_radius = 1.0
m1 = around_atoms(
structure.unit_cell(),
structure.space_group().order_z(),
structure.sites_frac(),
atmrad,
nxyz,
solvent_radius,
shrink_truncation_radius)
assert m1.solvent_radius == 1
assert m1.shrink_truncation_radius == 1
assert flex.max(m1.data) == 1
assert flex.min(m1.data) == 0
assert m1.data.size() == m1.data.count(1) + m1.data.count(0)
m2 = mmtbx.masks.bulk_solvent(
xray_structure=structure,
gridding_n_real=nxyz,
ignore_zero_occupancy_atoms = False,
solvent_radius=solvent_radius,
shrink_truncation_radius=shrink_truncation_radius)
assert m2.data.all_eq(m1.data)
m3 = mmtbx.masks.bulk_solvent(
xray_structure=structure,
grid_step=step,
ignore_zero_occupancy_atoms = False,
solvent_radius=solvent_radius,
shrink_truncation_radius=shrink_truncation_radius)
assert m3.data.all_eq(m1.data)
f_mask2 = m2.structure_factors(miller_set=miller_set)
f_mask3 = m3.structure_factors(miller_set=miller_set)
assert approx_equal(f_mask2.data(), f_mask3.data())
assert approx_equal(flex.sum(flex.abs(f_mask3.data())), 1095.17999134)
def exercise_real_space_refinement(verbose):
if (verbose):
out = sys.stdout
else:
out = StringIO()
out_of_bounds_clamp = maptbx.out_of_bounds_clamp(0)
out_of_bounds_raise = maptbx.out_of_bounds_raise()
crystal_symmetry = crystal.symmetry(unit_cell=(10, 10, 10, 90, 90, 90),
space_group_symbol="P 1")
xray_structure = xray.structure(crystal_symmetry=crystal_symmetry,
scatterers=flex.xray_scatterer([
xray.scatterer(label="C",
site=(0, 0, 0))
]))
miller_set = miller.build_set(crystal_symmetry=crystal_symmetry,
anomalous_flag=False,
d_min=1)
f_calc = miller_set.structure_factors_from_scatterers(
xray_structure=xray_structure).f_calc()
fft_map = f_calc.fft_map()
fft_map.apply_sigma_scaling()
real_map = fft_map.real_map_unpadded()
#### unit_cell test
delta_h = .005
basic_map = maptbx.basic_map(
maptbx.basic_map_unit_cell_flag(), real_map, real_map.focus(),
crystal_symmetry.unit_cell().orthogonalization_matrix(),
out_of_bounds_clamp.as_handle(), crystal_symmetry.unit_cell())
testing_function_for_rsfit(basic_map, delta_h, xray_structure, out)
### non_symmetric test
#
minfrac = crystal_symmetry.unit_cell().fractionalize((-5, -5, -5))
maxfrac = crystal_symmetry.unit_cell().fractionalize((5, 5, 5))
gridding_first = [ifloor(n * b) for n, b in zip(fft_map.n_real(), minfrac)]
gridding_last = [iceil(n * b) for n, b in zip(fft_map.n_real(), maxfrac)]
data = maptbx.copy(real_map, gridding_first, gridding_last)
#
basic_map = maptbx.basic_map(
maptbx.basic_map_non_symmetric_flag(), data, fft_map.n_real(),
crystal_symmetry.unit_cell().orthogonalization_matrix(),
out_of_bounds_clamp.as_handle(), crystal_symmetry.unit_cell())
testing_function_for_rsfit(basic_map, delta_h, xray_structure, out)
### asu test
#
minfrac = crystal_symmetry.unit_cell().fractionalize((0, 0, 0))
maxfrac = crystal_symmetry.unit_cell().fractionalize((10, 10, 10))
gridding_first = [ifloor(n * b) for n, b in zip(fft_map.n_real(), minfrac)]
gridding_last = [iceil(n * b) for n, b in zip(fft_map.n_real(), maxfrac)]
data = maptbx.copy(real_map, gridding_first, gridding_last)
#
basic_map = maptbx.basic_map(
maptbx.basic_map_asu_flag(), data, crystal_symmetry.space_group(),
crystal_symmetry.direct_space_asu().as_float_asu(), real_map.focus(),
crystal_symmetry.unit_cell().orthogonalization_matrix(),
out_of_bounds_clamp.as_handle(), crystal_symmetry.unit_cell(), 0.5,
True)
testing_function_for_rsfit(basic_map, delta_h, xray_structure, out)
def __init__(self,
xray_structure,
solvent_radius,
shrink_truncation_radius,
ignore_hydrogen_atoms=False,
crystal_gridding=None,
grid_step=None,
d_min=None,
resolution_factor=1 / 4,
atom_radii_table=None,
use_space_group_symmetry=False):
self.xray_structure = xray_structure
if crystal_gridding is None:
self.crystal_gridding = maptbx.crystal_gridding(
unit_cell=xray_structure.unit_cell(),
space_group_info=xray_structure.space_group_info(),
step=grid_step,
d_min=d_min,
resolution_factor=resolution_factor,
symmetry_flags=sgtbx.search_symmetry_flags(
use_space_group_symmetry=use_space_group_symmetry))
else:
self.crystal_gridding = crystal_gridding
if use_space_group_symmetry:
atom_radii = cctbx.masks.vdw_radii(
xray_structure, table=atom_radii_table).atom_radii
asu_mappings = xray_structure.asu_mappings(
buffer_thickness=flex.max(atom_radii) + solvent_radius)
scatterers_asu_plus_buffer = flex.xray_scatterer()
frac = xray_structure.unit_cell().fractionalize
for sc, mappings in zip(xray_structure.scatterers(),
asu_mappings.mappings()):
for mapping in mappings:
scatterers_asu_plus_buffer.append(
sc.customized_copy(site=frac(mapping.mapped_site())))
xs = xray.structure(crystal_symmetry=xray_structure,
scatterers=scatterers_asu_plus_buffer)
else:
xs = xray_structure.expand_to_p1()
self.vdw_radii = cctbx.masks.vdw_radii(xs, table=atom_radii_table)
self.mask = cctbx.masks.around_atoms(
unit_cell=xs.unit_cell(),
space_group_order_z=xs.space_group().order_z(),
sites_frac=xs.sites_frac(),
atom_radii=self.vdw_radii.atom_radii,
gridding_n_real=self.crystal_gridding.n_real(),
solvent_radius=solvent_radius,
shrink_truncation_radius=shrink_truncation_radius)
if use_space_group_symmetry:
tags = self.crystal_gridding.tags()
tags.tags().apply_symmetry_to_mask(self.mask.data)
self.flood_fill = cctbx.masks.flood_fill(self.mask.data,
xray_structure.unit_cell())
self.exclude_void_flags = [False] * self.flood_fill.n_voids()
self.solvent_accessible_volume = self.n_solvent_grid_points() \
/ self.mask.data.size() * xray_structure.unit_cell().volume()
def run(self):
# I'm guessing self.data_manager, self.params and self.logger
# are already defined here...
# this must be mmtbx.model.manager?
model = self.data_manager.get_model()
atoms = model.get_atoms()
all_bsel = flex.bool(atoms.size(), False)
for selection_string in self.params.atom_selection_program.inselection:
print("Selecting '%s'" % selection_string, file=self.logger)
isel = model.iselection(string=selection_string)
all_bsel.set_selected(isel, True)
if self.params.atom_selection_program.write_pdb_file is None:
print(" %d atom%s selected" % plural_s(isel.size()),
file=self.logger)
for atom in atoms.select(isel):
print(" %s" % atom.format_atom_record(),
file=self.logger)
print("", file=self.logger)
if self.params.atom_selection_program.write_pdb_file is not None:
print("Writing file:",
show_string(
self.params.atom_selection_program.write_pdb_file),
file=self.logger)
ss_ann = model.get_ss_annotation()
if not model.crystal_symmetry() or \
(not model.crystal_symmetry().unit_cell()):
model = shift_and_box_model(model, shift_model=False)
selected_model = model.select(all_bsel)
if (ss_ann is not None):
selected_model.set_ss_annotation(ss_ann.\
filter_annotation(
hierarchy=selected_model.get_hierarchy(),
asc=selected_model.get_atom_selection_cache(),
remove_short_annotations=False,
remove_3_10_helices=False,
remove_empty_annotations=True,
concatenate_consecutive_helices=False,
split_helices_with_prolines=False,
filter_sheets_with_long_hbonds=False))
if self.params.atom_selection_program.cryst1_replacement_buffer_layer is not None:
box = uctbx.non_crystallographic_unit_cell_with_the_sites_in_its_center(
sites_cart=selected_model.get_atoms().extract_xyz(),
buffer_layer=self.params.atom_selection_program.
cryst1_replacement_buffer_layer)
sp = crystal.special_position_settings(box.crystal_symmetry())
sites_frac = box.sites_frac()
xrs_box = selected_model.get_xray_structure(
).replace_sites_frac(box.sites_frac())
xray_structure_box = xray.structure(sp, xrs_box.scatterers())
selected_model.set_xray_structure(xray_structure_box)
pdb_str = selected_model.model_as_pdb()
f = open(self.params.atom_selection_program.write_pdb_file, 'w')
f.write(pdb_str)
f.close()
print("", file=self.logger)
def as_xray_structure(self, scatterer=None):
from cctbx import xray
if (scatterer is None):
scatterer = xray.scatterer(scattering_type="const")
result = xray.structure(special_position_settings=self)
for position in self.positions():
result.add_scatterer(scatterer.customized_copy(
label=position.label,
site=position.site))
return result
def as_xray_structure(self, scatterer=None):
from cctbx import xray
if (scatterer is None):
scatterer = xray.scatterer(scattering_type="const")
result = xray.structure(special_position_settings=self)
for position in self.positions():
result.add_scatterer(
scatterer.customized_copy(label=position.label,
site=position.site))
return result
def exercise_unmerged () :
quartz_structure = xray.structure(
special_position_settings=crystal.special_position_settings(
crystal_symmetry=crystal.symmetry(
unit_cell=(5.01,5.01,5.47,90,90,120),
space_group_symbol="P6222")),
scatterers=flex.xray_scatterer([
xray.scatterer(
label="Si",
site=(1/2.,1/2.,1/3.),
u=0.2),
xray.scatterer(
label="O",
site=(0.197,-0.197,0.83333),
u=0.1)]))
quartz_structure.set_inelastic_form_factors(
photon=1.54,
table="sasaki")
fc = abs(quartz_structure.structure_factors(d_min=1.0).f_calc())
symm = fc.crystal_symmetry()
icalc = fc.expand_to_p1().f_as_f_sq().set_observation_type_xray_intensity()
# generate 'unmerged' data
i_obs = icalc.customized_copy(crystal_symmetry=symm)
# now make up sigmas and some (hopefully realistic) error
flex.set_random_seed(12345)
n_refl = i_obs.size()
sigmas = flex.random_double(n_refl) * flex.mean(fc.data())
sigmas = icalc.customized_copy(data=sigmas).apply_debye_waller_factors(
u_iso=0.15)
err = (flex.double(n_refl, 0.5) - flex.random_double(n_refl)) * 2
i_obs = i_obs.customized_copy(
sigmas=sigmas.data(),
data=i_obs.data() + err)
# check for unmerged acentrics
assert i_obs.is_unmerged_intensity_array()
i_obs_centric = i_obs.select(i_obs.centric_flags().data())
i_obs_acentric = i_obs.select(~(i_obs.centric_flags().data()))
i_mrg_acentric = i_obs_acentric.merge_equivalents().array()
i_mixed = i_mrg_acentric.concatenate(i_obs_centric)
assert not i_mixed.is_unmerged_intensity_array()
# XXX These results of these functions are heavily dependent on the
# behavior of the random number generator, which is not consistent across
# platforms - therefore we can only check for very approximate values.
# Exact numerical results are tested with real data (stored elsewhere).
# CC1/2, etc.
assert approx_equal(i_obs.cc_one_half(), 0.9998, eps=0.001)
assert i_obs.resolution_filter(d_max=1.2).cc_one_half() > 0
assert i_obs.cc_anom() > 0.1
r_ano = i_obs.r_anom()
assert approx_equal(r_ano, 0.080756, eps=0.0001)
# merging stats
i_mrg = i_obs.merge_equivalents()
assert i_mrg.r_merge() < 0.1
assert i_mrg.r_meas() < 0.1
assert i_mrg.r_pim() < 0.05
def exercise_lbfgs(test_case, use_geo, out, d_min=2):
sites_cart, geo_manager = cctbx.geometry_restraints.manager.\
construct_non_crystallographic_conserving_bonds_and_angles(
sites_cart=flex.vec3_double(test_case.sites),
edge_list_bonds=test_case.bonds,
edge_list_angles=test_case.angles())
scatterers = flex.xray_scatterer(sites_cart.size(),
xray.scatterer(scattering_type="C", b=20))
for sc, lbl in zip(scatterers, test_case.labels):
sc.label = lbl
structure = xray.structure(crystal_symmetry=geo_manager.crystal_symmetry,
scatterers=scatterers)
structure.set_sites_cart(sites_cart=sites_cart)
f_calc = structure.structure_factors(d_min=d_min,
anomalous_flag=False).f_calc()
fft_map = f_calc.fft_map()
fft_map.apply_sigma_scaling()
if (use_geo):
axis = matrix.col(flex.random_double_point_on_sphere())
rot = scitbx.math.r3_rotation_axis_and_angle_as_matrix(axis=axis,
angle=25,
deg=True)
trans = matrix.col(flex.random_double_point_on_sphere()) * 1.0
structure.apply_rigid_body_shift(rot=rot, trans=trans)
geo_manager.energies_sites(sites_cart=structure.sites_cart()).show(
f=out)
minimized = real_space_refinement_simple.lbfgs(
sites_cart=structure.sites_cart(),
density_map=fft_map.real_map(),
geometry_restraints_manager=geo_manager,
gradients_method="fd",
real_space_target_weight=1,
real_space_gradients_delta=d_min / 3)
geo_manager.energies_sites(sites_cart=minimized.sites_cart).show(f=out)
else:
minimized = real_space_refinement_simple.lbfgs(
sites_cart=structure.sites_cart(),
density_map=fft_map.real_map(),
unit_cell=structure.unit_cell(),
gradients_method="fd",
real_space_gradients_delta=d_min / 3)
rmsd_start = sites_cart.rms_difference(structure.sites_cart())
rmsd_final = sites_cart.rms_difference(minimized.sites_cart)
print("RMSD start, final:", rmsd_start, rmsd_final, file=out)
if (use_geo):
assert rmsd_start >= 1 - 1e-6
assert rmsd_final < 0.2
def show_f_g(label, f, g):
print(label, "f, |g|:", f, flex.mean_sq(g)**0.5, file=out)
show_f_g(label="start", f=minimized.f_start, g=minimized.g_start)
show_f_g(label="final", f=minimized.f_final, g=minimized.g_final)
assert minimized.f_final <= minimized.f_start
return minimized
def exercise_u_iso_proportional_to_pivot_u_iso():
# Test working constraint
xs = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=(),
space_group_symbol='hall: P 2x 2y'),
scatterers=flex.xray_scatterer((
xray.scatterer('C0', u=0.12),
xray.scatterer('C1'),
)))
r = constraints.ext.reparametrisation(xs.unit_cell())
sc = xs.scatterers()
u_iso = r.add(constraints.independent_u_iso_parameter, sc[0])
u_iso_1 = r.add(constraints.u_iso_proportional_to_pivot_u_iso,
pivot_u_iso=u_iso,
multiplier=2,
scatterer=sc[1])
r.finalise()
r.linearise()
assert approx_equal(u_iso_1.value, 0.24, eps=1e-15)
# Test conflicting constraints
xs = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=(),
space_group_symbol='hall: P 2x 2y'),
scatterers=flex.xray_scatterer((
xray.scatterer('C0', u=0.12),
xray.scatterer('C1', u=0.21),
xray.scatterer('C2')
)))
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
r = constraints.reparametrisation(
structure=xs,
constraints=[constraints.adp.shared_u((0, 2)),
constraints.adp.shared_u((1, 2))],
connectivity_table=smtbx.utils.connectivity_table(xs))
assert len(w) == 1
assert w[-1].category == constraints.ConflictingConstraintWarning
assert w[-1].message.conflicts == set(((2, 'U'),))
def debug_write_reciprocal_lattice_points_as_pdb(self,
file_name='reciprocal_lattice.pdb'):
from cctbx import crystal, xray
cs = crystal.symmetry(unit_cell=(1000,1000,1000,90,90,90),
space_group="P1")
xs = xray.structure(crystal_symmetry=cs)
for site in self.trial_sites:
xs.add_scatterer(xray.scatterer("C", site=site))
xs.sites_mod_short()
with open(file_name, 'wb') as f:
print >> f, xs.as_pdb_file()
def __init__(
self,
xray_structure,
solvent_radius,
shrink_truncation_radius,
ignore_hydrogen_atoms=False,
crystal_gridding=None,
grid_step=None,
d_min=None,
resolution_factor=1 / 4,
atom_radii_table=None,
use_space_group_symmetry=False,
):
self.xray_structure = xray_structure
if crystal_gridding is None:
self.crystal_gridding = maptbx.crystal_gridding(
unit_cell=xray_structure.unit_cell(),
space_group_info=xray_structure.space_group_info(),
step=grid_step,
d_min=d_min,
resolution_factor=resolution_factor,
symmetry_flags=sgtbx.search_symmetry_flags(use_space_group_symmetry=use_space_group_symmetry),
)
else:
self.crystal_gridding = crystal_gridding
if use_space_group_symmetry:
atom_radii = cctbx.masks.vdw_radii(xray_structure, table=atom_radii_table).atom_radii
asu_mappings = xray_structure.asu_mappings(buffer_thickness=flex.max(atom_radii) + solvent_radius)
scatterers_asu_plus_buffer = flex.xray_scatterer()
frac = xray_structure.unit_cell().fractionalize
for sc, mappings in zip(xray_structure.scatterers(), asu_mappings.mappings()):
for mapping in mappings:
scatterers_asu_plus_buffer.append(sc.customized_copy(site=frac(mapping.mapped_site())))
xs = xray.structure(crystal_symmetry=xray_structure, scatterers=scatterers_asu_plus_buffer)
else:
xs = xray_structure.expand_to_p1()
self.vdw_radii = cctbx.masks.vdw_radii(xs, table=atom_radii_table)
self.mask = cctbx.masks.around_atoms(
unit_cell=xs.unit_cell(),
space_group_order_z=xs.space_group().order_z(),
sites_frac=xs.sites_frac(),
atom_radii=self.vdw_radii.atom_radii,
gridding_n_real=self.crystal_gridding.n_real(),
solvent_radius=solvent_radius,
shrink_truncation_radius=shrink_truncation_radius,
)
if use_space_group_symmetry:
tags = self.crystal_gridding.tags()
tags.tags().apply_symmetry_to_mask(self.mask.data)
self.flood_fill = cctbx.masks.flood_fill(self.mask.data, xray_structure.unit_cell())
self.exclude_void_flags = [False] * self.flood_fill.n_voids()
self.solvent_accessible_volume = (
self.n_solvent_grid_points() / self.mask.data.size() * xray_structure.unit_cell().volume()
)
def demo():
"""
Result of ICSD query:
N * -Cr2O3-[R3-CH] Baster, M.;Bouree, F.;Kowalska, A.;Latacz, Z(2000)
C 4.961950 4.961950 13.597400 90.000000 90.000000 120.000000
S GRUP R -3 C
A Cr1 0.000000 0.000000 0.347570 0.000000
A O1 0.305830 0.000000 0.250000
"""
crystal_symmetry = crystal.symmetry(
unit_cell="4.961950 4.961950 13.597400 90.000000 90.000000 120.000000",
space_group_symbol="R -3 C")
scatterers = flex.xray_scatterer()
scatterers.append(xray.scatterer(
label="Cr1", site=(0.000000,0.000000,0.347570)))
scatterers.append(xray.scatterer(
label="O1", site=(0.305830,0.000000,0.250000)))
icsd_structure = xray.structure(
crystal_symmetry=crystal_symmetry,
scatterers=scatterers)
icsd_structure.show_summary().show_scatterers()
print
icsd_pairs = icsd_structure.show_distances(
distance_cutoff=2.5, keep_pair_asu_table=True)
print
primitive_structure = icsd_structure.primitive_setting()
primitive_structure.show_summary().show_scatterers()
print
p1_structure = primitive_structure.expand_to_p1()
p1_structure.show_summary().show_scatterers()
print
p1_pairs = p1_structure.show_distances(
distance_cutoff=2.5, keep_pair_asu_table=True)
print
for label,structure,pairs in [("ICSD", icsd_structure,icsd_pairs),
("P1", p1_structure,p1_pairs)]:
print "Coordination sequences for", label, "structure"
term_table = crystal.coordination_sequences.simple(
pair_asu_table=pairs.pair_asu_table,
max_shell=10)
crystal.coordination_sequences.show_terms(
structure=structure,
term_table=term_table)
print
icsd_f_calc = icsd_structure.structure_factors(
d_min=1, algorithm="direct").f_calc()
icsd_f_calc_in_p1 = icsd_f_calc.primitive_setting().expand_to_p1()
p1_f_calc = icsd_f_calc_in_p1.structure_factors_from_scatterers(
xray_structure=p1_structure, algorithm="direct").f_calc()
for h,i,p in zip(icsd_f_calc_in_p1.indices(),
icsd_f_calc_in_p1.data(),
p1_f_calc.data()):
print h, abs(i), abs(p)*3
print "OK"
def run():
print __doc__
crystal_symmetry = crystal.symmetry(
unit_cell=(5, 5, 6, 90, 90, 120),
space_group_symbol="P 31")
distance_cutoff = 2.5
scatterers = flex.xray_scatterer()
for i,site in enumerate([(0.7624, 0.5887, 0.3937),
(0.2813, 0.9896, 0.9449),
(0.4853, 0.8980, 0.4707)]):
scatterers.append(xray.scatterer(
label="Se%d"%(i+1), site=site))
given_structure = xray.structure(
crystal_symmetry=crystal_symmetry,
scatterers=scatterers)
print "=================="
print "Original structure"
print "=================="
given_structure.show_summary().show_scatterers()
print "Interatomic distances:"
given_structure.show_distances(distance_cutoff=distance_cutoff)
print
print
print "====================================================="
print "Other hand with sites flipped and space group changed"
print "====================================================="
other_hand = given_structure.change_hand()
other_hand.show_summary().show_scatterers()
print "Interatomic distances:"
other_hand.show_distances(distance_cutoff=distance_cutoff)
print
print "=================================="
print "Other hand with sites flipped only"
print "=================================="
other_sites_orig_symmetry = xray.structure(
crystal_symmetry=crystal_symmetry,
scatterers=other_hand.scatterers())
other_sites_orig_symmetry.show_summary().show_scatterers()
print "Interatomic distances:"
other_sites_orig_symmetry.show_distances(distance_cutoff=distance_cutoff)
print
def pdb_atoms_as_xray_structure(pdb_atoms, crystal_symmetry):
xray_structure = xray.structure(crystal_symmetry = crystal_symmetry)
unit_cell = xray_structure.unit_cell()
for atom in pdb_atoms:
scatterer = xray.scatterer(
label = atom.name,
site = unit_cell.fractionalize(atom.xyz),
b = atom.b,
occupancy = atom.occ,
scattering_type = atom.element)
xray_structure.add_scatterer(scatterer)
return xray_structure
def exercise_covariance():
xs = xray.structure(
crystal_symmetry=crystal.symmetry(
(5.01,5.01,5.47,90,90,120), "P6222"),
scatterers=flex.xray_scatterer([
xray.scatterer("Si", (1/2.,1/2.,1/3.)),
xray.scatterer("O", (0.197,-0.197,0.83333))]))
uc = xs.unit_cell()
flags = xs.scatterer_flags()
for f in flags:
f.set_grad_site(True)
xs.set_scatterer_flags(flags)
cov = flex.double((1e-8,1e-9,2e-9,3e-9,4e-9,5e-9,
2e-8,1e-9,2e-9,3e-9,4e-9,
3e-8,1e-9,2e-9,3e-9,
2e-8,1e-9,2e-9,
3e-8,1e-9,
4e-8))
param_map = xs.parameter_map()
assert approx_equal(cov,
covariance.extract_covariance_matrix_for_sites(flex.size_t([0,1]), cov, param_map))
cov_cart = covariance.orthogonalize_covariance_matrix(cov, uc, param_map)
O = matrix.sqr(uc.orthogonalization_matrix())
for i in range(param_map.n_scatterers):
cov_i = covariance.extract_covariance_matrix_for_sites(flex.size_t([i]), cov, param_map)
cov_i_cart = covariance.extract_covariance_matrix_for_sites(flex.size_t([i]), cov_cart, param_map)
assert approx_equal(
O * matrix.sym(sym_mat3=cov_i) * O.transpose(),
matrix.sym(sym_mat3=cov_i_cart).as_mat3())
for f in flags: f.set_grads(False)
flags[0].set_grad_u_aniso(True)
flags[0].set_use_u_aniso(True)
flags[1].set_grad_u_iso(True)
flags[1].set_use_u_iso(True)
xs.set_scatterer_flags(flags)
param_map = xs.parameter_map()
cov = flex.double(7*7, 0)
cov.reshape(flex.grid(7,7))
cov.matrix_diagonal_set_in_place(flex.double([i for i in range(7)]))
cov = cov.matrix_symmetric_as_packed_u()
assert approx_equal([i for i in range(6)],
covariance.extract_covariance_matrix_for_u_aniso(
0, cov, param_map).matrix_packed_u_diagonal())
assert covariance.variance_for_u_iso(1, cov, param_map) == 6
try: covariance.variance_for_u_iso(0, cov, param_map)
except RuntimeError: pass
else: raise Exception_expected
try: covariance.extract_covariance_matrix_for_u_aniso(1, cov, param_map)
except RuntimeError: pass
else: raise Exception_expected
approx_equal(covariance.extract_covariance_matrix_for_sites(
flex.size_t([1]), cov, param_map), (0,0,0,0,0,0))
def build_xray_structure_with_carbon_along_x(a, b_iso, x=[0]):
result = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=(a,a,a,90,90,90),
space_group_symbol="P1"))
for i,v in enumerate(x):
result.add_scatterer(xray.scatterer(
label="C%d" % (i+1), scattering_type="C", site=(v,0,0), b=b_iso))
reg = result.scattering_type_registry(table="n_gaussian", d_min=1/12)
g = reg.as_type_gaussian_dict()["C"]
assert g.n_terms() == 5
assert not g.use_c()
return result
def dummy_structure(space_group_info, volume, n_scatterers):
structure = xray.structure(
special_position_settings=crystal.special_position_settings(
crystal_symmetry=crystal.symmetry(
unit_cell=space_group_info.any_compatible_unit_cell(volume=volume),
space_group_info=space_group_info)))
b_iso = 20
u_iso = adptbx.b_as_u(b_iso)
u_star = adptbx.u_iso_as_u_star(structure.unit_cell(), u_iso)
scatterer = xray.scatterer(label="C", site=(0.123,0.234,0.345), u=u_star)
for i in xrange(n_scatterers):
structure.add_scatterer(scatterer)
return structure
def as_xray_structure(self, crystal_symmetry=None, force_symmetry=False,
min_distance_sym_equiv=0.5):
crystal_symmetry = self.crystal_symmetry().join_symmetry(
other_symmetry=crystal_symmetry,
force=force_symmetry)
assert crystal_symmetry.unit_cell() is not None
assert crystal_symmetry.space_group_info() is not None
structure = xray.structure(crystal.special_position_settings(
crystal_symmetry=crystal_symmetry,
min_distance_sym_equiv=min_distance_sym_equiv))
for site in self.sites:
structure.add_scatterer(site.as_xray_scatterer(structure.unit_cell()))
return structure
def debug_write_reciprocal_lattice_points_as_pdb(
points, file_name='reciprocal_lattice.pdb'):
from cctbx import crystal, xray
cs = crystal.symmetry(unit_cell=(1000,1000,1000,90,90,90), space_group="P1")
xs = xray.structure(crystal_symmetry=cs)
sel = flex.random_selection(points.size(),
min(20000, points.size()))
rsp = points.select(sel)
for site in rsp:
xs.add_scatterer(xray.scatterer("C", site=site))
xs.sites_mod_short()
with open(file_name, 'wb') as f:
print >> f, xs.as_pdb_file()