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 __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 exercise_site_symmetry(space_group_info):
special_position_settings = crystal.special_position_settings(
crystal_symmetry=space_group_info.any_compatible_crystal_symmetry(
volume=1000))
z2p_op = space_group_info.group().z2p_op()
special_position_settings_p = crystal.special_position_settings(
crystal_symmetry=special_position_settings.change_basis(z2p_op),
min_distance_sym_equiv=special_position_settings.
min_distance_sym_equiv() * 0.99)
wyckoff_table = space_group_info.wyckoff_table()
for i_position in range(wyckoff_table.size()):
site_symmetry = wyckoff_table.random_site_symmetry(
special_position_settings=special_position_settings,
i_position=i_position)
s = site_symmetry.special_op()
assert s.multiply(s) == s
for m in site_symmetry.matrices():
assert m.multiply(s) == s
tab = sgtbx.site_symmetry_table()
tab.process(site_symmetry)
ss_ops = tab.get(0)
assert ss_ops.multiplicity() == site_symmetry.multiplicity()
assert ss_ops.multiplicity() * ss_ops.n_matrices() \
== site_symmetry.space_group().order_z()
site_p = z2p_op.c() * site_symmetry.exact_site()
site_symmetry_p = special_position_settings_p.site_symmetry(site_p)
ss_ops_p = ss_ops.change_basis(z2p_op)
assert ss_ops_p.multiplicity() == site_symmetry_p.multiplicity()
assert ss_ops_p.special_op() == site_symmetry_p.special_op()
assert ss_ops_p.multiplicity() * ss_ops_p.n_matrices() \
== site_symmetry_p.space_group().order_z()
references = [str(m) for m in site_symmetry_p.matrices()]
testees = [str(m) for m in ss_ops_p.matrices()]
references.sort()
testees.sort()
assert " ".join(testees) == " ".join(references)
def exercise_site_symmetry(space_group_info):
special_position_settings = crystal.special_position_settings(
crystal_symmetry=space_group_info.any_compatible_crystal_symmetry(
volume=1000))
z2p_op = space_group_info.group().z2p_op()
special_position_settings_p = crystal.special_position_settings(
crystal_symmetry=special_position_settings.change_basis(z2p_op),
min_distance_sym_equiv
=special_position_settings.min_distance_sym_equiv()*0.99)
wyckoff_table = space_group_info.wyckoff_table()
for i_position in xrange(wyckoff_table.size()):
site_symmetry = wyckoff_table.random_site_symmetry(
special_position_settings=special_position_settings,
i_position=i_position)
s = site_symmetry.special_op()
assert s.multiply(s) == s
for m in site_symmetry.matrices():
assert m.multiply(s) == s
tab = sgtbx.site_symmetry_table()
tab.process(site_symmetry)
ss_ops = tab.get(0)
assert ss_ops.multiplicity() == site_symmetry.multiplicity()
assert ss_ops.multiplicity() * ss_ops.n_matrices() \
== site_symmetry.space_group().order_z()
site_p = z2p_op.c() * site_symmetry.exact_site()
site_symmetry_p = special_position_settings_p.site_symmetry(site_p)
ss_ops_p = ss_ops.change_basis(z2p_op)
assert ss_ops_p.multiplicity() == site_symmetry_p.multiplicity()
assert ss_ops_p.special_op() == site_symmetry_p.special_op()
assert ss_ops_p.multiplicity() * ss_ops_p.n_matrices() \
== site_symmetry_p.space_group().order_z()
references = [str(m) for m in site_symmetry_p.matrices()]
testees = [str(m) for m in ss_ops_p.matrices()]
references.sort()
testees.sort()
assert " ".join(testees) == " ".join(references)
def exercise(verbose=0):
distance_ideal = 1.8
default_vdw_distance = 3.6
vdw_1_4_factor = 3.5 / 3.6
sites_cart_manual = flex.vec3_double([(1, 3, 0), (2, 3, 0), (3, 2, 0),
(3, 1, 0), (4, 1, 0), (3, 4, 0),
(4, 3, 0), (5, 3, 0), (6, 2, 0),
(7, 2, 0), (8, 3, 0), (7, 4, 0),
(6, 4, 0), (7, 5, 0), (6, 6, 0),
(8, 6, 0)])
bond_proxies = geometry_restraints.bond_sorted_asu_proxies(
asu_mappings=None)
for i_seqs in [(0, 1), (1, 2), (2, 3), (3, 4), (1, 5), (2, 6), (5, 6),
(6, 7), (7, 8), (8, 9), (9, 10), (10, 11), (11, 12),
(12, 7), (11, 13), (13, 14), (14, 15), (15, 13)]:
bond_proxies.process(
geometry_restraints.bond_simple_proxy(
i_seqs=i_seqs, distance_ideal=distance_ideal, weight=100))
angle_proxies = geometry_restraints.shared_angle_proxy()
for i_seqs, angle_ideal in [[(0, 1, 2), 135], [(0, 1, 5), 135],
[(1, 2, 3), 135], [(3, 2, 6), 135],
[(2, 3, 4), 120], [(1, 2, 6), 90],
[(2, 6, 5), 90], [(6, 5, 1), 90],
[(5, 1, 2), 90], [(2, 6, 7), 135],
[(5, 6, 7), 135], [(6, 7, 8), 120],
[(6, 7, 12), 120], [(7, 8, 9), 120],
[(8, 9, 10), 120], [(9, 10, 11), 120],
[(10, 11, 12), 120], [(11, 12, 7), 120],
[(12, 7, 8), 120], [(10, 11, 13), 120],
[(12, 11, 13), 120], [(11, 13, 15), 150],
[(11, 13, 14), 150], [(13, 15, 14), 60],
[(15, 14, 13), 60], [(14, 13, 15), 60]]:
angle_proxies.append(
geometry_restraints.angle_proxy(i_seqs=i_seqs,
angle_ideal=angle_ideal,
weight=1))
if (0 or verbose):
dump_pdb(file_name="manual.pdb", sites_cart=sites_cart_manual)
for traditional_convergence_test in [True, False]:
for sites_cart_selection in [True, False]:
sites_cart = sites_cart_manual.deep_copy()
if sites_cart_selection:
sites_cart_selection = flex.bool(sites_cart.size(), True)
sites_cart_selection[1] = False
assert bond_proxies.asu.size() == 0
bond_params_table = geometry_restraints.extract_bond_params(
n_seq=sites_cart.size(),
bond_simple_proxies=bond_proxies.simple)
manager = geometry_restraints.manager.manager(
bond_params_table=bond_params_table,
angle_proxies=angle_proxies)
minimized = geometry_restraints.lbfgs.lbfgs(
sites_cart=sites_cart,
geometry_restraints_manager=manager,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
traditional_convergence_test=traditional_convergence_test,
drop_convergence_test_max_drop_eps=1.e-20,
drop_convergence_test_iteration_coefficient=1,
max_iterations=1000),
sites_cart_selection=sites_cart_selection,
)
assert minimized.minimizer.iter() > 100
sites_cart_minimized_1 = sites_cart.deep_copy()
if (0 or verbose):
dump_pdb(file_name="minimized_1.pdb",
sites_cart=sites_cart_minimized_1)
bond_deltas = geometry_restraints.bond_deltas(
sites_cart=sites_cart_minimized_1, proxies=bond_proxies.simple)
angle_deltas = geometry_restraints.angle_deltas(
sites_cart=sites_cart_minimized_1, proxies=angle_proxies)
if (0 or verbose):
for proxy, delta in zip(bond_proxies.simple, bond_deltas):
print "bond:", proxy.i_seqs, delta
for proxy, delta in zip(angle_proxies, angle_deltas):
print "angle:", proxy.i_seqs, delta
assert is_below_limit(value=flex.max(flex.abs(bond_deltas)),
limit=0,
eps=1.e-6)
assert is_below_limit(value=flex.max(flex.abs(angle_deltas)),
limit=0,
eps=2.e-6)
sites_cart += matrix.col((1, 1, 0)) - matrix.col(sites_cart.min())
unit_cell_lengths = list(
matrix.col(sites_cart.max()) + matrix.col((1, -1.2, 4)))
unit_cell_lengths[1] *= 2
unit_cell_lengths[2] *= 2
xray_structure = xray.structure(crystal_symmetry=crystal.symmetry(
unit_cell=unit_cell_lengths, space_group_symbol="P112"))
for serial, site in zip(count(1), sites_cart):
xray_structure.add_scatterer(
xray.scatterer(
label="C%02d" % serial,
site=xray_structure.unit_cell().fractionalize(site)))
if (0 or verbose):
xray_structure.show_summary().show_scatterers()
p1_structure = (xray_structure.apply_shift(
(-.5, -.5, 0)).expand_to_p1().apply_shift((.5, .5, 0)))
for shift in [(1, 0, 0), (0, 1, 0), (0, 0, 1)]:
p1_structure.add_scatterers(
p1_structure.apply_shift(shift).scatterers())
if (0 or verbose):
open("p1_structure.pdb", "w").write(p1_structure.as_pdb_file())
nonbonded_cutoff = 6.5
asu_mappings = xray_structure.asu_mappings(
buffer_thickness=nonbonded_cutoff)
bond_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
geometry_restraints.add_pairs(bond_asu_table, bond_proxies.simple)
shell_asu_tables = crystal.coordination_sequences.shell_asu_tables(
pair_asu_table=bond_asu_table, max_shell=3)
shell_sym_tables = [
shell_asu_table.extract_pair_sym_table()
for shell_asu_table in shell_asu_tables
]
bond_params_table = geometry_restraints.extract_bond_params(
n_seq=sites_cart.size(), bond_simple_proxies=bond_proxies.simple)
atom_energy_types = flex.std_string(sites_cart.size(), "Default")
nonbonded_params = geometry_restraints.nonbonded_params(
factor_1_4_interactions=vdw_1_4_factor,
const_shrink_1_4_interactions=0,
default_distance=default_vdw_distance)
nonbonded_params.distance_table.setdefault(
"Default")["Default"] = default_vdw_distance
pair_proxies = geometry_restraints.pair_proxies(
bond_params_table=bond_params_table,
shell_asu_tables=shell_asu_tables,
model_indices=None,
conformer_indices=None,
nonbonded_params=nonbonded_params,
nonbonded_types=atom_energy_types,
nonbonded_distance_cutoff_plus_buffer=nonbonded_cutoff)
if (0 or verbose):
print "pair_proxies.bond_proxies.n_total():", \
pair_proxies.bond_proxies.n_total(),
print "simple:", pair_proxies.bond_proxies.simple.size(),
print "sym:", pair_proxies.bond_proxies.asu.size()
print "pair_proxies.nonbonded_proxies.n_total():", \
pair_proxies.nonbonded_proxies.n_total(),
print "simple:", pair_proxies.nonbonded_proxies.simple.size(),
print "sym:", pair_proxies.nonbonded_proxies.asu.size()
print "min_distance_nonbonded: %.2f" % flex.min(
geometry_restraints.nonbonded_deltas(
sites_cart=sites_cart,
sorted_asu_proxies=pair_proxies.nonbonded_proxies))
s = StringIO()
pair_proxies.bond_proxies.show_histogram_of_model_distances(
sites_cart=sites_cart, f=s, prefix="[]")
assert s.getvalue().splitlines()[0] == "[]Histogram of bond lengths:"
assert s.getvalue().splitlines()[5].startswith("[] 1.80 - 1.80:")
s = StringIO()
pair_proxies.bond_proxies.show_histogram_of_deltas(sites_cart=sites_cart,
f=s,
prefix="][")
assert s.getvalue().splitlines()[0] == "][Histogram of bond deltas:"
assert s.getvalue().splitlines()[5].startswith("][ 0.000 - 0.000:")
s = StringIO()
pair_proxies.bond_proxies.show_sorted(by_value="residual",
sites_cart=sites_cart,
max_items=3,
f=s,
prefix=":;")
l = s.getvalue().splitlines()
assert l[0] == ":;Bond restraints: 18"
assert l[1] == ":;Sorted by residual:"
assert l[2].startswith(":;bond ")
assert l[3].startswith(":; ")
assert l[4] == ":; ideal model delta sigma weight residual"
for i in [5, -2]:
assert l[i].startswith(":; 1.800 1.800 ")
assert l[-1] == ":;... (remaining 15 not shown)"
s = StringIO()
pair_proxies.nonbonded_proxies.show_histogram_of_model_distances(
sites_cart=sites_cart, f=s, prefix="]^")
assert not show_diff(
s.getvalue(), """\
]^Histogram of nonbonded interaction distances:
]^ 2.16 - 3.03: 3
]^ 3.03 - 3.89: 12
]^ 3.89 - 4.75: 28
]^ 4.75 - 5.61: 44
]^ 5.61 - 6.48: 54
""")
s = StringIO()
pair_proxies.nonbonded_proxies.show_sorted(by_value="delta",
sites_cart=sites_cart,
max_items=7,
f=s,
prefix=">,")
assert not show_diff(s.getvalue(),
"""\
>,Nonbonded interactions: 141
>,Sorted by model distance:
>,nonbonded 15
>, 15
>, model vdw sym.op.
>, 2.164 3.600 -x+2,-y+1,z
...
>,nonbonded 4
>, 8
>, model vdw
>, 3.414 3.600
>,... (remaining 134 not shown)
""",
selections=[range(6), range(-5, 0)])
vdw_1_sticks = []
vdw_2_sticks = []
for proxy in pair_proxies.nonbonded_proxies.simple:
if (proxy.vdw_distance == default_vdw_distance):
vdw_1_sticks.append(
pml_stick(begin=sites_cart[proxy.i_seqs[0]],
end=sites_cart[proxy.i_seqs[1]]))
else:
vdw_2_sticks.append(
pml_stick(begin=sites_cart[proxy.i_seqs[0]],
end=sites_cart[proxy.i_seqs[1]]))
mps = asu_mappings.mappings()
for proxy in pair_proxies.nonbonded_proxies.asu:
if (proxy.vdw_distance == default_vdw_distance):
vdw_1_sticks.append(
pml_stick(begin=mps[proxy.i_seq][0].mapped_site(),
end=mps[proxy.j_seq][proxy.j_sym].mapped_site()))
else:
vdw_2_sticks.append(
pml_stick(begin=mps[proxy.i_seq][0].mapped_site(),
end=mps[proxy.j_seq][proxy.j_sym].mapped_site()))
if (0 or verbose):
pml_write(f=open("vdw_1.pml", "w"), label="vdw_1", sticks=vdw_1_sticks)
pml_write(f=open("vdw_2.pml", "w"), label="vdw_2", sticks=vdw_2_sticks)
#
i_pdb = count(2)
for use_crystal_symmetry in [False, True]:
if (not use_crystal_symmetry):
crystal_symmetry = None
site_symmetry_table = None
else:
crystal_symmetry = xray_structure
site_symmetry_table = xray_structure.site_symmetry_table()
for sites_cart in [
sites_cart_manual.deep_copy(),
sites_cart_minimized_1.deep_copy()
]:
manager = geometry_restraints.manager.manager(
crystal_symmetry=crystal_symmetry,
site_symmetry_table=site_symmetry_table,
nonbonded_params=nonbonded_params,
nonbonded_types=atom_energy_types,
nonbonded_function=geometry_restraints.
prolsq_repulsion_function(),
bond_params_table=bond_params_table,
shell_sym_tables=shell_sym_tables,
nonbonded_distance_cutoff=nonbonded_cutoff,
nonbonded_buffer=1,
angle_proxies=angle_proxies,
plain_pairs_radius=5)
manager = manager.select(
selection=flex.bool(sites_cart.size(), True))
manager = manager.select(iselection=flex.size_t_range(
stop=sites_cart.size()))
pair_proxies = manager.pair_proxies(sites_cart=sites_cart)
minimized = geometry_restraints.lbfgs.lbfgs(
sites_cart=sites_cart,
geometry_restraints_manager=manager,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=1000))
if (0 or verbose):
minimized.final_target_result.show()
print "number of function evaluations:", minimized.minimizer.nfun(
)
print "n_updates_pair_proxies:", manager.n_updates_pair_proxies
if (not use_crystal_symmetry):
assert minimized.final_target_result.bond_residual_sum < 1.e-3
assert minimized.final_target_result.nonbonded_residual_sum < 0.1
else:
assert minimized.final_target_result.bond_residual_sum < 1.e-2
assert minimized.final_target_result.nonbonded_residual_sum < 0.1
assert minimized.final_target_result.angle_residual_sum < 1.e-3
if (0 or verbose):
pdb_file_name = "minimized_%d.pdb" % i_pdb.next()
print "Writing file:", pdb_file_name
dump_pdb(file_name=pdb_file_name, sites_cart=sites_cart)
if (manager.site_symmetry_table is None):
additional_site_symmetry_table = None
else:
additional_site_symmetry_table = sgtbx.site_symmetry_table()
assert manager.new_including_isolated_sites(
n_additional_sites=0,
site_symmetry_table=additional_site_symmetry_table,
nonbonded_types=flex.std_string()).plain_pairs_radius \
== manager.plain_pairs_radius
if (crystal_symmetry is not None):
assert len(manager.plain_pair_sym_table) == 16
if (0 or verbose):
manager.plain_pair_sym_table.show()
#
xray_structure.set_u_iso(values=flex.double([
0.77599982480241358, 0.38745781137212021, 0.20667558236418682,
0.99759840171302094, 0.8917287406687805, 0.64780251325379845,
0.24878590382983534, 0.59480621182194615, 0.58695637792905142,
0.33997130213653637, 0.51258699130743735, 0.79760289141276675,
0.39996577657875021, 0.4329328819341467, 0.70422156561726479,
0.87260110626999332
]))
class parameters:
pass
parameters.sphere_radius = 5
parameters.distance_power = 0.7
parameters.average_power = 0.9
parameters.wilson_b_weight = 1.3952
parameters.wilson_b_weight_auto = False
adp_energies = adp_restraints.energies_iso(
geometry_restraints_manager=manager,
xray_structure=xray_structure,
parameters=parameters,
wilson_b=None,
use_hd=False,
use_u_local_only=False,
compute_gradients=False,
gradients=None,
normalization=False,
collect=True)
assert adp_energies.number_of_restraints == 69
assert approx_equal(adp_energies.residual_sum, 6.24865382467)
assert adp_energies.gradients is None
assert adp_energies.u_i.size() == adp_energies.number_of_restraints
assert adp_energies.u_j.size() == adp_energies.number_of_restraints
assert adp_energies.r_ij.size() == adp_energies.number_of_restraints
for wilson_b in [None, 10, 100]:
finite_difference_gradients = flex.double()
eps = 1.e-6
for i_scatterer in xrange(xray_structure.scatterers().size()):
rs = []
for signed_eps in [eps, -eps]:
xray_structure_eps = xray_structure.deep_copy_scatterers()
xray_structure_eps.scatterers(
)[i_scatterer].u_iso += signed_eps
adp_energies = adp_restraints.energies_iso(
geometry_restraints_manager=manager,
xray_structure=xray_structure_eps,
parameters=parameters,
wilson_b=wilson_b,
use_u_local_only=False,
use_hd=False,
compute_gradients=True,
gradients=None,
normalization=False,
collect=False)
rs.append(adp_energies.residual_sum)
assert adp_energies.gradients.size() \
== xray_structure.scatterers().size()
assert adp_energies.u_i == None
assert adp_energies.u_j == None
assert adp_energies.r_ij == None
finite_difference_gradients.append((rs[0] - rs[1]) / (2 * eps))
sel = flex.bool(xray_structure.scatterers().size(), True)
xray_structure.scatterers().flags_set_grad_u_iso(sel.iselection())
adp_energies = adp_restraints.energies_iso(
geometry_restraints_manager=manager,
xray_structure=xray_structure,
parameters=parameters,
wilson_b=wilson_b,
use_u_local_only=False,
use_hd=False,
compute_gradients=True,
gradients=None,
normalization=False,
collect=False)
assert approx_equal(adp_energies.gradients,
finite_difference_gradients)
print "OK"
def demo():
#
# define unit cell parameters and a compatible space group
#
unit_cell = uctbx.unit_cell((10, 10, 15, 90, 90, 120))
space_group = sgtbx.space_group("-P 3 2") # Hall symbol
#
# define a site_symmetry_table with a few sites
#
site_symmetry_table = sgtbx.site_symmetry_table()
site_symmetry_table.reserve(3) # optional: optimizes memory allocation
for site_frac in [(0, 0, 0), (0.5, 0.5, 0.5), (0.25, 0.66, 0.0),
(0.75, 0.66, 0.0)]:
site_symmetry = sgtbx.site_symmetry(unit_cell=unit_cell,
space_group=space_group,
original_site=site_frac,
min_distance_sym_equiv=0.5,
assert_min_distance_sym_equiv=True)
site_symmetry_table.process(site_symmetry_ops=site_symmetry)
#
# there are two sets of indices:
# 1. "i_seq" = index into the sequence of sites as passed to
# site_symmetry.process().
# 2. The indices of the tabulated special_position_ops instances.
# site_symmetry_table.indices() establishes the relation between
# these two sets of indices:
# site_symmetry_table.indices().size() = number of sites processed
# site_symmetry_table.indices()[i_seq] = index of special_position_ops
# instance in the internal site_symmetry_table.table()
assert list(site_symmetry_table.indices()) == [1, 2, 0, 0]
#
# table entry 0 is always the general position
#
assert str(site_symmetry_table.table()[0].special_op()) == "x,y,z"
#
# all other table entries are special positions
#
assert str(site_symmetry_table.table()[1].special_op()) == "0,0,0"
assert str(site_symmetry_table.table()[2].special_op()) == "1/2,1/2,1/2"
#
# To obtain the special_position_ops for a certain i_seq:
#
for i_seq in [0, 1, 2]:
print(site_symmetry_table.get(i_seq=i_seq).special_op())
#
# Most of the time the (many) general positions don't need a
# special treatment, and it is much more convenient to loop
# only over the (few) special positions. For example, to
# define symmetry constraints for anisotropic displacement
# parameters:
#
for i_seq in site_symmetry_table.special_position_indices():
site_constraints = site_symmetry_table.get(
i_seq=i_seq).site_constraints()
adp_constraints = site_symmetry_table.get(
i_seq=i_seq).adp_constraints()
#
# See also:
# cctbx/examples/site_symmetry_constraints.py
# cctbx/examples/adp_symmetry_constraints.py
# C++ reference documentation for
# cctbx::sgtbx::site_symmetry_ops
# cctbx::sgtbx::site_symmetry
#
print("OK")
def demo():
#
# define unit cell parameters and a compatible space group
#
unit_cell = uctbx.unit_cell((10,10,15,90,90,120))
space_group = sgtbx.space_group("-P 3 2") # Hall symbol
#
# define a site_symmetry_table with a few sites
#
site_symmetry_table = sgtbx.site_symmetry_table()
site_symmetry_table.reserve(3) # optional: optimizes memory allocation
for site_frac in [(0,0,0), (0.5,0.5,0.5), (0.25,0.66,0.0), (0.75,0.66,0.0)]:
site_symmetry = sgtbx.site_symmetry(
unit_cell=unit_cell,
space_group=space_group,
original_site=site_frac,
min_distance_sym_equiv=0.5,
assert_min_distance_sym_equiv=True)
site_symmetry_table.process(site_symmetry_ops=site_symmetry)
#
# there are two sets of indices:
# 1. "i_seq" = index into the sequence of sites as passed to
# site_symmetry.process().
# 2. The indices of the tabulated special_position_ops instances.
# site_symmetry_table.indices() establishes the relation between
# these two sets of indices:
# site_symmetry_table.indices().size() = number of sites processed
# site_symmetry_table.indices()[i_seq] = index of special_position_ops
# instance in the internal site_symmetry_table.table()
assert list(site_symmetry_table.indices()) == [1, 2, 0, 0]
#
# table entry 0 is always the general position
#
assert str(site_symmetry_table.table()[0].special_op()) == "x,y,z"
#
# all other table entries are special positions
#
assert str(site_symmetry_table.table()[1].special_op()) == "0,0,0"
assert str(site_symmetry_table.table()[2].special_op()) == "1/2,1/2,1/2"
#
# To obtain the special_position_ops for a certain i_seq:
#
for i_seq in [0,1,2]:
print site_symmetry_table.get(i_seq=i_seq).special_op()
#
# Most of the time the (many) general positions don't need a
# special treatment, and it is much more convenient to loop
# only over the (few) special positions. For example, to
# define symmetry constraints for anisotropic displacement
# parameters:
#
for i_seq in site_symmetry_table.special_position_indices():
site_constraints = site_symmetry_table.get(i_seq=i_seq).site_constraints()
adp_constraints = site_symmetry_table.get(i_seq=i_seq).adp_constraints()
#
# See also:
# cctbx/examples/site_symmetry_constraints.py
# cctbx/examples/adp_symmetry_constraints.py
# C++ reference documentation for
# cctbx::sgtbx::site_symmetry_ops
# cctbx::sgtbx::site_symmetry
#
print "OK"
def exercise(verbose=0):
distance_ideal = 1.8
default_vdw_distance = 3.6
vdw_1_4_factor = 3.5/3.6
sites_cart_manual = flex.vec3_double([
(1,3,0), (2,3,0), (3,2,0), (3,1,0), (4,1,0), (3,4,0), (4,3,0), (5,3,0),
(6,2,0), (7,2,0), (8,3,0), (7,4,0), (6,4,0), (7,5,0), (6,6,0), (8,6,0)])
bond_proxies = geometry_restraints.bond_sorted_asu_proxies(asu_mappings=None)
for i_seqs in [(0,1),(1,2),(2,3),(3,4),(1,5),(2,6),(5,6),
(6,7),(7,8),(8,9),(9,10),(10,11),(11,12),
(12,7),(11,13),(13,14),(14,15),(15,13)]:
bond_proxies.process(geometry_restraints.bond_simple_proxy(
i_seqs=i_seqs, distance_ideal=distance_ideal, weight=100))
angle_proxies = geometry_restraints.shared_angle_proxy()
for i_seqs,angle_ideal in [[(0,1,2),135],
[(0,1,5),135],
[(1,2,3),135],
[(3,2,6),135],
[(2,3,4),120],
[(1,2,6),90],
[(2,6,5),90],
[(6,5,1),90],
[(5,1,2),90],
[(2,6,7),135],
[(5,6,7),135],
[(6,7,8),120],
[(6,7,12),120],
[(7,8,9),120],
[(8,9,10),120],
[(9,10,11),120],
[(10,11,12),120],
[(11,12,7),120],
[(12,7,8),120],
[(10,11,13),120],
[(12,11,13),120],
[(11,13,15),150],
[(11,13,14),150],
[(13,15,14),60],
[(15,14,13),60],
[(14,13,15),60]]:
angle_proxies.append(geometry_restraints.angle_proxy(
i_seqs=i_seqs, angle_ideal=angle_ideal, weight=1))
if (0 or verbose):
dump_pdb(file_name="manual.pdb", sites_cart=sites_cart_manual)
for traditional_convergence_test in [True,False]:
for sites_cart_selection in [True, False]:
sites_cart = sites_cart_manual.deep_copy()
if sites_cart_selection:
sites_cart_selection = flex.bool(sites_cart.size(), True)
sites_cart_selection[1] = False
assert bond_proxies.asu.size() == 0
bond_params_table = geometry_restraints.extract_bond_params(
n_seq=sites_cart.size(),
bond_simple_proxies=bond_proxies.simple)
manager = geometry_restraints.manager.manager(
bond_params_table=bond_params_table,
angle_proxies=angle_proxies)
minimized = geometry_restraints.lbfgs.lbfgs(
sites_cart=sites_cart,
geometry_restraints_manager=manager,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
traditional_convergence_test=traditional_convergence_test,
drop_convergence_test_max_drop_eps=1.e-20,
drop_convergence_test_iteration_coefficient=1,
max_iterations=1000),
sites_cart_selection=sites_cart_selection,
)
assert minimized.minimizer.iter() > 100
sites_cart_minimized_1 = sites_cart.deep_copy()
if (0 or verbose):
dump_pdb(
file_name="minimized_1.pdb", sites_cart=sites_cart_minimized_1)
bond_deltas = geometry_restraints.bond_deltas(
sites_cart=sites_cart_minimized_1,
proxies=bond_proxies.simple)
angle_deltas = geometry_restraints.angle_deltas(
sites_cart=sites_cart_minimized_1,
proxies=angle_proxies)
if (0 or verbose):
for proxy,delta in zip(bond_proxies.simple, bond_deltas):
print "bond:", proxy.i_seqs, delta
for proxy,delta in zip(angle_proxies, angle_deltas):
print "angle:", proxy.i_seqs, delta
assert is_below_limit(
value=flex.max(flex.abs(bond_deltas)), limit=0, eps=1.e-6)
assert is_below_limit(
value=flex.max(flex.abs(angle_deltas)), limit=0, eps=2.e-6)
sites_cart += matrix.col((1,1,0)) - matrix.col(sites_cart.min())
unit_cell_lengths = list( matrix.col(sites_cart.max())
+ matrix.col((1,-1.2,4)))
unit_cell_lengths[1] *= 2
unit_cell_lengths[2] *= 2
xray_structure = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=unit_cell_lengths,
space_group_symbol="P112"))
for serial,site in zip(count(1), sites_cart):
xray_structure.add_scatterer(xray.scatterer(
label="C%02d"%serial,
site=xray_structure.unit_cell().fractionalize(site)))
if (0 or verbose):
xray_structure.show_summary().show_scatterers()
p1_structure = (xray_structure
.apply_shift((-.5,-.5,0))
.expand_to_p1()
.apply_shift((.5,.5,0)))
for shift in [(1,0,0), (0,1,0), (0,0,1)]:
p1_structure.add_scatterers(p1_structure.apply_shift(shift).scatterers())
if (0 or verbose):
open("p1_structure.pdb", "w").write(p1_structure.as_pdb_file())
nonbonded_cutoff = 6.5
asu_mappings = xray_structure.asu_mappings(
buffer_thickness=nonbonded_cutoff)
bond_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
geometry_restraints.add_pairs(bond_asu_table, bond_proxies.simple)
shell_asu_tables = crystal.coordination_sequences.shell_asu_tables(
pair_asu_table=bond_asu_table,
max_shell=3)
shell_sym_tables = [shell_asu_table.extract_pair_sym_table()
for shell_asu_table in shell_asu_tables]
bond_params_table = geometry_restraints.extract_bond_params(
n_seq=sites_cart.size(),
bond_simple_proxies=bond_proxies.simple)
atom_energy_types = flex.std_string(sites_cart.size(), "Default")
nonbonded_params = geometry_restraints.nonbonded_params(
factor_1_4_interactions=vdw_1_4_factor,
const_shrink_1_4_interactions=0,
default_distance=default_vdw_distance)
nonbonded_params.distance_table.setdefault(
"Default")["Default"] = default_vdw_distance
pair_proxies = geometry_restraints.pair_proxies(
bond_params_table=bond_params_table,
shell_asu_tables=shell_asu_tables,
model_indices=None,
conformer_indices=None,
nonbonded_params=nonbonded_params,
nonbonded_types=atom_energy_types,
nonbonded_distance_cutoff_plus_buffer=nonbonded_cutoff)
if (0 or verbose):
print "pair_proxies.bond_proxies.n_total():", \
pair_proxies.bond_proxies.n_total(),
print "simple:", pair_proxies.bond_proxies.simple.size(),
print "sym:", pair_proxies.bond_proxies.asu.size()
print "pair_proxies.nonbonded_proxies.n_total():", \
pair_proxies.nonbonded_proxies.n_total(),
print "simple:", pair_proxies.nonbonded_proxies.simple.size(),
print "sym:", pair_proxies.nonbonded_proxies.asu.size()
print "min_distance_nonbonded: %.2f" % flex.min(
geometry_restraints.nonbonded_deltas(
sites_cart=sites_cart,
sorted_asu_proxies=pair_proxies.nonbonded_proxies))
s = StringIO()
pair_proxies.bond_proxies.show_histogram_of_model_distances(
sites_cart=sites_cart,
f=s,
prefix="[]")
assert s.getvalue().splitlines()[0] == "[]Histogram of bond lengths:"
assert s.getvalue().splitlines()[5].startswith("[] 1.80 - 1.80:")
s = StringIO()
pair_proxies.bond_proxies.show_histogram_of_deltas(
sites_cart=sites_cart,
f=s,
prefix="][")
assert s.getvalue().splitlines()[0] == "][Histogram of bond deltas:"
assert s.getvalue().splitlines()[5].startswith("][ 0.000 - 0.000:")
s = StringIO()
pair_proxies.bond_proxies.show_sorted(
by_value="residual",
sites_cart=sites_cart,
max_items=3,
f=s,
prefix=":;")
l = s.getvalue().splitlines()
assert l[0] == ":;Bond restraints: 18"
assert l[1] == ":;Sorted by residual:"
assert l[2].startswith(":;bond ")
assert l[3].startswith(":; ")
assert l[4] == ":; ideal model delta sigma weight residual"
for i in [5,-2]:
assert l[i].startswith(":; 1.800 1.800 ")
assert l[-1] == ":;... (remaining 15 not shown)"
s = StringIO()
pair_proxies.nonbonded_proxies.show_histogram_of_model_distances(
sites_cart=sites_cart,
f=s,
prefix="]^")
assert not show_diff(s.getvalue(), """\
]^Histogram of nonbonded interaction distances:
]^ 2.16 - 3.03: 3
]^ 3.03 - 3.89: 12
]^ 3.89 - 4.75: 28
]^ 4.75 - 5.61: 44
]^ 5.61 - 6.48: 54
""")
s = StringIO()
pair_proxies.nonbonded_proxies.show_sorted(
by_value="delta",
sites_cart=sites_cart,
max_items=7,
f=s,
prefix=">,")
assert not show_diff(s.getvalue(), """\
>,Nonbonded interactions: 141
>,Sorted by model distance:
>,nonbonded 15
>, 15
>, model vdw sym.op.
>, 2.164 3.600 -x+2,-y+1,z
...
>,nonbonded 4
>, 8
>, model vdw
>, 3.414 3.600
>,... (remaining 134 not shown)
""",
selections=[range(6), range(-5,0)])
vdw_1_sticks = []
vdw_2_sticks = []
for proxy in pair_proxies.nonbonded_proxies.simple:
if (proxy.vdw_distance == default_vdw_distance):
vdw_1_sticks.append(pml_stick(
begin=sites_cart[proxy.i_seqs[0]],
end=sites_cart[proxy.i_seqs[1]]))
else:
vdw_2_sticks.append(pml_stick(
begin=sites_cart[proxy.i_seqs[0]],
end=sites_cart[proxy.i_seqs[1]]))
mps = asu_mappings.mappings()
for proxy in pair_proxies.nonbonded_proxies.asu:
if (proxy.vdw_distance == default_vdw_distance):
vdw_1_sticks.append(pml_stick(
begin=mps[proxy.i_seq][0].mapped_site(),
end=mps[proxy.j_seq][proxy.j_sym].mapped_site()))
else:
vdw_2_sticks.append(pml_stick(
begin=mps[proxy.i_seq][0].mapped_site(),
end=mps[proxy.j_seq][proxy.j_sym].mapped_site()))
if (0 or verbose):
pml_write(f=open("vdw_1.pml", "w"), label="vdw_1", sticks=vdw_1_sticks)
pml_write(f=open("vdw_2.pml", "w"), label="vdw_2", sticks=vdw_2_sticks)
#
i_pdb = count(2)
for use_crystal_symmetry in [False, True]:
if (not use_crystal_symmetry):
crystal_symmetry = None
site_symmetry_table = None
else:
crystal_symmetry = xray_structure
site_symmetry_table = xray_structure.site_symmetry_table()
for sites_cart in [sites_cart_manual.deep_copy(),
sites_cart_minimized_1.deep_copy()]:
manager = geometry_restraints.manager.manager(
crystal_symmetry=crystal_symmetry,
site_symmetry_table=site_symmetry_table,
nonbonded_params=nonbonded_params,
nonbonded_types=atom_energy_types,
nonbonded_function=geometry_restraints.prolsq_repulsion_function(),
bond_params_table=bond_params_table,
shell_sym_tables=shell_sym_tables,
nonbonded_distance_cutoff=nonbonded_cutoff,
nonbonded_buffer=1,
angle_proxies=angle_proxies,
plain_pairs_radius=5)
manager = manager.select(selection=flex.bool(sites_cart.size(), True))
manager = manager.select(
iselection=flex.size_t_range(stop=sites_cart.size()))
pair_proxies = manager.pair_proxies(sites_cart=sites_cart)
minimized = geometry_restraints.lbfgs.lbfgs(
sites_cart=sites_cart,
geometry_restraints_manager=manager,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=1000))
if (0 or verbose):
minimized.final_target_result.show()
print "number of function evaluations:", minimized.minimizer.nfun()
print "n_updates_pair_proxies:", manager.n_updates_pair_proxies
if (not use_crystal_symmetry):
assert minimized.final_target_result.bond_residual_sum < 1.e-3
assert minimized.final_target_result.nonbonded_residual_sum < 0.1
else:
assert minimized.final_target_result.bond_residual_sum < 1.e-2
assert minimized.final_target_result.nonbonded_residual_sum < 0.1
assert minimized.final_target_result.angle_residual_sum < 1.e-3
if (0 or verbose):
pdb_file_name = "minimized_%d.pdb" % i_pdb.next()
print "Writing file:", pdb_file_name
dump_pdb(file_name=pdb_file_name, sites_cart=sites_cart)
if (manager.site_symmetry_table is None):
additional_site_symmetry_table = None
else:
additional_site_symmetry_table = sgtbx.site_symmetry_table()
assert manager.new_including_isolated_sites(
n_additional_sites=0,
site_symmetry_table=additional_site_symmetry_table,
nonbonded_types=flex.std_string()).plain_pairs_radius \
== manager.plain_pairs_radius
if (crystal_symmetry is not None):
assert len(manager.plain_pair_sym_table) == 16
if (0 or verbose):
manager.plain_pair_sym_table.show()
#
xray_structure.set_u_iso(values=flex.double([
0.77599982480241358, 0.38745781137212021, 0.20667558236418682,
0.99759840171302094, 0.8917287406687805, 0.64780251325379845,
0.24878590382983534, 0.59480621182194615, 0.58695637792905142,
0.33997130213653637, 0.51258699130743735, 0.79760289141276675,
0.39996577657875021, 0.4329328819341467, 0.70422156561726479,
0.87260110626999332]))
class parameters: pass
parameters.sphere_radius = 5
parameters.distance_power = 0.7
parameters.average_power = 0.9
parameters.wilson_b_weight = 1.3952
parameters.wilson_b_weight_auto = False
adp_energies = adp_restraints.energies_iso(
geometry_restraints_manager=manager,
xray_structure=xray_structure,
parameters=parameters,
wilson_b=None,
use_hd=False,
use_u_local_only = False,
compute_gradients=False,
gradients=None,
normalization=False,
collect=True)
assert adp_energies.number_of_restraints == 69
assert approx_equal(adp_energies.residual_sum, 6.24865382467)
assert adp_energies.gradients is None
assert adp_energies.u_i.size() == adp_energies.number_of_restraints
assert adp_energies.u_j.size() == adp_energies.number_of_restraints
assert adp_energies.r_ij.size() == adp_energies.number_of_restraints
for wilson_b in [None, 10, 100]:
finite_difference_gradients = flex.double()
eps = 1.e-6
for i_scatterer in xrange(xray_structure.scatterers().size()):
rs = []
for signed_eps in [eps, -eps]:
xray_structure_eps = xray_structure.deep_copy_scatterers()
xray_structure_eps.scatterers()[i_scatterer].u_iso += signed_eps
adp_energies = adp_restraints.energies_iso(
geometry_restraints_manager=manager,
xray_structure=xray_structure_eps,
parameters=parameters,
wilson_b=wilson_b,
use_u_local_only = False,
use_hd=False,
compute_gradients=True,
gradients=None,
normalization=False,
collect=False)
rs.append(adp_energies.residual_sum)
assert adp_energies.gradients.size() \
== xray_structure.scatterers().size()
assert adp_energies.u_i == None
assert adp_energies.u_j == None
assert adp_energies.r_ij == None
finite_difference_gradients.append((rs[0]-rs[1])/(2*eps))
sel = flex.bool(xray_structure.scatterers().size(), True)
xray_structure.scatterers().flags_set_grad_u_iso(sel.iselection())
adp_energies = adp_restraints.energies_iso(
geometry_restraints_manager=manager,
xray_structure=xray_structure,
parameters=parameters,
wilson_b=wilson_b,
use_u_local_only = False,
use_hd=False,
compute_gradients=True,
gradients=None,
normalization=False,
collect=False)
assert approx_equal(adp_energies.gradients, finite_difference_gradients)
print "OK"