def run_call_back(flags, space_group_info):
crystal_symmetry = crystal.symmetry(
unit_cell=space_group_info.any_compatible_unit_cell(volume=1000),
space_group_info=space_group_info)
if (flags.Verbose):
print crystal_symmetry.unit_cell()
symmetry_flags=sgtbx.search_symmetry_flags(
use_space_group_symmetry=True,
use_space_group_ltr=0,
use_seminvariants=True,
use_normalizer_k2l=False,
use_normalizer_l2n=False)
point_distance = 2
buffer_thickness = -1
all_twelve_neighbors = False
if (flags.strictly_inside):
buffer_thickness = 0
if (flags.all_twelve_neighbors):
all_twelve_neighbors = True
if (flags.Verbose):
print "buffer_thickness:", buffer_thickness
print "all_twelve_neighbors:", all_twelve_neighbors
sites_cart = hexagonal_close_packing_sampling(
crystal_symmetry=crystal_symmetry,
symmetry_flags=symmetry_flags,
point_distance=point_distance,
buffer_thickness=buffer_thickness,
all_twelve_neighbors=all_twelve_neighbors)
if (1):
check_distances(
sites_cart=sites_cart,
point_distance=point_distance,
verbose=flags.Verbose)
if (1):
check_with_grid_tags(
inp_symmetry=crystal_symmetry,
symmetry_flags=symmetry_flags,
sites_cart=sites_cart,
point_distance=point_distance,
strictly_inside=flags.strictly_inside,
flag_write_pdb=flags.write_pdb,
verbose=flags.Verbose)
if (flags.write_pdb):
dump_pdb(
file_name="hex_sites.pdb",
crystal_symmetry=crystal_symmetry,
sites_cart=sites_cart)
def run_call_back(flags, space_group_info):
crystal_symmetry = crystal.symmetry(
unit_cell=space_group_info.any_compatible_unit_cell(volume=1000),
space_group_info=space_group_info)
if (flags.Verbose):
print(crystal_symmetry.unit_cell())
symmetry_flags = sgtbx.search_symmetry_flags(use_space_group_symmetry=True,
use_space_group_ltr=0,
use_seminvariants=True,
use_normalizer_k2l=False,
use_normalizer_l2n=False)
point_distance = 2
buffer_thickness = -1
all_twelve_neighbors = False
if (flags.strictly_inside):
buffer_thickness = 0
if (flags.all_twelve_neighbors):
all_twelve_neighbors = True
if (flags.Verbose):
print("buffer_thickness:", buffer_thickness)
print("all_twelve_neighbors:", all_twelve_neighbors)
sites_cart = hexagonal_close_packing_sampling(
crystal_symmetry=crystal_symmetry,
symmetry_flags=symmetry_flags,
point_distance=point_distance,
buffer_thickness=buffer_thickness,
all_twelve_neighbors=all_twelve_neighbors)
if (1):
check_distances(sites_cart=sites_cart,
point_distance=point_distance,
verbose=flags.Verbose)
if (1):
check_with_grid_tags(inp_symmetry=crystal_symmetry,
symmetry_flags=symmetry_flags,
sites_cart=sites_cart,
point_distance=point_distance,
strictly_inside=flags.strictly_inside,
flag_write_pdb=flags.write_pdb,
verbose=flags.Verbose)
if (flags.write_pdb):
dump_pdb(file_name="hex_sites.pdb",
crystal_symmetry=crystal_symmetry,
sites_cart=sites_cart)
def exercise_chirality(verbose=0):
# monomer library: CA N CB C
sites = [
col(site)
for site in [(27.660, 9.903,
2.078), (28.049, 9.675,
3.486), (28.183, 11.269,
1.625), (28.085, 8.759, 1.165)]
]
chir = geometry_restraints.chirality(sites=sites,
volume_ideal=-2.48,
both_signs=False,
weight=1)
assert approx_equal(chir.volume_model, -2.411548478)
assert approx_equal(chir.residual(), 0.00468561086412)
dih = geometry_restraints.dihedral(sites=improper_permutation(sites),
angle_ideal=35.26439,
weight=1)
assert approx_equal(dih.angle_model, 32.2587249641)
assert approx_equal(dih.residual(), 9.03402230782)
if (verbose):
dump_pdb("sites.pdb", sites)
print("volume_ideal:", chir.volume_ideal)
print("volume_model:", chir.volume_model)
print("angle_ideal:", dih.angle_ideal)
print("angle model:", dih.angle_model)
for i_trial in range(50):
volume_ideal = chir.volume_ideal
for both_signs in [False, True]:
sites_mod = []
for site in sites:
shift = col([random.uniform(-.5, .5) for i in range(3)])
sites_mod.append(site + shift)
if (both_signs): volume_ideal = abs(volume_ideal)
c = geometry_restraints.chirality(sites=sites_mod,
volume_ideal=volume_ideal,
both_signs=both_signs,
weight=500 * 1 / 0.2**2)
residual_obj = residual_functor(
restraint_type=geometry_restraints.chirality,
volume_ideal=c.volume_ideal,
both_signs=c.both_signs,
weight=c.weight)
fg = flex.vec3_double(finite_differences(
sites_mod, residual_obj)).as_double()
ag = flex.vec3_double(c.gradients()).as_double()
scale = max(1, flex.mean(flex.abs(fg)))
assert approx_equal(ag / scale, fg / scale)
d = geometry_restraints.dihedral(
sites=improper_permutation(sites_mod),
angle_ideal=dih.angle_ideal,
weight=750)
ag_dih = dih.gradients()
if (verbose and i_trial == 0 and not both_signs):
dump_pdb("sites_mod.pdb", sites_mod)
max_g_len = 0
for g in ag_dih:
max_g_len = max(max_g_len, abs(col(g)))
for g in flex.vec3_double(fg):
max_g_len = max(max_g_len, abs(col(g)))
sticks = []
for site, g in zip(improper_permutation(sites_mod), ag_dih):
sticks.append(
pml_stick(begin=site,
end=site + col(g) / max_g_len,
colors=[[1, 0, 0]] * 2,
width=0.01))
pml_write(f=open("dih.pml", "w"), label="dih", sticks=sticks)
sticks = []
for site, g in zip(sites_mod, flex.vec3_double(fg)):
sticks.append(
pml_stick(begin=site,
end=site + col(g) / max_g_len,
colors=[[0, 1, 0]] * 2,
width=0.01))
pml_write(f=open("chir.pml", "w"), label="chir", sticks=sticks)
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 check_with_grid_tags(inp_symmetry, symmetry_flags, sites_cart,
point_distance, strictly_inside, flag_write_pdb,
verbose):
cb_op_inp_ref = inp_symmetry.change_of_basis_op_to_reference_setting()
if (verbose):
print("cb_op_inp_ref.c():", cb_op_inp_ref.c())
ref_symmetry = inp_symmetry.change_basis(cb_op_inp_ref)
search_symmetry = sgtbx.search_symmetry(
flags=symmetry_flags,
space_group_type=ref_symmetry.space_group_info().type(),
seminvariant=ref_symmetry.space_group_info().structure_seminvariants())
assert search_symmetry.continuous_shifts_are_principal()
continuous_shift_flags = search_symmetry.continuous_shift_flags()
if (flag_write_pdb):
tag_sites_frac = flex.vec3_double()
else:
tag_sites_frac = None
if (strictly_inside):
inp_tags = inp_symmetry.gridding(step=point_distance * .7,
symmetry_flags=symmetry_flags).tags()
if (tag_sites_frac is not None):
for point in flex.nested_loop(inp_tags.n_real()):
if (inp_tags.tags().tag_array()[point] < 0):
point_frac_inp = [
float(n) / d for n, d in zip(point, inp_tags.n_real())
]
tag_sites_frac.append(point_frac_inp)
if (inp_tags.tags().n_independent() < sites_cart.size()):
print("FAIL:", inp_symmetry.space_group_info(), \
inp_tags.tags().n_independent(), sites_cart.size())
raise AssertionError
else:
inp_tags = inp_symmetry.gridding(step=point_distance / 2.,
symmetry_flags=symmetry_flags).tags()
sites_frac_inp = inp_symmetry.unit_cell().fractionalize(
sites_cart=sites_cart)
rt = cb_op_inp_ref.c().as_double_array()
sites_frac_ref = rt[:9] * sites_frac_inp
sites_frac_ref += rt[9:]
max_distance = 2 * ((.5 * math.sqrt(3) * point_distance) * 2 / 3.)
if (verbose):
print("max_distance:", max_distance)
for point in flex.nested_loop(inp_tags.n_real()):
if (inp_tags.tags().tag_array()[point] < 0):
point_frac_inp = [
float(n) / d for n, d in zip(point, inp_tags.n_real())
]
if (tag_sites_frac is not None):
tag_sites_frac.append(point_frac_inp)
point_frac_ref = cb_op_inp_ref.c() * point_frac_inp
equiv_points = sgtbx.sym_equiv_sites(
unit_cell=ref_symmetry.unit_cell(),
space_group=search_symmetry.subgroup(),
original_site=point_frac_ref,
minimum_distance=2.e-6,
tolerance=1.e-6)
min_dist = sgtbx.min_sym_equiv_distance_info(
reference_sites=equiv_points,
others=sites_frac_ref,
principal_continuous_allowed_origin_shift_flags=
continuous_shift_flags).dist()
if (min_dist > max_distance):
print("FAIL:", inp_symmetry.space_group_info(), \
point_frac_ref, min_dist)
raise AssertionError
if (inp_tags.tags().n_independent() + 10 < sites_cart.size()):
print("FAIL:", inp_symmetry.space_group_info(), \
inp_tags.tags().n_independent(), sites_cart.size())
raise AssertionError
if (tag_sites_frac is not None):
dump_pdb(file_name="tag_sites.pdb",
crystal_symmetry=inp_symmetry,
sites_cart=inp_symmetry.unit_cell().orthogonalize(
sites_frac=tag_sites_frac))
def exercise_chirality(verbose=0):
# monomer library: CA N CB C
sites = [col(site) for site in [
(27.660, 9.903, 2.078),
(28.049, 9.675, 3.486),
(28.183, 11.269, 1.625),
(28.085, 8.759, 1.165)]]
chir = geometry_restraints.chirality(
sites=sites,
volume_ideal=-2.48,
both_signs=False,
weight=1)
assert approx_equal(chir.volume_model, -2.411548478)
assert approx_equal(chir.residual(), 0.00468561086412)
dih = geometry_restraints.dihedral(
sites=improper_permutation(sites),
angle_ideal=35.26439,
weight=1)
assert approx_equal(dih.angle_model, 32.2587249641)
assert approx_equal(dih.residual(), 9.03402230782)
if (verbose):
dump_pdb("sites.pdb", sites)
print "volume_ideal:", chir.volume_ideal
print "volume_model:", chir.volume_model
print "angle_ideal:", dih.angle_ideal
print "angle model:", dih.angle_model
for i_trial in xrange(50):
volume_ideal = chir.volume_ideal
for both_signs in [False, True]:
sites_mod = []
for site in sites:
shift = col([random.uniform(-.5,.5) for i in xrange(3)])
sites_mod.append(site+shift)
if (both_signs): volume_ideal = abs(volume_ideal)
c = geometry_restraints.chirality(
sites=sites_mod,
volume_ideal=volume_ideal,
both_signs=both_signs,
weight=500*1/0.2**2)
residual_obj = residual_functor(
restraint_type=geometry_restraints.chirality,
volume_ideal=c.volume_ideal,
both_signs=c.both_signs,
weight=c.weight)
fg = flex.vec3_double(
finite_differences(sites_mod, residual_obj)).as_double()
ag = flex.vec3_double(
c.gradients()).as_double()
scale = max(1, flex.mean(flex.abs(fg)))
assert approx_equal(ag/scale, fg/scale)
d = geometry_restraints.dihedral(
sites=improper_permutation(sites_mod),
angle_ideal=dih.angle_ideal,
weight=750)
ag_dih = dih.gradients()
if (verbose and i_trial == 0 and not both_signs):
dump_pdb("sites_mod.pdb", sites_mod)
max_g_len = 0
for g in ag_dih:
max_g_len = max(max_g_len, abs(col(g)))
for g in flex.vec3_double(fg):
max_g_len = max(max_g_len, abs(col(g)))
sticks = []
for site,g in zip(improper_permutation(sites_mod),ag_dih):
sticks.append(
pml_stick(
begin=site,
end=site+col(g)/max_g_len,
colors=[[1,0,0]]*2,
width=0.01))
pml_write(f=open("dih.pml", "w"), label="dih", sticks=sticks)
sticks = []
for site,g in zip(sites_mod,flex.vec3_double(fg)):
sticks.append(
pml_stick(
begin=site,
end=site+col(g)/max_g_len,
colors=[[0,1,0]]*2,
width=0.01))
pml_write(f=open("chir.pml", "w"), label="chir", sticks=sticks)
def check_with_grid_tags(inp_symmetry, symmetry_flags,
sites_cart, point_distance,
strictly_inside, flag_write_pdb, verbose):
cb_op_inp_ref = inp_symmetry.change_of_basis_op_to_reference_setting()
if (verbose):
print "cb_op_inp_ref.c():", cb_op_inp_ref.c()
ref_symmetry = inp_symmetry.change_basis(cb_op_inp_ref)
search_symmetry = sgtbx.search_symmetry(
flags=symmetry_flags,
space_group_type=ref_symmetry.space_group_info().type(),
seminvariant=ref_symmetry.space_group_info().structure_seminvariants())
assert search_symmetry.continuous_shifts_are_principal()
continuous_shift_flags = search_symmetry.continuous_shift_flags()
if (flag_write_pdb):
tag_sites_frac = flex.vec3_double()
else:
tag_sites_frac = None
if (strictly_inside):
inp_tags = inp_symmetry.gridding(
step=point_distance*.7,
symmetry_flags=symmetry_flags).tags()
if (tag_sites_frac is not None):
for point in flex.nested_loop(inp_tags.n_real()):
if (inp_tags.tags().tag_array()[point] < 0):
point_frac_inp=[float(n)/d for n,d in zip(point, inp_tags.n_real())]
tag_sites_frac.append(point_frac_inp)
if (inp_tags.tags().n_independent() < sites_cart.size()):
print "FAIL:", inp_symmetry.space_group_info(), \
inp_tags.tags().n_independent(), sites_cart.size()
raise AssertionError
else:
inp_tags = inp_symmetry.gridding(
step=point_distance/2.,
symmetry_flags=symmetry_flags).tags()
sites_frac_inp = inp_symmetry.unit_cell().fractionalize(
sites_cart=sites_cart)
rt = cb_op_inp_ref.c().as_double_array()
sites_frac_ref = rt[:9] * sites_frac_inp
sites_frac_ref += rt[9:]
max_distance = 2 * ((.5 * math.sqrt(3) * point_distance) * 2/3.)
if (verbose):
print "max_distance:", max_distance
for point in flex.nested_loop(inp_tags.n_real()):
if (inp_tags.tags().tag_array()[point] < 0):
point_frac_inp = [float(n)/d for n,d in zip(point, inp_tags.n_real())]
if (tag_sites_frac is not None):
tag_sites_frac.append(point_frac_inp)
point_frac_ref = cb_op_inp_ref.c() * point_frac_inp
equiv_points = sgtbx.sym_equiv_sites(
unit_cell=ref_symmetry.unit_cell(),
space_group=search_symmetry.subgroup(),
original_site=point_frac_ref,
minimum_distance=2.e-6,
tolerance=1.e-6)
min_dist = sgtbx.min_sym_equiv_distance_info(
reference_sites=equiv_points,
others=sites_frac_ref,
principal_continuous_allowed_origin_shift_flags
=continuous_shift_flags).dist()
if (min_dist > max_distance):
print "FAIL:", inp_symmetry.space_group_info(), \
point_frac_ref, min_dist
raise AssertionError
if (inp_tags.tags().n_independent()+10 < sites_cart.size()):
print "FAIL:", inp_symmetry.space_group_info(), \
inp_tags.tags().n_independent(), sites_cart.size()
raise AssertionError
if (tag_sites_frac is not None):
dump_pdb(
file_name="tag_sites.pdb",
crystal_symmetry=inp_symmetry,
sites_cart=inp_symmetry.unit_cell().orthogonalize(
sites_frac=tag_sites_frac))
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"
