def exercise():
exercise_bond()
for irexp in [1,2,3,4,5]:
for rexp in [3,4]:
exercise_nonbonded(
nonbonded_type=geometry_restraints.nonbonded_prolsq,
repulsion_function=geometry_restraints.prolsq_repulsion_function(
irexp=irexp,
rexp=rexp))
for irexp in [1,2,3,4,5]:
exercise_nonbonded(
nonbonded_type=geometry_restraints.nonbonded_inverse_power,
repulsion_function=geometry_restraints.inverse_power_repulsion_function(
nonbonded_distance_cutoff=1.e20,
irexp=irexp))
for exponent in [1,2,3]:
exercise_nonbonded(
nonbonded_type=geometry_restraints.nonbonded_cos,
repulsion_function=geometry_restraints.cos_repulsion_function(
max_residual=13,
exponent=exponent))
for norm_height_at_vdw_distance in [0.1,0.2,0.3]:
exercise_nonbonded(
nonbonded_type=geometry_restraints.nonbonded_gaussian,
repulsion_function=geometry_restraints.gaussian_repulsion_function(
max_residual=12,
norm_height_at_vdw_distance=norm_height_at_vdw_distance))
exercise_angle()
exercise_dihedral()
exercise_chirality(verbose="--verbose" in sys.argv[1:])
exercise_planarity()
print "OK"
def __init__(self,
si_structure,
distance_cutoff,
nonbonded_distance_cutoff=None,
nonbonded_buffer=1,
nonbonded_repulsion_function_type="gaussian",
nonbonded_max_residual_bond_stretch_factor=1.0,
n_trials=1,
n_macro_cycles=2,
max_exceptions_handled=10,
connectivities=None,
out=None,
dev=False):
assert nonbonded_repulsion_function_type in ["gaussian", "cos", "prolsq"]
assert n_trials > 0
assert n_macro_cycles > 0
assert max_exceptions_handled >= 0
if (out is None): out = sys.stdout
si_structure.show_summary(f=out).show_scatterers(f=out)
print >> out
out.flush()
def get_si_si_sym_table():
si_asu_mappings = si_structure.asu_mappings(
buffer_thickness=distance_cutoff)
asu_table = crystal.pair_asu_table(asu_mappings=si_asu_mappings)
asu_table.add_all_pairs(distance_cutoff=distance_cutoff)
si_si_sym_table = asu_table.extract_pair_sym_table()
si_pair_counts = si_structure.pair_sym_table_show_distances(
pair_sym_table=si_si_sym_table,
out=out)
if (connectivities is not None):
assert list(si_pair_counts) == connectivities
print >> out
return si_si_sym_table, si_pair_counts
si_si_sym_table, si_pair_counts = get_si_si_sym_table()
out.flush()
si_o = add_oxygen(
si_structure=si_structure,
si_si_sym_table=si_si_sym_table)
si_o.structure.show_summary(f=out).show_scatterers(f=out)
si_o_sst = si_o.structure.site_symmetry_table()
print >> out
out.flush()
si_o_pair_counts = si_o.structure.pair_sym_table_show_distances(
pair_sym_table=si_o.bond_sym_table,
out=out)
n_si = si_pair_counts.size()
n_si_o = si_o_pair_counts.size()
assert si_o_pair_counts[:n_si].all_eq(si_pair_counts)
assert si_o_pair_counts[n_si:].count(2) == n_si_o-n_si
print >> out
out.flush()
o_si_o_sym_table = make_o_si_o_sym_table(
si_o_structure=si_o.structure,
si_o_bond_sym_table=si_o.bond_sym_table)
o_si_o_pair_counts = si_o.structure.pair_sym_table_show_distances(
pair_sym_table=o_si_o_sym_table,
out=out)
assert o_si_o_pair_counts[:n_si].all_eq(0)
if (si_pair_counts.count(4) == n_si):
assert o_si_o_pair_counts[n_si:].all_eq(6)
print >> out
out.flush()
shell_sym_tables = crystal.coordination_sequences.shell_sym_tables(
full_pair_sym_table=si_o.bond_sym_table.full_connectivity(
site_symmetry_table=si_o_sst),
site_symmetry_table=si_o_sst,
max_shell=3)
if (1):
shell_sym_tables[0].add_pair_sym_table_in_place(other=si_si_sym_table)
if (1):
shell_sym_tables[0].add_pair_sym_table_in_place(other=o_si_o_sym_table)
shell_sym_tables = [_.tidy(site_symmetry_table=si_o_sst)
for _ in shell_sym_tables]
bond_params_table = setup_bond_params_table(
structure=si_o.structure,
bond_sym_table=shell_sym_tables[0])
nonbonded_params = setup_nonbonded_params()
nonbonded_types = flex.std_string()
for scatterer in si_o.structure.scatterers():
nonbonded_types.append(scatterer.scattering_type)
if (nonbonded_repulsion_function_type == "gaussian"):
nonbonded_function = geometry_restraints.gaussian_repulsion_function(
max_residual=bond_params_table.mean_residual(
bond_stretch_factor=nonbonded_max_residual_bond_stretch_factor))
if (nonbonded_distance_cutoff is None):
nonbonded_distance_cutoff = 7
elif (nonbonded_repulsion_function_type == "cos"):
nonbonded_function = geometry_restraints.cos_repulsion_function(
max_residual=bond_params_table.mean_residual(
bond_stretch_factor=nonbonded_max_residual_bond_stretch_factor))
else:
nonbonded_function = geometry_restraints.prolsq_repulsion_function()
geometry_restraints_manager = geometry_restraints.manager.manager(
crystal_symmetry=si_o.structure,
site_symmetry_table=si_o_sst,
bond_params_table=bond_params_table,
shell_sym_tables=shell_sym_tables,
nonbonded_params=nonbonded_params,
nonbonded_types=nonbonded_types,
nonbonded_function=nonbonded_function,
nonbonded_distance_cutoff=nonbonded_distance_cutoff,
nonbonded_buffer=nonbonded_buffer,
max_reasonable_bond_distance=100)
minimized = None
for i_trial in xrange(n_trials):
for i_exceptions_handled in xrange(max_exceptions_handled+1):
trial_structure = si_o.structure.deep_copy_scatterers()
if (i_trial > 0):
n_scatterers = trial_structure.scatterers().size()
trial_structure.set_sites_cart(flex.vec3_double(flex.random_double(
size=n_scatterers*3)*10-5))
trial_structure.apply_symmetry_sites()
trial_minimized = []
trial_sites_cart = None
for i_macro_cycle in xrange(n_macro_cycles):
if (trial_sites_cart is not None):
trial_structure.set_sites_cart(sites_cart=trial_sites_cart)
trial_structure = trial_structure.random_shift_sites(
max_shift_cart=0.2)
trial_structure.apply_symmetry_sites()
trial_sites_cart = trial_structure.sites_cart()
geometry_restraints_flags = geometry_restraints.flags.flags(
bond=True,
nonbonded=((i_macro_cycle % 2) != (n_macro_cycles % 2)))
if (not dev):
try:
m = geometry_restraints.lbfgs.lbfgs(
sites_cart=trial_sites_cart,
correct_special_position_tolerance=1.0,
geometry_restraints_manager=geometry_restraints_manager,
geometry_restraints_flags=geometry_restraints_flags,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=100),
lbfgs_exception_handling_params=
scitbx.lbfgs.exception_handling_parameters(
ignore_line_search_failed_step_at_lower_bound=True))
except RuntimeError, lbfgs_error:
if (i_trial == 0): raise
if (not str(lbfgs_error).startswith(
"Bond distance > max_reasonable_bond_distance: ")): raise
m = None
break
else:
trial_minimized.append(m)
trial_structure.set_sites_cart(sites_cart=trial_sites_cart)
else:
m = dev_lbfgs(
sites_cart=trial_sites_cart,
geometry_restraints_manager=geometry_restraints_manager,
geometry_restraints_flags=geometry_restraints_flags,
lbfgs_termination_params=scitbx.lbfgs.termination_parameters(
max_iterations=100),
lbfgs_exception_handling_params=
scitbx.lbfgs.exception_handling_parameters(
ignore_line_search_failed_step_at_lower_bound=True))
trial_minimized.append(m)
trial_structure.set_sites_cart(sites_cart=trial_sites_cart)
if (m is not None):
break
else:
raise RuntimeError(
"max_exceptions_handled=%d exceeded: %s" % (
max_exceptions_handled, str(lbfgs_error)))
ftr = trial_minimized[-1].final_target_result
pair_proxies = geometry_restraints_manager.pair_proxies(
sites_cart=trial_sites_cart)
min_nonbonded_distance = flex.min_default(
pair_proxies.nonbonded_proxies.deltas(sites_cart=trial_sites_cart),
None)
print >> out, \
"i_trial, bond, nonbonded, min distance: %d, %.6g, %.6g, %s" % (
i_trial,
ftr.bond_residual_sum,
ftr.nonbonded_residual_sum,
format_value(format="%.4g", value=min_nonbonded_distance))
out.flush()
if (minimized is None or minimized[-1].final_target_result.target
> trial_minimized[-1].final_target_result.target):
minimized = trial_minimized
minimized_structure = trial_structure
best_i_trial = i_trial
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(), end=' ')
print("simple:", pair_proxies.bond_proxies.simple.size(), end=' ')
print("sym:", pair_proxies.bond_proxies.asu.size())
print("pair_proxies.nonbonded_proxies.n_total():", \
pair_proxies.nonbonded_proxies.n_total(), end=' ')
print("simple:", pair_proxies.nonbonded_proxies.simple.size(), end=' ')
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" % next(i_pdb)
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(
plain_pair_sym_table=manager.plain_pair_sym_table,
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 range(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(
plain_pair_sym_table=manager.plain_pair_sym_table,
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(
plain_pair_sym_table=manager.plain_pair_sym_table,
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 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"
