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 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
