def setup_bond_params_table(structure, bond_sym_table):
scatterers = structure.scatterers()
t = geometry_restraints.bond_params_table(scatterers.size())
for i_seq,bond_sym_dict in enumerate(bond_sym_table):
for j_seq in bond_sym_dict.keys():
i_seqs = [i_seq, j_seq]
i_seqs.sort()
scattering_types = [scatterers[i].scattering_type for i in i_seqs]
scattering_types.sort()
if (scattering_types == ["Si", "Si"]):
params = restraint_parameters_si_o_si
elif (scattering_types == ["O", "Si"]):
params = restraint_parameters_si_o
elif (scattering_types == ["O", "O"]):
params = restraint_parameters_o_si_o
else:
raise AssertionError("Unknown scattering type pair.")
if (not t[i_seq].has_key(j_seq)):
t[i_seq][j_seq] = geometry_restraints.bond_params(
distance_ideal=params.distance_ideal,
weight=params.weight)
else:
prev_params = t[i_seq][j_seq]
assert abs(prev_params.distance_ideal - params.distance_ideal) < 1.e-8
assert abs(prev_params.weight - params.weight) < 1.e-8
return t
def exercise_bond_sorted_asu_proxies(structure, distance_cutoff):
asu_mappings = structure.asu_mappings(buffer_thickness=distance_cutoff)
bond_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
bond_asu_table.add_all_pairs(distance_cutoff=distance_cutoff)
bond_sym_table = bond_asu_table.extract_pair_sym_table()
el = bond_sym_table.simple_edge_list()
es = bond_sym_table.full_simple_connectivity()
assert es.size() == bond_sym_table.size()
for i, j in el:
assert j in es[i]
assert i in es[j]
npis = bond_sym_table.number_of_pairs_involving_symmetry()
assert len(list(bond_sym_table.iterator())) == len(el) + npis
bond_params_table = geometry_restraints.bond_params_table(
structure.scatterers().size())
for i_seq, bond_sym_dict in enumerate(bond_sym_table):
for j_seq in bond_sym_dict.keys():
if (i_seq > j_seq):
j_seq, i_seq = i_seq, j_seq
bond_params_table[i_seq][j_seq] = geometry_restraints.bond_params(
distance_ideal=3.1, weight=1)
proxies_fast = geometry_restraints.bond_sorted_asu_proxies(
bond_params_table=bond_params_table, bond_asu_table=bond_asu_table)
proxies_conservative = geometry_restraints.bond_sorted_asu_proxies(
pair_asu_table=bond_asu_table)
pair_generator = crystal.neighbors_simple_pair_generator(
asu_mappings=asu_mappings,
distance_cutoff=distance_cutoff,
minimal=False)
proxies_slow = geometry_restraints.bond_sorted_asu_proxies(
asu_mappings=asu_mappings)
for pair in pair_generator:
proxies_slow.process(
geometry_restraints.bond_asu_proxy(pair=pair,
distance_ideal=3.1,
weight=1))
def compare_proxies(proxies_1, proxies_2):
assert proxies_1.simple.size() == proxies_2.simple.size()
assert proxies_1.asu.size() == proxies_2.asu.size()
ctrl = {}
for proxy in proxies_1.simple:
assert proxy.i_seqs not in ctrl
ctrl[proxy.i_seqs] = 0
for proxy in proxies_2.simple:
assert proxy.i_seqs in ctrl
ctrl[proxy.i_seqs] += 1
assert list(ctrl.values()) == [1] * len(ctrl)
ctrl = {}
for proxy in proxies_1.asu:
key = proxy.i_seq, proxy.j_seq, proxy.j_sym
assert key not in ctrl
ctrl[key] = 0
for proxy in proxies_2.asu:
key = proxy.i_seq, proxy.j_seq, proxy.j_sym
assert key in ctrl
ctrl[key] += 1
assert list(ctrl.values()) == [1] * len(ctrl)
compare_proxies(proxies_1=proxies_fast, proxies_2=proxies_conservative)
compare_proxies(proxies_1=proxies_fast, proxies_2=proxies_slow)
sites_cart = structure.sites_cart()
for proxy in proxies_conservative.simple:
i, j = proxy.i_seqs
assert approx_equal(
abs(matrix.col(sites_cart[i]) - matrix.col(sites_cart[j])),
proxy.distance_ideal)
assert proxy.weight == 1
distance = proxies_conservative.asu_mappings().unit_cell().distance
get_rt_mx_ji = proxies_conservative.asu_mappings().get_rt_mx_ji
sites_frac = structure.sites_frac()
for proxy in proxies_conservative.asu:
assert approx_equal(
distance(sites_frac[proxy.i_seq],
get_rt_mx_ji(pair=proxy) * sites_frac[proxy.j_seq]),
proxy.distance_ideal)
assert proxy.weight == 1
def exercise_bond_sorted_asu_proxies(
structure,
distance_cutoff):
asu_mappings = structure.asu_mappings(buffer_thickness=distance_cutoff)
bond_asu_table = crystal.pair_asu_table(asu_mappings=asu_mappings)
bond_asu_table.add_all_pairs(distance_cutoff=distance_cutoff)
bond_sym_table = bond_asu_table.extract_pair_sym_table()
el = bond_sym_table.simple_edge_list()
es = bond_sym_table.full_simple_connectivity()
assert es.size() == bond_sym_table.size()
for i,j in el:
assert j in es[i]
assert i in es[j]
npis = bond_sym_table.number_of_pairs_involving_symmetry()
assert len(list(bond_sym_table.iterator())) == len(el) + npis
bond_params_table = geometry_restraints.bond_params_table(
structure.scatterers().size())
for i_seq,bond_sym_dict in enumerate(bond_sym_table):
for j_seq in bond_sym_dict.keys():
if (i_seq > j_seq):
j_seq,i_seq = i_seq,j_seq
bond_params_table[i_seq][j_seq] = geometry_restraints.bond_params(
distance_ideal=3.1, weight=1)
proxies_fast = geometry_restraints.bond_sorted_asu_proxies(
bond_params_table=bond_params_table,
bond_asu_table=bond_asu_table)
proxies_conservative = geometry_restraints.bond_sorted_asu_proxies(
pair_asu_table=bond_asu_table)
pair_generator = crystal.neighbors_simple_pair_generator(
asu_mappings=asu_mappings,
distance_cutoff=distance_cutoff,
minimal=False)
proxies_slow = geometry_restraints.bond_sorted_asu_proxies(
asu_mappings=asu_mappings)
for pair in pair_generator:
proxies_slow.process(geometry_restraints.bond_asu_proxy(
pair=pair,
distance_ideal=3.1,
weight=1))
def compare_proxies(proxies_1, proxies_2):
assert proxies_1.simple.size() == proxies_2.simple.size()
assert proxies_1.asu.size() == proxies_2.asu.size()
ctrl = {}
for proxy in proxies_1.simple:
assert not ctrl.has_key(proxy.i_seqs)
ctrl[proxy.i_seqs] = 0
for proxy in proxies_2.simple:
assert ctrl.has_key(proxy.i_seqs)
ctrl[proxy.i_seqs] += 1
assert ctrl.values() == [1]*len(ctrl)
ctrl = {}
for proxy in proxies_1.asu:
key = proxy.i_seq,proxy.j_seq,proxy.j_sym
assert not ctrl.has_key(key)
ctrl[key] = 0
for proxy in proxies_2.asu:
key = proxy.i_seq,proxy.j_seq,proxy.j_sym
assert ctrl.has_key(key)
ctrl[key] += 1
assert ctrl.values() == [1]*len(ctrl)
compare_proxies(proxies_1=proxies_fast, proxies_2=proxies_conservative)
compare_proxies(proxies_1=proxies_fast, proxies_2=proxies_slow)
sites_cart = structure.sites_cart()
for proxy in proxies_conservative.simple:
i,j = proxy.i_seqs
assert approx_equal(
abs(matrix.col(sites_cart[i]) - matrix.col(sites_cart[j])),
proxy.distance_ideal)
assert proxy.weight == 1
distance = proxies_conservative.asu_mappings().unit_cell().distance
get_rt_mx_ji = proxies_conservative.asu_mappings().get_rt_mx_ji
sites_frac = structure.sites_frac()
for proxy in proxies_conservative.asu:
assert approx_equal(
distance(
sites_frac[proxy.i_seq],
get_rt_mx_ji(pair=proxy) * sites_frac[proxy.j_seq]),
proxy.distance_ideal)
assert proxy.weight == 1