def exercise_is_simple_interaction():
for space_group_symbol in ["P1", "P41"]:
for shifts in flex.nested_loop((-2, -2, -2), (2, 2, 2), False):
shifts = matrix.col(shifts)
structure = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=(10, 10, 20, 90, 90, 90),
space_group_symbol=space_group_symbol),
scatterers=flex.xray_scatterer([
xray.scatterer(label="O",
site=shifts + matrix.col((0, 0, 0))),
xray.scatterer(label="N",
site=shifts + matrix.col((0.5, 0.5, 0))),
xray.scatterer(label="C",
site=shifts + matrix.col((0.25, 0.25, 0)))
]))
asu_mappings = structure.asu_mappings(buffer_thickness=7)
pair_generator = crystal.neighbors_simple_pair_generator(
asu_mappings=asu_mappings, distance_cutoff=7)
simple_interactions = {}
for i_pair, pair in enumerate(pair_generator):
if (asu_mappings.is_simple_interaction(pair)):
assert asu_mappings_is_simple_interaction_emulation(
asu_mappings, pair)
key = (pair.i_seq, pair.j_seq)
assert simple_interactions.get(key, None) is None
simple_interactions[key] = 1
else:
assert not asu_mappings_is_simple_interaction_emulation(
asu_mappings, pair)
assert len(simple_interactions) == 2
assert simple_interactions[(0, 2)] == 1
assert simple_interactions[(1, 2)] == 1
def exercise_is_simple_interaction():
for space_group_symbol in ["P1", "P41"]:
for shifts in flex.nested_loop((-2,-2,-2),(2,2,2),False):
shifts = matrix.col(shifts)
structure = xray.structure(
crystal_symmetry=crystal.symmetry(
unit_cell=(10,10,20,90,90,90),
space_group_symbol=space_group_symbol),
scatterers=flex.xray_scatterer([
xray.scatterer(label="O", site=shifts+matrix.col((0,0,0))),
xray.scatterer(label="N", site=shifts+matrix.col((0.5,0.5,0))),
xray.scatterer(label="C", site=shifts+matrix.col((0.25,0.25,0)))]))
asu_mappings = structure.asu_mappings(buffer_thickness=7)
pair_generator = crystal.neighbors_simple_pair_generator(
asu_mappings=asu_mappings,
distance_cutoff=7)
simple_interactions = {}
for i_pair,pair in enumerate(pair_generator):
if (asu_mappings.is_simple_interaction(pair)):
assert asu_mappings_is_simple_interaction_emulation(
asu_mappings, pair)
key = (pair.i_seq,pair.j_seq)
assert simple_interactions.get(key, None) is None
simple_interactions[key] = 1
else:
assert not asu_mappings_is_simple_interaction_emulation(
asu_mappings, pair)
assert len(simple_interactions) == 2
assert simple_interactions[(0,2)] == 1
assert simple_interactions[(1,2)] == 1
def check_distances(sites_cart, point_distance, verbose):
asu_mappings = non_crystallographic_asu_mappings(sites_cart=sites_cart)
distance_cutoff = point_distance * math.sqrt(2) * 0.99
simple_pair_generator = crystal.neighbors_simple_pair_generator(
asu_mappings=asu_mappings,
distance_cutoff=distance_cutoff)
pair_generator = crystal.neighbors_fast_pair_generator(
asu_mappings=asu_mappings,
distance_cutoff=distance_cutoff)
assert simple_pair_generator.count_pairs() == pair_generator.count_pairs()
pair_generator.restart()
neighbors = {}
for pair in pair_generator:
assert pair.j_seq != pair.i_seq
assert pair.j_sym == 0
assert approx_equal(pair.dist_sq, point_distance**2)
neighbors[pair.i_seq] = neighbors.get(pair.i_seq, 0) + 1
neighbors[pair.j_seq] = neighbors.get(pair.j_seq, 0) + 1
n_dict = {}
for n in neighbors.values():
n_dict[n] = n_dict.get(n, 0) + 1
if (verbose):
print n_dict
if (len(neighbors) > 0):
assert max(neighbors.values()) <= 12
def check_distances(sites_cart, point_distance, verbose):
asu_mappings = non_crystallographic_asu_mappings(sites_cart=sites_cart)
distance_cutoff = point_distance * math.sqrt(2) * 0.99
simple_pair_generator = crystal.neighbors_simple_pair_generator(
asu_mappings=asu_mappings, distance_cutoff=distance_cutoff)
pair_generator = crystal.neighbors_fast_pair_generator(
asu_mappings=asu_mappings, distance_cutoff=distance_cutoff)
assert simple_pair_generator.count_pairs() == pair_generator.count_pairs()
pair_generator.restart()
neighbors = {}
for pair in pair_generator:
assert pair.j_seq != pair.i_seq
assert pair.j_sym == 0
assert approx_equal(pair.dist_sq, point_distance**2)
neighbors[pair.i_seq] = neighbors.get(pair.i_seq, 0) + 1
neighbors[pair.j_seq] = neighbors.get(pair.j_seq, 0) + 1
n_dict = {}
for n in neighbors.values():
n_dict[n] = n_dict.get(n, 0) + 1
if (verbose):
print(n_dict)
if (len(neighbors) > 0):
assert max(neighbors.values()) <= 12
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
