def exercise_stl_vector_unsigned(): a = shared.stl_vector_unsigned() assert a.size() == 0 assert len(a) == 0 a.append([]) assert a.size() == 1 a.append([1]) assert len(a) == 2 a.append([1,2]) assert native(a) == [(), (1,), (1, 2)] a.extend(a) a.reserve(len(a) + 100) assert native(a) == [(), (1,), (1, 2), (), (1,), (1, 2)] a.insert(1, [2,3]) assert native(a) == [(), (2,3), (1,), (1, 2), (), (1,), (1, 2)] a[4] = [3,4] assert native(a) == [(), (2,3), (1,), (1, 2), (3,4), (1,), (1, 2)] a = a[2:5] assert native(a) == [(1,), (1, 2), (3, 4)] del a[0] assert native(a) == [(1, 2), (3, 4)] a.append([2,3]) a.append([5,6]) assert native(a) == [(1, 2), (3, 4), (2, 3), (5, 6)] del a[1:3] assert native(a) == [(1, 2), (5, 6)] del a[:] assert a.size() == 0 a.append([1,2]) a.append([2,3]) a.append([3,4]) del a[-1:] assert native(a) == [(1, 2), (2, 3)] del a[:1] assert native(a) == [(2, 3)] b = a.deep_copy() assert native(b) == [(2, 3)] a.clear() assert a.size() == 0 assert b.size() == 1 a = shared.stl_vector_unsigned([[1,2],[2,3]]) assert native(a) == [(1, 2), (2, 3)] a = shared.stl_vector_unsigned(0) assert native(a) == [] a = shared.stl_vector_unsigned(3) assert native(a) == [(),(),()] a = shared.stl_vector_unsigned(3, [1,2]) assert native(a) == [(1,2),(1,2),(1,2)]
def exercise_stl_set_unsigned():
a = shared.stl_set_unsigned()
assert a.size() == 0
a = shared.stl_set_unsigned([(2,1)])
assert a.size() == 1
assert tuple(a[0]) == (1, 2)
a = shared.stl_set_unsigned([(2,1),(3,5,2)])
assert native(a) == [(1, 2), (2, 3, 5)]
#
from scitbx.array_family import flex
b = shared.stl_vector_unsigned()
s = flex.size_t()
a.append_union_of_selected_arrays(arrays=b, selection=s)
assert a.size() == 3
assert a[2].size() == 0
b.append([2,1])
b.append([])
b.append([4,3,2])
s.append(2)
s.append(1)
a.append_union_of_selected_arrays(arrays=b, selection=s)
assert tuple(a[3]) == (2,3,4)
s[1] = 0
a.append_union_of_selected_arrays(arrays=b, selection=s)
assert tuple(a[4]) == (1,2,3,4)
assert native(a) == [(1, 2), (2, 3, 5), (), (2, 3, 4), (1, 2, 3, 4)]
#
s = pickle.dumps(a, 1)
l = pickle.loads(s)
assert len(l) == len(a)
for ae,le in zip(a,l):
assert list(ae) == list(le)
def __init__(O, labels, sites_cart, masses, geo_manager):
from scitbx.array_family import shared
edge_list = geo_manager.simple_edge_list(omit_slack_greater_than=0)
tt = scitbx.graph.tardy_tree.construct(
n_vertices=len(sites_cart),
edge_list=edge_list,
external_clusters=geo_manager.rigid_clusters_due_to_dihedrals_and_planes(
constrain_dihedrals_with_sigma_less_than=10))
orcs = tt.cluster_manager.overlapping_rigid_clusters(
edge_sets=tt.edge_sets)
O.labels = flex.std_string()
O.sites_cart = flex.vec3_double()
O.masses = flex.double()
O.indices = []
O.external_clusters = []
O.related_x_i_seqs = shared.stl_vector_unsigned(sites_cart.size())
orca_dof = 0
for i_orc,orc in enumerate(orcs):
external_cluster = []
for i_seq in orc:
x_i_seq = len(O.sites_cart)
O.related_x_i_seqs[i_seq].append(x_i_seq)
external_cluster.append(x_i_seq)
O.labels.append("%s:%d" % (labels[i_seq], i_orc))
O.sites_cart.append(sites_cart[i_seq])
O.masses.append(masses[i_seq])
O.indices.append((i_orc, i_seq))
O.external_clusters.append(external_cluster)
if (len(orc) == 1):
orca_dof += 3
elif (len(orc) == 2):
orca_dof += 5
else:
orca_dof += 6
print "sites_cart.size():", sites_cart.size()
print "O.sites_cart.size():", O.sites_cart.size()
print "original Cartesian dof:", sites_cart.size()*3
print "orca dof:", orca_dof
for i_seq,x_i_seqs in enumerate(O.related_x_i_seqs):
O.masses /= len(x_i_seqs)
# XXX find more direct way to get x_edge_list
x_edge_list = []
for i,j in edge_list:
for x_i in O.related_x_i_seqs[i]:
i_orc = O.indices[x_i][0]
for x_j in O.related_x_i_seqs[j]:
j_orc = O.indices[x_j][0]
if (i_orc == j_orc):
x_edge_list.append(tuple(sorted((x_i,x_j))))
O.tardy_tree = scitbx.graph.tardy_tree.construct(
sites=O.sites_cart,
edge_list=x_edge_list,
external_clusters=O.external_clusters)
x_model_indices = expand_model_or_conformer_indices(
indices=geo_manager.model_indices,
x_n_seq=O.sites_cart.size(),
related_x_i_seqs=O.related_x_i_seqs)
x_conformer_indices = expand_model_or_conformer_indices(
indices=geo_manager.conformer_indices,
x_n_seq=O.sites_cart.size(),
related_x_i_seqs=O.related_x_i_seqs)
x_site_symmetry_table = expand_site_symmetry_table(
site_symmetry_table=geo_manager.site_symmetry_table,
x_n_seq=O.sites_cart.size(),
related_x_i_seqs=O.related_x_i_seqs)
x_bond_params_table = expand_bond_params_table(
bond_params_table=geo_manager.bond_params_table,
x_n_seq=O.sites_cart.size(),
related_x_i_seqs=O.related_x_i_seqs)
x_shell_sym_tables = []
for shell_sym_table in geo_manager.shell_sym_tables:
x_shell_sym_tables.append(expand_pair_sym_table(
pair_sym_table=shell_sym_table,
x_n_seq=O.sites_cart.size(),
related_x_i_seqs=O.related_x_i_seqs))
x_nonbonded_types = expand_nonbonded_types(
nonbonded_types=geo_manager.nonbonded_types,
x_n_seq=O.sites_cart.size(),
related_x_i_seqs=O.related_x_i_seqs)
x_angle_proxies = expand_angle_proxies(
angle_proxies=geo_manager.angle_proxies,
x_n_seq=O.sites_cart.size(),
related_x_i_seqs=O.related_x_i_seqs)
x_dihedral_proxies = expand_dihedral_or_chirality_proxies(
proxies=geo_manager.dihedral_proxies,
proxy_type=cctbx.geometry_restraints.dihedral_proxy,
proxy_array_type=cctbx.geometry_restraints.shared_dihedral_proxy,
x_n_seq=O.sites_cart.size(),
related_x_i_seqs=O.related_x_i_seqs)
x_chirality_proxies = expand_dihedral_or_chirality_proxies(
proxies=geo_manager.chirality_proxies,
proxy_type=cctbx.geometry_restraints.chirality_proxy,
proxy_array_type=cctbx.geometry_restraints.shared_chirality_proxy,
x_n_seq=O.sites_cart.size(),
related_x_i_seqs=O.related_x_i_seqs)
x_planarity_proxies = expand_planarity_proxies(
planarity_proxies=geo_manager.planarity_proxies,
x_n_seq=O.sites_cart.size(),
related_x_i_seqs=O.related_x_i_seqs)
O.geo_manager = cctbx.geometry_restraints.manager.manager(
crystal_symmetry=geo_manager.crystal_symmetry,
model_indices=x_model_indices,
conformer_indices=x_conformer_indices,
site_symmetry_table=x_site_symmetry_table,
bond_params_table=x_bond_params_table,
shell_sym_tables=x_shell_sym_tables,
nonbonded_params=geo_manager.nonbonded_params,
nonbonded_types=x_nonbonded_types,
nonbonded_function=geo_manager.nonbonded_function,
nonbonded_distance_cutoff=geo_manager.nonbonded_distance_cutoff,
nonbonded_buffer=geo_manager.nonbonded_buffer,
angle_proxies=x_angle_proxies,
dihedral_proxies=x_dihedral_proxies,
chirality_proxies=x_chirality_proxies,
planarity_proxies=x_planarity_proxies,
plain_pairs_radius=geo_manager.plain_pairs_radius,
max_reasonable_bond_distance=geo_manager.max_reasonable_bond_distance,
min_cubicle_edge=geo_manager.min_cubicle_edge)
O.tardy_tree_rmsd_calculator = None
def __init__(O, labels, sites_cart, masses, geo_manager):
from scitbx.array_family import shared
edge_list = geo_manager.simple_edge_list(omit_slack_greater_than=0)
tt = scitbx.graph.tardy_tree.construct(
n_vertices=len(sites_cart),
edge_list=edge_list,
external_clusters=geo_manager.
rigid_clusters_due_to_dihedrals_and_planes(
constrain_dihedrals_with_sigma_less_than=10))
orcs = tt.cluster_manager.overlapping_rigid_clusters(
edge_sets=tt.edge_sets)
O.labels = flex.std_string()
O.sites_cart = flex.vec3_double()
O.masses = flex.double()
O.indices = []
O.external_clusters = []
O.related_x_i_seqs = shared.stl_vector_unsigned(sites_cart.size())
orca_dof = 0
for i_orc, orc in enumerate(orcs):
external_cluster = []
for i_seq in orc:
x_i_seq = len(O.sites_cart)
O.related_x_i_seqs[i_seq].append(x_i_seq)
external_cluster.append(x_i_seq)
O.labels.append("%s:%d" % (labels[i_seq], i_orc))
O.sites_cart.append(sites_cart[i_seq])
O.masses.append(masses[i_seq])
O.indices.append((i_orc, i_seq))
O.external_clusters.append(external_cluster)
if (len(orc) == 1):
orca_dof += 3
elif (len(orc) == 2):
orca_dof += 5
else:
orca_dof += 6
print "sites_cart.size():", sites_cart.size()
print "O.sites_cart.size():", O.sites_cart.size()
print "original Cartesian dof:", sites_cart.size() * 3
print "orca dof:", orca_dof
for i_seq, x_i_seqs in enumerate(O.related_x_i_seqs):
O.masses /= len(x_i_seqs)
# XXX find more direct way to get x_edge_list
x_edge_list = []
for i, j in edge_list:
for x_i in O.related_x_i_seqs[i]:
i_orc = O.indices[x_i][0]
for x_j in O.related_x_i_seqs[j]:
j_orc = O.indices[x_j][0]
if (i_orc == j_orc):
x_edge_list.append(tuple(sorted((x_i, x_j))))
O.tardy_tree = scitbx.graph.tardy_tree.construct(
sites=O.sites_cart,
edge_list=x_edge_list,
external_clusters=O.external_clusters)
x_model_indices = expand_model_or_conformer_indices(
indices=geo_manager.model_indices,
x_n_seq=O.sites_cart.size(),
related_x_i_seqs=O.related_x_i_seqs)
x_conformer_indices = expand_model_or_conformer_indices(
indices=geo_manager.conformer_indices,
x_n_seq=O.sites_cart.size(),
related_x_i_seqs=O.related_x_i_seqs)
x_site_symmetry_table = expand_site_symmetry_table(
site_symmetry_table=geo_manager.site_symmetry_table,
x_n_seq=O.sites_cart.size(),
related_x_i_seqs=O.related_x_i_seqs)
x_bond_params_table = expand_bond_params_table(
bond_params_table=geo_manager.bond_params_table,
x_n_seq=O.sites_cart.size(),
related_x_i_seqs=O.related_x_i_seqs)
x_shell_sym_tables = []
for shell_sym_table in geo_manager.shell_sym_tables:
x_shell_sym_tables.append(
expand_pair_sym_table(pair_sym_table=shell_sym_table,
x_n_seq=O.sites_cart.size(),
related_x_i_seqs=O.related_x_i_seqs))
x_nonbonded_types = expand_nonbonded_types(
nonbonded_types=geo_manager.nonbonded_types,
x_n_seq=O.sites_cart.size(),
related_x_i_seqs=O.related_x_i_seqs)
x_angle_proxies = expand_angle_proxies(
angle_proxies=geo_manager.angle_proxies,
x_n_seq=O.sites_cart.size(),
related_x_i_seqs=O.related_x_i_seqs)
x_dihedral_proxies = expand_dihedral_or_chirality_proxies(
proxies=geo_manager.dihedral_proxies,
proxy_type=cctbx.geometry_restraints.dihedral_proxy,
proxy_array_type=cctbx.geometry_restraints.shared_dihedral_proxy,
x_n_seq=O.sites_cart.size(),
related_x_i_seqs=O.related_x_i_seqs)
x_chirality_proxies = expand_dihedral_or_chirality_proxies(
proxies=geo_manager.chirality_proxies,
proxy_type=cctbx.geometry_restraints.chirality_proxy,
proxy_array_type=cctbx.geometry_restraints.shared_chirality_proxy,
x_n_seq=O.sites_cart.size(),
related_x_i_seqs=O.related_x_i_seqs)
x_planarity_proxies = expand_planarity_proxies(
planarity_proxies=geo_manager.planarity_proxies,
x_n_seq=O.sites_cart.size(),
related_x_i_seqs=O.related_x_i_seqs)
O.geo_manager = cctbx.geometry_restraints.manager.manager(
crystal_symmetry=geo_manager.crystal_symmetry,
model_indices=x_model_indices,
conformer_indices=x_conformer_indices,
site_symmetry_table=x_site_symmetry_table,
bond_params_table=x_bond_params_table,
shell_sym_tables=x_shell_sym_tables,
nonbonded_params=geo_manager.nonbonded_params,
nonbonded_types=x_nonbonded_types,
nonbonded_function=geo_manager.nonbonded_function,
nonbonded_distance_cutoff=geo_manager.nonbonded_distance_cutoff,
nonbonded_buffer=geo_manager.nonbonded_buffer,
angle_proxies=x_angle_proxies,
dihedral_proxies=x_dihedral_proxies,
chirality_proxies=x_chirality_proxies,
planarity_proxies=x_planarity_proxies,
plain_pairs_radius=geo_manager.plain_pairs_radius,
max_reasonable_bond_distance=geo_manager.
max_reasonable_bond_distance,
min_cubicle_edge=geo_manager.min_cubicle_edge)
O.tardy_tree_rmsd_calculator = None
