def angles(O):
return graph_utils.extract_edge_list(
graph_utils.bond_bending_edge_sets(
edge_sets=graph_utils.construct_edge_sets(
n_vertices=len(O.sites),
edge_list=O.bonds),
omit_bonds=True))
def angles(O):
return graph_utils.extract_edge_list(
graph_utils.bond_bending_edge_sets(
edge_sets=graph_utils.construct_edge_sets(n_vertices=len(
O.sites),
edge_list=O.bonds),
omit_bonds=True))
def arch_dof(n_vertices, edge_list):
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=edge_list)
bbes = utils.bond_bending_edge_sets(edge_sets=es)
bbel = utils.extract_edge_list(edge_sets=bbes)
dofs = [rigidity.determine_degrees_of_freedom(
n_dim=3, n_vertices=n_vertices, edge_list=bbel, method=method)
for method in ["float", "integer"]]
assert dofs[0] == dofs[1]
return es, dofs[0]
def arch_dof(n_vertices, edge_list):
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=edge_list)
bbes = utils.bond_bending_edge_sets(edge_sets=es)
bbel = utils.extract_edge_list(edge_sets=bbes)
dofs = [rigidity.determine_degrees_of_freedom(
n_dim=3, n_vertices=n_vertices, edge_list=bbel, method=method)
for method in ["float", "integer"]]
assert dofs[0] == dofs[1]
return es, dofs[0]
def build_clash_detector(n_sites, bond_list, threshold):
import scitbx.r3_utils
result = scitbx.r3_utils.clash_detector_simple(
n_sites=n_sites, threshold=threshold)
from scitbx.graph import utils
bond_sets = utils.construct_edge_sets(
n_vertices=n_sites, edge_list=bond_list)
def add_exclusions(edge_sets):
for i,edge_set in enumerate(edge_sets):
for j in edge_set:
if (i < j):
result.add_exclusion(i=i, j=j)
add_exclusions(edge_sets=bond_sets)
angle_sets = utils.bond_bending_edge_sets(edge_sets=bond_sets)
add_exclusions(edge_sets=angle_sets)
for i,j in utils.potential_implied_edge_list(
edge_sets=bond_sets, bond_bending_edge_sets=angle_sets):
result.add_exclusion(i=i, j=j)
return result
def run(args):
assert len(args) == 0
#
el = []
n_vertices = 0
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
assert len(es) == 0
bbes = utils.bond_bending_edge_sets(edge_sets=es)
assert len(bbes) == 0
bbel = utils.extract_edge_list(edge_sets=bbes)
assert len(bbel) == 0
piel = utils.potential_implied_edge_list(
edge_sets=es, bond_bending_edge_sets=bbes)
assert len(piel) == 0
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
assert len(bbesob) == 0
#
el = [(0,1), (1,2), (2,3)]
n_vertices = 4
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
assert len(es) == n_vertices
bbes = utils.bond_bending_edge_sets(edge_sets=es)
assert len(bbes) == n_vertices
bbel = utils.extract_edge_list(edge_sets=bbes)
assert bbel == [(0,1), (0,2), (1,2), (1,3), (2,3)]
assert set(el).issubset(set(bbel))
piel = utils.potential_implied_edge_list(
edge_sets=es, bond_bending_edge_sets=bbes)
assert piel == [(0,3)]
assert set(bbel).isdisjoint(set(piel))
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
assert len(bbesob) == n_vertices
bbelob = utils.extract_edge_list(edge_sets=bbesob)
assert bbelob == [(0,2), (1,3)]
#
el = [(0,1), (1,2), (2,3), (3,4), (4,5), (5,6), (6,7)]
n_vertices = 8
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
bbes = utils.bond_bending_edge_sets(edge_sets=es)
bbel = utils.extract_edge_list(edge_sets=bbes)
assert bbel == [
(0, 1), (0, 2),
(1, 2), (1, 3),
(2, 3), (2, 4),
(3, 4), (3, 5),
(4, 5), (4, 6),
(5, 6), (5, 7),
(6, 7)]
assert set(el).issubset(set(bbel))
piel = utils.potential_implied_edge_list(
edge_sets=es, bond_bending_edge_sets=bbes)
assert piel == [(0,3), (1,4), (2,5), (3,6), (4,7)]
assert set(bbel).isdisjoint(set(piel))
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
bbelob = utils.extract_edge_list(edge_sets=bbesob)
assert bbelob == [
(0, 2),
(1, 3),
(2, 4),
(3, 5),
(4, 6),
(5, 7)]
#
el = [(0,1), (1,2), (2,3), (0,3)]
n_vertices = 4
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
bbes = utils.bond_bending_edge_sets(edge_sets=es)
bbel = utils.extract_edge_list(edge_sets=bbes)
assert bbel == [(0,1), (0,2), (0,3), (1,2), (1,3), (2,3)]
assert set(el).issubset(set(bbel))
piel = utils.potential_implied_edge_list(
edge_sets=es, bond_bending_edge_sets=bbes)
assert piel == []
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
bbelob = utils.extract_edge_list(edge_sets=bbesob)
assert bbelob == [(0, 2), (1, 3)]
#
el = [(0,1), (1,2), (2,3), (3,4), (4,5), (0,5)]
n_vertices = 6
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
bbes = utils.bond_bending_edge_sets(edge_sets=es)
bbel = utils.extract_edge_list(edge_sets=bbes)
assert bbel == [
(0,1), (0,2), (0,4), (0,5),
(1,2), (1,3), (1,5),
(2,3), (2,4),
(3,4), (3,5),
(4,5)]
assert set(el).issubset(set(bbel))
piel = utils.potential_implied_edge_list(
edge_sets=es, bond_bending_edge_sets=bbes)
assert piel == [(0,3), (1,4), (2,5)]
assert set(bbel).isdisjoint(set(piel))
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
bbelob = utils.extract_edge_list(edge_sets=bbesob)
assert bbelob == [
(0,2), (0,4),
(1,3), (1,5),
(2,4),
(3,5)]
#
el = [(0,1), (1,2), (2,3), (2,6), (3,4), (3,7), (4,5), (0,5)]
n_vertices = 8
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
bbes = utils.bond_bending_edge_sets(edge_sets=es)
bbel = utils.extract_edge_list(edge_sets=bbes)
assert bbel == [
(0,1), (0,2), (0,4), (0,5),
(1,2), (1,3), (1,5), (1,6),
(2,3), (2,4), (2,6), (2,7),
(3,4), (3,5), (3,6), (3,7),
(4,5), (4,7)]
assert set(el).issubset(set(bbel))
piel = utils.potential_implied_edge_list(
edge_sets=es, bond_bending_edge_sets=bbes)
assert piel == [(0,3), (0,6), (1,4), (1,7), (2,5), (4,6), (5,7), (6,7)]
assert set(bbel).isdisjoint(set(piel))
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
bbelob = utils.extract_edge_list(edge_sets=bbesob)
assert bbelob == [
(0,2), (0,4),
(1,3), (1,5), (1,6),
(2,4), (2,7),
(3,5), (3,6),
(4,7)]
#
el = [(0,1), (1,2), (2,3), (2,6), (3,4), (3,7), (4,5), (0,5)]
n_vertices = 8
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
sub = utils.sub_edge_list(edge_sets=es, vertex_indices=[])
assert len(sub.edge_list) == 0
assert len(sub.edge_sets()) == 0
sub = utils.sub_edge_list(edge_sets=es, vertex_indices=[1])
assert len(sub.edge_list) == 0
assert len(sub.edge_sets()) == 1
sub = utils.sub_edge_list(edge_sets=es, vertex_indices=[1,3])
assert len(sub.edge_list) == 0
assert len(sub.edge_sets()) == 2
sub = utils.sub_edge_list(edge_sets=es, vertex_indices=[1,0])
assert sub.edge_list == [(0,1)]
assert len(sub.edge_sets()) == 2
assert sub.reindexing_dict == {0: 1, 1: 0}
sub = utils.sub_edge_list(edge_sets=es, vertex_indices=[6,7,3,2])
assert sub.edge_list == [(1,2), (2,3), (0,3)]
assert len(sub.edge_sets()) == 4
assert sub.reindexing_dict == {2: 3, 3: 2, 6: 0, 7: 1}
#
exercise_tree_marking()
#
print "OK"
def run(args):
assert len(args) == 0
#
el = []
n_vertices = 0
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
assert len(es) == 0
bbes = utils.bond_bending_edge_sets(edge_sets=es)
assert len(bbes) == 0
bbel = utils.extract_edge_list(edge_sets=bbes)
assert len(bbel) == 0
piel = utils.potential_implied_edge_list(edge_sets=es,
bond_bending_edge_sets=bbes)
assert len(piel) == 0
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
assert len(bbesob) == 0
#
el = [(0, 1), (1, 2), (2, 3)]
n_vertices = 4
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
assert len(es) == n_vertices
bbes = utils.bond_bending_edge_sets(edge_sets=es)
assert len(bbes) == n_vertices
bbel = utils.extract_edge_list(edge_sets=bbes)
assert bbel == [(0, 1), (0, 2), (1, 2), (1, 3), (2, 3)]
assert set(el).issubset(set(bbel))
piel = utils.potential_implied_edge_list(edge_sets=es,
bond_bending_edge_sets=bbes)
assert piel == [(0, 3)]
assert set(bbel).isdisjoint(set(piel))
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
assert len(bbesob) == n_vertices
bbelob = utils.extract_edge_list(edge_sets=bbesob)
assert bbelob == [(0, 2), (1, 3)]
#
el = [(0, 1), (1, 2), (2, 3), (3, 4), (4, 5), (5, 6), (6, 7)]
n_vertices = 8
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
bbes = utils.bond_bending_edge_sets(edge_sets=es)
bbel = utils.extract_edge_list(edge_sets=bbes)
assert bbel == [(0, 1), (0, 2), (1, 2), (1, 3), (2, 3), (2, 4), (3, 4),
(3, 5), (4, 5), (4, 6), (5, 6), (5, 7), (6, 7)]
assert set(el).issubset(set(bbel))
piel = utils.potential_implied_edge_list(edge_sets=es,
bond_bending_edge_sets=bbes)
assert piel == [(0, 3), (1, 4), (2, 5), (3, 6), (4, 7)]
assert set(bbel).isdisjoint(set(piel))
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
bbelob = utils.extract_edge_list(edge_sets=bbesob)
assert bbelob == [(0, 2), (1, 3), (2, 4), (3, 5), (4, 6), (5, 7)]
#
el = [(0, 1), (1, 2), (2, 3), (0, 3)]
n_vertices = 4
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
bbes = utils.bond_bending_edge_sets(edge_sets=es)
bbel = utils.extract_edge_list(edge_sets=bbes)
assert bbel == [(0, 1), (0, 2), (0, 3), (1, 2), (1, 3), (2, 3)]
assert set(el).issubset(set(bbel))
piel = utils.potential_implied_edge_list(edge_sets=es,
bond_bending_edge_sets=bbes)
assert piel == []
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
bbelob = utils.extract_edge_list(edge_sets=bbesob)
assert bbelob == [(0, 2), (1, 3)]
#
el = [(0, 1), (1, 2), (2, 3), (3, 4), (4, 5), (0, 5)]
n_vertices = 6
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
bbes = utils.bond_bending_edge_sets(edge_sets=es)
bbel = utils.extract_edge_list(edge_sets=bbes)
assert bbel == [(0, 1), (0, 2), (0, 4), (0, 5), (1, 2), (1, 3), (1, 5),
(2, 3), (2, 4), (3, 4), (3, 5), (4, 5)]
assert set(el).issubset(set(bbel))
piel = utils.potential_implied_edge_list(edge_sets=es,
bond_bending_edge_sets=bbes)
assert piel == [(0, 3), (1, 4), (2, 5)]
assert set(bbel).isdisjoint(set(piel))
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
bbelob = utils.extract_edge_list(edge_sets=bbesob)
assert bbelob == [(0, 2), (0, 4), (1, 3), (1, 5), (2, 4), (3, 5)]
#
el = [(0, 1), (1, 2), (2, 3), (2, 6), (3, 4), (3, 7), (4, 5), (0, 5)]
n_vertices = 8
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
bbes = utils.bond_bending_edge_sets(edge_sets=es)
bbel = utils.extract_edge_list(edge_sets=bbes)
assert bbel == [(0, 1), (0, 2), (0, 4), (0, 5), (1, 2), (1, 3), (1, 5),
(1, 6), (2, 3), (2, 4), (2, 6), (2, 7), (3, 4), (3, 5),
(3, 6), (3, 7), (4, 5), (4, 7)]
assert set(el).issubset(set(bbel))
piel = utils.potential_implied_edge_list(edge_sets=es,
bond_bending_edge_sets=bbes)
assert piel == [(0, 3), (0, 6), (1, 4), (1, 7), (2, 5), (4, 6), (5, 7),
(6, 7)]
assert set(bbel).isdisjoint(set(piel))
bbesob = utils.bond_bending_edge_sets(edge_sets=es, omit_bonds=True)
bbelob = utils.extract_edge_list(edge_sets=bbesob)
assert bbelob == [(0, 2), (0, 4), (1, 3), (1, 5), (1, 6), (2, 4), (2, 7),
(3, 5), (3, 6), (4, 7)]
#
el = [(0, 1), (1, 2), (2, 3), (2, 6), (3, 4), (3, 7), (4, 5), (0, 5)]
n_vertices = 8
es = utils.construct_edge_sets(n_vertices=n_vertices, edge_list=el)
sub = utils.sub_edge_list(edge_sets=es, vertex_indices=[])
assert len(sub.edge_list) == 0
assert len(sub.edge_sets()) == 0
sub = utils.sub_edge_list(edge_sets=es, vertex_indices=[1])
assert len(sub.edge_list) == 0
assert len(sub.edge_sets()) == 1
sub = utils.sub_edge_list(edge_sets=es, vertex_indices=[1, 3])
assert len(sub.edge_list) == 0
assert len(sub.edge_sets()) == 2
sub = utils.sub_edge_list(edge_sets=es, vertex_indices=[1, 0])
assert sub.edge_list == [(0, 1)]
assert len(sub.edge_sets()) == 2
assert sub.reindexing_dict == {0: 1, 1: 0}
sub = utils.sub_edge_list(edge_sets=es, vertex_indices=[6, 7, 3, 2])
assert sub.edge_list == [(1, 2), (2, 3), (0, 3)]
assert len(sub.edge_sets()) == 4
assert sub.reindexing_dict == {2: 3, 3: 2, 6: 0, 7: 1}
#
exercise_tree_marking()
#
print("OK")
