def __init__(
self,
molecule1,
molecule2,
prematched=[],
vertex_equality=None,
edge_equality=None,
maxsol=0,
):
if vertex_equality is None:
import operator
vertex_equality = operator.eq
if edge_equality is None:
import operator
edge_equality = operator.eq
self.molecule1 = molecule1.atom_for
self.molecule2 = molecule2.atom_for
self.best = [[]]
self.largest = 0
from graph import maximum_clique
self.compat_graph = maximum_clique.compatibility_graph(
first=molecule1.graph,
second=molecule2.graph,
vertex_equality=vertex_equality,
edge_equality=edge_equality)
self.prematched = prematched
if self.prematched:
desc_for_1 = molecule1.descriptor_for
desc_for_2 = molecule2.descriptor_for
pairs = set([(desc_for_1[l], desc_for_2[r])
for (l, r) in self.prematched])
vertices = [
v for v in self.compat_graph.vertices()
if self.compat_graph.vertex_label(vertex=v) in pairs
]
assert len(vertices) == len(self.prematched)
neighbours = set(
self.compat_graph.adjacent_vertices(vertex=vertices[0]))
for v in vertices[1:]:
neighbours.intersection_update(
self.compat_graph.adjacent_vertices(vertex=v))
self.compat_graph = maximum_clique.selected_subgraph(
graph=self.compat_graph,
vertices=neighbours,
)
self.result = maximum_clique.greedy(graph=self.compat_graph,
maxsol=maxsol)
def __init__(
self,
molecule1,
molecule2,
prematched = [],
vertex_equality = None,
edge_equality = None,
maxsol = 0,
):
if vertex_equality is None:
import operator
vertex_equality = operator.eq
if edge_equality is None:
import operator
edge_equality = operator.eq
self.molecule1 = molecule1.atom_for
self.molecule2 = molecule2.atom_for
self.best = [ [] ]
self.largest = 0
from graph import maximum_clique
self.compat_graph = maximum_clique.compatibility_graph(
first = molecule1.graph,
second = molecule2.graph,
vertex_equality = vertex_equality,
edge_equality = edge_equality
)
self.prematched = prematched
if self.prematched:
desc_for_1 = molecule1.descriptor_for
desc_for_2 = molecule2.descriptor_for
pairs = set(
[ ( desc_for_1[ l ], desc_for_2[ r ] ) for ( l, r ) in self.prematched ]
)
vertices = [ v for v in self.compat_graph.vertices()
if self.compat_graph.vertex_label( vertex = v ) in pairs ]
assert len( vertices ) == len( self.prematched )
neighbours = set( self.compat_graph.adjacent_vertices( vertex = vertices[0] ) )
for v in vertices[1:]:
neighbours.intersection_update( self.compat_graph.adjacent_vertices( vertex = v ) )
self.compat_graph = maximum_clique.selected_subgraph(
graph = self.compat_graph,
vertices = neighbours,
)
self.result = maximum_clique.greedy( graph = self.compat_graph, maxsol = maxsol )
def manipulation(self, left, right):
u1 = left.add_vertex( label = "O" )
u2 = left.add_vertex( label = "C" )
u3 = left.add_vertex( label = "C" )
u4 = left.add_vertex( label = "N" )
u5 = left.add_vertex( label = "O" )
left.add_edge( vertex1 = u1, vertex2 = u2, weight = 1 )
left.add_edge( vertex1 = u2, vertex2 = u3, weight = 1 )
left.add_edge( vertex1 = u3, vertex2 = u4, weight = 1 )
left.add_edge( vertex1 = u3, vertex2 = u5, weight = 2 )
v1 = right.add_vertex( label = "O" )
v2 = right.add_vertex( label = "C" )
v3 = right.add_vertex( label = "C" )
v4 = right.add_vertex( label = "N" )
v5 = right.add_vertex( label = "O" )
right.add_edge( vertex1 = v1, vertex2 = v2, weight = 2 )
right.add_edge( vertex1 = v2, vertex2 = v3, weight = 1 )
right.add_edge( vertex1 = v3, vertex2 = v4, weight = 1 )
right.add_edge( vertex1 = v3, vertex2 = v5, weight = 2 )
result = maximum_clique.compatibility_graph(
first = left,
second = right,
)
vertices = list( result.vertices() )
edges = list( result.edges() )
self.assertEqual( len( vertices ), 9 )
self.assertEqual( len( edges ), 16 )
self.assertEqual(
set( result.vertex_label( vertex = v ) for v in result.vertices() ),
set(
[
( u1, v1 ), ( u1, v5 ), ( u5, v1 ), ( u5, v5 ),
( u2, v2 ), ( u2, v3 ), ( u3, v2 ), ( u3, v3 ),
( u4, v4 ),
]
)
)
edges_between = set(
[
frozenset(
[
result.vertex_label( vertex = result.source( edge = e ) ),
result.vertex_label( vertex = result.target( edge = e ) ),
]
)
for e in result.edges()
]
)
self.assertEqual(
edges_between,
set(
[
frozenset( [ ( u1, v1 ), ( u3, v3 ) ] ),
frozenset( [ ( u1, v1 ), ( u4, v4 ) ] ),
frozenset( [ ( u1, v1 ), ( u5, v5 ) ] ),
frozenset( [ ( u1, v5 ), ( u3, v2 ) ] ),
frozenset( [ ( u1, v5 ), ( u4, v4 ) ] ),
frozenset( [ ( u1, v5 ), ( u5, v1 ) ] ),
frozenset( [ ( u2, v2 ), ( u3, v3 ) ] ),
frozenset( [ ( u2, v2 ), ( u4, v4 ) ] ),
frozenset( [ ( u2, v2 ), ( u5, v5 ) ] ),
frozenset( [ ( u2, v3 ), ( u3, v2 ) ] ),
frozenset( [ ( u2, v3 ), ( u5, v1 ) ] ),
frozenset( [ ( u3, v2 ), ( u5, v1 ) ] ),
frozenset( [ ( u3, v3 ), ( u4, v4 ) ] ),
frozenset( [ ( u3, v3 ), ( u5, v5 ) ] ),
frozenset( [ ( u4, v4 ), ( u5, v1 ) ] ),
frozenset( [ ( u4, v4 ), ( u5, v5 ) ] ),
]
)
)
def manipulation(self, left, right):
u1 = left.add_vertex(label="O")
u2 = left.add_vertex(label="C")
u3 = left.add_vertex(label="C")
u4 = left.add_vertex(label="N")
u5 = left.add_vertex(label="O")
left.add_edge(vertex1=u1, vertex2=u2, weight=1)
left.add_edge(vertex1=u2, vertex2=u3, weight=1)
left.add_edge(vertex1=u3, vertex2=u4, weight=1)
left.add_edge(vertex1=u3, vertex2=u5, weight=2)
v1 = right.add_vertex(label="O")
v2 = right.add_vertex(label="C")
v3 = right.add_vertex(label="C")
v4 = right.add_vertex(label="N")
v5 = right.add_vertex(label="O")
right.add_edge(vertex1=v1, vertex2=v2, weight=2)
right.add_edge(vertex1=v2, vertex2=v3, weight=1)
right.add_edge(vertex1=v3, vertex2=v4, weight=1)
right.add_edge(vertex1=v3, vertex2=v5, weight=2)
result = maximum_clique.compatibility_graph(
first=left,
second=right,
)
vertices = list(result.vertices())
edges = list(result.edges())
self.assertEqual(len(vertices), 9)
self.assertEqual(len(edges), 16)
self.assertEqual(
set(result.vertex_label(vertex=v) for v in result.vertices()),
set([
(u1, v1),
(u1, v5),
(u5, v1),
(u5, v5),
(u2, v2),
(u2, v3),
(u3, v2),
(u3, v3),
(u4, v4),
]))
edges_between = set([
frozenset([
result.vertex_label(vertex=result.source(edge=e)),
result.vertex_label(vertex=result.target(edge=e)),
]) for e in result.edges()
])
self.assertEqual(
edges_between,
set([
frozenset([(u1, v1), (u3, v3)]),
frozenset([(u1, v1), (u4, v4)]),
frozenset([(u1, v1), (u5, v5)]),
frozenset([(u1, v5), (u3, v2)]),
frozenset([(u1, v5), (u4, v4)]),
frozenset([(u1, v5), (u5, v1)]),
frozenset([(u2, v2), (u3, v3)]),
frozenset([(u2, v2), (u4, v4)]),
frozenset([(u2, v2), (u5, v5)]),
frozenset([(u2, v3), (u3, v2)]),
frozenset([(u2, v3), (u5, v1)]),
frozenset([(u3, v2), (u5, v1)]),
frozenset([(u3, v3), (u4, v4)]),
frozenset([(u3, v3), (u5, v5)]),
frozenset([(u4, v4), (u5, v1)]),
frozenset([(u4, v4), (u5, v5)]),
]))
