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 boost_adaptbx.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, g):
n = {}
n["1,1'"] = g.add_vertex(label="1,1'") # 0
n["1,5'"] = g.add_vertex(label="1,5'") # 1
n["2,2'"] = g.add_vertex(label="2,2'") # 2
n["2,3'"] = g.add_vertex(label="2,3'") # 3
n["3,2'"] = g.add_vertex(label="3,2'") # 4
n["3,3'"] = g.add_vertex(label="3,3'") # 5
n["4,4'"] = g.add_vertex(label="4,4'") # 6
n["5,1'"] = g.add_vertex(label="5,1'") # 7
n["5,5'"] = g.add_vertex(label="5,5'") # 8
g.add_edge(vertex1=n["1,1'"], vertex2=n["3,3'"])
g.add_edge(vertex1=n["1,1'"], vertex2=n["4,4'"])
g.add_edge(vertex1=n["1,1'"], vertex2=n["5,5'"])
g.add_edge(vertex1=n["1,5'"], vertex2=n["3,2'"])
g.add_edge(vertex1=n["1,5'"], vertex2=n["4,4'"])
g.add_edge(vertex1=n["1,5'"], vertex2=n["5,1'"])
g.add_edge(vertex1=n["2,2'"], vertex2=n["3,3'"])
g.add_edge(vertex1=n["2,2'"], vertex2=n["4,4'"])
g.add_edge(vertex1=n["2,2'"], vertex2=n["5,5'"])
g.add_edge(vertex1=n["2,3'"], vertex2=n["3,2'"])
g.add_edge(vertex1=n["2,3'"], vertex2=n["5,1'"])
g.add_edge(vertex1=n["3,2'"], vertex2=n["5,1'"])
g.add_edge(vertex1=n["3,3'"], vertex2=n["4,4'"])
g.add_edge(vertex1=n["3,3'"], vertex2=n["5,5'"])
g.add_edge(vertex1=n["4,4'"], vertex2=n["5,1'"])
g.add_edge(vertex1=n["4,4'"], vertex2=n["5,5'"])
subgraph = maximum_clique.selected_subgraph(
graph=g, vertices=g.adjacent_vertices(vertex=n["2,2'"]))
vertices = list(subgraph.vertices())
self.assertEqual(len(vertices), 3)
self.assertEqual(
set(subgraph.vertex_label(vertex=v) for v in vertices),
set(["3,3'", "4,4'", "5,5'"]))
edges = list(subgraph.edges())
self.assertEqual(len(edges), 3)
self.assertEqual(
set(
frozenset([
subgraph.vertex_label(vertex=subgraph.source(edge=e)),
subgraph.vertex_label(vertex=subgraph.target(edge=e)),
]) for e in edges),
set([
frozenset(["3,3'", "4,4'"]),
frozenset(["3,3'", "5,5'"]),
frozenset(["4,4'", "5,5'"]),
]))
def subset(self, atoms):
if not all(a in self.descriptor_for for a in atoms):
raise ValueError, "Unknown atoms: %s" % atoms
from boost_adaptbx.graph import maximum_clique
subgraph = maximum_clique.selected_subgraph(
graph=self.graph,
vertices=(self.descriptor_for[a] for a in atoms),
)
return self.__class__(graph=subgraph)