def get_knob_graphs(self, min_scut=7.0, max_scut=9.0, scut_increment=0.5):
"""
Parameters
----------
min_scut: float
max_scut: float
scut_increment: float
values between min and max scut at scut_increment are used as iSocket cutoffs for getting graphs
Returns
-------
knob_graphs: list[nextworkx.Graph]
List of graph objects representing each connected component subgraph at range of scut and kcut values.
Each graph g has a g.graph dictionary containing the data needed to populate the database.
"""
kg = self.get_knob_group(cutoff=max_scut)
if kg is not None:
scuts = list(
numpy.arange(min_scut, max_scut + scut_increment,
scut_increment))
kcuts = list(range(4))
g = kg.graph
knob_graphs = []
for scut, kcut in itertools.product(scuts[::-1], kcuts):
h = kg.filter_graph(g=g, cutoff=scut, min_kihs=kcut)
h = graph_to_plain_graph(g=h)
# if is null graph
if h.number_of_nodes() == 0:
continue
if networkx.connected.is_connected(h):
ccs = [h]
else:
ccs = sorted(networkx.connected_component_subgraphs(
h, copy=True),
key=lambda x: len(x.nodes()),
reverse=True)
for cc_num, cc in enumerate(ccs):
name = isomorphism_checker(cc, graph_list=_graph_list)
d = dict(scut=scut,
kcut=kcut,
code=self.code,
cc_num=cc_num,
preferred=self.is_preferred,
mmol=self.mmol,
name=name,
nodes=cc.number_of_nodes(),
edges=cc.number_of_edges())
cc.graph.update(d)
knob_graphs.append(cc)
else:
knob_graphs = []
return knob_graphs
def add_unknowns(knob_graphs, mode):
""" Name all new unknown graphs, add them to unknown_pickle and to database.
Parameters
----------
knob_graphs: list(networkx.Graph)
mode: str
Allowed values: 'production' or 'testing'.
Returns
-------
None
"""
large_graph_list = AtlasHandler().get_graph_list(atlas=False,
cyclics=False,
paths=False,
unknowns=True)
assert not all_graphs_named(knob_graphs=knob_graphs)
assert all(
isomorphism_checker(x, graph_list=large_graph_list)
for x in knob_graphs)
next_number_to_add = max([int(x.name[1:]) for x in large_graph_list]) + 1
to_add_to_atlas = []
for i, g in enumerate(knob_graphs):
n = isomorphism_checker(g, graph_list=knob_graphs[:i])
if n is None:
h = graph_to_plain_graph(g)
n = 'U{}'.format(next_number_to_add)
h.name = n
to_add_to_atlas.append(h)
next_number_to_add += 1
g.graph['name'] = n
large_graph_list += to_add_to_atlas
unknown_pickle = global_settings["unknown_graphs"][mode]
with open(unknown_pickle, 'wb') as foo:
pickle.dump(large_graph_list, foo)
populate_atlas(graph_list=to_add_to_atlas)
return
def name_against_unknowns(knob_graphs):
""" Checks each unnamed graph for isomorphism against list of 'unknown' (large) graphs.
Parameters
----------
knob_graphs: list(networkx.Graph)
Returns
-------
None
"""
large_graph_list = AtlasHandler().get_graph_list(atlas=False,
cyclics=False,
paths=False,
unknowns=True)
for g in knob_graphs:
if g.graph['name'] is None:
name = isomorphism_checker(g, graph_list=large_graph_list)
if name is not None:
g.graph['name'] = name
return
def test_complete_graph(self):
g = complete_graph(8)
self.assertIsNone(isomorphism_checker(g))
def test_pentamer(self):
pent = cycle_graph(5)
self.assertEqual(isomorphism_checker(pent), "G38")
def test_octomer(self):
octamer = cycle_graph(8)
self.assertEqual(
isomorphism_checker(octamer, graph_list=self.graph_list), "C8")