def full_subgraph_isomorphism(gra1, gra2):
""" gra2 is fully isomorphic to a subgraph of gra1
"""
assert gra1 == explicit(gra1) and gra2 == explicit(gra2)
nxg1 = _networkx.from_graph(gra1)
nxg2 = _networkx.from_graph(gra2)
iso_dct = _networkx.subgraph_isomorphism(nxg1, nxg2)
return iso_dct
def full_isomorphism(xgr1, xgr2):
""" full graph isomorphism
"""
assert xgr1 == explicit(xgr1) and xgr2 == explicit(xgr2)
nxg1 = _networkx.from_graph(xgr1)
nxg2 = _networkx.from_graph(xgr2)
iso_dct = _networkx.isomorphism(nxg1, nxg2)
return iso_dct
def full_isomorphism(gra1, gra2):
""" full graph isomorphism
"""
assert gra1 == explicit(gra1) and gra2 == explicit(gra2)
nxg1 = _networkx.from_graph(gra1)
nxg2 = _networkx.from_graph(gra2)
iso_dct = _networkx.isomorphism(nxg1, nxg2)
return iso_dct
def backbone_isomorphism(xgr1, xgr2):
""" graph backbone isomorphism
for implicit graphs, this is the relabeling of `xgr1` to produce `xgr2`
for other graphs, it gives the correspondences between backbone atoms
"""
xgr1 = implicit(xgr1)
xgr2 = implicit(xgr2)
nxg1 = _networkx.from_graph(xgr1)
nxg2 = _networkx.from_graph(xgr2)
iso_dct = _networkx.isomorphism(nxg1, nxg2)
return iso_dct
def _isomorphism(gra1, gra2, igraph=False):
"""
"""
if igraph:
igr1 = _igraph.from_graph(gra1)
igr2 = _igraph.from_graph(gra2)
iso_dcts = _igraph.isomorphisms(igr1, igr2)
iso_dct = iso_dcts[0] if iso_dcts else None
else:
nxg1 = _networkx.from_graph(gra1)
nxg2 = _networkx.from_graph(gra2)
iso_dct = _networkx.isomorphism(nxg1, nxg2)
return iso_dct
def full_isomorphism(gra1, gra2, igraph=False):
""" full graph isomorphism
"""
assert gra1 == explicit(gra1) and gra2 == explicit(gra2)
if igraph:
igr1 = _igraph.from_graph(gra1)
igr2 = _igraph.from_graph(gra2)
iso_dcts = _igraph.isomorphisms(igr1, igr2)
iso_dct = iso_dcts[0] if iso_dcts else None
else:
nxg1 = _networkx.from_graph(gra1)
nxg2 = _networkx.from_graph(gra2)
iso_dct = _networkx.isomorphism(nxg1, nxg2)
return iso_dct
def atom_shortest_paths(gra):
""" shortest paths between any two atoms in the graph
:returns: a 2d dictionary keyed by pairs of atoms
"""
nxg = _networkx.from_graph(gra)
sp_dct = dict(_networkx.all_pairs_shortest_path(nxg))
return sp_dct
def backbone_isomorphism(gra1, gra2, igraph=False):
""" graph backbone isomorphism
for implicit graphs, this is the relabeling of `gra1` to produce `gra2`
for other graphs, it gives the correspondences between backbone atoms
"""
gra1 = implicit(gra1)
gra2 = implicit(gra2)
if igraph:
igr1 = _igraph.from_graph(gra1)
igr2 = _igraph.from_graph(gra2)
iso_dcts = _igraph.isomorphisms(igr1, igr2)
iso_dct = iso_dcts[0] if iso_dcts else None
else:
nxg1 = _networkx.from_graph(gra1)
nxg2 = _networkx.from_graph(gra2)
iso_dct = _networkx.isomorphism(nxg1, nxg2)
return iso_dct
def rings_bond_keys(gra):
""" bond keys for each ring in the graph (minimal basis)
"""
bnd_keys = bond_keys(gra)
def _ring_bond_keys(rng_atm_keys):
return frozenset(filter(lambda x: x <= rng_atm_keys, bnd_keys))
nxg = _networkx.from_graph(gra)
rng_atm_keys_lst = _networkx.minimum_cycle_basis(nxg)
rng_bnd_keys_lst = frozenset(map(_ring_bond_keys, rng_atm_keys_lst))
return rng_bnd_keys_lst
def connected_components_atom_keys(gra):
""" atom keys for each connected component in the graph
"""
nxg = _networkx.from_graph(gra)
cmp_gra_atm_keys_lst = _networkx.connected_component_atom_keys(nxg)
return cmp_gra_atm_keys_lst
