def isomorphism(gra1, gra2, backbone_only=False, stereo=True, dummy=True):
""" Obtain an isomorphism between two graphs
This should eventually replace the other isomorphism functions.
:param backbone_only: Compare backbone atoms only?
:type backbone_only: bool
:param stereo: Consider stereo?
:type stereo: bool
:param dummy: Consider dummy atoms?
:type dummy: bool
:returns: The isomorphism mapping `gra1` onto `gra2`
:rtype: dict
"""
if backbone_only:
gra1 = implicit(gra1)
gra2 = implicit(gra2)
if not stereo:
gra1 = without_stereo_parities(gra1)
gra2 = without_stereo_parities(gra2)
if not dummy:
gra1 = without_dummy_atoms(gra1)
gra2 = without_dummy_atoms(gra2)
return _isomorphism(gra1, gra2)
def linear_segments_atom_keys(gra, lin_keys=None):
""" atom keys for linear segments in the graph
"""
ngb_keys_dct = atoms_neighbor_atom_keys(without_dummy_atoms(gra))
lin_keys = (linear_atom_keys(gra, dummy=True)
if lin_keys is None else lin_keys)
lin_keys = [k for k in lin_keys if len(ngb_keys_dct[k]) <= 2]
lin_segs = connected_components(subgraph(gra, lin_keys))
lin_keys_lst = []
for lin_seg in lin_segs:
lin_seg_keys = atom_keys(lin_seg)
if len(lin_seg_keys) == 1:
key, = lin_seg_keys
lin_keys_lst.append([key])
else:
end_key1, end_key2 = sorted([
key
for key, ngb_keys in atoms_neighbor_atom_keys(lin_seg).items()
if len(ngb_keys) == 1
])
ngb_keys_dct = atoms_neighbor_atom_keys(lin_seg)
key = None
keys = [end_key1]
while key != end_key2:
key, = ngb_keys_dct[keys[-1]] - set(keys)
keys.append(key)
lin_keys_lst.append(keys)
lin_keys_lst = tuple(map(tuple, lin_keys_lst))
return lin_keys_lst
def rotational_symmetry_number(gra, key1, key2, lin_keys=None):
""" get the rotational symmetry number along a given rotational axis
:param gra: the graph
:param key1: the first atom key
:param key2: the second atom key
"""
ngb_keys_dct = atoms_neighbor_atom_keys(without_dummy_atoms(gra))
imp_hyd_vlc_dct = atom_implicit_hydrogen_valences(implicit(gra))
axis_keys = {key1, key2}
# If the keys are part of a linear chain, use the ends of that for the
# symmetry number calculation
lin_keys_lst = linear_segments_atom_keys(gra, lin_keys=lin_keys)
for keys in lin_keys_lst:
if key1 in keys or key2 in keys:
if len(keys) == 1:
key1, key2 = sorted(ngb_keys_dct[keys[0]])
else:
key1, = ngb_keys_dct[keys[0]] - {keys[1]}
key2, = ngb_keys_dct[keys[-1]] - {keys[-2]}
axis_keys |= set(keys)
break
sym_num = 1
for key in (key1, key2):
if key in imp_hyd_vlc_dct:
ngb_keys = ngb_keys_dct[key] - axis_keys
if len(ngb_keys) == imp_hyd_vlc_dct[key] == 3:
sym_num = 3
break
return sym_num
def reverse(tsg, dummies=True):
""" reverse a transition state graph
"""
if not dummies:
tsg = without_dummy_atoms(tsg)
return graph(gra=tsg,
frm_bnd_keys=breaking_bond_keys(tsg),
brk_bnd_keys=forming_bond_keys(tsg))
def rotational_groups(gra, key1, key2, dummy=False):
""" get the rotational groups for a given rotational axis
:param gra: the graph
:param key1: the first atom key
:param key2: the second atom key
"""
if not dummy:
gra = without_dummy_atoms(gra)
bnd_key = frozenset({key1, key2})
assert bnd_key in bond_keys(gra)
grp1 = branch_atom_keys(gra, key2, bnd_key) - {key1}
grp2 = branch_atom_keys(gra, key1, bnd_key) - {key2}
grp1 = tuple(sorted(grp1))
grp2 = tuple(sorted(grp2))
return grp1, grp2