def forming_rings_bond_keys(tsg):
""" get the bond keys to rings forming in the TS graph
"""
frm_bnd_keys = forming_bond_keys(tsg)
frm_rngs_bnd_keys = tuple(bks for bks in rings_bond_keys(tsg)
if frm_bnd_keys & bks)
return frm_rngs_bnd_keys
def breaking_rings_bond_keys(tsg):
""" get the bond keys to rings breaking in the TS graph
"""
brk_bnd_keys = breaking_bond_keys(tsg)
brk_rngs_bnd_keys = tuple(bks for bks in rings_bond_keys(tsg)
if brk_bnd_keys & bks)
return brk_rngs_bnd_keys
def rotational_bond_keys(gra, lin_keys=None, with_h_rotors=True):
""" get all rotational bonds for a graph
:param gra: the graph
:param lin_keys: keys to linear atoms in the graph
"""
gra = explicit(gra)
sym_dct = atom_symbols(gra)
ngb_keys_dct = atoms_neighbor_atom_keys(gra)
bnd_ord_dct = resonance_dominant_bond_orders(gra)
rng_bnd_keys = list(itertools.chain(*rings_bond_keys(gra)))
def _is_rotational_bond(bnd_key):
ngb_keys_lst = [ngb_keys_dct[k] - bnd_key for k in bnd_key]
is_single = max(bnd_ord_dct[bnd_key]) <= 1
has_neighbors = all(ngb_keys_lst)
not_in_ring = bnd_key not in rng_bnd_keys
is_h_rotor = any(
set(map(sym_dct.__getitem__, ks)) == {'H'} for ks in ngb_keys_lst)
return is_single and has_neighbors and not_in_ring and (
not is_h_rotor or with_h_rotors)
rot_bnd_keys = frozenset(filter(_is_rotational_bond, bond_keys(gra)))
lin_keys_lst = linear_segments_atom_keys(gra, lin_keys=lin_keys)
dum_keys = tuple(atom_keys(gra, sym='X'))
for keys in lin_keys_lst:
bnd_keys = sorted((k for k in rot_bnd_keys if k & set(keys)),
key=sorted)
# Check whether there are neighboring atoms on either side of the
# linear segment
excl_keys = set(keys) | set(dum_keys)
end_key1 = atom_neighbor_atom_key(gra,
keys[0],
excl_atm_keys=excl_keys)
excl_keys |= {end_key1}
end_key2 = atom_neighbor_atom_key(gra,
keys[-1],
excl_atm_keys=excl_keys)
end_keys = {end_key1, end_key2}
ngb_keys_lst = [ngb_keys_dct[k] - excl_keys for k in end_keys]
has_neighbors = all(ngb_keys_lst)
if not has_neighbors:
rot_bnd_keys -= set(bnd_keys)
else:
rot_bnd_keys -= set(bnd_keys[:-1])
return rot_bnd_keys
def stereogenic_bond_keys(gra, assigned=False):
""" Find stereogenic bonds in this graph.
If the `assigned` flag is set to `False`, only unassigned stereogenic
bonds will be detected.
:param gra: the graph
:param assigned: Include bonds that already have stereo assignments?
:param assigned: bool
:returns: the stereogenic bond keys
:rtype: frozenset
"""
gra = without_bond_orders(gra)
gra = explicit(gra) # for simplicity, add the explicit hydrogens back in
# get candidates: planar bonds
bnd_keys = sp2_bond_keys(gra)
if not assigned:
# remove bonds that already have stereo assignments
bnd_keys -= bond_stereo_keys(gra)
bnd_keys -= functools.reduce( # remove double bonds in small rings
frozenset.union, filter(lambda x: len(x) < 8, rings_bond_keys(gra)),
frozenset())
atm_ngb_keys_dct = atoms_neighbor_atom_keys(gra)
def _is_stereogenic(bnd_key):
atm1_key, atm2_key = bnd_key
def _is_symmetric_on_bond(atm_key, atm_ngb_key):
atm_ngb_keys = list(atm_ngb_keys_dct[atm_key] - {atm_ngb_key})
if not atm_ngb_keys: # C=:O:
ret = True
elif len(atm_ngb_keys) == 1: # C=N:-X
ret = False
else:
assert len(atm_ngb_keys) == 2 # C=C(-X)-Y
ret = (stereo_priority_vector(
gra, atm_key, atm_ngb_keys[0]) == stereo_priority_vector(
gra, atm_key, atm_ngb_keys[1]))
return ret
return not (_is_symmetric_on_bond(atm1_key, atm2_key)
or _is_symmetric_on_bond(atm2_key, atm1_key))
ste_gen_bnd_keys = frozenset(filter(_is_stereogenic, bnd_keys))
return ste_gen_bnd_keys