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