def atoms_sorted_neighbor_atom_keys(gra,
symbs_first=('C', ),
symbs_last=('H', ),
ords_last=(0.1, ),
prioritize_keys=()):
""" keys of neighboring atoms, by atom
:param gra: the graph
:param symbs_first: atomic symbols to put put first in the sort order
:param symbs_last: atomic symbols to put last in the sort order
:param ords_last: neighors connected with a bond of this order will be put
last in the sort order
:param prioritize_keys: keys to put first no matter what
"""
atm_symb_dct = atom_symbols(gra)
bnd_ord_dct = bond_orders(gra)
def _neighbor_keys(atm_key, atm_nbh):
keys = sorted(atom_keys(atm_nbh) - {atm_key})
bnd_keys = [frozenset({atm_key, k}) for k in keys]
ords = list(map(bnd_ord_dct.__getitem__, bnd_keys))
ords = [-1 if o not in ords_last else ords_last.index(o) for o in ords]
symbs = list(map(atm_symb_dct.__getitem__, keys))
pris = [0 if k in prioritize_keys else 1 for k in keys]
srt_vals = list(zip(ords, pris, symbs))
srt = automol.formula.argsort_symbols(srt_vals,
symbs_first,
symbs_last,
idx=2)
keys = tuple(map(keys.__getitem__, srt))
return keys
atm_ngb_keys_dct = dict_.transform_items_to_values(atom_neighborhoods(gra),
_neighbor_keys)
return atm_ngb_keys_dct
def bonds_neighbor_atom_keys(gra):
""" keys of neighboring atoms, by bond
"""
def _neighbor_keys(bnd_key, bnd_nbh):
return frozenset(atom_keys(bnd_nbh) - bnd_key)
bnd_ngb_keys_dct = dict_.transform_items_to_values(bond_neighborhoods(gra),
_neighbor_keys)
return bnd_ngb_keys_dct
def atoms_neighbor_atom_keys(gra):
""" keys of neighboring atoms, by atom
"""
def _neighbor_keys(atm_key, atm_nbh):
return frozenset(atom_keys(atm_nbh) - {atm_key})
atm_ngb_keys_dct = dict_.transform_items_to_values(atom_neighborhoods(gra),
_neighbor_keys)
return atm_ngb_keys_dct
def bonds_neighbor_bond_keys(gra):
""" keys of neighboring bonds, by bond
"""
def _neighbor_keys(bnd_key, bnd_nbh):
bnd_keys = bond_keys(bnd_nbh)
bnd_keys -= {bnd_key}
bnd_keys = frozenset(key for key in bnd_keys if key & bnd_key)
return bnd_keys
bnd_ngb_keys_dct = dict_.transform_items_to_values(bond_neighborhoods(gra),
_neighbor_keys)
return bnd_ngb_keys_dct