def graph(gra, frm_bnd_keys, brk_bnd_keys):
""" generate a transition-state graph
"""
frm_bnd_keys = frozenset(map(frozenset, frm_bnd_keys))
brk_bnd_keys = frozenset(map(frozenset, brk_bnd_keys))
frm_ord_dct = {k: 0.1 for k in frm_bnd_keys}
brk_ord_dct = {k: 0.9 for k in brk_bnd_keys}
tsg = add_bonds(gra, frm_bnd_keys, ord_dct=frm_ord_dct, check=False)
tsg = add_bonds(tsg, brk_bnd_keys, ord_dct=brk_ord_dct, check=False)
return tsg
def addition(xgr1, xgr2):
""" find an addition transformation
"""
assert xgr1 == _explicit(xgr1) and xgr2 == _explicit(xgr2)
tra = None
xgrs1 = _connected_components(xgr1)
xgrs2 = _connected_components(xgr2)
if len(xgrs1) == 2 and len(xgrs2) == 1:
x_xgr, y_xgr = xgrs1
xgr2, = xgrs2
x_atm_keys = _unsaturated_atom_keys(x_xgr)
y_atm_keys = _unsaturated_atom_keys(y_xgr)
# xgeo = geometry(xgr2)
for x_atm_key, y_atm_key in itertools.product(x_atm_keys, y_atm_keys):
xy_xgr = add_bonds(_union(x_xgr, y_xgr), [{x_atm_key, y_atm_key}])
# xgeo = geometry(xy_xgr)
atm_key_dct = _full_isomorphism(xy_xgr, xgr2)
if atm_key_dct:
tra = from_data('addition',
frm_bnd_keys=[{x_atm_key, y_atm_key}],
brk_bnd_keys=[])
return tra
def apply(tra, xgr):
""" apply this transformation to a graph
"""
brk_bnd_keys = broken_bond_keys(tra)
frm_bnd_keys = formed_bond_keys(tra)
# in case some bonds are broken *and* formed, we subtract the other set
xgr = remove_bonds(xgr, brk_bnd_keys - frm_bnd_keys)
xgr = add_bonds(xgr, frm_bnd_keys - brk_bnd_keys)
return xgr
def _substitution(atmsa, neighsa, bndsa, atmsb, xgr1, xgr2):
ret_tra = None
for atmi in atmsa:
if _is_heavy(atmi, atmsa):
i_neighs = neighsa[atmi]
for atmj in i_neighs:
bnd_break_key_ij = _get_bnd_key(atmi, atmj, bndsa)
new_xgr = remove_bonds(xgr1, [bnd_break_key_ij])
for atmk in atmsb:
if atmk not in (atmi, atmj):
bnd_form_key_ik = frozenset({atmi, atmk})
newnew_xgr = add_bonds(new_xgr, [bnd_form_key_ik])
atm_key_dct = _full_isomorphism(newnew_xgr, xgr2)
if atm_key_dct:
tra = [[bnd_form_key_ik], [bnd_break_key_ij]]
ret_tra = tra
return ret_tra
def add_bonded_atom(gra,
sym,
atm_key,
bnd_atm_key=None,
imp_hyd_vlc=None,
atm_ste_par=None,
bnd_ord=None,
bnd_ste_par=None):
""" add a single atom with a bond to an atom already in the graph
"""
atm_keys = atom_keys(gra)
bnd_atm_key = max(atm_keys) + 1 if bnd_atm_key is None else bnd_atm_key
symb_dct = {bnd_atm_key: sym}
imp_hyd_vlc_dct = ({
bnd_atm_key: imp_hyd_vlc
} if imp_hyd_vlc is not None else None)
atm_ste_par_dct = ({
bnd_atm_key: atm_ste_par
} if atm_ste_par is not None else None)
gra = add_atoms(gra,
symb_dct,
imp_hyd_vlc_dct=imp_hyd_vlc_dct,
ste_par_dct=atm_ste_par_dct)
bnd_key = frozenset({bnd_atm_key, atm_key})
bnd_ord_dct = {bnd_key: bnd_ord} if bnd_ord is not None else None
bnd_ste_par_dct = ({
bnd_key: bnd_ste_par
} if bnd_ste_par is not None else None)
gra = add_bonds(gra, [bnd_key],
ord_dct=bnd_ord_dct,
ste_par_dct=bnd_ste_par_dct)
return gra
def _insertion(atmsa, neighsa, bndsa, atmsb, neighsb, xgr1, xgr2):
"""Do the insertion for an order of reactants
"""
ret_tra = None
for i in atmsa:
if _is_heavy(i, atmsa):
i_neighs = neighsa[i]
for j in i_neighs:
bnd_break_key_ij = _get_bnd_key(i, j, bndsa)
new_xgr = remove_bonds(xgr1, [bnd_break_key_ij])
for k in atmsb:
if _is_heavy(k, atmsb) and (k != i and k != j
and i not in neighsb[k]
and j not in neighsb[k]):
bnd_form_key_ik = {i, k}
bnd_form_key_jk = {j, k}
newnew_xgr = add_bonds(
new_xgr, [bnd_form_key_ik, bnd_form_key_jk])
atm_key_dct = _full_isomorphism(newnew_xgr, xgr2)
if atm_key_dct:
tra = [[bnd_form_key_ik, bnd_form_key_jk],
[bnd_break_key_ij]]
ret_tra = tra
return ret_tra
def elimination(xgr1, xgr2):
"""identifies elimination reactions
"""
assert xgr1 == _explicit(xgr1) and xgr2 == _explicit(xgr2)
tra = None
xgrs1 = _connected_components(xgr1)
xgrs2 = _connected_components(xgr2)
tras = []
if len(xgrs1) == 1 and len(xgrs2) == 2:
atms = atoms(xgr1)
neighs = atom_neighbor_keys(xgr1)
bnds = bond_keys(xgr1)
radicals = _resonance_dominant_radical_atom_keys(xgr1)
lonepairs = atom_lone_pair_counts(xgr1)
for atmi in atms:
i_neighs = neighs[atmi]
for atmj in i_neighs:
bnd_break_key_ij = _get_bnd_key(atmi, atmj, bnds)
new_xgr = remove_bonds(xgr1, [bnd_break_key_ij])
new_xgrs = _connected_components(new_xgr)
if len(new_xgrs) == 2:
xgra, xgrb = new_xgrs
atmsa = atoms(xgra)
if atmi not in atmsa.keys():
xgrb, xgra = xgra, xgrb
atmsa = atoms(xgra)
neighsa = atom_neighbor_keys(xgra)
atmsb = atoms(xgrb)
neighs_i = neighsa[atmi]
for atmk in atmsb:
if atmk in radicals:
for atml in neighs_i:
neighs_l = neighsa[atml]
if atml != atmj:
bnd_break_key_il = _get_bnd_key(
atmi, atml, bnds)
bnd_form_key_kl = frozenset({atmk, atml})
newnew_xgr = remove_bonds(
new_xgr, [bnd_break_key_il])
newnew_xgr = add_bonds(
newnew_xgr, [bnd_form_key_kl])
atm_key_dct = _full_isomorphism(
newnew_xgr, xgr2)
if atm_key_dct:
tra = [[bnd_form_key_kl],
[
bnd_break_key_ij,
bnd_break_key_il
]]
return tra
for atmm in neighs_l:
if atmm != atmi:
bnd_break_key_lm = _get_bnd_key(
atml, atmm, bnds)
bnd_form_key_km = frozenset(
{atmk, atmm})
newnew_xgr = remove_bonds(
new_xgr, [bnd_break_key_lm])
newnew_xgr = add_bonds(
newnew_xgr, [bnd_form_key_km])
atm_key_dct = _full_isomorphism(
newnew_xgr, xgr2)
if atm_key_dct:
tras.append([[bnd_form_key_km],
[
bnd_break_key_ij,
bnd_break_key_lm
]])
for atmi in atms:
i_neighs = neighs[atmi]
print('atmi test:', atmi)
print('i_neighs test:', i_neighs)
for atmj in i_neighs:
bnd_break_key_ij = _get_bnd_key(atmi, atmj, bnds)
new_xgr = remove_bonds(xgr1, [bnd_break_key_ij])
new_xgrs = _connected_components(new_xgr)
if len(new_xgrs) == 2:
xgra, xgrb = new_xgrs
atmsa = atoms(xgra)
if atmi not in atmsa.keys():
xgrb, xgra = xgra, xgrb
atmsa = atoms(xgra)
neighsa = atom_neighbor_keys(xgra)
atmsb = atoms(xgrb)
neighs_i = neighsa[atmi]
print('len atmsb test:', len(atmsb))
for atmk in atmsb:
if lonepairs[atmk] > 0 or len(atmsb) == 1:
# if lonepairs[atmk] > 0:
for atml in neighs_i:
neighs_l = neighsa[atml]
if atml != atmj:
bnd_break_key_il = _get_bnd_key(
atmi, atml, bnds)
bnd_form_key_kl = frozenset({atmk, atml})
newnew_xgr = remove_bonds(
new_xgr, [bnd_break_key_il])
newnew_xgr = add_bonds(
newnew_xgr, [bnd_form_key_kl])
atm_key_dct = _full_isomorphism(
newnew_xgr, xgr2)
if atm_key_dct:
tra = [[bnd_form_key_kl],
[
bnd_break_key_ij,
bnd_break_key_il
]]
return tra
for atmm in neighs_l:
if atmm != atmi:
bnd_break_key_lm = _get_bnd_key(
atml, atmm, bnds)
bnd_form_key_km = frozenset(
{atmk, atmm})
newnew_xgr = remove_bonds(
new_xgr, [bnd_break_key_lm])
newnew_xgr = add_bonds(
newnew_xgr, [bnd_form_key_km])
atm_key_dct = _full_isomorphism(
newnew_xgr, xgr2)
if atm_key_dct:
tras.append([[bnd_form_key_km],
[
bnd_break_key_ij,
bnd_break_key_lm
]])
if len(tras) < 1:
tras = None
return tras
