def cbhone(ich, balance=True):
"""
Fragments molecule in a way that conserves each heavy-atom/heavy-atom bond
INPUT:
ich -- STR inchi name for molecule
OUTPUT
frags -- DIC dictionary with keys as STR inchi name for fragments
and value as INT their coefficient
"""
# Graphical info about molecule
gra = automol.inchi.graph(ich)
atms = automol.graph.atoms(gra)
bnd_ords = automol.graph.one_resonance_dominant_bond_orders(gra)
rad_atms = list(automol.graph.sing_res_dom_radical_atom_keys(gra))
atm_vals = automol.graph.atom_element_valences(gra)
adj_atms = automol.graph.atoms_neighbor_atom_keys(gra)
# Determine CBHone fragments
frags = {}
for atm in atm_vals:
for adj in list(adj_atms[atm]):
if atm > adj:
vali = atm_vals[atm]
valj = atm_vals[adj]
if atm in rad_atms:
vali -= 1
if adj in rad_atms:
valj -= 1
key = frozenset({atm, adj})
bnd_ord = list(bnd_ords[key])[0]
vali -= bnd_ord
valj -= bnd_ord
atm_dic = {
0: (atms[atm][0], int(vali), None),
1: (atms[adj][0], int(valj), None)
}
bnd_dic = {frozenset({0, 1}): (1, None)}
gra = (atm_dic, bnd_dic)
frag = automol.graph.inchi(gra)
util.add2dic(frags, frag)
frags = {k: v for k, v in frags.items() if v}
if not frags:
frags = cbhzed(ich)
# Balance
if balance:
balance_ = util.balance(ich, frags)
balance_ = {k: v for k, v in balance_.items() if v}
if balance_:
zedfrags = cbhzed(ich, balance=False)
newfrags = frags.copy()
for frag in zedfrags:
util.add2dic(newfrags, frag, -zedfrags[frag])
frags = {k: v for k, v in newfrags.items() if v}
balance_ = util.balance(ich, frags)
balance_ = {k: v for k, v in balance_.items() if v}
if balance_:
frags = util.balance_frags(ich, frags)
return frags
def cbhzed(ich, balance=True):
"""
Fragments molecule so that each heavy-atom is a seperate fragment
INPUT:
ich -- STR inchi name for molecule
OUTPUT
frags -- DIC dictionary with keys as STR inchi name for fragments
and value as INT their coefficient
"""
# Graphical info about molecule
gra = automol.inchi.graph(ich)
rad_atms = list(automol.graph.sing_res_dom_radical_atom_keys(gra))
atm_vals = automol.graph.atom_element_valences(gra)
atms = automol.graph.atoms(gra)
adj_atms = automol.graph.atoms_neighbor_atom_keys(gra)
# Determine CBHzed fragments
frags = {}
for atm in atm_vals:
coeff = 1
if not balance:
coeff = (util.branch_point(adj_atms[atm]) *
util.terminal_moiety(adj_atms[atm]))
if atm in rad_atms:
atm_vals[atm] -= 1
atm_dic = {0: (atms[atm][0], int(atm_vals[atm]), None)}
gra = (atm_dic, {})
frag = automol.graph.inchi(gra)
util.add2dic(frags, frag, coeff)
if balance:
balance_ = util.balance(ich, frags)
balance_ = {k: v for k, v in balance_.items() if v}
if balance_:
frags = util.balance_frags(ich, frags)
return frags
def cbhthree(ich, balance=True):
"""
Fragments molecule to retain each heavy-atom -- heavy-atom bond,
and keep the bonds of each atm1 b1 atm2 b2 atm3 b3 atm4 b4 atm5
would give atm1 [b1] atm2 b2 atm3, atm1 b1 atm2 [b2] atm3 b3 atm4,
atm2 b2 atm3 [b3] atm4 b4 atm5, and atm3 b3 atm4 [b4] atm5
INPUT:
ich -- STR inchi name for molecule
OUTPUT
frags -- DIC dictionary with keys as STR inchi name
for fragments and value as INT their coefficient
"""
# Graphical info about molecule
gra = automol.inchi.graph(ich)
atms = automol.graph.atoms(gra)
bnd_ords = automol.graph.one_resonance_dominant_bond_orders(gra)
rad_atms = list(automol.graph.sing_res_dom_radical_atom_keys(gra))
atm_vals = automol.graph.atom_element_valences(gra)
adj_atms = automol.graph.atoms_neighbor_atom_keys(gra)
# Determine CBHfour fragments
frags = {}
for bnd in list(bnd_ords):
atm_dic = {}
bnd_dic = {}
bnd_dic[frozenset({0, 1})] = (list(bnd_ords[bnd])[0], None)
for i, atm in enumerate(list(bnd)):
vali = atm_vals[atm]
if atm in rad_atms:
vali -= 1
for adj in list(adj_atms[atm]):
key = frozenset({atm, adj})
bnd_ord = list(bnd_ords[key])[0]
vali -= bnd_ord
atm_dic[i] = (atms[atm][0], int(vali), None)
for j, adj in enumerate(list(adj_atms[atm]), start=1):
if adj not in list(bnd):
valj = atm_vals[adj]
if adj in rad_atms:
valj -= 1
key = frozenset({atm, adj})
bnd_ord = list(bnd_ords[key])[0]
valj -= bnd_ord
atm_dic[i * 4 + j + 1] = (atms[adj][0], int(valj), None)
bnd_dic[frozenset({i, i * 4 + j + 1})] = (bnd_ord, None)
gra = (atm_dic, bnd_dic)
frag = automol.graph.inchi(gra)
util.add2dic(frags, frag)
if not frags:
frags = cbhtwo(frags)
if balance:
balance_ = util.balance(ich, frags)
balance_ = {k: v for k, v in balance_.items() if v}
if balance_:
newfrags = frags.copy()
twofrags = cbhtwo(ich, balance=False)
for frag in twofrags:
util.add2dic(newfrags, frag, -twofrags[frag])
frags = {k: v for k, v in newfrags.items() if v}
# balance_ = util.balancec(ich, frags)
# balance_ = {k: v for k, v in balance_.items() if v}
# if balance_:
# newfrags = frags.copy()
# newerfrags = {}
# onefrags = cbhone(ich, balance=False)
# for frag in onefrags:
# util.add2dic(newfrags, frag, - onefrags[frag])
# frags = {k: v for k, v in newfrags.items() if v}
# balance_ = util.balancec(ich, frags)
# balance_ = {k: v for k, v in balance_.items() if v}
# if balance_:
# newfrags = frags.copy()
# zedfrags = cbhzed(ich, balance=False)
# for frag in zedfrags:
# util.add2dic(newfrags, frag, zedfrags[frag])
# frags = {k: v for k, v in newfrags.items() if v}
# balance_ = util.balancec(ich, frags)
# balance_ = {k: v for k, v in balance_.items() if v}
# if balance_:
# frags = util.balancec_frags(ich, frags)
# balance = util.balancec(ich, frags)
# balance_ = {k: v for k, v in balance_.items() if v}
return frags
def cbhtwo(ich, balance=True):
"""
Fragments molecule for each heavy-atom to stay bonded to its adjacent atoms
INPUT:
ich -- STR inchi name for molecule
OUTPUT
frags -- DIC dictionary with keys as STR inchi name for fragments and
value as INT their coefficient
"""
# Graphical info about molecule
gra = automol.inchi.graph(ich)
atms = automol.graph.atoms(gra)
bnd_ords = automol.graph.one_resonance_dominant_bond_orders(gra)
rad_atms = list(automol.graph.sing_res_dom_radical_atom_keys(gra))
atm_vals = automol.graph.atom_element_valences(gra)
adj_atms = automol.graph.atoms_neighbor_atom_keys(gra)
# Determine CBHtwo fragments
frags = {}
for atm in atms:
vali = atm_vals[atm]
if atm in rad_atms:
vali -= 1
# First loop over all atoms of this frag to get saturation of atomi
for adj in list(adj_atms[atm]):
key = frozenset({atm, adj})
bnd_ord = list(bnd_ords[key])[0]
vali -= bnd_ord
atm_dic = {0: (atms[atm][0], int(vali), None)}
bnd_dic = {}
# Then start adding bonds to the bnddic and atomdic
j = 0
coeff = 1
if not balance:
coeff = (util.branch_point(adj_atms[atm]) *
util.terminal_moiety(adj_atms[atm]))
for adj in list(adj_atms[atm]):
j += 1
valj = atm_vals[adj]
if adj in rad_atms:
valj -= 1
key = frozenset({atm, adj})
bnd_ord = list(bnd_ords[key])[0]
valj -= bnd_ord
atm_dic[j] = (atms[adj][0], int(valj), None)
bnd_dic[frozenset({0, j})] = (1, None)
gra = (atm_dic, bnd_dic)
frag = automol.graph.inchi(gra)
util.add2dic(frags, frag, coeff)
frags = {k: v for k, v in frags.items() if v}
if not frags:
frags = cbhone(frags)
# Balance
if balance:
balance_ = util.balance(ich, frags)
balance_ = {k: v for k, v in balance_.items() if v}
if balance_:
newfrags = frags.copy()
onefrags = cbhone(ich, balance=False)
for frag in onefrags:
util.add2dic(newfrags, frag, -onefrags[frag])
frags = {k: v for k, v in newfrags.items() if v}
balance_ = util.balance(ich, frags)
balance_ = {k: v for k, v in balance_.items() if v}
if balance_:
newfrags = frags.copy()
zedfrags = cbhzed(ich, balance=False)
for frag in zedfrags:
util.add2dic(newfrags, frag, zedfrags[frag])
frags = {k: v for k, v in newfrags.items() if v}
balance_ = util.balance(ich, frags)
balance_ = {k: v for k, v in balance_.items() if v}
if balance_:
frags = util.balance_frags(ich, frags)
return frags