def cbhzed_elim(gra,
site1,
site2,
atms,
bnd_ords,
atm_vals,
adj_atms,
bal=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
"""
frags = {}
if not site1[0] == site2[2]:
site2, site1 = site1, site2
for atm in atm_vals:
grai = (atms.copy(), bnd_ords.copy())
if (atms[atm][0] != 'H' or atm in site1 + site2):
if atm in [site1[1], site1[2], site2[0], site2[1]]:
# Dont overcount reactions site
# Ignore atm if its any of these because we'll count
# all these through site1[0] and site2[0]
continue
coeff = 1.0
if not bal:
# The coefficient changes for branch and terminal points if
# cbhzed is being used to balance cbhx then coeffs are normal
coeff = _coeff_for_elim_sites(atm, atms, adj_atms, site1,
site2)
if atm == site1[0]:
key = 'ts_gra'
extended_site = [*site1, *site2]
else:
key = 'exp_gra'
extended_site = [atm]
for site_atm in extended_site:
for atm_x in adj_atms[site_atm]:
if atm_x not in extended_site and atms[atm_x][0] != 'H':
grai = cleave_group_and_saturate(
grai, bnd_ords, site_atm, atm_x)
grai = automol.graph.explicit(grai)
frags = _add_frag_to_frags(key, coeff, grai, frags)
frags = tsutil.simplify_gra_frags(frags)
if bal:
balance_ = util.balance_ts(gra, frags)
balance_ = {k: v for k, v in balance_.items() if v}
if balance_:
frags = util.balance_frags_ts(gra, frags)
frags = tsutil.simplify_gra_frags(frags)
return frags
def cbhzed_radradabs(gra,
site1,
site2,
atms,
bnd_ords,
atm_vals,
adj_atms,
bal=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
"""
frags = {}
for atm in atm_vals:
grai = (atms.copy(), bnd_ords.copy())
if (atms[atm][0] != 'H' or atm in site1 + site2):
if atm in site1 + site2 and atm != site1[0]:
continue
coeff = 1.0
if not bal:
if atm in site1 + site2:
coeff = _coeff_for_extended_site(atms, adj_atms,
site1 + site2)
else:
nonhyd_adj_atms = tsutil.remove_hyd_from_adj_atms(
atms, adj_atms[atm])
coeff = (util.branch_point(nonhyd_adj_atms) *
util.terminal_moiety(nonhyd_adj_atms))
if atm == site1[0]:
key = 'ts_gra'
extended_site = [*site1, *site2]
else:
key = 'exp_gra'
extended_site = [atm]
for site_atm in extended_site:
for atm_x in adj_atms[site_atm]:
if atm_x not in extended_site and atms[atm_x][0] != 'H':
grai = cleave_group_and_saturate(
grai, bnd_ords, site_atm, atm_x)
grai = automol.graph.explicit(grai)
frags = _add_frag_to_frags(key, coeff, grai, frags)
frags = tsutil.simplify_gra_frags(frags)
if bal:
balance_ = util.balance_ts(gra, frags)
balance_ = {k: v for k, v in balance_.items() if v}
if balance_:
frags = util.balance_frags_ts(gra, frags)
frags = tsutil.simplify_gra_frags(frags)
return frags
def cbhone_habs(gra, site, atms, bnd_ords, atm_vals, adj_atms, bal=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
"""
frags = {}
for bnd in bnd_ords:
atma, atmb = bnd
grai = (atms.copy(), bnd_ords.copy())
extended_site = None
if ((atms[atma][0] != 'H' or atma in site)
and (atms[atmb][0] != 'H' or atmb in site)):
if atma in site and atmb in site:
continue
coeff = 1.0
if atmb in site:
atmb, atma = atma, atmb
if atma in site:
key = 'ts_gra'
extended_site = [*site, atmb]
elif atms[atma][0] != 'H' and atms[atmb][0] != 'H':
key = 'exp_gra'
extended_site = [atma, atmb]
if extended_site is not None:
for site_atm in extended_site:
for atm_x in adj_atms[site_atm]:
if atm_x not in extended_site and atms[atm_x][0] != 'H':
grai = cleave_group_and_saturate(
grai, bnd_ords, site_atm, atm_x)
grai = automol.graph.explicit(grai)
frags = _add_frag_to_frags(key, coeff, grai, frags)
frags = tsutil.simplify_gra_frags(frags)
if bal:
balance_ = util.balance_ts(gra, frags)
balance_ = {k: v for k, v in balance_.items() if v}
if balance_:
if not frags:
zedfrags = cbhzed_habs(gra,
site,
atms,
bnd_ords,
atm_vals,
adj_atms,
bal=True)
else:
zedfrags = cbhzed_habs(gra,
site,
atms,
bnd_ords,
atm_vals,
adj_atms,
bal=False)
newfrags = frags.copy()
for zedfrags_dct in zedfrags.values():
newname = None
repeat = False
if 'exp_gra' in zedfrags_dct:
key = 'exp_gra'
for onename in newfrags:
if 'exp_gra' in newfrags[onename]:
if automol.graph.full_isomorphism(
newfrags[onename][key], zedfrags_dct[key]):
newname = onename
repeat = True
else:
key = 'ts_gra'
if not repeat:
newname = len(newfrags.keys())
newfrags[newname] = {}
newfrags[newname][key] = zedfrags_dct[key]
if not frags:
util.add2dic(newfrags[newname], 'coeff',
zedfrags_dct['coeff'])
else:
util.add2dic(newfrags[newname], 'coeff',
-zedfrags_dct['coeff'])
frags = newfrags
balance_ = util.balance_ts(gra, frags)
balance_ = {k: v for k, v in balance_.items() if v}
if balance_:
frags = util.balance_frags_ts(gra, frags)
frags = tsutil.simplify_gra_frags(frags)
return frags
def cbhone_habs(gra, site, bal=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
_, atms, bnd_ords, atm_vals, _ = tsutil.ts_graph(gra, site)
# Determine CBHone fragments
frags = {}
for bnd in bnd_ords:
atma, atmb = bnd
if ((atms[atma][0] != 'H' or atma in site) and
(atms[atmb][0] != 'H' or atmb in site)):
if atma in site and atmb in site:
continue
coeff = 1.0
if atmb in site:
atmb, atma = atma, atmb
if atma in site:
key1 = [site[0], site[1]]
key1.sort()
key = frozenset({*key1})
bnd_ord1 = list(bnd_ords[key])[0]
atm_dic = {
0: (atms[site[0]][0], atm_vals[site[0]]-bnd_ord1, None)}
bnd_dct = {frozenset({0, 1}): (bnd_ord1, None)}
key1 = [site[2], site[1]]
key1.sort()
key = frozenset({*key1})
bnd_ord2 = list(bnd_ords[key])[0]
atm_dic[2] = (
atms[site[2]][0], atm_vals[site[2]]-bnd_ord2, None)
atm_dic[1] = (
atms[site[1]][0],
atm_vals[site[1]]-bnd_ord1-bnd_ord2, None)
bnd_dct[frozenset({1, 2})] = (bnd_ord2, None)
key1 = [atma, atmb]
key1.sort()
key = frozenset({*key1})
bnd_ord1 = list(bnd_ords[key])[0]
atm_dic[3] = (atms[atmb][0], atm_vals[atmb]-bnd_ord1, None)
if atma == site[0]:
atm_dic[0] = (
atm_dic[0][0], atm_dic[0][1] - bnd_ord1, None)
bnd_dct[frozenset({0, 3})] = (bnd_ord1, None)
elif atma == site[2]:
atm_dic[2] = (
atm_dic[2][0], atm_dic[2][1] - bnd_ord1, None)
bnd_dct[frozenset({2, 3})] = (bnd_ord1, None)
elif atma == site[1]:
atm_dic[1] = (
atm_dic[1][0], atm_dic[1][1] - bnd_ord1, None)
bnd_dct[frozenset({1, 3})] = (bnd_ord1, None)
else:
bnd_ord = list(bnd_ords[bnd])[0]
atm_dic = {
0: (atms[atma][0], int(atm_vals[atma])-bnd_ord, None)}
atm_dic[1] = (atms[atmb][0], int(atm_vals[atmb])-bnd_ord, None)
bnd_dct = {frozenset({0, 1}): (bnd_ord, None)}
grai = (atm_dic, bnd_dct)
try:
grai = automol.graph.explicit(grai)
key = 'exp_gra'
except:
key = 'ts_gra'
newname = None
repeat = False
for name in frags:
if key in frags[name]:
if key == 'exp_gra':
if automol.graph.full_isomorphism(
frags[name][key], grai):
newname = name
repeat = True
else:
if frags[name][key] == grai:
newname = name
repeat = True
if not repeat:
newname = len(frags.keys())
frags[newname] = {}
frags[newname][key] = grai
util.add2dic(frags[newname], 'coeff', coeff)
frags = tsutil.simplify_gra_frags(frags)
if bal:
balance_ = util.balance_ts(gra, frags)
balance_ = {k: v for k, v in balance_.items() if v}
if balance_:
zedfrags = cbhzed_habs(gra, site, bal=False)
newfrags = frags.copy()
for zedname in zedfrags:
newname = None
repeat = False
if 'exp_gra' in zedfrags[zedname]:
key = 'exp_gra'
for onename in newfrags:
if 'exp_gra' in newfrags[onename]:
if automol.graph.full_isomorphism(
newfrags[onename][key],
zedfrags[zedname][key]):
newname = onename
repeat = True
else:
key = 'ts_gra'
if not repeat:
newname = len(newfrags.keys())
newfrags[newname] = {}
newfrags[newname][key] = zedfrags[zedname][key]
util.add2dic(
newfrags[newname], 'coeff', -zedfrags[zedname]['coeff'])
frags = newfrags
balance_ = util.balance_ts(gra, frags)
balance_ = {k: v for k, v in balance_.items() if v}
if balance_:
frags = util.balance_frags_ts(gra, frags)
frags = tsutil.simplify_gra_frags(frags)
return frags
def cbhzed_habs(gra, site, bal=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
_, atms, bnd_ords, atm_vals, adj_atms = tsutil.ts_graph(gra, site)
# Determine CBHzed fragments
frags = {}
for atm in atm_vals:
if (atms[atm][0] != 'H' or atm in site):
if atm in (site[1], site[2]):
continue
coeff = 1.0
if not bal:
if atm in site:
nonhyd_adj_atms1 = tsutil.remove_hyd_from_adj_atms(
atms, adj_atms[site[0]], site,
other_adj=adj_atms[site[2]])
nonhyd_adj_atms2 = tsutil.remove_hyd_from_adj_atms(
atms, adj_atms[site[2]],
site, other_adj=adj_atms[site[0]])
nonhyd_adj_atms3 = []
for adj in adj_atms[site[0]]:
if adj in adj_atms[site[2]]:
nonhyd_adj_atms3 = tsutil.remove_hyd_from_adj_atms(
atms, adj_atms[adj], othersite=site)
coeff = (
util.branch_point(
nonhyd_adj_atms1, nonhyd_adj_atms2,
nonhyd_adj_atms3) *
util.terminal_moiety(
nonhyd_adj_atms1, nonhyd_adj_atms2,
nonhyd_adj_atms3, endisterm=False)
)
else:
nonhyd_adj_atms = tsutil.remove_hyd_from_adj_atms(
atms, adj_atms[atm])
coeff = (
util.branch_point(nonhyd_adj_atms) *
util.terminal_moiety(nonhyd_adj_atms)
)
if atm == site[0]:
key1 = [site[0], site[1]]
key1.sort()
key = frozenset({*key1})
bnd_ord1 = list(bnd_ords[key])[0]
atm_dic = {0: (atms[atm][0], atm_vals[atm]-bnd_ord1, None)}
bnd_dct = {frozenset({0, 1}): (bnd_ord1, None)}
key1 = [site[2], site[1]]
key1.sort()
key = frozenset({*key1})
bnd_ord2 = list(bnd_ords[key])[0]
atm_dic[2] = (
atms[site[2]][0], atm_vals[site[2]]-bnd_ord2, None)
atm_dic[1] = (
atms[site[1]][0],
atm_vals[site[1]]-bnd_ord1-bnd_ord2, None)
bnd_dct[frozenset({1, 2})] = (bnd_ord2, None)
else:
bnd_dct = {}
atm_dic = {0: (atms[atm][0], int(atm_vals[atm]), None)}
grai = (atm_dic, bnd_dct)
try:
grai = automol.graph.explicit(grai)
key = 'exp_gra'
except:
key = 'ts_gra'
newname = None
repeat = False
for name in frags:
if key in frags[name]:
if automol.graph.full_isomorphism(frags[name][key], grai):
newname = name
repeat = True
if not repeat:
newname = len(frags.keys())
frags[newname] = {}
frags[newname][key] = grai
util.add2dic(frags[newname], 'coeff', coeff)
frags = tsutil.simplify_gra_frags(frags)
if bal:
balance_ = util.balance_ts(gra, frags)
balance_ = {k: v for k, v in balance_.items() if v}
if balance_:
frags = util.balance_frags_ts(gra, frags)
frags = tsutil.simplify_gra_frags(frags)
return frags