def without_stereo_parities(xgr):
""" graph with stereo assignments wiped out
"""
atm_ste_par_dct = dict_.by_key({}, atom_keys(xgr), fill_val=None)
bnd_ste_par_dct = dict_.by_key({}, bond_keys(xgr), fill_val=None)
xgr = set_atom_stereo_parities(xgr, atm_ste_par_dct)
xgr = set_bond_stereo_parities(xgr, bnd_ste_par_dct)
return xgr
def subgraph(xgr, atm_keys):
""" the subgraph induced by a subset of the atoms
"""
atm_keys = set(atm_keys)
assert atm_keys <= atom_keys(xgr)
bnd_keys = set(filter(lambda x: x <= atm_keys, bond_keys(xgr)))
atm_dct = dict_.by_key(atoms(xgr), atm_keys)
bnd_dct = dict_.by_key(bonds(xgr), bnd_keys)
return _create.from_atoms_and_bonds(atm_dct, bnd_dct)
def bond_induced_subgraph(gra, bnd_keys):
""" the subgraph induced by a subset of the bonds
"""
atm_keys = set(itertools.chain(*bnd_keys))
bnd_keys = set(bnd_keys)
assert atm_keys <= atom_keys(gra)
atm_dct = dict_.by_key(atoms(gra), atm_keys)
bnd_dct = dict_.by_key(bonds(gra), bnd_keys)
return _create.from_atoms_and_bonds(atm_dct, bnd_dct)
def bond_induced_subgraph(xgr, bnd_keys, saddle=False):
""" the subgraph induced by a subset of the bonds
"""
atm_keys = set(itertools.chain(*bnd_keys))
bnd_keys = set(bnd_keys)
assert atm_keys <= atom_keys(xgr)
if not saddle:
assert bnd_keys <= bond_keys(xgr)
atm_dct = dict_.by_key(atoms(xgr), atm_keys)
bnd_dct = dict_.by_key(bonds(xgr), bnd_keys)
return _create.from_atoms_and_bonds(atm_dct, bnd_dct)
def standard_form(ich, remove_stereo=False):
""" return an inchi string in standard form
(eventually we should just designate standard-form as standard inchi
ordering for all but the hardcoded exceptions, which we can put at the end)
"""
if remove_stereo:
fml_slyr = formula_sublayer(ich)
main_dct = main_sublayers(ich)
char_dct = charge_sublayers(ich)
ste_dct = {}
iso_dct = dict_.by_key(isotope_sublayers(ich),
automol.create.inchi.ISO_NONSTE_PFXS)
else:
fml_slyr = formula_sublayer(ich)
main_dct = main_sublayers(ich)
char_dct = charge_sublayers(ich)
ste_dct = stereo_sublayers(ich)
iso_dct = isotope_sublayers(ich)
ich = from_data(fml_slyr,
main_dct=main_dct,
char_dct=char_dct,
ste_dct=ste_dct,
iso_dct=iso_dct)
return recalculate(ich)
def _join_sublayers(dcts):
pfxs = sorted(functools.reduce(set.union, map(set, dcts)))
if 's' in pfxs:
pfxs.remove('s')
dcts = [dict_.by_key(dct, pfxs, fill_val='') for dct in dcts]
slyrs_lst = [[dct[pfx] for dct in dcts] for pfx in pfxs]
dct = {pfx: (_join_sublayer_strings(slyrs) if pfx != 'm' else
_join_m_sublayer_strings(slyrs))
for pfx, slyrs in zip(pfxs, slyrs_lst)}
return dct
def remove_bonds(xgr, bnd_keys):
""" remove bonds from the molecular graph
"""
all_bnd_keys = bond_keys(xgr)
bnd_keys = set(bnd_keys)
assert bnd_keys <= all_bnd_keys
bnd_keys = all_bnd_keys - bnd_keys
atm_dct = atoms(xgr)
bnd_dct = dict_.by_key(bonds(xgr), bnd_keys)
return _create.from_atoms_and_bonds(atm_dct, bnd_dct)
def bond_symmetry_numbers(gra, frm_bnd_key=None, brk_bnd_key=None):
""" symmetry numbers, by bond
the (approximate) symmetry number of the torsional potential for this bond,
based on the hydrogen counts for each atom
It is reduced to 1 if one of the H atoms in the torsional bond is a
neighbor to the special bonding atom (the atom that is being transferred)
"""
imp_gra = implicit(gra)
atm_imp_hyd_vlc_dct = atom_implicit_hydrogen_valences(imp_gra)
bnd_keys = bond_keys(imp_gra)
tfr_atm = None
if frm_bnd_key and brk_bnd_key:
for atm_f in list(frm_bnd_key):
for atm_b in list(brk_bnd_key):
if atm_f == atm_b:
tfr_atm = atm_f
if tfr_atm:
neighbor_dct = atom_neighbor_keys(gra)
nei_tfr = neighbor_dct[tfr_atm]
atms = gra[0]
all_hyds = []
for atm in atms:
if atms[atm][0] == 'H':
all_hyds.append(atm)
else:
nei_tfr = {}
bnd_sym_num_dct = {}
bnd_sym_nums = []
for bnd_key in bnd_keys:
bnd_sym = 1
vlc = max(map(atm_imp_hyd_vlc_dct.__getitem__, bnd_key))
if vlc == 3:
bnd_sym = 3
if tfr_atm:
for atm in nei_tfr:
nei_s = neighbor_dct[atm]
h_nei = 0
for nei in nei_s:
if nei in all_hyds:
h_nei += 1
if h_nei == 3:
bnd_sym = 1
bnd_sym_nums.append(bnd_sym)
bnd_sym_num_dct = dict(zip(bnd_keys, bnd_sym_nums))
# fill in the rest of the bonds for completeness
bnd_sym_num_dct = dict_.by_key(bnd_sym_num_dct, bond_keys(gra), fill_val=1)
return bnd_sym_num_dct
def explicit(xgr, atm_keys=None):
""" make the hydrogens at these atoms explicit
"""
atm_keys = backbone_keys(xgr) if atm_keys is None else atm_keys
atm_keys = sorted(atm_keys)
atm_imp_hyd_vlc_dct = dict_.by_key(atom_implicit_hydrogen_valences(xgr),
atm_keys)
atm_exp_hyd_keys_dct = {}
next_atm_key = max(atom_keys(xgr)) + 1
for atm_key in atm_keys:
imp_hyd_vlc = atm_imp_hyd_vlc_dct[atm_key]
atm_exp_hyd_keys_dct[atm_key] = set(
range(next_atm_key, next_atm_key + imp_hyd_vlc))
next_atm_key += imp_hyd_vlc
xgr = set_atom_implicit_hydrogen_valences(
xgr, dict_.by_key({}, atm_keys, fill_val=0))
xgr = add_atom_explicit_hydrogen_keys(xgr, atm_exp_hyd_keys_dct)
return xgr
def remove_bonds(gra, bnd_keys, check=True):
""" remove bonds from the molecular graph
"""
all_bnd_keys = bond_keys(gra)
bnd_keys = set(map(frozenset, bnd_keys))
if check:
assert bnd_keys <= all_bnd_keys
bnd_keys = all_bnd_keys - bnd_keys
atm_dct = atoms(gra)
bnd_dct = dict_.by_key(bonds(gra), bnd_keys)
return _create.from_atoms_and_bonds(atm_dct, bnd_dct)
def implicit(xgr, atm_keys=None):
""" make the hydrogens at these atoms implicit
"""
atm_keys = backbone_keys(xgr) if atm_keys is None else atm_keys
atm_exp_hyd_keys_dct = dict_.by_key(atom_explicit_hydrogen_keys(xgr),
atm_keys)
inc_imp_hyd_keys_dct = dict_.transform_values(atm_exp_hyd_keys_dct, len)
xgr = add_atom_implicit_hydrogen_valences(xgr, inc_imp_hyd_keys_dct)
exp_hyd_keys = set(itertools.chain(*atm_exp_hyd_keys_dct.values()))
xgr = remove_atoms(xgr, exp_hyd_keys)
return xgr
def add_atom_explicit_hydrogen_keys(xgr, atm_exp_hyd_keys_dct):
""" add explicit hydrogens by atom
"""
assert set(atm_exp_hyd_keys_dct.keys()) <= atom_keys(xgr)
for atm_key, atm_exp_hyd_keys in atm_exp_hyd_keys_dct.items():
assert not set(atm_exp_hyd_keys) & atom_keys(xgr)
atm_exp_hyd_bnd_keys = {
frozenset({atm_key, atm_exp_hyd_key})
for atm_exp_hyd_key in atm_exp_hyd_keys
}
atm_exp_hyd_sym_dct = dict_.by_key({}, atm_exp_hyd_keys, fill_val='H')
xgr = add_atoms(xgr, atm_exp_hyd_sym_dct)
xgr = add_bonds(xgr, atm_exp_hyd_bnd_keys)
return xgr
def add_atom_explicit_hydrogen_keys(gra, atm_exp_hyd_keys_dct):
""" add explicit hydrogens by atom
"""
assert set(atm_exp_hyd_keys_dct.keys()) <= atom_keys(gra), (
'{} !<= {}'.format(set(atm_exp_hyd_keys_dct.keys()), atom_keys(gra)))
for atm_key, atm_exp_hyd_keys in atm_exp_hyd_keys_dct.items():
assert not set(atm_exp_hyd_keys) & atom_keys(gra)
atm_exp_hyd_bnd_keys = {
frozenset({atm_key, atm_exp_hyd_key})
for atm_exp_hyd_key in atm_exp_hyd_keys
}
atm_exp_hyd_sym_dct = dict_.by_key({}, atm_exp_hyd_keys, fill_val='H')
gra = add_atoms(gra, atm_exp_hyd_sym_dct)
gra = add_bonds(gra, atm_exp_hyd_bnd_keys)
return gra
def without_bond_orders(xgr):
""" resonance graph with maximum spin (i.e. no pi bonds)
"""
bnd_keys = bond_keys(xgr) - dummy_bond_keys(xgr)
bnd_ord_dct = dict_.by_key({}, bnd_keys, fill_val=1)
return set_bond_orders(xgr, bnd_ord_dct)
