def _radical_graph_isomorphisms(gra):
""" Generate a set of graphs where the radical has been migrated to a
new atom and then calculate the isomorphism between the input
graph and all of the new graphs generated by moving the radical
"""
# Determine useful keys
symbols = atom_symbols(gra)
unsat_keys = unsaturated_atom_keys(gra)
unsat_key = next(iter(unsat_keys))
h_atm_key = max(symbols.keys()) + 1
new_gras, isomorphisms = [], []
for aidx, symbol in enumerate(symbols.values()):
# Loop over saturated (non-radical) heavy atoms
if symbol != 'H' and aidx != unsat_key:
# Add hydrogen atom to radical atom
new_graph = add_atom_explicit_hydrogen_keys(
gra, {unsat_key: [h_atm_key]})
# Remove hydrogen from saturated atom
neighbors = atoms_neighbor_atom_keys(new_graph)
for neigh in neighbors[aidx]:
if symbols[neigh] == 'H':
aneighbor = neigh
break
new_graph = remove_atoms(new_graph, [aneighbor])
# Build lists to return
new_gras.append(new_graph)
isomorphisms.append(full_isomorphism(gra, new_graph))
return tuple(zip(new_gras, isomorphisms))
def _shift_remove_dummy_atom(gra, dummy_key):
keys = sorted(automol.graph.atom_keys(gra))
idx = keys.index(dummy_key)
key_dct = {}
key_dct.update({k: k for k in keys[:idx]})
key_dct.update({k: k - 1 for k in keys[(idx + 1):]})
gra = remove_atoms(gra, [dummy_key])
gra = relabel(gra, key_dct)
return gra
def radical_dissociation_prods(gra, pgra1):
""" given a dissociation product, determine the other product
"""
gra = without_fractional_bonds(gra)
pgra2 = None
rads = sing_res_dom_radical_atom_keys(gra)
adj_atms = atoms_neighbor_atom_keys(gra)
# adj_idxs = tuple(adj_atms[rad] for rad in rads)
for rad in rads:
for adj in adj_atms[rad]:
for group in atom_groups(gra, adj):
if full_isomorphism(explicit(group), explicit(pgra1)):
pgra2 = remove_atoms(gra, atom_keys(group))
# pgra2 = remove_bonds(pgra2, bond_keys(group))
if bond_keys(group) in pgra2:
pgra2 = remove_bonds(pgra2, bond_keys(group))
return (pgra1, pgra2)
def standard_keys_without_dummy_atoms(gra):
""" remove dummy atoms and standardize keys, returning the dummy key
dictionary for converting back
Requires that graph follows z-matrix ordering (this is checked)
"""
dummy_ngb_key_dct = dummy_atoms_neighbor_atom_key(gra)
dummy_keys_dct = {}
last_dummy_key = -1
decr = 0
for dummy_key, key in sorted(dummy_ngb_key_dct.items()):
assert last_dummy_key <= key, (
"{:d} must follow previous dummy {:d}".format(key, last_dummy_key))
dummy_keys_dct[key - decr] = dummy_key - decr
gra = remove_atoms(gra, [dummy_key])
decr += 1
last_dummy_key = dummy_key - decr
gra = standard_keys(gra)
return gra, dummy_keys_dct
def chem_unique_atoms_of_type(gra, symb):
""" For the given atom type, determine the idxs of all the
chemically unique atoms.
:param gra: molecular graph
:type gra: molecular graph data structure
:param symb: atomic symbol to determine symbols for
:type symb: str
:rtype: tuple(int)
"""
# Get the indices for the atom type
symb_idx_dct = atom_symbol_idxs(gra)
atom_idxs = symb_idx_dct[symb]
# Loop over each idx
uni_idxs = tuple()
uni_del_gras = []
for idx in atom_idxs:
# Remove the atom from the graph
del_gra = remove_atoms(gra, [idx])
# Test if the del_gra is isomorphic to any of the uni_del_gras
new_uni = True
for uni_del_gra in uni_del_gras:
iso_dct = full_isomorphism(del_gra, uni_del_gra)
if iso_dct:
new_uni = False
break
# Add graph and idx to lst if del gra is unique
if new_uni:
uni_del_gras.append(del_gra)
uni_idxs += (idx, )
return uni_idxs