def radical_group_dct(gra):
""" return a dictionary of lists of groups attached each radical
"""
gra = without_fractional_bonds(gra)
groups = {}
rads = list(sing_res_dom_radical_atom_keys(gra))
atms = atoms(gra)
for rad in rads:
key = atms[rad][0]
if key in groups:
groups[atms[rad][0]] += atom_groups(gra, rad)
else:
groups[atms[rad][0]] = atom_groups(gra, rad)
return groups
def radical_groups(gra):
""" returns a list of lists of groups attached each radical
"""
gra = without_fractional_bonds(gra)
groups = []
rads = sing_res_dom_radical_atom_keys(gra)
for rad in rads:
groups.append(atom_groups(gra, rad))
return groups
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, stereo=False):
if isomorphism(group, pgra1, backbone_only=True):
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 radical_dissociation_products(gra, pgra1):
""" For a given species, determine the products of a dissociation
occuring around a radical site. We assume one of the
dissociation products is known, and we attempt to find the
corresponding product.
Currently, we assume that the input pgra1 is appropriately
stereolabeled.
:param gra: species undergoing dissociation
:type gra: automol.graph object
:param pgra1: one of the known products of dissociation
:type pgra1: automol.graph object
:rtype: tuple(automol.graph.object)
"""
# Remove gractional bonds for functions to work
gra = without_fractional_bonds(gra)
# Attempt to find a graph of product corresponding to pgra1
pgra2 = None
for rad in sing_res_dom_radical_atom_keys(gra):
for adj in atoms_neighbor_atom_keys(gra)[rad]:
for group in atom_groups(gra, adj, stereo=False):
if isomorphism(group, pgra1, backbone_only=True):
pgra2 = remove_atoms(gra, atom_keys(group))
if bond_keys(group) in pgra2:
pgra2 = remove_bonds(pgra2, bond_keys(group))
# If pgra2 is ID'd, rebuild the two product graphs with stereo labels
if pgra2 is not None:
keys2 = atom_keys(pgra2)
idx_gra = to_index_based_stereo(gra)
idx_pgra2 = subgraph(idx_gra, keys2, stereo=True)
pgra2 = from_index_based_stereo(idx_pgra2)
return pgra1, pgra2