def stereo_priority_vector(gra, atm_key, atm_ngb_key):
""" generates a sortable one-to-one representation of the branch extending
from `atm_key` through its bonded neighbor `atm_ngb_key`
"""
bbn_keys = backbone_keys(gra)
exp_hyd_keys = explicit_hydrogen_keys(gra)
if atm_ngb_key not in bbn_keys:
assert atm_ngb_key in exp_hyd_keys
assert frozenset({atm_key, atm_ngb_key}) in bond_keys(gra)
pri_vec = ()
else:
gra = implicit(gra)
atm_dct = atoms(gra)
bnd_dct = bonds(gra)
assert atm_key in bbn_keys
assert frozenset({atm_key, atm_ngb_key}) in bnd_dct
# here, switch to an implicit graph
atm_ngb_keys_dct = atoms_neighbor_atom_keys(gra)
def _priority_vector(atm1_key, atm2_key, seen_keys):
# we keep a list of seen keys to cut off cycles, avoiding infinite
# loops
bnd_val = bnd_dct[frozenset({atm1_key, atm2_key})]
atm_val = atm_dct[atm2_key]
bnd_val = _replace_nones_with_negative_infinity(bnd_val)
atm_val = _replace_nones_with_negative_infinity(atm_val)
if atm2_key in seen_keys:
ret = (bnd_val, )
else:
seen_keys.update({atm1_key, atm2_key})
atm3_keys = atm_ngb_keys_dct[atm2_key] - {atm1_key}
if atm3_keys:
next_vals, seen_keys = zip(*[
_priority_vector(atm2_key, atm3_key, seen_keys)
for atm3_key in atm3_keys
])
ret = (bnd_val, atm_val) + next_vals
else:
ret = (bnd_val, atm_val)
return ret, seen_keys
pri_vec, _ = _priority_vector(atm_key, atm_ngb_key, set())
return pri_vec
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 from_graph(gra):
""" igraph object from a molecular graph
"""
atm_keys = sorted(atom_keys(gra))
bnd_keys = sorted(bond_keys(gra), key=sorted)
atm_vals = dict_.values_by_key(atoms(gra), atm_keys)
bnd_vals = dict_.values_by_key(bonds(gra), bnd_keys)
atm_colors = list(itertools.starmap(_encode_vertex_attributes, atm_vals))
bnd_colors = list(itertools.starmap(_encode_edge_attributes, bnd_vals))
atm_idx_dct = dict(map(reversed, enumerate(atm_keys)))
bnd_idxs = [sorted(map(atm_idx_dct.__getitem__, k)) for k in bnd_keys]
igr = igraph.Graph(bnd_idxs)
igr.vs['keys'] = atm_keys
igr.vs['color'] = atm_colors
igr.es['color'] = bnd_colors
return igr