def ts_bond_keys(gra):
""" get keys for all order-0 bonds in the graph
"""
bnd_ord_dct = bond_orders(gra)
ts_bnd_keys = tuple(bnd_key for bnd_key, bnd_ord in bnd_ord_dct.items()
if bnd_ord == 0)
return ts_bnd_keys
def add_bonds(gra, keys, ord_dct=None, ste_par_dct=None, check=True):
""" add bonds to this molecular graph
"""
bnd_keys = set(bond_keys(gra))
bnd_ord_dct = bond_orders(gra)
bnd_ste_par_dct = bond_stereo_parities(gra)
keys = set(map(frozenset, keys))
ord_dct = {} if ord_dct is None else ord_dct
ste_par_dct = {} if ste_par_dct is None else ste_par_dct
if check:
assert not keys & bnd_keys, (
'{} and {} have a non-empty intersection'.format(keys, bnd_keys))
assert set(ord_dct.keys()) <= keys
assert set(ste_par_dct.keys()) <= keys
bnd_keys.update(keys)
bnd_ord_dct.update(ord_dct)
bnd_ste_par_dct.update(ste_par_dct)
atm_dct = atoms(gra)
bnd_dct = _create.bonds_from_data(bond_keys=bnd_keys,
bond_orders=bnd_ord_dct,
bond_stereo_parities=bnd_ste_par_dct)
gra = _create.from_atoms_and_bonds(atoms=atm_dct, bonds=bnd_dct)
return gra
def without_bond_orders(gra):
""" resonance graph with maximum spin (i.e. no pi bonds)
"""
bnd_keys = list(bond_keys(gra))
# don't set dummy bonds to one!
bnd_ord_dct = bond_orders(gra)
bnd_vals = [
1 if v != 0 else 0 for v in map(bnd_ord_dct.__getitem__, bnd_keys)
]
bnd_ord_dct = dict(zip(bnd_keys, bnd_vals))
return set_bond_orders(gra, bnd_ord_dct)
def atom_bond_valences(gra, bond_order=True):
""" bond count (bond valence), by atom
"""
atm_keys = list(atom_keys(gra))
gra = explicit(gra)
if not bond_order:
gra = without_bond_orders(gra)
atm_nbhs = dict_.values_by_key(atom_neighborhoods(gra), atm_keys)
atm_bnd_vlcs = [sum(bond_orders(nbh).values()) for nbh in atm_nbhs]
atm_bnd_vlc_dct = dict_.transform_values(dict(zip(atm_keys, atm_bnd_vlcs)),
int)
return atm_bnd_vlc_dct
def from_graph(gra):
""" networkx graph object from a molecular graph
"""
nxg = networkx.Graph()
nxg.add_nodes_from(atom_keys(gra))
nxg.add_edges_from(bond_keys(gra))
networkx.set_node_attributes(nxg, atom_symbols(gra), 'symbol')
networkx.set_node_attributes(nxg, atom_implicit_hydrogen_valences(gra),
'implicit_hydrogen_valence')
networkx.set_node_attributes(nxg, atom_stereo_parities(gra),
'stereo_parity')
networkx.set_edge_attributes(nxg, bond_orders(gra), 'order')
networkx.set_edge_attributes(nxg, bond_stereo_parities(gra),
'stereo_parity')
return nxg