def decode(v):
"""Decode a molvector into a molecule
:param v: molvector
:result rdkit.RWMol:
"""
chunksize = atom_size + bond_chunk_size
nchunks = len(v) // chunksize
m = RWMol()
bonds = {}
for i in range(nchunks):
start = i * (atom_size + bond_chunk_size)
el, c, h, b1, o1, b2, o2, b3, o3, b4, o4 = v[start:start + chunksize]
atom = Atom(el)
atom.SetFormalCharge(c)
atom.SetNumExplicitHs(h)
atom_idx = m.AddAtom(atom)
assert atom_idx == i
for b, o in ((b1, o1), (b2, o2), (b3, o3), (b4, o4)):
if o:
to_atom = atom_idx + o
bonds[tuple(sorted((atom_idx, to_atom)))] = b
for (a1, a2), btype in bonds.items():
try:
m.AddBond(a1 % m.GetNumAtoms(), a2 % m.GetNumAtoms(),
BondType.values[btype])
except:
pass
return m
def set_atom_feat(a: Atom, key: str, val: int):
if key == 'atomic_num':
a.SetAtomicNum(val)
elif key == 'formal_charge':
a.SetFormalCharge(val)
elif key == 'chiral_tag':
a_chiral = rdchem.ChiralType.values[val]
a.SetChiralTag(a_chiral)
elif key == 'num_explicit_hs':
a.SetNumExplicitHs(val)
elif key == 'is_aromatic':
a.SetIsAromatic(bool(val))
return a