def copy_edit_mol(mol: Chem.rdchem.Mol) -> Chem.rdchem.Mol:
new_mol = Chem.RWMol(Chem.MolFromSmiles(''))
for atom in mol.GetAtoms():
new_atom = copy_atom(atom)
new_mol.AddAtom(new_atom)
for bond in mol.GetBonds():
a1 = bond.GetBeginAtom().GetIdx()
a2 = bond.GetEndAtom().GetIdx()
bt = bond.GetBondType()
new_mol.AddBond(a1, a2, bt)
return new_mol
def atom_graph(mol: Chem.rdchem.Mol):
"""
Generates the atom graph from an RDKit Mol object.
Function taken from https://github.com/maxhodak/keras-molecules/pull/32/files.
"""
if mol:
G = nx.Graph()
for atom in mol.GetAtoms():
G.add_node(
atom.GetIdx(),
atomic_num=atom.GetAtomicNum(
), # this should be instantiated once, and later reused for defining the feature vector
formal_charge=atom.GetFormalCharge(),
chiral_tag=atom.GetChiralTag(),
hybridization=atom.GetHybridization(),
num_explicit_hs=atom.GetNumExplicitHs(),
is_aromatic=atom.GetIsAromatic(),
mass=atom.GetMass(),
implicit_valence=atom.GetImplicitValence(),
total_hydrogens=atom.GetTotalNumHs(),
features=np.array([
atom.GetAtomicNum(),
atom.GetFormalCharge(),
atom.GetChiralTag(),
atom.GetHybridization(),
atom.GetNumExplicitHs(),
atom.GetIsAromatic(),
atom.GetMass(),
atom.GetImplicitValence(),
atom.GetTotalNumHs(),
]),
)
for bond in mol.GetBonds():
G.add_edge(
bond.GetBeginAtomIdx(),
bond.GetEndAtomIdx(),
bond_type=bond.GetBondType(),
)
return G
def bond_graph(mol: Chem.rdchem.Mol):
"""
Generates the bond graph from an RDKit Mol object.
Here, unlike the atom gaph, bonds are nodes, and are
connected to each other by atoms.
:returns: a NetworkX graph.
"""
if mol:
G = nx.Graph()
for bond in mol.GetBonds():
G.add_node(
(bond.GetBeginAtomIdx(), bond.GetEndAtomIdx()),
bond_type=bond.GetBondTypeAsDouble(),
aromatic=bond.GetIsAromatic(),
stereo=bond.GetStereo(),
in_ring=bond.IsInRing(),
is_conjugated=bond.GetIsConjugated(),
features=[
bond.GetBondTypeAsDouble(),
int(bond.GetIsAromatic()),
# bond.GetStereo(),
int(bond.IsInRing()),
int(bond.GetIsConjugated()),
],
)
for atom in mol.GetAtoms():
bonds = atom.GetBonds()
if len(bonds) >= 2:
for b1, b2 in combinations(bonds, 2):
n1 = (b1.GetBeginAtomIdx(), b1.GetEndAtomIdx())
n2 = (b2.GetBeginAtomIdx(), b2.GetEndAtomIdx())
joining_node = list(set(n1).intersection(n2))[0]
G.add_edge(n1, n2, atom=joining_node)
G.add_edge(n2, n1)
return G
def tree_decomp(
mol: Chem.rdchem.Mol) -> Tuple[List[List[int]], List[Tuple[int, int]]]:
n_atoms = mol.GetNumAtoms()
cliques = []
for atom in mol.GetAtoms():
if atom.GetDegree() == 0:
cliques.append([atom.GetIdx()])
for bond in mol.GetBonds():
a1 = bond.GetBeginAtom().GetIdx()
a2 = bond.GetEndAtom().GetIdx()
if not bond.IsInRing():
cliques.append([a1, a2])
ssr = [list(x) for x in Chem.GetSymmSSSR(mol)]
cliques.extend(ssr)
nei_list = [[] for i in range(n_atoms)]
for i in range(len(cliques)):
for atom in cliques[i]:
nei_list[atom].append(i)
# Merge Rings with intersection > 2 atoms
for i in range(len(cliques)):
if len(cliques[i]) <= 2: continue
for atom in cliques[i]:
for j in nei_list[atom]:
if i >= j or len(cliques[j]) <= 2: continue
inter = set(cliques[i]) & set(cliques[j])
if len(inter) > 2:
cliques[i].extend(cliques[j])
cliques[i] = list(set(cliques[i]))
cliques[j] = []
cliques = [c for c in cliques if len(c) > 0]
nei_list = [[] for i in range(n_atoms)]
for i in range(len(cliques)):
for atom in cliques[i]:
nei_list[atom].append(i)
# Build edges and add singleton cliques
edges = defaultdict(int)
for atom in range(n_atoms):
if len(nei_list[atom]) <= 1:
continue
cnei = nei_list[atom]
bonds = [c for c in cnei if len(cliques[c]) == 2]
rings = [c for c in cnei if len(cliques[c]) > 4]
if len(bonds) > 2 or (
len(bonds) == 2 and len(cnei) > 2
): # In general, if len(cnei) >= 3, a singleton should be added, but 1 bond + 2 ring is currently not dealt with.
cliques.append([atom])
c2 = len(cliques) - 1
for c1 in cnei:
edges[(c1, c2)] = 1
elif len(rings) > 2: # Multiple (n>2) complex rings
cliques.append([atom])
c2 = len(cliques) - 1
for c1 in cnei:
edges[(c1, c2)] = MST_MAX_WEIGHT - 1
else:
for i in range(len(cnei)):
for j in range(i + 1, len(cnei)):
c1, c2 = cnei[i], cnei[j]
inter = set(cliques[c1]) & set(cliques[c2])
if edges[(c1, c2)] < len(inter):
edges[(c1, c2)] = len(
inter) # cnei[i] < cnei[j] by construction
edges = [u + (MST_MAX_WEIGHT - v, ) for u, v in edges.items()]
if len(edges) == 0:
return cliques, edges
# Compute Maximum Spanning Tree
row, col, data = zip(*edges)
n_clique = len(cliques)
clique_graph = csr_matrix((data, (row, col)), shape=(n_clique, n_clique))
junc_tree = minimum_spanning_tree(clique_graph)
row, col = junc_tree.nonzero()
edges = [(row[i], col[i]) for i in range(len(row))]
return cliques, edges
def all_bond_remove(
mol: Chem.rdchem.Mol,
as_mol: bool = True,
allow_bond_decrease: bool = True,
allow_atom_trim: bool = True,
max_num_action=float("Inf"),
):
"""Remove bonds from a molecule
Warning:
This can be computationally expensive.
Args:
mol: Input molecule
allow_bond_decrease: Allow decreasing bond type in addition to bond cut
max_num_action: Maximum number of action to reduce complexity
allow_atom_trim: Allow bond removal even when it results in dm.SINGLE_BOND
Returns:
All possible molecules from removing bonds
"""
new_mols = []
try:
Chem.Kekulize(mol, clearAromaticFlags=True)
except:
pass
for bond in mol.GetBonds():
if len(new_mols) > max_num_action:
break
original_bond_type = bond.GetBondType()
emol = Chem.RWMol(mol)
emol.RemoveBond(bond.GetBeginAtomIdx(), bond.GetEndAtomIdx())
new_mol = dm.sanitize_mol(emol.GetMol())
if not new_mol:
continue
frag_list = list(rdmolops.GetMolFrags(new_mol, asMols=True))
has_single_atom = any([x.GetNumAtoms() < 2 for x in frag_list])
if not has_single_atom or allow_atom_trim:
new_mols.extend(frag_list)
if allow_bond_decrease:
if original_bond_type in [dm.DOUBLE_BOND, dm.TRIPLE_BOND]:
new_mol = update_bond(mol, bond, dm.SINGLE_BOND)
if new_mol is not None:
new_mols.extend(
list(rdmolops.GetMolFrags(new_mol, asMols=True)))
if original_bond_type == dm.TRIPLE_BOND:
new_mol = update_bond(mol, bond, dm.DOUBLE_BOND)
if new_mol is not None:
new_mols.extend(
list(rdmolops.GetMolFrags(new_mol, asMols=True)))
new_mols = [mol for mol in new_mols if mol is not None]
if not as_mol:
return [dm.to_smiles(x) for x in new_mols if x]
return new_mols