def _compute_fragment_join(
mol,
fragment,
mol_atom_count,
bond_between_rings=True,
asMols=True,
):
"""List all posibilities of where a fragment can be attached to a mol"""
fragment = copy.copy(
fragment
) # need to copy the fragment copy is faster than all the other methods
with dm.without_rdkit_log():
combined = Chem.CombineMols(mol, fragment)
for i1 in range(mol.GetNumAtoms()):
a1 = combined.GetAtomWithIdx(i1)
if a1.GetImplicitValence() == 0:
continue
for i2 in range(fragment.GetNumAtoms()):
i2 += mol_atom_count
a2 = combined.GetAtomWithIdx(i2)
if a2.GetImplicitValence() == 0:
continue
# no bond between atoms already in rings
if not bond_between_rings and a1.IsInRing() and a2.IsInRing():
continue
# no bond to form large rings
else:
possibilities = _all_atom_join(combined, a1, a2)
for x in possibilities:
x = dm.sanitize_mol(x)
if x is not None:
if not asMols:
x = dm.to_smiles(x)
yield x
def _all_atom_join(mol, a1, a2):
"""Join two atoms (a1, a2) in a molecule in all possible valid manner"""
new_mols = []
with dm.without_rdkit_log():
try:
Chem.Kekulize(mol, clearAromaticFlags=True)
except:
pass
v1, v2 = a1.GetImplicitValence(), a2.GetImplicitValence()
bond = mol.GetBondBetweenAtoms(a1.GetIdx(), a2.GetIdx())
if bond is None:
if v1 > 0 and v2 > 0:
new_mols.append(add_bond_between(mol, a1, a2, dm.SINGLE_BOND))
if v1 > 1 and v2 > 1:
new_mols.append(add_bond_between(mol, a1, a2, dm.DOUBLE_BOND))
if v1 > 2 and v2 > 2:
new_mols.append(add_bond_between(mol, a1, a2, dm.TRIPLE_BOND))
elif bond.GetBondType() == dm.SINGLE_BOND:
if v1 > 0 and v2 > 0:
new_mols.append(update_bond(mol, bond, dm.DOUBLE_BOND))
if v1 > 1 and v2 > 1:
new_mols.append(update_bond(mol, bond, dm.TRIPLE_BOND))
elif bond.GetBondType() == dm.DOUBLE_BOND:
if v1 > 0 and v2 > 0:
new_mols.append(update_bond(mol, bond, dm.TRIPLE_BOND))
return [mol for mol in new_mols if mol is not None]
def update_bond(mol, bond, bond_type):
"""Update bond type between atoms"""
new_mol = dm.copy_mol(mol)
with dm.without_rdkit_log():
new_bond = new_mol.GetBondWithIdx(bond.GetIdx())
new_bond.SetBondType(bond_type)
return dm.sanitize_mol(new_mol)
def test_rdkit_log(capfd):
"""Test multiple rdkit log scenarios."""
check_logs_are_shown(capfd)
with dm.without_rdkit_log():
check_logs_are_not_shown(capfd)
check_logs_are_shown(capfd)
dm.disable_rdkit_log()
check_logs_are_not_shown(capfd)
dm.enable_rdkit_log()
check_logs_are_shown(capfd)
dm.disable_rdkit_log()
with dm.without_rdkit_log():
check_logs_are_not_shown(capfd)
check_logs_are_not_shown(capfd)
def all_atom_add(
mol,
atom_types=["C", "N", "O", "F", "Cl", "Br"],
asMols=True,
max_num_action=float("Inf"),
**kwargs,
):
"""Add a new atom on the mol, by considering all bond type
.. warning::
This is computationally expensive
Args:
mol: <Chem.Mol>
Input molecule
atom_types: list
List of atom symbol to use as replacement
(Default: ["C", "N", "O", "F", "Cl", "Br"])
asMols: bool, optional
Whether to return output as molecule or smiles
max_num_action: float, optional
Maximum number of action to reduce complexity
Returns:
All possible molecules with one additional atom added
"""
new_mols = []
stop = False
with dm.without_rdkit_log():
for atom in mol.GetAtoms():
if stop:
break
if atom.GetImplicitValence() == 0:
continue
for atom_symb in atom_types:
emol = Chem.RWMol(mol)
new_index = emol.AddAtom(Chem.Atom(atom_symb))
emol.UpdatePropertyCache(strict=False)
new_mols.extend(
_all_atom_join(emol, atom,
emol.GetMol().GetAtomWithIdx(new_index)))
if len(new_mols) > max_num_action:
stop = True
break
new_mols = [dm.sanitize_mol(mol) for mol in new_mols]
new_mols = [mol for mol in new_mols if mol is not None]
if not asMols:
return [dm.to_smiles(x) for x in new_mols if x]
return new_mols
def all_transform_apply(
mol,
rxns,
max_num_action=float("Inf"),
asMols=True,
**kwargs,
):
"""
Apply a transformation defined as a reaction from a set of reaction to the input molecule.
The reaction need to be one reactant-only
Arguments
----------
mol: <Chem.Mol>
Input molecule
rnxs: list
list of reactions/ reaction smarts
max_num_action: int, optional
Maximum number of result to return
(Default: inf)
asMols: bool, optional
Whether to return smiles or mols
Returns
-------
Products obtained from applying the chemical reactions
"""
mols = set([])
with dm.without_rdkit_log():
for rxn in rxns:
if len(mols) >= max_num_action:
break
if isinstance(rxn, str):
rxn = AllChem.ReactionFromSmarts(rxn)
try:
pcdts = [products[0] for products in rxn.RunReactants([mol])]
pcdts = [dm.sanitize_mol(x) for x in pcdts]
mols.update([dm.to_smiles(x) for x in pcdts if x])
except:
pass
mols = [x for x in mols if x is not None]
if np.isfinite(max_num_action):
mols = mols[:max_num_action]
mols = [dm.to_mol(x) for x in mols]
if not asMols:
mols = [dm.to_smiles(x) for x in mols if x is not None]
return mols
def all_atom_replace(mol,
atom_types=["C", "N", "S", "O"],
asMols=True,
max_num_action=float("Inf"),
**kwargs):
"""Replace all non-hydrogen atoms by other possibilities.
.. warning::
This is computationally expensive
Args:
mol: <Chem.Mol>
Input molecule
atom_types: list
List of atom symbol to use as replacement
(Default: ['C', 'N', 'S', 'O'])
asMols: bool, optional
Whether to return output as molecule or smiles
max_num_action: float, optional
Maximum number of action to reduce complexity
Returns:
All possible molecules with atoms replaced
"""
new_mols = []
stop = False
with dm.without_rdkit_log():
for atom in mol.GetAtoms():
if stop:
break
if atom.GetAtomicNum() > 1:
for atom_symb in atom_types:
emol = Chem.RWMol(mol)
emol.ReplaceAtom(atom.GetIdx(), Chem.Atom(atom_symb))
new_mols.append(emol)
if len(new_mols) > max_num_action:
stop = True
break
# Sanitize and remove bad molecules
new_mols = [dm.sanitize_mol(mol) for mol in new_mols]
new_mols = [mol for mol in new_mols if mol is not None]
if not asMols: # Return SMILES
return [dm.to_smiles(x) for x in new_mols]
return new_mols
