datamol.reactions

apply_reaction(rxn, reactants, product_index=None, single_product_group=False, as_smiles=False, rm_attach=False, disable_logs=True, sanitize=True)

Apply a chemical reaction on a molecule

Parameters:

Name	Type	Description	Default
rxn	dm.ChemicalReaction	Reaction object.	required
reactants	tuple	A tuple of reactants.	required
product_index	Optional[Union[int, list]]	The index of the product of interest.	None
single_product_group	bool	Whether return one product group from all possible product groups.	False
as_smiles	bool	Whether return products in SMILES.	False
rm_attach	bool	Whether remove the attachment point from products.	False
disable_logs	bool	Whether disable rdkit logs.	True
sanitize	bool	Whether sanitize the products.	True

Returns:

Type	Description
Union[list, str, dm.Mol]	Reaction products.

Source code in datamol/reactions/_reactions.py

def apply_reaction(
    rxn: dm.ChemicalReaction,
    reactants: tuple,
    product_index: Optional[Union[int, list]] = None,
    single_product_group: bool = False,
    as_smiles: bool = False,
    rm_attach: bool = False,
    disable_logs: bool = True,
    sanitize: bool = True,
) -> Union[list, str, dm.Mol]:
    """
    Apply a chemical reaction on a molecule

    Args:
       rxn: Reaction object.
       reactants: A tuple of reactants.
       product_index: The index of the product of interest.
       single_product_group: Whether return one product group from all possible product groups.
       as_smiles: Whether return products in SMILES.
       rm_attach: Whether remove the attachment point from products.
       disable_logs: Whether disable rdkit logs.
       sanitize: Whether sanitize the products.

    Returns:
       Reaction products.
    """
    with dm.without_rdkit_log(enable=disable_logs):
        if not rxn.IsInitialized():
            rxn.Initialize()  # pragma: no cover

        product = rxn.RunReactants(reactants)
        outputs = select_reaction_output(
            product=product,
            product_index=product_index,
            single_product_group=single_product_group,
            as_smiles=as_smiles,
            rm_attach=rm_attach,
            sanitize=sanitize,
        )

    return outputs

can_react(rxn, mol)

Check if a molecule is a reactant to a chemical reaction.

Parameters:

Name	Type	Description	Default
rxn	dm.ChemicalReaction	Reaction to check.	required
mol	dm.Mol	Molecule to check if it is a reactant.	required

Returns:

Type	Description
bool	True if mol is a reactant of rxn.

Source code in datamol/reactions/_reactions.py

def can_react(rxn: dm.ChemicalReaction, mol: dm.Mol) -> bool:
    """Check if a molecule is a reactant to a chemical reaction.

    Args:
        rxn: Reaction to check.
        mol: Molecule to check if it is a reactant.

    Returns:
        True if `mol` is a reactant of rxn.
    """
    if not rxn.IsInitialized():
        rxn.Initialize()  # pragma: no cover
    if rxn.IsMoleculeReactant(mol):
        return find_reactant_position(rxn, mol) != -1
    return False

find_reactant_position(rxn, mol)

Find the position of a reactant in a reaction.

Parameters:

Name	Type	Description	Default
rxn	dm.ChemicalReaction	Reaction	required
mol	dm.Mol	Molecule	required

Returns:

Type	Description
int	Reactant position or -1 if mol is not a reactant.

Source code in datamol/reactions/_reactions.py

def find_reactant_position(rxn: dm.ChemicalReaction, mol: dm.Mol) -> int:
    """Find the position of a reactant in a reaction.

    Args:
        rxn: Reaction
        mol: Molecule

    Returns:
        Reactant position or -1 if `mol` is not a reactant.
    """

    if not rxn.IsInitialized():
        rxn.Initialize()  # pragma: no cover

    react_pos = -1
    for pos, rct in enumerate(rxn.GetReactants()):
        if mol.HasSubstructMatch(rct):
            react_pos = pos
    return react_pos

inverse_reaction(rxn)

Get the reverse reaction of the input reaction

Parameters:

Name	Type	Description	Default
rxn	dm.ChemicalReaction	Reaction to inverse.	required

Returns:

Type	Description
dm.ChemicalReaction	Inversed reaction.

Source code in datamol/reactions/_reactions.py

def inverse_reaction(rxn: dm.ChemicalReaction) -> dm.ChemicalReaction:
    """
    Get the reverse reaction of the input reaction

    Args:
        rxn: Reaction to inverse.

    Returns:
        Inversed reaction.
    """
    rxn2 = rdChemReactions.ChemicalReaction()
    for i in range(rxn.GetNumReactantTemplates()):
        rxn2.AddProductTemplate(rxn.GetReactantTemplate(i))
    for i in range(rxn.GetNumProductTemplates()):
        rxn2.AddReactantTemplate(rxn.GetProductTemplate(i))
    rxn2.Initialize()
    return rxn2

is_reaction_ok(rxn, enable_logs=False)

Check if the given reaction is synthetically valid.

Parameters:

Name	Type	Description	Default
rxn	dm.ChemicalReaction	dm.ChemicalReaction object	required
enable_logs	bool	Whether to enable logs.	False

Returns:

Type	Description
bool	Boolean whether reaction is valid

Source code in datamol/reactions/_reactions.py

def is_reaction_ok(rxn: dm.ChemicalReaction, enable_logs: bool = False) -> bool:
    """Check if the given reaction is synthetically valid.

    Args:
        rxn: dm.ChemicalReaction object
        enable_logs: Whether to enable logs.

    Returns:
        Boolean whether reaction is valid
    """
    nWarn, nError, nReactants, nProducts, labels = rdChemReactions.PreprocessReaction(rxn)

    if enable_logs:
        logger.info(f"Number of warnings:{nWarn}")
        logger.info(f"Number of preprocessing errors: {nError}")
        logger.info(f"Number of reactants in reaction: {nReactants}")
        logger.info(f"Number of products in reaction: {nProducts}")
        logger.info(f"Preprocess labels added:{labels}")

    return rdChemReactions.SanitizeRxn(rxn) in [
        rdChemReactions.SanitizeFlags.SANITIZE_NONE,
        None,
    ]

rxn_from_block(rxn_block, sanitize=False)

Create a reaction from a block.

Parameters:

Name	Type	Description	Default
rxn_block	str	A reaction block.	required
sanitize	bool	Whether to sanitize the reaction.	False

Returns:

Type	Description
dm.ChemicalReaction	Initialized reaction.

Source code in datamol/reactions/_reactions.py

def rxn_from_block(
    rxn_block: str,
    sanitize: bool = False,
) -> dm.ChemicalReaction:
    """Create a reaction from a block.

    Args:
        rxn_block: A reaction block.
        sanitize: Whether to sanitize the reaction.

    Returns:
        Initialized reaction.

    """
    rxn = rdChemReactions.ReactionFromRxnBlock(rxnblock=rxn_block, sanitize=sanitize)
    rxn.Initialize()
    return rxn

rxn_from_block_file(rxn_block_path, sanitize=False)

Create a reaction from a block file.

Parameters:

Name	Type	Description	Default
rxn_block_path	Union[str, os.PathLike]	Filepath to a reaction block file.	required
sanitize	bool	Whether to sanitize the reaction.	False

Returns:

Type	Description
dm.ChemicalReaction	Initialized reaction.

Source code in datamol/reactions/_reactions.py

def rxn_from_block_file(
    rxn_block_path: Union[str, os.PathLike],
    sanitize: bool = False,
) -> dm.ChemicalReaction:
    """Create a reaction from a block file.

    Args:
        rxn_block_path: Filepath to a reaction block file.
        sanitize: Whether to sanitize the reaction.

    Returns:
        Initialized reaction.
    """
    with fsspec.open(rxn_block_path) as f:
        rxn_block = f.read()  # type: ignore
        rxn = rxn_from_block(rxn_block=rxn_block, sanitize=sanitize)
    return rxn

rxn_from_smarts(rxn_smarts)

Create a reaction from smarts

Parameters:

Name	Type	Description	Default
rxn_smarts	str	Reaction SMARTS string	required

Returns:

Type	Description
dm.ChemicalReaction	Initilized reaction.

Source code in datamol/reactions/_reactions.py

def rxn_from_smarts(rxn_smarts: str) -> dm.ChemicalReaction:
    """
    Create a reaction from smarts

    Args:
        rxn_smarts:  Reaction SMARTS string

    Returns:
        Initilized reaction.
    """
    rxn = rdChemReactions.ReactionFromSmarts(SMARTS=rxn_smarts)
    rxn.Initialize()
    return rxn

rxn_to_block(rxn, separate_agents=False, force_V3000=False)

Create a block from a reaction object.

Parameters:

Name	Type	Description	Default
rxn	dm.ChemicalReaction	A reaction object.	required
separate_agents	bool	Whether to separate agents from the reactants block. Not supported if force_V3000=True.	False
force_V3000	bool	Write the block in a V3000 format.	False

Returns:

Type	Description
str	Reaction block as string

Source code in datamol/reactions/_reactions.py

def rxn_to_block(
    rxn: dm.ChemicalReaction,
    separate_agents: bool = False,
    force_V3000: bool = False,
) -> str:
    """Create a block from a reaction object.

    Args:
        rxn: A reaction object.
        separate_agents: Whether to separate agents from the reactants block. Not supported
            if `force_V3000=True`.
        force_V3000: Write the block in a V3000 format.

    Returns:
        Reaction block as string
    """

    args = {}
    if dm.is_lower_than_current_rdkit_version("2022"):
        logger.warning("RDKit version prior to 2022.* does not support the `force_V3000` flag.")
    else:
        args["forceV3000"] = force_V3000

    return rdChemReactions.ReactionToRxnBlock(reaction=rxn, separateAgents=separate_agents, **args)

rxn_to_block_file(rxn, output_block_path, separate_agents=False, force_V3000=False)

Create a block from a reaction object.

Parameters:

Name	Type	Description	Default
rxn	dm.ChemicalReaction	A reaction object.	required
output_block_path	Union[str, os.PathLike]	Filepath to a reaction block file.	required
separate_agents	bool	Whether to separate agents from the reactants block. Not supported if force_V3000=True.	False
force_V3000	bool	Write the block in a V3000 format.	False

Source code in datamol/reactions/_reactions.py

def rxn_to_block_file(
    rxn: dm.ChemicalReaction,
    output_block_path: Union[str, os.PathLike],
    separate_agents: bool = False,
    force_V3000: bool = False,
):
    """Create a block from a reaction object.

    Args:
        rxn: A reaction object.
        output_block_path: Filepath to a reaction block file.
        separate_agents: Whether to separate agents from the reactants block. Not supported
            if `force_V3000=True`.
        force_V3000: Write the block in a V3000 format.
    """
    block = rxn_to_block(
        rxn=rxn,
        separate_agents=separate_agents,
        force_V3000=force_V3000,
    )

    with fsspec.open(output_block_path, "w") as f:
        f = cast(io.TextIOWrapper, f)
        f.write(block)

rxn_to_smarts(rxn)

Create a SMARTS from a reaction.

Parameters:

Name	Type	Description	Default
rxn	dm.ChemicalReaction	dm.ChemicalReaction object.	required

Returns:

Type	Description
str	SMARTS as string.

Source code in datamol/reactions/_reactions.py

def rxn_to_smarts(rxn: dm.ChemicalReaction) -> str:
    """Create a SMARTS from a reaction.

    Args:
        rxn: dm.ChemicalReaction object.

    Returns:
        SMARTS as string.
    """
    return rdChemReactions.ReactionToSmarts(reaction=rxn)

select_reaction_output(product, product_index=None, single_product_group=True, rm_attach=False, as_smiles=False, sanitize=True)

Compute the products from a reaction. It only takes the first product of the

Parameters:

Name	Type	Description	Default
product	Sequence[Sequence[dm.Mol]]	All the products from a reaction. A sequence of the list of products.	required
product_index	Optional[Union[int, list]]	Index of the product to select. Examples: A.B -> C.D. The indices of products are 0 and 1. Both C and D will be returned if index is None or product indices are to [0, 1].	None
single_product_group	bool	Whether return a single group of products from a reaction.	True
rm_attach	bool	Whether remove the attachment point from the products.	False
as_smiles	bool	Whether return the result in smiles.	False
sanitize	bool	Whether sanitize the products to return.	True

Returns:

Type	Description
Union[list, str, dm.Mol]	Processed products from reaction.

Source code in datamol/reactions/_reactions.py

def select_reaction_output(
    product: Sequence[Sequence[dm.Mol]],
    product_index: Optional[Union[int, list]] = None,
    single_product_group: bool = True,
    rm_attach: bool = False,
    as_smiles: bool = False,
    sanitize: bool = True,
) -> Union[list, str, dm.Mol]:
    """
    Compute the products from a reaction. It only takes the first product of the

    Args:
        product: All the products from a reaction. A sequence of the list of products.
        product_index: Index of the product to select.
            Examples: A.B -> C.D. The indices of products are 0 and 1.
            Both C and D will be returned if index is None or product indices are to [0, 1].
        single_product_group: Whether return a single group of products from a reaction.
        rm_attach: Whether remove the attachment point from the products.
        as_smiles: Whether return the result in smiles.
        sanitize: Whether sanitize the products to return.

    Returns:
        Processed products from reaction.
    """
    if len(product) == 0:
        return list(product)
    product = np.array(product)
    if product_index is not None:
        product = product[:, product_index]
    if single_product_group:
        index = np.random.randint(product.shape[0], size=1)
        product = product[index]
    if sanitize:
        product = np.vectorize(dm.sanitize_mol)(product)
    if rm_attach:
        fn = lambda x: dm.remove_dummies(x) if x is not None else x
        product = np.vectorize(fn)(product)
    if as_smiles:
        fn = lambda x: dm.to_smiles(x, allow_to_fail=True) if x is not None else x
        product = np.vectorize(fn)(product)
    product = product.tolist()
    if single_product_group:
        return product[0]
    return product

add_brackets_to_attachment_points(smiles)

Adds brackets to the attachment points (if they don't have them). Example: "CC(C)CO" to "CC(C)CO[]"

Parameters:

Name	Type	Description	Default
smiles	str	A smiles string.	required

Returns:

Type	Description
str	A smiles string with brackets.

Source code in datamol/reactions/_attachments.py

def add_brackets_to_attachment_points(smiles: str) -> str:
    """
    Adds brackets to the attachment points (if they don't have them).
    Example: "CC(C)CO*" to "CC(C)CO[*]"

    Args:
        smiles: A smiles string.

    Returns:
        A smiles string with brackets.
    """
    return re.sub(
        ATTACHMENT_POINT_NO_BRACKETS_REGEXP,
        "[{}]".format(ATTACHMENT_POINT_TOKEN),
        smiles,
    )

convert_attach_to_isotope(mol_or_smiles, same_isotope=False, as_smiles=False)

Convert attachment to isotope mapping.

"O=C(NCc1cnc([*])c1)[*]" to "O=C(NCc1cnc([1*])c1)[2*]"

Parameters:

Name	Type	Description	Default
mol_or_smiles	Union[dm.Mol, str]	A Mol object or a smiles to be converted	required
same_isotope	bool	Whether convert to the same isotope. Example: "O=C(NCc1cnc([])c1)[]" to "O=C(NCc1cnc([1])c1)[1]"	False

Returns:

Type	Description
Union[dm.Mol, str]	Converted Mol object or SMILES.

Source code in datamol/reactions/_attachments.py

def convert_attach_to_isotope(
    mol_or_smiles: Union[dm.Mol, str],
    same_isotope: bool = False,
    as_smiles: bool = False,
) -> Union[dm.Mol, str]:
    """Convert attachment to isotope mapping.

    Examples: "O=C(NCc1cnc([*])c1)[*]" to  "O=C(NCc1cnc([1*])c1)[2*]"

    Args:
        mol_or_smiles: A Mol object or a smiles to be converted
        same_isotope: Whether convert to the same isotope.
            Example: "O=C(NCc1cnc([*])c1)[*]" to  "O=C(NCc1cnc([1*])c1)[1*]"

    Returns:
        Converted Mol object or SMILES.
    """
    mol = dm.to_mol(mol_or_smiles)
    smiles = dm.to_smiles(mol)
    smiles = cast(str, smiles)

    smiles = add_brackets_to_attachment_points(smiles)

    # reg matching seems to be the most effective
    subs_reg = r"[\g<1>{}]"
    if same_isotope:
        subs_reg = "[1{}]"

    smiles = re.sub(ATTACHMENT_POINT_NUM_REGEXP, subs_reg.format(ATTACHMENT_POINT_TOKEN), smiles)

    if as_smiles:
        return smiles
    return dm.to_mol(smiles)

num_attachment_points(mol_or_smiles)

Get the number of attachment point in the

Parameters:

Name	Type	Description	Default
mol_or_smiles	Union[dm.Mol, str]	A Mol object or a smiles to be converted	required

Returns:

Type	Description
int	Number of attachment points of the given molecule.

Source code in datamol/reactions/_attachments.py

def num_attachment_points(mol_or_smiles: Union[dm.Mol, str]) -> int:
    """
    Get the number of attachment point in the

    Args:
        mol_or_smiles: A Mol object or a smiles to be converted

    Returns:
        Number of attachment points of the given molecule.
    """
    if isinstance(mol_or_smiles, dm.Mol):
        mol = cast(dm.Mol, mol_or_smiles)
        n_points = len(
            [atom for atom in mol.GetAtoms() if atom.GetSymbol() == ATTACHMENT_POINT_TOKEN]
        )
    else:
        n_points = len(re.findall(ATTACHMENT_POINT_REGEXP, mol_or_smiles))

    return n_points

open_attach_points(mol, fix_atom_map=False, bond_type=dm.SINGLE_BOND)

Compute attachment points on a molecule. This will highlight all valid attachment point on the current molecule instead.

Parameters:

Name	Type	Description	Default
mol	dm.Mol	A Mol object to be processed.	required
fix_atom_map	bool	Whether fix the atom mapping of the molecule.	False
bond_type	dm.BondType	The bond type to be opened.	dm.SINGLE_BOND

Returns:

Type	Description
dm.Mol	Molecule with open attachment points

Source code in datamol/reactions/_attachments.py

def open_attach_points(
    mol: dm.Mol,
    fix_atom_map: bool = False,
    bond_type: dm.BondType = dm.SINGLE_BOND,
) -> dm.Mol:
    """Compute attachment points on a molecule.
    This will highlight all valid attachment point on the current molecule instead.

    Args:
        mol: A Mol object to be processed.
        fix_atom_map: Whether fix the atom mapping of the molecule.
        bond_type: The bond type to be opened.

    Returns:
        Molecule with open attachment points
    """

    emol = Chem.rdchem.RWMol(dm.to_mol(mol))
    with dm.log.without_rdkit_log():
        atoms = [
            (a.GetIdx(), a)
            for a in emol.GetAtoms()
            if a.GetSymbol() != ATTACHMENT_POINT_TOKEN
            and a.GetImplicitValence() > 0
            and (not a.HasProp("_protected") or a.GetProp("_protected") != "1")
        ]
        atoms.sort(reverse=True, key=operator.itemgetter(0))

        for atom in atoms:
            new_atom = Chem.rdchem.Atom(ATTACHMENT_POINT_TOKEN)
            new_atom.SetAtomMapNum(1 if fix_atom_map else atom[0])
            new_index = emol.AddAtom(new_atom)
            emol.UpdatePropertyCache(strict=False)
            if bond_type is not None:
                emol.AddBond(atom[0], new_index, bond_type)
            else:
                emol.AddBond(atom[0], new_index)

    mol = dm.sanitize_mol(emol)
    return mol