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datamol.reactions

Working with chemical reactions

apply_reaction(rxn, mol, react_pos, single_output=False)

Apply a chemical reaction on a molecule

Source code in datamol/reactions/_reactions.py 
@singledispatch
def apply_reaction(rxn, mol, react_pos, single_output=False):
    """Apply a chemical reaction on a molecule"""
    raise ValueError

can_react(rxn, mol)

Check if a molecule is a reactant to a chemical reaction and return position

Source code in datamol/reactions/_reactions.py 
@singledispatch
def can_react(rxn, mol):
    """Check if a molecule is a reactant to a chemical reaction and return position"""
    raise ValueError

compute_reaction_product(out, single_output=True)

Compute the product of a reaction

Source code in datamol/reactions/_reactions.py 
def compute_reaction_product(out, single_output=True):
    """Compute the product of a reaction"""
    out = [dm.fix_mol(x[0], n_iter=0) for x in out]
    if not single_output:
        return [dm.sanitize_mol(x) for x in out]
    # Might be a important to make a tradeoff decision in selecting products for greater speed.
    # product = sorted(out, key=lambda x: MoleculeEnv.compute_reward_from_mol(x, True))[-1]
    # sampling from list of products is an alternative
    return dm.sanitize_first(np.random.permutation(out))

inverse_reaction(rxn)

Get the reverse reaction of the input reaction

Source code in datamol/reactions/_reactions.py 
def inverse_reaction(rxn):
    """Get the reverse reaction of the input reaction"""
    rxn2 = AllChem.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)

Check is the reaction is synthetically valid

Source code in datamol/reactions/_reactions.py 
def is_reaction_ok(rxn):
    """Check is the reaction is synthetically valid"""
    return rdChemReactions.SanitizeRxn(rxn) == rdChemReactions.SanitizeFlags.SANITIZE_NONE