Python rdkit.Chem.RenumberAtoms() Examples

The following are 6 code examples of rdkit.Chem.RenumberAtoms(). You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may also want to check out all available functions/classes of the module rdkit.Chem , or try the search function .
Example #1
Source File: chem.py    From reinvent-randomized with MIT License 6 votes vote down vote up 
def randomize_smiles(mol, random_type="restricted"):
    """
    Returns a random SMILES given a SMILES of a molecule.
    :param mol: A Mol object
    :param random_type: The type (unrestricted, restricted) of randomization performed.
    :return : A random SMILES string of the same molecule or None if the molecule is invalid.
    """
    if not mol:
        return None

    if random_type == "unrestricted":
        return rkc.MolToSmiles(mol, canonical=False, doRandom=True, isomericSmiles=False)
    if random_type == "restricted":
        new_atom_order = list(range(mol.GetNumAtoms()))
        random.shuffle(new_atom_order)
        random_mol = rkc.RenumberAtoms(mol, newOrder=new_atom_order)
        return rkc.MolToSmiles(random_mol, canonical=False, isomericSmiles=False)
    raise ValueError("Type '{}' is not valid".format(random_type))
Example #2
Source File: preprocessing.py    From cddd with MIT License 6 votes vote down vote up 
def randomize_smile(sml):
    """Function that randomizes a SMILES sequnce. This was adapted from the
    implemetation of E. Bjerrum 2017, SMILES Enumeration as Data Augmentation
    for Neural Network Modeling of Molecules.
    Args:
        sml: SMILES sequnce to randomize.
    Return:
        randomized SMILES sequnce or
        nan if SMILES is not interpretable.
    """
    try:
        m = Chem.MolFromSmiles(sml)
        ans = list(range(m.GetNumAtoms()))
        np.random.shuffle(ans)
        nm = Chem.RenumberAtoms(m, ans)
        return Chem.MolToSmiles(nm, canonical=False)
    except:
        return float('nan')
Example #3
Source File: smiles_enumerator.py    From OpenChem with MIT License 5 votes vote down vote up 
def randomize_smiles(self, smiles):
        """Perform a randomization of a SMILES string
        must be RDKit sanitizable"""
        m = Chem.MolFromSmiles(smiles)
        ans = list(range(m.GetNumAtoms()))
        np.random.shuffle(ans)
        nm = Chem.RenumberAtoms(m, ans)
        return Chem.MolToSmiles(nm, canonical=self.canonical,
                                isomericSmiles=self.isomericSmiles)
Example #4
Source File: vectorizers.py    From Deep-Drug-Coder with MIT License 5 votes vote down vote up 
def randomize_mol(self, mol):
        """Performs a randomization of the atom order of an RDKit molecule"""
        ans = list(range(mol.GetNumAtoms()))
        np.random.shuffle(ans)
        return Chem.RenumberAtoms(mol,ans)
Example #5
Source File: chem.py    From reinvent-scaffold-decorator with MIT License 5 votes vote down vote up 
def to_smiles(mol, variant="canonical"):
    """
    Converts a Mol object into a canonical SMILES string.
    :param mol: Mol object.
    :return: A SMILES string.
    """
    if mol:
        if variant.startswith("random"):
            new_atom_order = list(range(mol.GetNumAtoms()))
            random.shuffle(new_atom_order)
            random_mol = rkc.RenumberAtoms(mol, newOrder=new_atom_order)
            return rkc.MolToSmiles(random_mol, canonical=False, isomericSmiles=False)
        else:
            return rkc.MolToSmiles(mol, isomericSmiles=False, canonical=True)
Example #6
Source File: SmilesEnumerator.py    From SMILES-enumeration with MIT License 5 votes vote down vote up 
def randomize_smiles(self, smiles):
        """Perform a randomization of a SMILES string
        must be RDKit sanitizable"""
        m = Chem.MolFromSmiles(smiles)
        ans = list(range(m.GetNumAtoms()))
        np.random.shuffle(ans)
        nm = Chem.RenumberAtoms(m,ans)
        return Chem.MolToSmiles(nm, canonical=self.canonical, isomericSmiles=self.isomericSmiles)