DeepSMILES

This Python module can convert well-formed SMILES (that is, as written by a cheminformatics toolkit) to DeepSMILES. It also does the reverse conversion.

Install the latest version with::

pip install --upgrade deepsmiles

DeepSMILES is a SMILES-like syntax suited to machine learning. Rings are indicated using a single symbol instead of two, while branches do not use matching parentheses but rather use a right parenthesis as a 'pop' operator.

For example, benzene is c1ccccc1 in SMILES but cccccc6 in DeepSMILES (where the 6 indicates the ring size). As a branch example, the SMILES C(Br)(OC)I can be converted to the DeepSMILES CBr)OC))I. For more information, please see the corresponding preprint (https://doi.org/10.26434/chemrxiv.7097960.v1) or the lightning talk at https://www.slideshare.net/NextMoveSoftware/deepsmiles.

The library is used as follows:

.. code-block:: python

    import deepsmiles
    print("DeepSMILES version: %s" % deepsmiles.__version__)
    converter = deepsmiles.Converter(rings=True, branches=True)
    print(converter) # record the options used

    encoded = converter.encode("c1cccc(C(=O)Cl)c1")
    print("Encoded: %s" % encoded)

    try:
        decoded = converter.decode(encoded)
    except deepsmiles.DecodeError as e:
        decoded = None
        print("DecodeError! Error message was '%s'" % e.message)

    if decoded:
        print("Decoded: %s" % decoded)