k-ujihara / deepsmiles

DeepSMILES - A variant of SMILES for use in machine-learning

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:

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)