smiles-encoder: One-hot encoding for simple molecular-input line-entry system (SMILES) strings

smiles-encoder is a Python package used to generate one-hot vectors representing SMILES strings (each string element is a one-hot vector).

Installation

Installation via pip:

$ pip install smiles-encoder

Installation via cloned repository:

$ git clone https://github.com/tjkessler/smiles-encoder
$ cd smiles-encoder
$ python setup.py install

smiles-encoder does not require any dependencies.

Basic Usage

First, assemble a list of SMILES strings:

smiles_strings = [
    'O=Cc1ccc(O)c(OC)c1',  # Vanillin
    'CC(=O)NCCC1=CNc2c1cc(OC)cc2',  # Melatonin
    'C1CCCCC1',  # Cyclohexane
    'C1=CC=CC=C1'  # Benzene
]

Import the SmilesEncoder object, and pass it the list of SMILES strings during initialization to construct the element dictionary:

from smiles_encoder import SmilesEncoder

encoder = SmilesEncoder(smiles_strings)

Use the encoder to encode SMILES strings:

encoded_smiles = encoder.encode_many(smiles_strings)

# OR

encoded_smiles = [encoder.encode(s) for s in smiles_strings]

Use the encoder to decode encoded SMILES strings:

decoded_smiles = encoder.decode_many(encoded_smiles)

# OR

decoded_smiles = [encoder.decode(e) for e in encoded_smiles]

Contributing, Reporting Issues and Other Support

To contribute to smiles-encoder, make a pull request. Contributions should include extensive documentation.

To report problems with the software or feature requests, file an issue. When reporting problems, include information such as error messages, your OS/environment and Python version.

For additional support/questions, contact Travis Kessler (travis.j.kessler@gmail.com).