SELFIES
SELFIES (SELF-referencIng Embedded Strings) is a general-purpose, sequence-based, robust representation of semantically constrained graphs. It is based on a Chomsky type-2 grammar, augmented with two self-referencing functions. A main objective is to use SELFIES as direct input into machine learning models, in particular in generative models, for the generation of graphs with high semantical and syntactical validity.
See the paper at arXiv: https://arxiv.org/abs/1905.13741
The code presented here is a concrete application of SELFIES in chemistry, for the robust representation of molecule. We show the encoding and decoding of three molecules from various databases, and the generation of a new, random molecule with high semantical and syntactical validity.
Installation
You can install SELFIES via
pip install selfies
Examples
Several examples can be seen in examples/selfies_example.py. Here is a simple encoding and decoding:
from selfies import encoder, decoder
test_molecule1='CN1C(=O)C2=C(c3cc4c(s3)-c3sc(-c5ncc(C#N)s5)cc3C43OCCO3)N(C)C(=O)C2=C1c1cc2c(s1)-c1sc(-c3ncc(C#N)s3)cc1C21OCCO1' # non-fullerene acceptors for organic solar cells
selfies1=encoder(test_molecule1)
smiles1=decoder(selfies1)
print('test_molecule1: '+test_molecule1+'\n')
print('selfies1: '+selfies1+'\n')
print('smiles1: '+smiles1+'\n')
print('equal: '+str(test_molecule1==smiles1)+'\n\n\n')- an example of SELFIES in a generative model can be seen in the directory 'VariationalAutoEncoder_with_SELFIES'. There, SMILES datasets are automatically translated into SELFIES, and used for training of a variational autoencoder (VAE).
Python version
fully tested with Python 3.7.1 on
- 134.000 molecules at QM9 database (https://www.nature.com/articles/sdata201422)
- 250.000 molecues from the ZINC database (https://en.wikipedia.org/wiki/ZINC_database)
- 72 million molecules from PubChem (https://pubchem.ncbi.nlm.nih.gov/)
- 50.000 molecules for organic solar cells (https://www.sciencedirect.com/science/article/pii/S2542435117301307)
- 1 million molecules from organic chemical reactions (https://pubs.rsc.org/en/content/articlehtml/2018/sc/c8sc02339e)
supported:
- Python 3.7.2, 3.7.1, 3.6.8, 3.6.7, 2.7.15