Skip to main content

DeepSMILES, a SMILES-like syntax suited to machine learning

Project description

This Python module can convert well-formed SMILES (that is, as writen 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.

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)

    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)

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for deepsmiles, version 1.0.1
Filename, size File type Python version Upload date Hashes
Filename, size deepsmiles-1.0.1-py2.py3-none-any.whl (12.6 kB) File type Wheel Python version py2.py3 Upload date Hashes View hashes
Filename, size deepsmiles-1.0.1.tar.gz (8.0 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page