selfies

library2.2.0pypypi✓ verified 83d ago

SELFIES (SELF-referencIng Embedded Strings) is a general-purpose, sequence-based, robust representation of semantically constrained graphs, primarily used for molecular structures in cheminformatics and ML. Current version 2.2.0, releases every few months.

ai-ml data

pip install selfies

github ↗package ↗homepage ↗

INSTALL

IMPORT

SIG · SELFIES

selfies

ai-mlpythonv2.2.0

Install

1.5s avg

Import

51ms

Disk

16MB

Pass rate

10/ 10

Env Coverage10 / 10

glibc

3.9–3.13

musl

3.9–3.13

Install & Compatibility

Where this runs

tested against v2.2.0 · pip install

no network on importno background threads

Install × environment matrix

Each cell = how many times install + import succeeded across repeated harness runs. Partial = flaky.
glibc = Debian/Ubuntu slim · musl = Alpine Linux

musl

py 3.10–3.95 runs

installs and imports cleanly · install 0.0s · import 0.052s · 18MB

glibc

py 3.10–3.95 runs

installs and imports cleanly · install 1.5s · import 0.050s · 18MB

16MB installed

● package 16MB

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

encoder

✓ from selfies import encoder

No common wrong import; just import the function.

decoder

✓ from selfies import decoder

No common wrong import; just import the function.

Basic encode/decode a SMILES string.

from selfies import encoder, decoder smiles = "CCO" # ethanol selfies_str = encoder(smiles) print(selfies_str) # [C][C][O] smiles_back = decoder(selfies_str) print(smiles_back) # CCO

Debug

Known issues

breakingIn v2.0.0, the encoder now defaults to strict=True, raising errors for SMILES violating bond constraints. Previously, invalid SMILES were silently allowed.

fix

Use encoder(smiles, strict=False) to mimic old behavior, or ensure input SMILES are valid.

affects: >=2.0.0

deprecatedSupport for Python 3.5-3.6 dropped in v2.1.0.

fix

Upgrade to Python >=3.7.

affects: >=2.1.0

Errors

Common errors & fixes

AttributeError: module 'selfies' has no attribute 'selfies'

Wrong import style: trying to access selfies.selfies.

fix

Use from selfies import encoder, decoder directly.

RuntimeError: The input SMILES could not be parsed due to semantic constraints.

SMILES violates bond constraints (e.g., hypervalent atoms) and strict=True is default.

fix

Either fix the SMILES or pass strict=False to encoder.

TypeError: encoder() got an unexpected keyword argument 'strict'

Using version <2.0.0 where strict parameter didn't exist.

fix

Upgrade selfies: pip install --upgrade selfies

Upgrade

Version history

2.2.0latest on PyPI · released Jan 15, 2025

Audit

Dependencies

rdkitoptionalRequired for SMILES/SELFIES conversion and validity checks

Agent activity

15 hits · last 30 days

node

OpenAI (training)

Resources

githubhttps://github.com/aspuru-guzik-group/selfies ↗

packagehttps://pypi.org/project/selfies/ ↗

homepagehttps://selfies.mit.edu ↗