Smiles Python Packages

epam-indigo

Universal cheminformatics toolkit, utilities and database search tools

pysmiles

A lightweight python-only library for reading and writing SMILES strings

cosmolkit

COSMolKit is a Rust-native cheminformatics and structural biology toolkit for molecules, SMILES/SDF/MolBlock parsing, molecular graphs, conformers, coordinates, and AI-ready batch workflows.

deepsmiles

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

rxnmapper

RXNMapper: Unsupervised attention-guided atom-mapping. Code complementing our Science Advances publication on "Extraction of organic chemistry grammar from unsupervised learning of chemical reactions" (https://advances.sciencemag.org/content/7/15/eabe4166).

bingo-elastic

Universal cheminformatics toolkit, utilities and database search tools

sciforma

High-performance 3D molecular conformer generation inspired by RDKit's ETKDG algorithm. Built with Rust for maximum speed, providing scientific accuracy and native support for Python, TypeScript (WASM), and CLI.

cheminformant

⚗️ An all-in-one solution for chemical property retrieval from PubChem.

glyles

A tool to convert IUPAC representations of glycans into SMILES strings.

pytoda

pytoda - PaccMann PyTorch Dataset Classes. Read the docs: https://paccmann.github.io/paccmann_datasets/

plotlymol

Interactive 3D molecular visualization in Python — ball-and-stick, VDW, orbital rendering, and a Dash GUI. Built on Plotly and RDKit.

chem-mrl

Chem-MRL: SMILES-based Matryoshka Representation Learning Embedding Model

mofstructure

A python package to deconstruct MOFs into building units, compute porosity, remove unbound guests and compute cheminfomatic data of building units

schemist

⬢⬢⬢ Organizing and processing tables of chemical structures.

peplink

Peptide <-> SMILES utilities for monomer peptides with non-canonical residues, terminal modifications, and selected cyclizations.

provesid

A Python package for chemical identifier resolution and experimental property extraction

chemdraw

Drawing molecules

protify

Low code molecular property prediction

rdkit-cli

Python command line tool for rdkit library, fast, simple and reactive

chemicalx

A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)

smiles-featurizers

Extract Molecular SMILES embeddings from language models pre-trained with various objectives architectures.

coho

SMILES parser

molbuilder

Professional-grade molecular engineering toolkit: atoms to retrosynthesis to process engineering

molbuilder-client

Python SDK for the MolBuilder REST API