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.

bingo-elastic

Universal cheminformatics toolkit, utilities and database search tools

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).

cheminformant

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

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.

pytoda

pytoda: PaccMann PyTorch Dataset Classes.

glyles

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

chem-mrl

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

schemist

Organizing and processing tables of chemical structures.

mofstructure

A comprehensive Python toolkit for deconstructing metal-organic frameworks (MOFs) into building units, analysing porosity, removing unbound guest molecules, determining framework topology with RCSR net identification and generating cheminformatics descriptors for structural components.

protify

Low code molecular property prediction

chemdraw

Draw molecules with plotly!

peplink

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

chemicalx

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

plotlymol

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

mols2grid-to-image

Convert CSV files with SMILES molecular data into grid PNG images using mols2grid and Playwright

rdkit-cli

A comprehensive CLI tool for RDKit cheminformatics operations

smiles-encoder

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

coho

SMILES parser

molbuilder

From molecule to manufacturing: retrosynthesis, process engineering, cost estimation, and safety analysis. Pure Python, no RDKit required.

smiles-featurizers

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