Smiles Python Packages

epam-indigo

Universal cheminformatics toolkit, utilities and database search tools

chematic

A pure-Rust cheminformatics library targeting RDKit feature parity — zero C/C++ by default.

pysmiles

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

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).

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

pytoda

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

cheminformant

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

chem-mrl

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

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.

glyles

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

molgen

Lightweight toolkit for de novo molecular generation: SMILES & SELFIES tokenizers, CharRNN / MolGPT / VAE models, training, sampling, and MOSES-style metrics.

harmonsmile

Toolkit for harmonizing SMILES strings to canonical + isomeric + Kekulized convention (RDKit)

chemdraw-mcp

MCP server for Claude: molecule names or SMILES → publication-style 2D structure drawings (PNG/SVG, offline via RDKit), reaction schemes, curved-arrow mechanisms and schematic spectra. Optional ChemDraw CDXML export — unofficial, not affiliated with Revvity.

molecode

Molecode presents molecules as code and enables LLMs to operate and reason on chemistry directly.

provesid

Access online services of chemical identifiers from Python

mofstructure

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

chemdraw

Draw molecules with plotly!

chemicalx

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

molbuilder

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

protify

Low code molecular property prediction

schemist

⬢⬢⬢ Organizing and processing tables of chemical structures.

mols2grid-to-image

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