Molecular Modeling Python Packages

meeko

Interface for AutoDock, molecule parameterization

moleculekit

MoleculeKit: Your favorite molecule manipulation kit

stk

A Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.

spindry

Low-cost host-guest conformer generation

molecularnodes

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

quantumtuna

A streamlined quantum chemistry program for atoms and diatomics.

pymolar

Repository for molar crate and its dependencies

pyemma

🚂 Python API for Emma's Markov Model Algorithms 🚂

bayesianflow-for-chem

ChemBFN: Bayesian Flow Network Framework for Chemistry Tasks. Developed in Hiroshima University.

quantui

QuantUI puts PySCF behind an interactive Jupyter/Voilà UI. Run DFT, MP2, TD-DFT, NMR, geometry optimization, frequencies, and PES scans — visualize structures, orbitals, IR and UV-Vis spectra, all on your laptop.

pyadmd

Setup and run aMDeNM simulations with Python

stko

A collection of molecular optimisers and property calculators for use with stk.

pylipid

A python toolkit for analysing membrane protein-lipid interactions.

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.

kmcos

Kinetic Monte Carlo of Systems (KMCOS): lattice based kinetic Monte Carlo with a python front-end and Fortran back-end.

bbprepared

Prepare your building blocks for stk construction and analysis

libarvo

Library to compute molecular surfaces and volumes.

synth-pdb

Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development. Jupyter Notebook tutorials are available to visualize the concepts..

cognichem-client

Client library for interacting with Cognichem's cheminformatics services, supporting molecular inference, job management, and utility functions for chemical data processing.

swarm-cg

Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization

dynsight

A framework for the analysis of the dynamics of particle trajectories

openpathsampling

An open source Python framework for transition interface and path sampling calculations.

buildamol

A fragment-based molecular assembly toolkit

xyz2graph

Convert an xyz file into a molecular graph and create a 3D visualisation of the graph.