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.

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..

spindry

Low-cost host-guest conformer generation

stko

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

quantumtuna

A streamlined quantum chemistry program for atoms and diatomics.

pylipid

A python toolkit for analysing membrane protein-lipid interactions.

pyemma

🚂 Python API for Emma's Markov Model Algorithms 🚂

pymolar

Repository for molar crate and its dependencies

bayesianflow-for-chem

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

atomic-datasets

An easy (and fast) API for popular 3D molecular datasets!

molecularnodes

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

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.

openpathsampling

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

kmcos

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

buildamol

A fragment-based molecular assembly toolkit

bbprepared

Prepare your building blocks for stk construction and analysis

molecode

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

dynsight

A framework for the analysis of the dynamics of particle trajectories

boltzyml

Preprocessing file generator (v1) and hosted Boltz-2 API builder/submitter (v2.0): binary, ternary, or N-body protein-ligand-DNA-RNA binding prediction.

xyz2graph

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

chorus

(archived) A simple chemical structure graph modeling, drawing and analysis toolkit

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