Molecular Modeling Python Packages

meeko

Interface for AutoDock, molecule parameterization

moleculekit

MoleculeKit: Your favorite molecule manipulation kit

pymolar

Repository for molar crate and its dependencies

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

stko

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

quantumtuna

A streamlined quantum chemistry program for atoms and diatomics.

synth-pdb

Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development

pyemma

🚂 Python API for Emma's Markov Model Algorithms 🚂

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.

pylipid

A python toolkit for analysing membrane protein-lipid interactions.

bayesianflow-for-chem

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

kmcos

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

molecularnodes

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

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

xyz2graph

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

atomic-datasets

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

openpathsampling

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

bbprepared

Prepare your building blocks for stk construction and analysis

chorus

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

ani1datatools

package used to access the ANI-1 data set

buildamol

A fragment-based molecular assembly toolkit

dynsight

A framework for the analysis of the dynamics of particle trajectories

libarvo

Library to compute molecular surfaces and volumes.