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.

pymolar

Repository for molar crate and its dependencies

synth-pdb

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

quantumtuna

A streamlined quantum chemistry program for atoms and diatomics.

spindry

Low-cost host-guest conformer generation

pyemma

PyEMMA: Emma's Markov Model Algorithms

stko

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

bayesianflow-for-chem

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

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.

xyz2graph

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

pylipid

A python toolkit for analysing membrane protein-lipid interactions.

atomic-datasets

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

molecularnodes

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

kmcos

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

openpathsampling

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

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

Simplifies analysis of simulation and experimental trajectories.

bbprepared

No description available

chorus

Simple chemical structure modeling toolkit

ani1datatools

A data set of 20 million calculated off-equilibrium conformations for organic molecules

buildamol

A fragment-based molecular assembly toolkit for python.

rcbs-py

RCBS.py (Reactivity of Chemical and Biochemical Systems) is a Python package that contains several scripts, functions and classes that simplify the analysis of chemical and biochemical simulations.