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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

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

stko

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

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.

pyemma

🚂 Python API for Emma's Markov Model Algorithms 🚂

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

openpathsampling

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

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!

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

dynsight

A framework for the analysis of the dynamics of particle trajectories

libarvo

Library to compute molecular surfaces and volumes.

buildamol

A fragment-based molecular assembly toolkit