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Molecular Modeling Python Packages

Python packages with the GitHub topic molecular-modeling. Sorted by relevance, with stars and monthly downloads.
forlilab
meeko

Interface for AutoDock, molecule parameterization

64K 365 71
Acellera
moleculekit

MoleculeKit: Your favorite molecule manipulation kit

33K 236 39
lukasturcani
stk

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

6K 284 52
yesint
pymolar

Repository for molar crate and its dependencies

6K 51 3
elkins
synth-pdb

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

5K 1 0
h-brough
quantumtuna

A streamlined quantum chemistry program for atoms and diatomics.

4K 2 0
andrewtarzia
spindry

Low-cost host-guest conformer generation

4K 1 0
markovmodel
pyemma

PyEMMA: Emma's Markov Model Algorithms

3K 339 126
JelfsMaterialsGroup
stko

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

3K 24 9
Augus1999
bayesianflow-for-chem

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

2K 28 5
jigonzalez930209
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.

1K 3 0
zotko
xyz2graph

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

1K 86 22
wlsong
pylipid

A python toolkit for analysing membrane protein-lipid interactions.

1K 71 34
atomicarchitects
atomic-datasets

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

1K 49 5
bradyajohnston
molecularnodes

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

951 1K 120
kmcos
kmcos

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

892 24 17
openpathsampling
openpathsampling

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

811 116 51
GMPavanLab
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

702 48 13
GMPavanLab
dynsight

Simplifies analysis of simulation and experimental trajectories.

678 5 10
andrewtarzia
bbprepared

No description available

676 4 0
mojaie
chorus

Simple chemical structure modeling toolkit

608 5 4
isayev
ani1datatools

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

573 102 18
NoahHenrikKleinschmidt
buildamol

A fragment-based molecular assembly toolkit for python.

500 44 1
dynamicsUAB
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.

412 3 0
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