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mdanalysis
mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

692K 2K 830
mir-group
nequip

NequIP is a code for building E(3)-equivariant interatomic potentials

371K 903 207
mir-group
nequip-allegro

Allegro is an open-source code for building highly scalable and accurate equivariant deep learning interatomic potentials

350K 477 72
glotzerlab
freud-analysis

Powerful, efficient particle trajectory analysis in scientific Python.

108K 319 52
m3g
packmol

Packmol - Initial configurations for molecular dynamics simulations

32K 352 60
mushroomfire
mdapy

A simple and fast python library to handle the data generated from molecular dynamics simulations

22K 98 13
alchemistry
alchemlyb

the simple alchemistry library

22K 237 56
alchemistry
alchemtest

the simple alchemistry test set

22K 10 13
chemosim-lab
prolif

Interaction Fingerprints for protein-ligand complexes and more

21K 497 99
deepmodeling
deepmd-kit

A deep learning package for many-body potential energy representation and molecular dynamics

15K 2K 608
bjmorgan
kinisi

A Python package for estimating diffusion properties from molecular dynamics simulations.

11K 84 15
shirtsgroup
physical-validation

Physical validation of molecular simulations

10K 64 21
metatensor
metatrain

Train, fine-tune, and manipulate machine learning models for atomistic systems

10K 68 26
N283T
pyztraj

High-performance molecular dynamics trajectory analysis library in Zig

9K 0 0
yesint
pymolar

Repository for molar crate and its dependencies

8K 49 3
N283T
zsasa

High-performance SASA (Solvent Accessible Surface Area) calculation in Zig with Python bindings

8K 0 0
lab-cosmo
upet

Universal interatomic potentials for advanced materials modeling

8K 201 19
zincware
znh5md

ZnH5MD - High Performance Interface for H5MD Trajectories

7K 14 0
abelcarreras
dynaphopy

Phonon anharmonicity analysis from molecular dynamics

6K 140 57
jewettaij
moltemplate

A general cross-platform text-based molecule builder for LAMMPS

6K 312 106
inductiva
inductiva

Large scale simulations made simple.

5K 41 8
Becksteinlab
gromacswrapper

GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).

5K 190 54
mdanalysis
mdanalysistests

MDAnalysis is a Python library to analyze molecular dynamics simulations.

5K 2K 830
marrink-lab
vermouth

Describe and apply transformation on molecular structures and topologies

4K 144 59
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