Molecular Simulation Python Packages

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

moleculekit

MoleculeKit: Your favorite molecule manipulation kit

torchani

TorchANI 2.0 is an open-source library that supports training, development, and research of ANI-style neural network interatomic potentials. It was originally developed and is currently maintained by the Roitberg group.

physical-validation

Physical validation of molecular simulations

mdanalysistests

MDAnalysis is a Python library to analyze molecular dynamics simulations.

quantumtuna

A streamlined quantum chemistry program for atoms and diatomics.

spindry

Low-cost host-guest conformer generation

mchammer

Implementation of cheap Monte Carlo optimisation of bonds in molecules

mbuild

A hierarchical, component based molecule builder

foyer

A package for atom-typing as well as applying and disseminating forcefields

westpa

WESTPA is a package for constructing and running stochastic simulations using the "weighted ensemble" approach of Huber and Kim (1996).

qc-iodata

Python library for reading, writing, and converting computational chemistry file formats and generating input files.

deerpredict

A package for DEER and PRE predictions based on molecular dynamics ensembles. Can be installed with pip.

hotpot-zzy

A python package designed to communicate among various chemical and materials calculational tools

adaptivepele

AdaptivePELE is a Python package aimed at enhancing the sampling of molecular simulations

iodata

Python library for reading, writing, and converting computational chemistry file formats and generating input files.

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.

cgexplore

No description available

poremapper

cavity shape and size mapping by growing a guest inside a host

chemtools

Python tools for quantum chemical calculations

mbgdml

Create, use, and analyze machine learning potentials within the many-body expansion framework.

xdimer

Simulation of multi-molecular emission spectra dominated by intermolecular vibrations

imd-cookie-cutter

A tool for removing atoms in IMD config files, just like a cookie cutter in higher dimensions

tensormol

Tensorflow + Molecules = TensorMol