awesome-python-chemistry

AQME

Ensemble of automated QM workflows that can be run through jupyter notebooks, command lines and yaml files

aizynthfinder

A tool for retrosynthetic planning

A GUI app based on wxPython for calculating the correct amount of reactants (batch) for a particular composition given by the molar ratio of its components

The Computational Crystallography Toolbox

ChemFormula

ChemFormula provides a class for working with chemical formulas. It allows parsing chemical formulas, calculating formula weights, and generating formatted output strings (e.g. in HTML, LaTeX, or Unicode)

A robust and easy-to-use package that solves a variety of chemistry problems

ChemPy is a package useful for chemistry (mainly physical/inorganic/analytical chemistry)

datamol

: - Molecular Manipulation Made Easy. A light wrapper build on top of RDKit

GoodVibes

A Python program to compute quasi-harmonic thermochemical data from Gaussian frequency calculations

hgraph2graph

Hierarchical Generation of Molecular Graphs using Structural Motifs

Calculates the properties of individual ionic species in aqueous solution, as well as aqueous solutions containing arbitrary sets of ions

Calculates the intrinsic chemical bond strength based on local vibrational mode theory in solids and molecules

A package that provides a python API for accessing various properties of elements from the periodic table of elements

nmrglue

A package for working with nuclear magnetic resonance (NMR) data including functions for reading common binary file formats and processing NMR data

molmass

Calculate mass, elemental composition, and mass distribution spectrum of a molecule given by its chemical formula, relative element weights, or sequence

A chemical toolbox designed to speak the many languages of chemical data

periodictable

This package provides a periodic table of the elements with support for mass, density and xray/neutron scattering information

propka

Predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure

A package for fitting baselines of spectra for baseline correction

Pybel provides convenience functions and classes that make it simpler to use the Open Babel libraries from Python

Scientific analysis of nanoscale materials imaging data

A set of tools for conventional calculations involving solutions (mixtures) and electrolytes

pyiron - an integrated development environment (IDE) for computational materials science

Python Materials Genomics is a robust, open-source library for materials analysis

pymatviz

A toolkit for visualizations in materials informatics

a curve-fitting library ideally suited to chemistry problems, including fitting experimental kinetics data

Symmetry is a library for materials symmetry analysis

stk

A library for building, manipulating, analyzing and automatic design of molecules, including a genetic algorithm

spectrochempy

A library for processing, analyzing and modeling spectroscopic data

Is an open-source package designed to easily bring machine-learning to atomistic calculations

atom3d

Enables machine learning on three-dimensional molecular structure

chainer-chemistry

A deep learning framework (based on Chainer) with applications in Biology and Chemistry

A machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data

chemprop

Message Passing Neural Networks for Molecule Property Prediction

cgcnn

Crystal graph convolutional neural networks for predicting material properties

Deep-learning models for Drug Discovery and Quantum Chemistry

DeepPurpose

A Deep Learning Library for Compound and Protein Modeling DTI, Drug Property, PPI, DDI, Protein Function Prediction

DescriptaStorus

Descriptor computation (chemistry) and (optional) storage for machine learning

DScribe

Descriptor library containing a variety of fingerprinting techniques, including the Smooth Overlap of Atomic Positions (SOAP)

graphein

Provides functionality for producing geometric representations of protein and RNA structures, and biological interaction networks

Matminer

Library of descriptors to aid in the data-mining of materials properties, created by the Lawrence Berkeley National Laboratory

MoleOOD

a robust molecular representation learning framework against distribution shifts

megnet

Graph Networks as a Universal Machine Learning Framework for Molecules and Crystals

MAML

Aims to provide useful high-level interfaces that make ML for materials science as easy as possible

MORFEUS

Library for fast calculations of lecula at re from 3D structures for machine learning with a focus on steric descriptors

olorenchemengine

Molecular property prediction with unified API for diverse models and respresentations, with integrated uncertainty quantification, interpretability, and hyperparameter/architecture tuning

ROBERT

Ensemble of automated machine learning protocols that can be run sequentially through a single command line. The program works for regression and classification problems

schnetpack

Deep Neural Networks for Atomistic Systems

selfies

Self-Referencing Embedded Strings (SELFIES): A 100% robust molecular string representation

Summit

Package for optimizing chemical reactions using machine learning (contains 10 algorithms + several benchmarks)

TDC

Therapeutics Data Commons (TDC) is the first unifying framework to systematically access and evaluate machine learning across the entire range of therapeutics

XenonPy

Library with several compositional and structural material descriptors, along with a few pre-trained neural network models of material properties

GraphINVENT

A platform for graph-based molecular generation using graph neural networks

GuacaMol

A package for benchmarking of models for molecular design

moses

A benchmarking platform for molecular generation models

perses

Experiments with expanded ensembles to explore chemical space

alchemlyb

Makes alchemical free energy calculations easier by leveraging the full power and flexibility of the PyData stack

atomate2

atomate2 is a library of computational materials science workflows

Is a set of tools and modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations

basis_set_exchange

A library containing basis sets for use in quantum chemistry calculations. In addition, this library has functionality for manipulation of basis set data

Cactvs is a universal, scriptable cheminformatics toolkit, with a large collection of modules for property computation, chemistry data file I/O and other tasks

CalcUS

Quantum chemisttry web platform that brings all the necessary tools to perform quantum chemistry in a user-friendly web interface

cantera

A collection of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and transport processes

CatKit

General purpose tools for high-throughput catalysis

ccinput

A tool and library for creating quantum chemistry input files

A library for parsing output files various quantum chemical programs

cctk

A library for computational chemistry (DFT) for input file generation, data extraction, method screening and analysis

A common API to several cheminformatics toolkits (Open Babel, RDKit, the CDK, Indigo, JChem, OPSIN and cheminformatics webservices)

Is a library that can help the user with chemistry-relevant calculations

emmet

A package to 'build' collections of materials properties from the output of computational materials calculations

fromage

The "FRamewOrk for Molecular AGgregate Excitations" enables localised QM/QM' excited state calculations in a solid state environment

Is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE)

Helpful Open-source Research TOol for N-fermion system, a quantum-chemistry program that can perform computations involving model Hamiltonians

HTMD

High-Throughput Molecular Dynamics: Programming Environment for Molecular Discovery

Indigo

Universal cheminformatics libraries, utilities and database search tools

IoData

File parser/converter for QM, MD and plane-wave DFT programs

Jarvis-tools

An open-access software package for atomistic data-driven materials design

Is a free open source package for calculating topological indices and other invariants of molecular graphs

Is an object-oriented library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats

Package for manipulating molecular dynamics trajectories with support for multiple formats

The Molecular Modeling Toolkit is an Open Source program library for molecular simulation applications

A library with many components that are useful to write molecular modeling programs

A library for simulating first- or second-order NMR spectra and dynamic NMR resonances

oddt

Open Drug Discovery Toolkit, a modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc

OPEM

Open source PEM (Proton Exchange Membrane) fuel cell simulation tool

openmmtools

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine

overreact

A library and command-line tool for building and analyzing complex homogeneous microkinetic models from quantum chemistry calculations, with support for quasi-harmonic thermochemistry, quantum tunnelling corrections, molecular symmetries and more

ParmEd

Parameter/topology editor and molecular simulator with visualization capability

pGrAdd

A library for estimating thermochemical properties of molecules and adsorbates using group additivity

An open source package for phonon calculations at harmonic and quasi-harmonic levels

PLAMS

Python Library for Automating Molecular Simulation: input preparation, job execution, file management, output processing and building data workflows

A library for ab-initio thermodynamic and kinetic parameter estimation

PorePy

A Simulation Tool for Fractured and Deformable Porous Media

An open source package for protein structural dynamics analysis with a flexible and responsive API

ProLIF

Interaction Fingerprints for protein-ligand complexes and more

A hybrid Python/C++ open-source package for quantum chemistry

Psi4NumPy

Psi4-based reference implementations and Jupyter notebook-based tutorials for foundational quantum chemistry methods

Library for the estimation, validation and analysis Markov models of molecular kinetics and other kinetic and thermodynamic models from molecular dynamics data

An interactive tool for supporting the life cycle of a computational molecular chemistry investigations

Is an open-source suite of programs for developing quantum chemistry methods

pysic

A calculator incorporating various empirical pair and many-body potentials

Pyscf

A quantum chemistry package written in Python

A program for analyzing vibrational motion and vibrational spectra

Open-Source Cheminformatics Software

ReNView

A program to visualize reaction networks

stk

A library for building, manipulating, analyzing and automatic design of molecules

QMsolve

A module for solving and visualizing the Schrödinger equation

A collection of software tools to carry out molecular dynamics simulations

torchmd

End-To-End Molecular Dynamics (MD) Engine using PyTorch

The library which depends on ASE to tackle transition state calculations

yank

An open, extensible Python framework for GPU-accelerated alchemical free energy calculations

acpype

Convert AMBER forcefields from ANTECHAMBER to GROMACS format

CHGNet

Pretrained universal neural network potential for charge-informed atomistic modeling

FitSNAP

A Package For Training SNAP Interatomic Potentials for use in the LAMMPS molecular dynamics package

fftool

Tool to build force field input files for molecular simulation

FLARE

A package for creating fast and accurate interatomic potentials

global-chem

A Chemical Knowledge Graph and Toolkit, writting in IUPAC/SMILES/SMARTS, for common small molecules from diverse communities to aid users in selecting compounds for forcefield parametirization

matbench-discovery

A benchmark for ML-guided high-throughput materials discovery

NeuralForceField

Neural Network Force Field based on PyTorch

openff-toolkit

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools

The graphical user-interface allows users to visualize, manipulate, and render molecular systems and atoms objects

chemiscope

An interactive structure/property explorer for materials and molecules

An interactive molecular viewer designed for the IPython notebook

An embeddable webGL molecule viewer and file format converter

moleculekit

A molecule manipulation library

nglview

A widget to interactively view molecular structures and trajectories

A user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger

A viewer for atomic clusters, crystalline and amorphous materials in a unit cell corresponding to one of the seven 3D Bravais lattices

rdeditor

Simple RDKit molecule editor GUI using PySide

A toolkit for plotting and analysis of ab initio solid-state calculation data

A library for the analysis, plotting and visualisation of ab initio surface calculation data

trident-chemwidgets

Jupyter Widgets to interact with molecular datasets

An API for the Cambridge Structural Database System

wrapper, that allows chemical searches, chemical file downloads, depiction and retrieval of chemical properties

An interface for the Chemical Identifier Resolver (CIR) by the CADD Group at the NCI/NIH

NistChemPy

A package for accessing data from the NIST webbook. API includes access to thermodynamic properties, molecular structures, IR/MS/UV-Vis spectra and more

PubChemPy provides a way to interact with PubChem in Python

chembl-downloader

Automate downloading and querying the latest (or a given) version of

drugbank-downloader

Automate downloading, opening, and parsing

An Introduction to Applied Bioinformatics

A Jupyter book demonstrating working with biochemical data using the scikit-bio library for tasks such as sequence alignment and calculating Hamming distances

This collection of Jupyter notebooks demonstrates solutions to a range of thermodynamic problems including solving chemical equilibria, comparing real versus ideal gas behavior, and calculating the temperature and composition of a combustion reaction

SciCompforChemists

Scientific Computing for Chemists with Python is a Jupyter book teaching basic python in chemistry skills, including relevant libraries, and applies them to solving chemical problems

A beatuful, interactive visualization of nuclides with access to a varirty of nuclear properties and allows saving high quality images for publications, presentations and outreach

awesome-cheminformatics

Another list focuses on Cheminformatics, including tools not only in Python

awesome-small-molecule-ml

A collection of papers, datasets, and packages for small-molecule drug discovery. Most links to code are in Python

awesome-molecular-docking

A curated list of molecular docking software, datasets, and papers

Joint Automated Repository for Various Integrated Simulations is a repository designed to automate materials discovery and optimization using classical force-field, density functional theory, machine learning calculations and experiments

polypharmacy-ddi-synergy-survey

A collection of research papers (with Python implementations) focusing on drug-drug interactions, synergy and polypharmacy