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awesome-python-chemistry

A curated list of Python packages related to chemistry
https://github.com/lmmentel/awesome-python-chemistry

Last synced: about 16 hours ago
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  • See Also

  • Simulations

      • cclib - A library for parsing output files various quantum chemical programs.
      • RDKit - Open-Source Cheminformatics Software.
      • Atomic Silumation Environment (ASE) - Is a set of tools and modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.
      • CACTVS - Cactvs is a universal, scriptable cheminformatics toolkit, with a large collection of modules for property computation, chemistry data file I/O and other tasks.
      • cinfony - A common API to several cheminformatics toolkits (Open Babel, RDKit, the CDK, Indigo, JChem, OPSIN and cheminformatics webservices).
      • chemlab - Is a library that can help the user with chemistry-relevant calculations.
      • GPAW - Is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE).
      • horton - Helpful Open-source Research TOol for N-fermion system, a quantum-chemistry program that can perform computations involving model Hamiltonians.
      • mathchem - Is a free open source package for calculating topological indices and other invariants of molecular graphs.
      • MDTraj - Package for manipulating molecular dynamics trajectories with support for multiple formats.
      • MMTK - The Molecular Modeling Toolkit is an Open Source program library for molecular simulation applications.
      • MolMod - A library with many components that are useful to write molecular modeling programs.
      • ProDy - An open source package for protein structural dynamics analysis with a flexible and responsive API.
      • Psi4 - A hybrid Python/C++ open-source package for quantum chemistry.
      • pyEMMA - Library for the estimation, validation and analysis Markov models of molecular kinetics and other kinetic and thermodynamic models from molecular dynamics data.
      • pygauss - An interactive tool for supporting the life cycle of a computational molecular chemistry investigations.
      • PyQuante - Is an open-source suite of programs for developing quantum chemistry methods.
      • pyvib2 - A program for analyzing vibrational motion and vibrational spectra.
      • ReNView - Usage-Instructions) - A program to visualize reaction networks.
      • tsase - The library which depends on ASE to tackle transition state calculations.
      • phonopy - An open source package for phonon calculations at harmonic and quasi-harmonic levels.
      • PorePy - A Simulation Tool for Fractured and Deformable Porous Media.
      • cantera - A collection of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and transport processes.
      • OPEM - Open source PEM (Proton Exchange Membrane) fuel cell simulation tool.
      • Jarvis-tools - An open-access software package for atomistic data-driven materials design
      • HTMD - High-Throughput Molecular Dynamics: Programming Environment for Molecular Discovery.
      • QMsolve - A module for solving and visualizing the Schrödinger equation.
      • torchmd - End-To-End Molecular Dynamics (MD) Engine using PyTorch.
      • emmet - A package to 'build' collections of materials properties from the output of computational materials calculations.
      • atomate2 - atomate2 is a library of computational materials science workflows.
      • IoData - File parser/converter for QM, MD and plane-wave DFT programs.
      • oddt - Open Drug Discovery Toolkit, a modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc.
      • alchemlyb - Makes alchemical free energy calculations easier by leveraging the full power and flexibility of the PyData stack.
      • yank - An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
      • openmmtools - A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
      • Indigo - Universal cheminformatics libraries, utilities and database search tools.
      • 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.
      • CalcUS - Quantum chemisttry web platform that brings all the necessary tools to perform quantum chemistry in a user-friendly web interface.
      • CatKit - General purpose tools for high-throughput catalysis.
      • ccinput - A tool and library for creating quantum chemistry input files.
      • cctk - A library for computational chemistry (DFT) for input file generation, data extraction, method screening and analysis.
      • fromage - The "FRamewOrk for Molecular AGgregate Excitations" enables localised QM/QM' excited state calculations in a solid state environment.
      • GPAW - Is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE).
      • horton - Helpful Open-source Research TOol for N-fermion system, a quantum-chemistry program that can perform computations involving model Hamiltonians.
      • mathchem - Is a free open source package for calculating topological indices and other invariants of molecular graphs.
      • MMTK - The Molecular Modeling Toolkit is an Open Source program library for molecular simulation applications.
      • MolMod - A library with many components that are useful to write molecular modeling programs.
      • nmrsim - A library for simulating first- or second-order NMR spectra and dynamic NMR resonances.
      • 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.
      • PLAMS - Python Library for Automating Molecular Simulation: input preparation, job execution, file management, output processing and building data workflows.
      • pMuTT - A library for ab-initio thermodynamic and kinetic parameter estimation.
      • ProDy - An open source package for protein structural dynamics analysis with a flexible and responsive API.
      • ProLIF - Interaction Fingerprints for protein-ligand complexes and more.
      • pyEMMA - Library for the estimation, validation and analysis Markov models of molecular kinetics and other kinetic and thermodynamic models from molecular dynamics data.
      • pysic - A calculator incorporating various empirical pair and many-body potentials.
      • Pyscf - A quantum chemistry package written in Python.
      • ReNView - Usage-Instructions) - A program to visualize reaction networks.
      • QUIP - A collection of software tools to carry out molecular dynamics simulations.
      • ProDy - An open source package for protein structural dynamics analysis with a flexible and responsive API.
      • QUIP - A collection of software tools to carry out molecular dynamics simulations.

    • Force Fields

      • FLARE - A package for creating fast and accurate interatomic potentials.
      • matbench-discovery - A benchmark for ML-guided high-throughput materials discovery.
      • CHGNet - Pretrained universal neural network potential for charge-informed atomistic modeling.
      • NeuralForceField - Neural Network Force Field based on PyTorch.
      • FitSNAP - A Package For Training SNAP Interatomic Potentials for use in the LAMMPS molecular dynamics package.
      • acpype - Convert AMBER forcefields from ANTECHAMBER to GROMACS format.
      • openff-toolkit - The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools.
      • fftool - Tool to build force field input files for molecular simulation.
      • 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.

  • General Chemistry

    • cctbx - The Computational Crystallography Toolbox.
    • batchcalculator - 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.
    • chemlib - A robust and easy-to-use package that solves a variety of chemistry problems.
    • chempy - ChemPy is a package useful for chemistry (mainly physical/inorganic/analytical chemistry).
    • LModeA-nano - Calculates the intrinsic chemical bond strength based on local vibrational mode theory in solids and molecules.
    • mendeleev - A package that provides a python API for accessing various properties of elements from the periodic table of elements.
    • pybel - Pybel provides convenience functions and classes that make it simpler to use the Open Babel libraries from Python.
    • pycroscopy - Scientific analysis of nanoscale materials imaging data.
    • pyEQL - A set of tools for conventional calculations involving solutions (mixtures) and electrolytes.
    • pyiron - pyiron - an integrated development environment (IDE) for computational materials science.
    • symfit - a curve-fitting library ideally suited to chemistry problems, including fitting experimental kinetics data.
    • symmetry - Symmetry is a library for materials symmetry analysis.
    • GoodVibes - A Python program to compute quasi-harmonic thermochemical data from Gaussian frequency calculations.
    • nmrglue - A package for working with nuclear magnetic resonance (NMR) data including functions for reading common binary file formats and processing NMR data.
    • aizynthfinder - A tool for retrosynthetic planning.
    • 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).
    • pymatviz - A toolkit for visualizations in materials informatics.
    • AQME - Ensemble of automated QM workflows that can be run through jupyter notebooks, command lines and yaml files.
    • stk - A library for building, manipulating, analyzing and automatic design of molecules, including a genetic algorithm.
    • molmass - Calculate mass, elemental composition, and mass distribution spectrum of a molecule given by its chemical formula, relative element weights, or sequence.
    • spectrochempy - A library for processing, analyzing and modeling spectroscopic data.
    • propka - Predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
    • batchcalculator - 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.
    • hgraph2graph - Hierarchical Generation of Molecular Graphs using Structural Motifs.
    • ionize - Calculates the properties of individual ionic species in aqueous solution, as well as aqueous solutions containing arbitrary sets of ions.
    • Open Babel - A chemical toolbox designed to speak the many languages of chemical data.
    • pybaselines - A package for fitting baselines of spectra for baseline correction.
    • pybel - Pybel provides convenience functions and classes that make it simpler to use the Open Babel libraries from Python.
    • ionize - Calculates the properties of individual ionic species in aqueous solution, as well as aqueous solutions containing arbitrary sets of ions.
    • Open Babel - A chemical toolbox designed to speak the many languages of chemical data.
    • datamol - Molecular Manipulation Made Easy. A light wrapper build on top of RDKit.

  • Machine Learning

    • amp - Is an open-source package designed to easily bring machine-learning to atomistic calculations.
    • MAML - Aims to provide useful high-level interfaces that make ML for materials science as easy as possible.
    • TDC - Therapeutics Data Commons (TDC) is the first unifying framework to systematically access and evaluate machine learning across the entire range of therapeutics.
    • chainer-chemistry - A deep learning framework (based on Chainer) with applications in Biology and Chemistry.
    • selfies - Self-Referencing Embedded Strings (SELFIES): A 100% robust molecular string representation.
    • DeepPurpose - A Deep Learning Library for Compound and Protein Modeling DTI, Drug Property, PPI, DDI, Protein Function Prediction.
    • Summit - Package for optimizing chemical reactions using machine learning (contains 10 algorithms + several benchmarks).
    • graphein - Provides functionality for producing geometric representations of protein and RNA structures, and biological interaction networks.
    • schnetpack - Deep Neural Networks for Atomistic Systems.
    • megnet - Graph Networks as a Universal Machine Learning Framework for Molecules and Crystals.
    • Matminer - Library of descriptors to aid in the data-mining of materials properties, created by the Lawrence Berkeley National Laboratory.
    • XenonPy - Library with several compositional and structural material descriptors, along with a few pre-trained neural network models of material properties.
    • DScribe - Descriptor library containing a variety of fingerprinting techniques, including the Smooth Overlap of Atomic Positions (SOAP).
    • chemprop - Message Passing Neural Networks for Molecule Property Prediction .
    • 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.
    • cgcnn - Crystal graph convolutional neural networks for predicting material properties.
    • DescriptaStorus - Descriptor computation (chemistry) and (optional) storage for machine learning.
    • atom3d - Enables machine learning on three-dimensional molecular structure.
    • chemml - A machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data.
    • MoleOOD - a robust molecular representation learning framework against distribution shifts.
    • olorenchemengine - Molecular property prediction with unified API for diverse models and respresentations,

  • Molecular Visualization

    • Force Fields

      • ase-gui - The graphical user-interface allows users to visualize, manipulate, and render molecular systems and atoms objects.
      • chemview - An interactive molecular viewer designed for the IPython notebook.
      • imolecule - An embeddable webGL molecule viewer and file format converter.
      • pymoldyn - A viewer for atomic clusters, crystalline and amorphous materials in a unit cell corresponding to one of the seven 3D Bravais lattices.
      • sumo - A toolkit for plotting and analysis of ab initio solid-state calculation data.
      • surfinpy - A library for the analysis, plotting and visualisation of ab initio surface calculation data.
      • PyMOL - A user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.
      • chemiscope - An interactive structure/property explorer for materials and molecules.
      • moleculekit - A molecule manipulation library.
      • trident-chemwidgets - Jupyter Widgets to interact with molecular datasets.
      • rdeditor - Simple RDKit molecule editor GUI using PySide.
      • nglview - A [Jupyter](https://jupyter.org/) widget to interactively view molecular structures and trajectories.

  • Database Wrappers

    • Force Fields

      • ccdc - An API for the Cambridge Structural Database System.
      • ChemSpiPy - [ChemSpider](http://www.chemspider.com/) wrapper, that allows chemical searches, chemical file downloads, depiction and retrieval of chemical properties.
      • chembl-downloader - Automate downloading and querying the latest (or a given) version of ChEMBL.
      • ChemInformant - High-throughput PubChem client for batch queries with caching, validation, rate-limit-aware retries, and a simple CLI.
      • NistChemPy - A package for accessing data from the NIST webbook...

  • Learning Resources

    • Force Fields

      • Computational Thermodynamics - 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.
      • 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.

  • Miscellaneous Awesome

    • Force Fields

      • Colorful Nuclide Chart - 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.

  • Table of contents

  • Generative Molecular Design

    • GuacaMol - A package for benchmarking of models for _de novo_ molecular design.
    • GraphINVENT - A platform for graph-based molecular generation using graph neural networks.
    • perses - Experiments with expanded ensembles to explore chemical space.
    • moses - A benchmarking platform for molecular generation models.
Programming Languages
Python 56 Jupyter Notebook 12 C++ 3 Fortran 2 TeX 1 JavaScript 1 CSS 1 Rich Text Format 1 TypeScript 1 HTML 1
Categories
Simulations 71 General Chemistry 31 Machine Learning 21 Molecular Visualization 12 See Also 5 Database Wrappers 5 Generative Molecular Design 4 Learning Resources 3 Table of contents 1 Miscellaneous Awesome 1
Sub Categories
Force Fields 35
Keywords
python 21 machine-learning 18 chemistry 14 drug-discovery 13 cheminformatics 11 materials-science 9 deep-learning 7 molecular-dynamics 7 computational-chemistry 6 bioinformatics 6 quantum-chemistry 5 automation 5 pytorch 4 neural-networks 4 materials-informatics 4 awesome 3 awesome-list 3 thermochemistry 3 molecule 3 visualization 3 neural-network 2 spectroscopy 2 chemical-kinetics 2 openmm 2 tensorflow 2 reactions 2 physics 2 atomistic-simulations 2 condensed-matter 2 smiles 2 vasp 2 scikit-learn 2 dft 2 biology 2 alchemical-free-energy-calculations 2 datasets 2 lammps 2 materials-discovery 2 cli 2 simulations 2 graph-neural-networks 2 molecular-dynamics-simulation 2 bayesian-optimization 2 python-library 2 molecular-simulations 2 computational-biology 2 molecular-modeling 2 molecular-simulation 2 workflows 2 reproducibility 2