[38;5;12m                             [39m[38;2;255;187;0m[1m[4mAwesome Python Chemistry [0m[38;5;14m[1m[4m![0m[38;2;255;187;0m[1m[4mAwesome[0m[38;5;14m[1m[4m (https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)[0m[38;2;255;187;0m[1m[4m (https://github.com/sindresorhus/awesome)[0m
[38;5;14m[1m![0m[38;5;12mLicense: CC BY 4.0[39m[38;5;14m[1m (https://img.shields.io/badge/License-CC%20BY%204.0-lightgrey.svg)[0m[38;5;12m (https://creativecommons.org/licenses/by/4.0/)[39m

[38;5;12mA curated list of awesome Python frameworks, libraries, software and resources related to Chemistry.[39m

[38;5;12mInspired by [39m[38;5;14m[1mawesome-python[0m[38;5;12m (https://awesome-python.com).[39m

[38;2;255;187;0m[4mTable of contents[0m

[38;5;12m- [39m[38;5;14m[1mAwesome Python Chemistry ![0m[38;5;12mAwesome[39m[38;5;14m[1m (https://github.com/sindresorhus/awesome)[0m[38;5;12m (#awesome-python-chemistry-)[39m
[38;5;12m  - [39m[38;5;14m[1mGeneral Chemistry[0m[38;5;12m (#general-chemistry)[39m
[38;5;12m  - [39m[38;5;14m[1mMachine Learning[0m[38;5;12m (#machine-learning)[39m
[38;5;12m  - [39m[38;5;14m[1mGenerative Molecular Design[0m[38;5;12m (#generative-molecular-design)[39m
[38;5;12m  - [39m[38;5;14m[1mSimulations[0m[38;5;12m (#simulations)[39m
[38;5;12m  - [39m[38;5;14m[1mMolecular Visualization[0m[38;5;12m (#molecular-visualization)[39m
[38;5;12m  - [39m[38;5;14m[1mDatabase Wrappers[0m[38;5;12m (#database-wrappers)[39m
[38;5;12m  - [39m[38;5;14m[1mLearning Resources[0m[38;5;12m (#learning-resources)[39m
[38;5;12m  - [39m[38;5;14m[1mSee Also[0m[38;5;12m (#see-also)[39m

[38;5;238m――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――――[39m

[38;2;255;187;0m[4mGeneral Chemistry[0m

[48;2;30;30;40m[38;5;13m[3mPackages and tools for general chemistry.[0m

[38;5;12m- [39m[38;5;14m[1mAQME[0m[38;5;12m (https://github.com/jvalegre/aqme) - Ensemble of automated QM workflows that can be run through jupyter notebooks, command lines and yaml files.[39m
[38;5;12m- [39m[38;5;14m[1maizynthfinder[0m[38;5;12m (https://github.com/MolecularAI/aizynthfinder) - A tool for retrosynthetic planning.[39m
[38;5;12m- [39m[38;5;14m[1mbatchcalculator[0m[38;5;12m (http://lukaszmentel.com/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.[39m
[38;5;12m- [39m[38;5;14m[1mcctbx[0m[38;5;12m (https://cctbx.github.io/) - The Computational Crystallography Toolbox.[39m
[38;5;12m-[39m[38;5;12m [39m[38;5;14m[1mChemFormula[0m[38;5;12m [39m[38;5;12m(https://github.com/molshape/ChemFormula)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mChemFormula[39m[38;5;12m [39m[38;5;12mprovides[39m[38;5;12m [39m[38;5;12ma[39m[38;5;12m [39m[38;5;12mclass[39m[38;5;12m [39m[38;5;12mfor[39m[38;5;12m [39m[38;5;12mworking[39m[38;5;12m [39m[38;5;12mwith[39m[38;5;12m [39m[38;5;12mchemical[39m[38;5;12m [39m[38;5;12mformulas.[39m[38;5;12m [39m[38;5;12mIt[39m[38;5;12m [39m[38;5;12mallows[39m[38;5;12m [39m[38;5;12mparsing[39m[38;5;12m [39m[38;5;12mchemical[39m[38;5;12m [39m[38;5;12mformulas,[39m[38;5;12m [39m[38;5;12mcalculating[39m[38;5;12m [39m[38;5;12mformula[39m[38;5;12m [39m[38;5;12mweights,[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mgenerating[39m[38;5;12m [39m[38;5;12mformatted[39m[38;5;12m [39m[38;5;12moutput[39m[38;5;12m [39m[38;5;12mstrings[39m[38;5;12m [39m[38;5;12m(e.g.[39m[38;5;12m [39m
[38;5;12min[39m[38;5;12m [39m[38;5;12mHTML,[39m[38;5;12m [39m[38;5;12mLaTeX,[39m[38;5;12m [39m[38;5;12mor[39m[38;5;12m [39m[38;5;12mUnicode).[39m
[38;5;12m- [39m[38;5;14m[1mchemlib[0m[38;5;12m (https://chemlib.readthedocs.io/en/latest/) - A robust and easy-to-use package that solves a variety of chemistry problems.[39m
[38;5;12m- [39m[38;5;14m[1mchempy[0m[38;5;12m (http://pythonhosted.org/chempy/) - ChemPy is a package useful for chemistry (mainly physical/inorganic/analytical chemistry).[39m
[38;5;12m- [39m[38;5;14m[1mdatamol[0m[38;5;12m (https://github.com/datamol-org/datamol): - Molecular Manipulation Made Easy. A light wrapper build on top of RDKit.[39m
[38;5;12m- [39m[38;5;14m[1mGoodVibes[0m[38;5;12m (https://github.com/bobbypaton/GoodVibes) - A Python program to compute quasi-harmonic thermochemical data from Gaussian frequency calculations.[39m
[38;5;12m- [39m[38;5;14m[1mhgraph2graph[0m[38;5;12m (https://github.com/wengong-jin/hgraph2graph) - Hierarchical Generation of Molecular Graphs using Structural Motifs.[39m
[38;5;12m- [39m[38;5;14m[1mionize[0m[38;5;12m (http://lewisamarshall.github.io/ionize/) - Calculates the properties of individual ionic species in aqueous solution, as well as aqueous solutions containing arbitrary sets of ions.[39m
[38;5;12m- [39m[38;5;14m[1mLModeA-nano[0m[38;5;12m (https://lmodea-nano.readthedocs.io/en/latest/) - Calculates the intrinsic chemical bond strength based on local vibrational mode theory in solids and molecules.[39m
[38;5;12m- [39m[38;5;14m[1mmendeleev[0m[38;5;12m (http://mendeleev.readthedocs.io/en/stable/) - A package that provides a python API for accessing various properties of elements from the periodic table of elements.[39m
[38;5;12m- [39m[38;5;14m[1mnmrglue[0m[38;5;12m (https://github.com/jjhelmus/nmrglue) - A package for working with nuclear magnetic resonance (NMR) data including functions for reading common binary file formats and processing NMR data.[39m
[38;5;12m- [39m[38;5;14m[1mOpen Babel[0m[38;5;12m (http://openbabel.org/wiki/Main_Page) - A chemical toolbox designed to speak the many languages of chemical data.[39m
[38;5;12m- [39m[38;5;14m[1mperiodictable[0m[38;5;12m (https://github.com/pkienzle/periodictable) - This package provides a periodic table of the elements with support for mass, density and xray/neutron scattering information.[39m
[38;5;12m- [39m[38;5;14m[1mpropka[0m[38;5;12m (https://github.com/jensengroup/propka) - Predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.[39m
[38;5;12m- [39m[38;5;14m[1mpybel[0m[38;5;12m (https://openbabel.org/docs/dev/UseTheLibrary/Python_Pybel.html) - Pybel provides convenience functions and classes that make it simpler to use the Open Babel libraries from Python.[39m
[38;5;12m- [39m[38;5;14m[1mpycroscopy[0m[38;5;12m (https://pycroscopy.github.io/pycroscopy/index.html) - Scientific analysis of nanoscale materials imaging data.[39m
[38;5;12m- [39m[38;5;14m[1mpyEQL[0m[38;5;12m (https://pyeql.readthedocs.io/en/latest/index.html) - A set of tools for conventional calculations involving solutions (mixtures) and electrolytes.[39m
[38;5;12m- [39m[38;5;14m[1mpyiron[0m[38;5;12m (http://pyiron.org/) - pyiron - an integrated development environment (IDE) for computational materials science.[39m
[38;5;12m- [39m[38;5;14m[1mpymatgen[0m[38;5;12m (http://pymatgen.org) - Python Materials Genomics is a robust, open-source library for materials analysis.[39m
[38;5;12m- [39m[38;5;14m[1mpymatviz[0m[38;5;12m (https://github.com/janosh/pymatviz) - A toolkit for visualizations in materials informatics.[39m
[38;5;12m- [39m[38;5;14m[1msymfit[0m[38;5;12m (https://symfit.readthedocs.io/en/stable/) - a curve-fitting library ideally suited to chemistry problems, including fitting experimental kinetics data.[39m
[38;5;12m- [39m[38;5;14m[1msymmetry[0m[38;5;12m (http://pythonhosted.org/symmetry/) - Symmetry is a library for materials symmetry analysis.[39m
[38;5;12m- [39m[38;5;14m[1mstk[0m[38;5;12m (https://github.com/lukasturcani/stk) - A library for building, manipulating, analyzing and automatic design of molecules, including a genetic algorithm.[39m
[38;5;12m- [39m[38;5;14m[1mspectrochempy[0m[38;5;12m (https://github.com/spectrochempy/spectrochempy) - A library for processing, analyzing and modeling spectroscopic data.[39m

[38;2;255;187;0m[4mMachine Learning[0m

[48;2;30;30;40m[38;5;13m[3mPackages and tools for employing machine learning and data science in chemistry.[0m

[38;5;12m- [39m[38;5;14m[1mamp[0m[38;5;12m (http://amp.readthedocs.io/en/latest/) - Is an open-source package designed to easily bring machine-learning to atomistic calculations.[39m
[38;5;12m- [39m[38;5;14m[1matom3d[0m[38;5;12m (https://github.com/drorlab/atom3d) - Enables machine learning on three-dimensional molecular structure.[39m
[38;5;12m- [39m[38;5;14m[1mchainer-chemistry[0m[38;5;12m (https://github.com/chainer/chainer-chemistry) - A deep learning framework (based on Chainer) with applications in Biology and Chemistry.[39m
[38;5;12m- [39m[38;5;14m[1mchemml[0m[38;5;12m (https://hachmannlab.github.io/chemml/) - A machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data.[39m
[38;5;12m- [39m[38;5;14m[1mchemprop[0m[38;5;12m (https://github.com/chemprop/chemprop) - Message Passing Neural Networks for Molecule Property Prediction .[39m
[38;5;12m- [39m[38;5;14m[1mcgcnn[0m[38;5;12m (https://github.com/txie-93/cgcnn) - Crystal graph convolutional neural networks for predicting material properties.[39m
[38;5;12m- [39m[38;5;14m[1mdeepchem[0m[38;5;12m (http://deepchem.io/) - Deep-learning models for Drug Discovery and Quantum Chemistry.[39m
[38;5;12m- [39m[38;5;14m[1mDeepPurpose[0m[38;5;12m (https://github.com/kexinhuang12345/DeepPurpose) - A Deep Learning Library for Compound and Protein Modeling DTI, Drug Property, PPI, DDI, Protein Function Prediction.[39m
[38;5;12m- [39m[38;5;14m[1mDescriptaStorus[0m[38;5;12m (https://github.com/bp-kelley/descriptastorus) - Descriptor computation (chemistry) and (optional) storage for machine learning.[39m
[38;5;12m- [39m[38;5;14m[1mDScribe[0m[38;5;12m (https://github.com/SINGROUP/dscribe) - Descriptor library containing a variety of fingerprinting techniques, including the Smooth Overlap of Atomic Positions (SOAP).[39m
[38;5;12m- [39m[38;5;14m[1mgraphein[0m[38;5;12m (https://github.com/a-r-j/graphein) - Provides functionality for producing geometric representations of protein and RNA structures, and biological interaction networks.[39m
[38;5;12m- [39m[38;5;14m[1mMatminer[0m[38;5;12m (https://github.com/hackingmaterials/matminer) - Library of descriptors to aid in the data-mining of materials properties, created by the Lawrence Berkeley National Laboratory.[39m
[38;5;12m- [39m[38;5;14m[1mMoleOOD[0m[38;5;12m (https://github.com/yangnianzu0515/MoleOOD) - a robust molecular representation learning framework against distribution shifts.[39m
[38;5;12m- [39m[38;5;14m[1mmegnet[0m[38;5;12m (https://github.com/materialsvirtuallab/megnet) - Graph Networks as a Universal Machine Learning Framework for Molecules and Crystals.[39m
[38;5;12m- [39m[38;5;14m[1mMAML[0m[38;5;12m (https://github.com/materialsvirtuallab/maml) - Aims to provide useful high-level interfaces that make ML for materials science as easy as possible.[39m
[38;5;12m- [39m[38;5;14m[1mMORFEUS[0m[38;5;12m (https://github.com/kjelljorner/morfeus) - Library for fast calculations of [39m[38;5;14m[1mmo[0m[38;5;12mlecula[39m[38;5;14m[1mr[0m[38;5;12m [39m[38;5;14m[1mfe[0m[38;5;12mat[39m[38;5;14m[1mu[0m[38;5;12mre[39m[38;5;14m[1ms[0m[38;5;12m from 3D structures for machine learning with a focus on steric descriptors.[39m
[38;5;12m- [39m[38;5;14m[1molorenchemengine[0m[38;5;12m (https://github.com/Oloren-AI/olorenchemengine) - Molecular property prediction with unified API for diverse models and respresentations,[39m
[38;5;12m  with integrated uncertainty quantification, interpretability, and hyperparameter/architecture tuning.[39m
[38;5;12m- [39m[38;5;14m[1mROBERT[0m[38;5;12m (https://github.com/jvalegre/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.[39m
[38;5;12m- [39m[38;5;14m[1mschnetpack[0m[38;5;12m (https://github.com/atomistic-machine-learning/schnetpack) - Deep Neural Networks for Atomistic Systems.[39m
[38;5;12m- [39m[38;5;14m[1mselfies[0m[38;5;12m (https://github.com/aspuru-guzik-group/selfies) - Self-Referencing Embedded Strings (SELFIES): A 100% robust molecular string representation.[39m
[38;5;12m- [39m[38;5;14m[1mSummit[0m[38;5;12m (https://github.com/sustainable-processes/summit) - Package for optimizing chemical reactions using machine learning (contains 10 algorithms + several benchmarks).[39m
[38;5;12m- [39m[38;5;14m[1mTDC[0m[38;5;12m (https://github.com/mims-harvard/TDC) - Therapeutics Data Commons (TDC) is the first unifying framework to systematically access and evaluate machine learning across the entire range of therapeutics.[39m
[38;5;12m- [39m[38;5;14m[1mXenonPy[0m[38;5;12m (https://github.com/yoshida-lab/XenonPy) - Library with several compositional and structural material descriptors, along with a few pre-trained neural network models of material properties.[39m

[38;2;255;187;0m[4mGenerative Molecular Design[0m

[48;2;30;30;40m[38;5;13m[3mPackages and tools for generating molecular species[0m

[38;5;12m- [39m[38;5;14m[1mGraphINVENT[0m[38;5;12m (https://github.com/MolecularAI/GraphINVENT) - A platform for graph-based molecular generation using graph neural networks.[39m
[38;5;12m- [39m[38;5;14m[1mGuacaMol[0m[38;5;12m (https://github.com/BenevolentAI/guacamol) - A package for benchmarking of models for _de novo_ molecular design.[39m
[38;5;12m- [39m[38;5;14m[1mmoses[0m[38;5;12m (https://github.com/molecularsets/moses) - A benchmarking platform for molecular generation models.[39m
[38;5;12m- [39m[38;5;14m[1mperses[0m[38;5;12m (https://github.com/choderalab/perses) - Experiments with expanded ensembles to explore chemical space.[39m

[38;2;255;187;0m[4mSimulations[0m

[48;2;30;30;40m[38;5;13m[3mPackages for atomistic simulations and computational chemistry.[0m

[38;5;12m- [39m[38;5;14m[1malchemlyb[0m[38;5;12m (https://github.com/alchemistry/alchemlyb) - Makes alchemical free energy calculations easier by leveraging the full power and flexibility of the PyData stack.[39m
[38;5;12m- [39m[38;5;14m[1matomate2[0m[38;5;12m (https://github.com/materialsproject/atomate2) - atomate2 is a library of computational materials science workflows.[39m
[38;5;12m- [39m[38;5;14m[1mAtomic Silumation Environment (ASE)[0m[38;5;12m (https://wiki.fysik.dtu.dk/ase/index.html) - Is a set of tools and modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.[39m
[38;5;12m- [39m[38;5;14m[1mbasis_set_exchange[0m[38;5;12m (https://github.com/MolSSI-BSE/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.[39m
[38;5;12m- [39m[38;5;14m[1mCACTVS[0m[38;5;12m (https://www.xemistry.com/academic/) - Cactvs is a universal, scriptable cheminformatics toolkit, with a large collection of modules for property computation, chemistry data file I/O and other tasks.[39m
[38;5;12m- [39m[38;5;14m[1mCalcUS[0m[38;5;12m (https://github.com/cyllab/CalcUS) - Quantum chemisttry web platform that brings all the necessary tools to perform quantum chemistry in a user-friendly web interface.[39m
[38;5;12m- [39m[38;5;14m[1mcantera[0m[38;5;12m (https://github.com/Cantera/cantera) - A collection of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and transport processes.[39m
[38;5;12m- [39m[38;5;14m[1mCatKit[0m[38;5;12m (https://github.com/SUNCAT-Center/CatKit) - General purpose tools for high-throughput catalysis.[39m
[38;5;12m- [39m[38;5;14m[1mccinput[0m[38;5;12m (https://github.com/cyllab/ccinput/) - A tool and library for creating quantum chemistry input files.[39m
[38;5;12m- [39m[38;5;14m[1mcclib[0m[38;5;12m (https://cclib.github.io/) - A library for parsing output files various quantum chemical programs.[39m
[38;5;12m- [39m[38;5;14m[1mcinfony[0m[38;5;12m (http://cinfony.github.io/) - A common API to several cheminformatics toolkits (Open Babel, RDKit, the CDK, Indigo, JChem, OPSIN and cheminformatics webservices).[39m
[38;5;12m- [39m[38;5;14m[1mchemlab[0m[38;5;12m (http://chemlab.readthedocs.io/en/latest/index.html) - Is a library that can help the user with chemistry-relevant calculations.[39m
[38;5;12m- [39m[38;5;14m[1memmet[0m[38;5;12m (https://github.com/materialsproject/emmet) - A package to 'build' collections of materials properties from the output of computational materials calculations.[39m
[38;5;12m- [39m[38;5;14m[1mfromage[0m[38;5;12m (https://github.com/Crespo-Otero-group/fromage/) - The "FRamewOrk for Molecular AGgregate Excitations" enables localised QM/QM' excited state calculations in a solid state environment.[39m
[38;5;12m- [39m[38;5;14m[1mGPAW[0m[38;5;12m (https://wiki.fysik.dtu.dk/gpaw/) - Is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE).[39m
[38;5;12m- [39m[38;5;14m[1mhorton[0m[38;5;12m (http://theochem.github.io/horton/2.0.1/index.html) - Helpful Open-source Research TOol for N-fermion system, a quantum-chemistry program that can perform computations involving model Hamiltonians.[39m
[38;5;12m- [39m[38;5;14m[1mHTMD[0m[38;5;12m (https://github.com/Acellera/htmd) - High-Throughput Molecular Dynamics: Programming Environment for Molecular Discovery.[39m
[38;5;12m- [39m[38;5;14m[1mIndigo[0m[38;5;12m (https://github.com/epam/Indigo) - Universal cheminformatics libraries, utilities and database search tools.[39m
[38;5;12m- [39m[38;5;14m[1mJarvis-tools[0m[38;5;12m (https://github.com/usnistgov/jarvis) - An open-access software package for atomistic data-driven materials design[39m
[38;5;12m- [39m[38;5;14m[1mmathchem[0m[38;5;12m (http://mathchem.iam.upr.si/) - Is a free open source package for calculating topological indices and other invariants of molecular graphs.[39m
[38;5;12m- [39m[38;5;14m[1mMDAnalysis[0m[38;5;12m (http://www.mdanalysis.org/) - Is an object-oriented library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats.[39m
[38;5;12m- [39m[38;5;14m[1mMDTraj[0m[38;5;12m (http://mdtraj.org) - Package for manipulating molecular dynamics trajectories with support for multiple formats.[39m
[38;5;12m- [39m[38;5;14m[1mMMTK[0m[38;5;12m (http://dirac.cnrs-orleans.fr/MMTK/) - The Molecular Modeling Toolkit is an Open Source program library for molecular simulation applications.[39m
[38;5;12m- [39m[38;5;14m[1mMolMod[0m[38;5;12m (http://molmod.github.io/molmod/index.html) - A library with many components that are useful to write molecular modeling programs.[39m
[38;5;12m- [39m[38;5;14m[1moddt[0m[38;5;12m (https://github.com/oddt/oddt) - Open Drug Discovery Toolkit, a modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc.[39m
[38;5;12m- [39m[38;5;14m[1mOPEM[0m[38;5;12m (https://github.com/ECSIM/opem) - Open source PEM (Proton Exchange Membrane) fuel cell simulation tool.[39m
[38;5;12m- [39m[38;5;14m[1mopenmmtools[0m[38;5;12m (https://github.com/choderalab/openmmtools) - A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.[39m
[38;5;12m-[39m[38;5;12m [39m[38;5;14m[1moverreact[0m[38;5;12m [39m[38;5;12m(https://github.com/geem-lab/overreact)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mA[39m[38;5;12m [39m[38;5;12mlibrary[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mcommand-line[39m[38;5;12m [39m[38;5;12mtool[39m[38;5;12m [39m[38;5;12mfor[39m[38;5;12m [39m[38;5;12mbuilding[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12manalyzing[39m[38;5;12m [39m[38;5;12mcomplex[39m[38;5;12m [39m[38;5;12mhomogeneous[39m[38;5;12m [39m[38;5;12mmicrokinetic[39m[38;5;12m [39m[38;5;12mmodels[39m[38;5;12m [39m[38;5;12mfrom[39m[38;5;12m [39m[38;5;12mquantum[39m[38;5;12m [39m[38;5;12mchemistry[39m[38;5;12m [39m[38;5;12mcalculations,[39m[38;5;12m [39m[38;5;12mwith[39m[38;5;12m [39m[38;5;12msupport[39m[38;5;12m [39m[38;5;12mfor[39m[38;5;12m [39m[38;5;12mquasi-harmonic[39m[38;5;12m [39m
[38;5;12mthermochemistry,[39m[38;5;12m [39m[38;5;12mquantum[39m[38;5;12m [39m[38;5;12mtunnelling[39m[38;5;12m [39m[38;5;12mcorrections,[39m[38;5;12m [39m[38;5;12mmolecular[39m[38;5;12m [39m[38;5;12msymmetries[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mmore.[39m
[38;5;12m- [39m[38;5;14m[1mParmEd[0m[38;5;12m (https://github.com/ParmEd/ParmEd) -  Parameter/topology editor and molecular simulator with visualization capability.[39m
[38;5;12m- [39m[38;5;14m[1mpGrAdd[0m[38;5;12m (https://github.com/VlachosGroup/PythonGroupAdditivity) - A library for estimating thermochemical properties of molecules and adsorbates using group additivity.[39m
[38;5;12m- [39m[38;5;14m[1mphonopy[0m[38;5;12m (http://atztogo.github.io/phonopy/) - An open source package for phonon calculations at harmonic and quasi-harmonic levels.[39m
[38;5;12m- [39m[38;5;14m[1mPLAMS[0m[38;5;12m (https://github.com/SCM-NV/PLAMS) - Python Library for Automating Molecular Simulation: input preparation, job execution, file management, output processing and building data workflows.[39m
[38;5;12m- [39m[38;5;14m[1mpMuTT[0m[38;5;12m (https://vlachosgroup.github.io/pMuTT/) - A library for ab-initio thermodynamic and kinetic parameter estimation.[39m
[38;5;12m- [39m[38;5;14m[1mPorePy[0m[38;5;12m (https://github.com/pmgbergen/porepy) - A Simulation Tool for Fractured and Deformable Porous Media.[39m
[38;5;12m- [39m[38;5;14m[1mProDy[0m[38;5;12m (http://prody.csb.pitt.edu/) - An open source package for protein structural dynamics analysis with a flexible and responsive API.[39m
[38;5;12m- [39m[38;5;14m[1mProLIF[0m[38;5;12m (https://github.com/chemosim-lab/ProLIF) - Interaction Fingerprints for protein-ligand complexes and more.[39m
[38;5;12m- [39m[38;5;14m[1mPsi4[0m[38;5;12m (http://psicode.org) - A hybrid Python/C++ open-source package for quantum chemistry.[39m
[38;5;12m- [39m[38;5;14m[1mPsi4NumPy[0m[38;5;12m (https://github.com/psi4/psi4numpy/) - Psi4-based reference implementations and Jupyter notebook-based tutorials for foundational quantum chemistry methods.[39m
[38;5;12m- [39m[38;5;14m[1mpyEMMA[0m[38;5;12m (http://www.emma-project.org/latest/) - Library for the estimation, validation and analysis Markov models of molecular kinetics and other kinetic and thermodynamic models from molecular dynamics data.[39m
[38;5;12m- [39m[38;5;14m[1mpygauss[0m[38;5;12m (https://pygauss.readthedocs.io/en/stable/index.html) - An interactive tool for supporting the life cycle of a computational molecular chemistry investigations.[39m
[38;5;12m- [39m[38;5;14m[1mPyQuante[0m[38;5;12m (http://pyquante.sourceforge.net/) - Is an open-source suite of programs for developing quantum chemistry methods.[39m
[38;5;12m- [39m[38;5;14m[1mpysic[0m[38;5;12m (https://github.com/thynnine/pysic) - A calculator incorporating various empirical pair and many-body potentials.[39m
[38;5;12m- [39m[38;5;14m[1mPyscf[0m[38;5;12m (https://github.com/sunqm/pyscf) - A quantum chemistry package written in Python.[39m
[38;5;12m- [39m[38;5;14m[1mpyvib2[0m[38;5;12m (http://pyvib2.sourceforge.net/) - A program for analyzing vibrational motion and vibrational spectra.[39m
[38;5;12m- [39m[38;5;14m[1mRDKit[0m[38;5;12m (http://www.rdkit.org/) - Open-Source Cheminformatics Software.[39m
[38;5;12m- [39m[38;5;14m[1mReNView[0m[38;5;12m (https://github.com/VlachosGroup/ReNView/wiki/Reaction-Network-Viewer-(ReNView)-Usage-Instructions) - A program to visualize reaction networks.[39m
[38;5;12m- [39m[38;5;14m[1mstk[0m[38;5;12m (https://github.com/lukasturcani/stk) - A library for building, manipulating, analyzing and automatic design of molecules.[39m
[38;5;12m- [39m[38;5;14m[1mQMsolve[0m[38;5;12m (https://github.com/quantum-visualizations/qmsolve) - A module for solving and visualizing the Schrödinger equation.[39m
[38;5;12m- [39m[38;5;14m[1mQUIP[0m[38;5;12m (http://libatoms.github.io/QUIP/) - A collection of software tools to carry out molecular dynamics simulations.[39m
[38;5;12m- [39m[38;5;14m[1mtorchmd[0m[38;5;12m (https://github.com/torchmd/torchmd) - End-To-End Molecular Dynamics (MD) Engine using PyTorch.[39m
[38;5;12m- [39m[38;5;14m[1mtsase[0m[38;5;12m (http://theory.cm.utexas.edu/tsase/) - The library which depends on ASE to tackle transition state calculations.[39m
[38;5;12m- [39m[38;5;14m[1myank[0m[38;5;12m (https://github.com/choderalab/yank) - An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.[39m

[38;2;255;187;0m[4mForce Fields[0m

[48;2;30;30;40m[38;5;13m[3mPackages related to force fields[0m

[38;5;12m- [39m[38;5;14m[1mCHGNet[0m[38;5;12m (https://github.com/CederGroupHub/chgnet) - Pretrained universal neural network potential for charge-informed atomistic modeling.[39m
[38;5;12m- [39m[38;5;14m[1mFitSNAP[0m[38;5;12m (https://github.com/FitSNAP/FitSNAP) - A Package For Training SNAP Interatomic Potentials for use in the LAMMPS molecular dynamics package.[39m
[38;5;12m- [39m[38;5;14m[1mfftool[0m[38;5;12m (https://github.com/paduagroup/fftool) - Tool to build force field input files for molecular simulation.[39m
[38;5;12m- [39m[38;5;14m[1mFLARE[0m[38;5;12m (https://github.com/mir-group/flare) - A package for creating fast and accurate interatomic potentials.[39m
[38;5;12m-[39m[38;5;12m [39m[38;5;14m[1mglobal-chem[0m[38;5;12m [39m[38;5;12m(https://github.com/Sulstice/global-chem)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mA[39m[38;5;12m [39m[38;5;12mChemical[39m[38;5;12m [39m[38;5;12mKnowledge[39m[38;5;12m [39m[38;5;12mGraph[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mToolkit,[39m[38;5;12m [39m[38;5;12mwritting[39m[38;5;12m [39m[38;5;12min[39m[38;5;12m [39m[38;5;12mIUPAC/SMILES/SMARTS,[39m[38;5;12m [39m[38;5;12mfor[39m[38;5;12m [39m[38;5;12mcommon[39m[38;5;12m [39m[38;5;12msmall[39m[38;5;12m [39m[38;5;12mmolecules[39m[38;5;12m [39m[38;5;12mfrom[39m[38;5;12m [39m[38;5;12mdiverse[39m[38;5;12m [39m[38;5;12mcommunities[39m[38;5;12m [39m[38;5;12mto[39m[38;5;12m [39m[38;5;12maid[39m[38;5;12m [39m[38;5;12musers[39m[38;5;12m [39m[38;5;12min[39m[38;5;12m [39m[38;5;12mselecting[39m[38;5;12m [39m[38;5;12mcompounds[39m[38;5;12m [39m[38;5;12mfor[39m[38;5;12m [39m[38;5;12mforcefield[39m[38;5;12m [39m
[38;5;12mparametirization.[39m
[38;5;12m- [39m[38;5;14m[1mmatbench-discovery[0m[38;5;12m (https://github.com/janosh/matbench-discovery) - A benchmark for ML-guided high-throughput materials discovery.[39m
[38;5;12m- [39m[38;5;14m[1mNeuralForceField[0m[38;5;12m (https://github.com/learningmatter-mit/NeuralForceField) - Neural Network Force Field based on PyTorch.[39m
[38;5;12m- [39m[38;5;14m[1mopenff-toolkit[0m[38;5;12m (https://github.com/openforcefield/openff-toolkit) - The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools.[39m

[38;2;255;187;0m[4mMolecular Visualization[0m

[48;2;30;30;40m[38;5;13m[3mPackages for viewing molecular structures.[0m

[38;5;12m- [39m[38;5;14m[1mase-gui[0m[38;5;12m (https://wiki.fysik.dtu.dk/ase/ase/gui/gui.html#module-ase.gui) - The graphical user-interface allows users to visualize, manipulate, and render molecular systems and atoms objects.[39m
[38;5;12m- [39m[38;5;14m[1mchemiscope[0m[38;5;12m (https://github.com/lab-cosmo/chemiscope) - An interactive structure/property explorer for materials and molecules.[39m
[38;5;12m- [39m[38;5;14m[1mchemview[0m[38;5;12m (http://chemview.readthedocs.io/en/latest/) - An interactive molecular viewer designed for the IPython notebook.[39m
[38;5;12m- [39m[38;5;14m[1mimolecule[0m[38;5;12m (http://patrickfuller.github.io/imolecule/) - An embeddable webGL molecule viewer and file format converter.[39m
[38;5;12m- [39m[38;5;14m[1mmoleculekit[0m[38;5;12m (https://github.com/Acellera/moleculekit) - A molecule manipulation library.[39m
[38;5;12m- [39m[38;5;14m[1mnglview[0m[38;5;12m (https://github.com/arose/nglview) - A [39m[38;5;14m[1mJupyter[0m[38;5;12m (https://jupyter.org/) widget to interactively view molecular structures and trajectories.[39m
[38;5;12m- [39m[38;5;14m[1mPyMOL[0m[38;5;12m (https://pymol.org/) - A user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.[39m
[38;5;12m- [39m[38;5;14m[1mpymoldyn[0m[38;5;12m (https://pgi-jcns.fz-juelich.de/portal/pages/pymoldyn-main.html) - A viewer for atomic clusters, crystalline and amorphous materials in a unit cell corresponding to one of the seven 3D Bravais lattices.[39m
[38;5;12m- [39m[38;5;14m[1msumo[0m[38;5;12m (http://sumo.readthedocs.io/en/latest/) - A toolkit for plotting and analysis of ab initio solid-state calculation data.[39m
[38;5;12m- [39m[38;5;14m[1msurfinpy[0m[38;5;12m (https://surfinpy.readthedocs.io/en/latest/) - A library for the analysis, plotting and visualisation of ab initio surface calculation data.[39m
[38;5;12m- [39m[38;5;14m[1mtrident-chemwidgets[0m[38;5;12m (https://github.com/tridentbio/trident-chemwidgets) - Jupyter Widgets to interact with molecular datasets.[39m

[38;2;255;187;0m[4mDatabase Wrappers[0m

[48;2;30;30;40m[38;5;13m[3mProviding a python layer for accessing chemical databases[0m

[38;5;12m- [39m[38;5;14m[1mccdc[0m[38;5;12m (https://downloads.ccdc.cam.ac.uk/documentation/API/index.html) - An API for the Cambridge Structural Database System.[39m
[38;5;12m- [39m[38;5;14m[1mChemSpiPy[0m[38;5;12m (http://chemspipy.readthedocs.io/en/latest/) - [39m[38;5;14m[1mChemSpider[0m[38;5;12m (http://www.chemspider.com/) wrapper, that allows chemical searches, chemical file downloads, depiction and retrieval of chemical properties.[39m
[38;5;12m- [39m[38;5;14m[1mCIRpy[0m[38;5;12m (http://cirpy.readthedocs.io/en/latest/) - An interface for the Chemical Identifier Resolver (CIR) by the CADD Group at the NCI/NIH.[39m
[38;5;12m- [39m[38;5;14m[1mpubchempy[0m[38;5;12m (http://pubchempy.readthedocs.io/en/latest/) - PubChemPy provides a way to interact with PubChem in Python.[39m
[38;5;12m- [39m[38;5;14m[1mchembl-downloader[0m[38;5;12m (https://github.com/cthoyt/chembl-downloader) - Automate downloading and querying the latest (or a given) version of [39m[38;5;14m[1mChEMBL[0m[38;5;12m (https://www.ebi.ac.uk/chembl/)[39m
[38;5;12m- [39m[38;5;14m[1mdrugbank-downloader[0m[38;5;12m (https://github.com/cthoyt/drugbank_downloader) - Automate downloading, opening, and parsing [39m[38;5;14m[1mDrugBank[0m[38;5;12m (https://www.drugbank.com/)[39m

[38;2;255;187;0m[4mLearning Resources[0m

[48;2;30;30;40m[38;5;13m[3mResources for learning to apply python to chemistry.[0m

[38;5;12m-[39m[38;5;12m [39m[38;5;14m[1mAn[0m[38;5;14m[1m [0m[38;5;14m[1mIntroduction[0m[38;5;14m[1m [0m[38;5;14m[1mto[0m[38;5;14m[1m [0m[38;5;14m[1mApplied[0m[38;5;14m[1m [0m[38;5;14m[1mBioinformatics[0m[38;5;12m [39m[38;5;12m(https://github.com/applied-bioinformatics/iab2)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mA[39m[38;5;12m [39m[38;5;12mJupyter[39m[38;5;12m [39m[38;5;12mbook[39m[38;5;12m [39m[38;5;12mdemonstrating[39m[38;5;12m [39m[38;5;12mworking[39m[38;5;12m [39m[38;5;12mwith[39m[38;5;12m [39m[38;5;12mbiochemical[39m[38;5;12m [39m[38;5;12mdata[39m[38;5;12m [39m[38;5;12musing[39m[38;5;12m [39m[38;5;12mthe[39m[38;5;12m [39m[38;5;12mscikit-bio[39m[38;5;12m [39m[38;5;12mlibrary[39m[38;5;12m [39m[38;5;12mfor[39m[38;5;12m [39m[38;5;12mtasks[39m[38;5;12m [39m[38;5;12msuch[39m[38;5;12m [39m[38;5;12mas[39m[38;5;12m [39m[38;5;12msequence[39m[38;5;12m [39m[38;5;12malignment[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mcalculating[39m[38;5;12m [39m
[38;5;12mHamming[39m[38;5;12m [39m[38;5;12mdistances.[39m
[38;5;12m-[39m[38;5;12m [39m[38;5;14m[1mComputational[0m[38;5;14m[1m [0m[38;5;14m[1mThermodynamics[0m[38;5;12m [39m[38;5;12m(https://kyleniemeyer.github.io/computational-thermo/content/intro.html)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mThis[39m[38;5;12m [39m[38;5;12mcollection[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m[38;5;12mJupyter[39m[38;5;12m [39m[38;5;12mnotebooks[39m[38;5;12m [39m[38;5;12mdemonstrates[39m[38;5;12m [39m[38;5;12msolutions[39m[38;5;12m [39m[38;5;12mto[39m[38;5;12m [39m[38;5;12ma[39m[38;5;12m [39m[38;5;12mrange[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m[38;5;12mthermodynamic[39m[38;5;12m [39m[38;5;12mproblems[39m[38;5;12m [39m[38;5;12mincluding[39m[38;5;12m [39m[38;5;12msolving[39m[38;5;12m [39m[38;5;12mchemical[39m[38;5;12m [39m
[38;5;12mequilibria,[39m[38;5;12m [39m[38;5;12mcomparing[39m[38;5;12m [39m[38;5;12mreal[39m[38;5;12m [39m[38;5;12mversus[39m[38;5;12m [39m[38;5;12mideal[39m[38;5;12m [39m[38;5;12mgas[39m[38;5;12m [39m[38;5;12mbehavior,[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mcalculating[39m[38;5;12m [39m[38;5;12mthe[39m[38;5;12m [39m[38;5;12mtemperature[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mcomposition[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m[38;5;12ma[39m[38;5;12m [39m[38;5;12mcombustion[39m[38;5;12m [39m[38;5;12mreaction.[39m
[38;5;12m-[39m[38;5;12m [39m[38;5;14m[1mSciCompforChemists[0m[38;5;12m [39m[38;5;12m(https://github.com/weisscharlesj/SciCompforChemists)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mScientific[39m[38;5;12m [39m[38;5;12mComputing[39m[38;5;12m [39m[38;5;12mfor[39m[38;5;12m [39m[38;5;12mChemists[39m[38;5;12m [39m[38;5;12mwith[39m[38;5;12m [39m[38;5;12mPython[39m[38;5;12m [39m[38;5;12mis[39m[38;5;12m [39m[38;5;12ma[39m[38;5;12m [39m[38;5;12mJupyter[39m[38;5;12m [39m[38;5;12mbook[39m[38;5;12m [39m[38;5;12mteaching[39m[38;5;12m [39m[38;5;12mbasic[39m[38;5;12m [39m[38;5;12mpython[39m[38;5;12m [39m[38;5;12min[39m[38;5;12m [39m[38;5;12mchemistry[39m[38;5;12m [39m[38;5;12mskills,[39m[38;5;12m [39m[38;5;12mincluding[39m[38;5;12m [39m[38;5;12mrelevant[39m[38;5;12m [39m[38;5;12mlibraries,[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mapplies[39m[38;5;12m [39m[38;5;12mthem[39m[38;5;12m [39m[38;5;12mto[39m[38;5;12m [39m
[38;5;12msolving[39m[38;5;12m [39m[38;5;12mchemical[39m[38;5;12m [39m[38;5;12mproblems.[39m

[38;2;255;187;0m[4mMiscellaneous Awesome[0m

[38;5;12m-[39m[38;5;12m [39m[38;5;14m[1mColorful[0m[38;5;14m[1m [0m[38;5;14m[1mNuclide[0m[38;5;14m[1m [0m[38;5;14m[1mChart[0m[38;5;12m [39m[38;5;12m(https://people.physics.anu.edu.au/~ecs103/chart/)[39m[38;5;12m [39m[38;5;12m-[39m[38;5;12m [39m[38;5;12mA[39m[38;5;12m [39m[38;5;12mbeatuful,[39m[38;5;12m [39m[38;5;12minteractive[39m[38;5;12m [39m[38;5;12mvisualization[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m[38;5;12mnuclides[39m[38;5;12m [39m[38;5;12mwith[39m[38;5;12m [39m[38;5;12maccess[39m[38;5;12m [39m[38;5;12mto[39m[38;5;12m [39m[38;5;12ma[39m[38;5;12m [39m[38;5;12mvarirty[39m[38;5;12m [39m[38;5;12mof[39m[38;5;12m [39m[38;5;12mnuclear[39m[38;5;12m [39m[38;5;12mproperties[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mallows[39m[38;5;12m [39m[38;5;12msaving[39m[38;5;12m [39m[38;5;12mhigh[39m[38;5;12m [39m[38;5;12mquality[39m[38;5;12m [39m[38;5;12mimages[39m[38;5;12m [39m[38;5;12mfor[39m[38;5;12m [39m[38;5;12mpublications,[39m[38;5;12m [39m
[38;5;12mpresentations[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12moutreach.[39m

[38;2;255;187;0m[4mSee Also[0m

[38;5;12m- [39m[38;5;14m[1mawesome-cheminformatics[0m[38;5;12m (https://github.com/hsiaoyi0504/awesome-cheminformatics) Another list focuses on Cheminformatics, including tools not only in Python.[39m
[38;5;12m- [39m[38;5;14m[1mawesome-small-molecule-ml[0m[38;5;12m (https://github.com/benb111/awesome-small-molecule-ml) A collection of papers, datasets, and packages for small-molecule drug discovery. Most links to code are in Python.[39m
[38;5;12m- [39m[38;5;14m[1mawesome-molecular-docking[0m[38;5;12m (https://github.com/yangnianzu0515/awesome-molecular-docking) A curated list of molecular docking software, datasets, and papers.[39m
[38;5;12m-[39m[38;5;12m [39m[38;5;14m[1mjarvis[0m[38;5;12m [39m[38;5;12m(https://jarvis.nist.gov/)[39m[38;5;12m [39m[38;5;12mJoint[39m[38;5;12m [39m[38;5;12mAutomated[39m[38;5;12m [39m[38;5;12mRepository[39m[38;5;12m [39m[38;5;12mfor[39m[38;5;12m [39m[38;5;12mVarious[39m[38;5;12m [39m[38;5;12mIntegrated[39m[38;5;12m [39m[38;5;12mSimulations[39m[38;5;12m [39m[38;5;12mis[39m[38;5;12m [39m[38;5;12ma[39m[38;5;12m [39m[38;5;12mrepository[39m[38;5;12m [39m[38;5;12mdesigned[39m[38;5;12m [39m[38;5;12mto[39m[38;5;12m [39m[38;5;12mautomate[39m[38;5;12m [39m[38;5;12mmaterials[39m[38;5;12m [39m[38;5;12mdiscovery[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12moptimization[39m[38;5;12m [39m[38;5;12musing[39m[38;5;12m [39m[38;5;12mclassical[39m[38;5;12m [39m[38;5;12mforce-field,[39m[38;5;12m [39m[38;5;12mdensity[39m[38;5;12m [39m[38;5;12mfunctional[39m[38;5;12m [39m[38;5;12mtheory,[39m[38;5;12m [39m[38;5;12mmachine[39m[38;5;12m [39m
[38;5;12mlearning[39m[38;5;12m [39m[38;5;12mcalculations[39m[38;5;12m [39m[38;5;12mand[39m[38;5;12m [39m[38;5;12mexperiments.[39m
[38;5;12m- [39m[38;5;14m[1mpolypharmacy-ddi-synergy-survey[0m[38;5;12m (https://github.com/AstraZeneca/polypharmacy-ddi-synergy-survey) A collection of research papers (with Python implementations) focusing on drug-drug interactions, synergy and polypharmacy.[39m
