awesome-python-chemistry

Chemistry toolkit

A curated list of packages and tools for chemistry-related tasks in Python.

A curated list of Python packages related to chemistry

GitHub
1k stars
56 watching
214 forks
last commit: about 1 month ago
Linked from 4 awesome lists

atomistic-simulationschemistrycomputational-chemistrymolecular-dynamicspython-chemistryquantum-chemistrysimulation

Awesome Python Chemistry / General Chemistry
AQME 99 9 days ago Ensemble of automated QM workflows that can be run through jupyter notebooks, command lines and yaml files
aizynthfinder 590 6 months ago A tool for retrosynthetic planning
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
cctbx The Computational Crystallography Toolbox
ChemFormula 24 almost 3 years ago 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)
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)
datamol 469 5 months ago : - Molecular Manipulation Made Easy. A light wrapper build on top of RDKit
GoodVibes 1 5 months ago A Python program to compute quasi-harmonic thermochemical data from Gaussian frequency calculations
hgraph2graph 378 over 2 years ago 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
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
nmrglue 211 23 days ago A package for working with nuclear magnetic resonance (NMR) data including functions for reading common binary file formats and processing NMR data
molmass 58 27 days ago Calculate mass, elemental composition, and mass distribution spectrum of a molecule given by its chemical formula, relative element weights, or sequence
Open Babel A chemical toolbox designed to speak the many languages of chemical data
periodictable 147 27 days ago This package provides a periodic table of the elements with support for mass, density and xray/neutron scattering information
propka 264 9 months ago Predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure
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
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
pymatgen Python Materials Genomics is a robust, open-source library for materials analysis
pymatviz 173 4 days ago A toolkit for visualizations in materials informatics
symfit a curve-fitting library ideally suited to chemistry problems, including fitting experimental kinetics data
symmetry Symmetry is a library for materials symmetry analysis
stk 252 about 1 month ago A library for building, manipulating, analyzing and automatic design of molecules, including a genetic algorithm
spectrochempy 130 about 1 month ago A library for processing, analyzing and modeling spectroscopic data

Awesome Python Chemistry / Machine Learning
amp Is an open-source package designed to easily bring machine-learning to atomistic calculations
atom3d 303 over 1 year ago Enables machine learning on three-dimensional molecular structure
chainer-chemistry 635 over 1 year ago A deep learning framework (based on Chainer) with applications in Biology and Chemistry
chemml A machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data
chemprop 1,786 11 days ago Message Passing Neural Networks for Molecule Property Prediction
cgcnn 657 about 3 years ago Crystal graph convolutional neural networks for predicting material properties
deepchem Deep-learning models for Drug Discovery and Quantum Chemistry
DeepPurpose 974 5 months ago A Deep Learning Library for Compound and Protein Modeling DTI, Drug Property, PPI, DDI, Protein Function Prediction
DescriptaStorus 231 26 days ago Descriptor computation (chemistry) and (optional) storage for machine learning
DScribe 404 9 days ago Descriptor library containing a variety of fingerprinting techniques, including the Smooth Overlap of Atomic Positions (SOAP)
graphein 1,036 29 days ago Provides functionality for producing geometric representations of protein and RNA structures, and biological interaction networks
Matminer 484 10 days ago Library of descriptors to aid in the data-mining of materials properties, created by the Lawrence Berkeley National Laboratory
MoleOOD 60 almost 2 years ago a robust molecular representation learning framework against distribution shifts
megnet 508 over 1 year ago Graph Networks as a Universal Machine Learning Framework for Molecules and Crystals
MAML 369 7 days ago Aims to provide useful high-level interfaces that make ML for materials science as easy as possible
MORFEUS 164 10 months ago Library for fast calculations of lecula at re from 3D structures for machine learning with a focus on steric descriptors
olorenchemengine 97 about 1 year ago Molecular property prediction with unified API for diverse models and respresentations, with integrated uncertainty quantification, interpretability, and hyperparameter/architecture tuning
ROBERT 38 16 days ago 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 789 7 days ago Deep Neural Networks for Atomistic Systems
selfies 679 3 months ago Self-Referencing Embedded Strings (SELFIES): A 100% robust molecular string representation
Summit 120 3 months ago Package for optimizing chemical reactions using machine learning (contains 10 algorithms + several benchmarks)
TDC 1,011 9 days ago Therapeutics Data Commons (TDC) is the first unifying framework to systematically access and evaluate machine learning across the entire range of therapeutics
XenonPy 139 4 months ago Library with several compositional and structural material descriptors, along with a few pre-trained neural network models of material properties

Awesome Python Chemistry / Generative Molecular Design
GraphINVENT 362 over 1 year ago A platform for graph-based molecular generation using graph neural networks
GuacaMol 414 9 months ago A package for benchmarking of models for molecular design
moses 829 5 months ago A benchmarking platform for molecular generation models
perses 181 11 months ago Experiments with expanded ensembles to explore chemical space

Awesome Python Chemistry / Simulations
alchemlyb 199 7 days ago Makes alchemical free energy calculations easier by leveraging the full power and flexibility of the PyData stack
atomate2 167 6 days ago atomate2 is a library of computational materials science workflows
Atomic Silumation Environment (ASE) Is a set of tools and modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations
basis_set_exchange 158 2 months ago A library containing basis sets for use in quantum chemistry calculations. In addition, this library has functionality for manipulation of basis set data
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
CalcUS 68 3 months ago Quantum chemisttry web platform that brings all the necessary tools to perform quantum chemistry in a user-friendly web interface
cantera 615 10 days ago A collection of object-oriented software tools for problems involving chemical kinetics, thermodynamics, and transport processes
CatKit 85 5 months ago General purpose tools for high-throughput catalysis
ccinput 42 8 days ago A tool and library for creating quantum chemistry input files
cclib A library for parsing output files various quantum chemical programs
cctk 13 3 months ago A library for computational chemistry (DFT) for input file generation, data extraction, method screening and analysis
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
emmet 55 3 days ago A package to 'build' collections of materials properties from the output of computational materials calculations
fromage 21 about 2 months ago 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
HTMD 260 14 days ago High-Throughput Molecular Dynamics: Programming Environment for Molecular Discovery
Indigo 315 4 days ago Universal cheminformatics libraries, utilities and database search tools
IoData 133 2 months ago File parser/converter for QM, MD and plane-wave DFT programs
Jarvis-tools 311 27 days ago An open-access software package for atomistic data-driven materials design
mathchem Is a free open source package for calculating topological indices and other invariants of molecular graphs
MDAnalysis Is an object-oriented library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats
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
nmrsim A library for simulating first- or second-order NMR spectra and dynamic NMR resonances
oddt 419 almost 2 years ago Open Drug Discovery Toolkit, a modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc
OPEM 202 26 days ago Open source PEM (Proton Exchange Membrane) fuel cell simulation tool
openmmtools 251 7 days ago A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine
overreact 51 6 days ago 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 398 22 days ago Parameter/topology editor and molecular simulator with visualization capability
pGrAdd 9 12 months ago A library for estimating thermochemical properties of molecules and adsorbates using group additivity
phonopy An open source package for phonon calculations at harmonic and quasi-harmonic levels
PLAMS 67 6 days ago 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
PorePy 250 4 days ago A Simulation Tool for Fractured and Deformable Porous Media
ProDy An open source package for protein structural dynamics analysis with a flexible and responsive API
ProLIF 371 26 days ago Interaction Fingerprints for protein-ligand complexes and more
Psi4 A hybrid Python/C++ open-source package for quantum chemistry
Psi4NumPy 346 11 months ago Psi4-based reference implementations and Jupyter notebook-based tutorials for foundational quantum chemistry methods
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
pysic 23 about 7 years ago A calculator incorporating various empirical pair and many-body potentials
Pyscf 68 4 days ago A quantum chemistry package written in Python
pyvib2 A program for analyzing vibrational motion and vibrational spectra
RDKit Open-Source Cheminformatics Software
ReNView 22 4 months ago A program to visualize reaction networks
stk 252 about 1 month ago A library for building, manipulating, analyzing and automatic design of molecules
QMsolve 904 6 months ago A module for solving and visualizing the Schrödinger equation
QUIP A collection of software tools to carry out molecular dynamics simulations
torchmd 570 about 1 month ago End-To-End Molecular Dynamics (MD) Engine using PyTorch
tsase The library which depends on ASE to tackle transition state calculations
yank 181 over 1 year ago An open, extensible Python framework for GPU-accelerated alchemical free energy calculations

Awesome Python Chemistry / Simulations / Force Fields
acpype 206 2 months ago Convert AMBER forcefields from ANTECHAMBER to GROMACS format
CHGNet 252 24 days ago Pretrained universal neural network potential for charge-informed atomistic modeling
FitSNAP 152 2 months ago A Package For Training SNAP Interatomic Potentials for use in the LAMMPS molecular dynamics package
fftool 149 about 1 month ago Tool to build force field input files for molecular simulation
FLARE 292 20 days ago A package for creating fast and accurate interatomic potentials
global-chem 20 about 1 year ago 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 107 5 days ago A benchmark for ML-guided high-throughput materials discovery
NeuralForceField 238 4 days ago Neural Network Force Field based on PyTorch
openff-toolkit 318 6 days ago The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools

Awesome Python Chemistry / Molecular Visualization
ase-gui The graphical user-interface allows users to visualize, manipulate, and render molecular systems and atoms objects
chemiscope 133 7 days ago An interactive structure/property explorer for materials and molecules
chemview An interactive molecular viewer designed for the IPython notebook
imolecule An embeddable webGL molecule viewer and file format converter
moleculekit 203 17 days ago A molecule manipulation library
nglview 821 3 months ago A widget to interactively view molecular structures and trajectories
PyMOL A user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger
pymoldyn A viewer for atomic clusters, crystalline and amorphous materials in a unit cell corresponding to one of the seven 3D Bravais lattices
rdeditor 134 2 months ago Simple RDKit molecule editor GUI using PySide
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
trident-chemwidgets 30 over 2 years ago Jupyter Widgets to interact with molecular datasets

Awesome Python Chemistry / Database Wrappers
ccdc An API for the Cambridge Structural Database System
ChemSpiPy wrapper, that allows chemical searches, chemical file downloads, depiction and retrieval of chemical properties
CIRpy An interface for the Chemical Identifier Resolver (CIR) by the CADD Group at the NCI/NIH
NistChemPy 26 about 2 months ago 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 PubChemPy provides a way to interact with PubChem in Python
chembl-downloader 69 10 months ago Automate downloading and querying the latest (or a given) version of
drugbank-downloader 37 17 days ago Automate downloading, opening, and parsing

Awesome Python Chemistry / Learning Resources
An Introduction to Applied Bioinformatics 125 over 1 year ago A Jupyter book demonstrating working with biochemical data using the scikit-bio library for tasks such as sequence alignment and calculating Hamming distances
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 227 about 1 month ago 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

Awesome Python Chemistry / Miscellaneous Awesome
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

Awesome Python Chemistry / See Also
awesome-cheminformatics 699 8 months ago Another list focuses on Cheminformatics, including tools not only in Python
awesome-small-molecule-ml 199 12 months ago A collection of papers, datasets, and packages for small-molecule drug discovery. Most links to code are in Python
awesome-molecular-docking 92 over 1 year ago A curated list of molecular docking software, datasets, and papers
jarvis 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 88 over 2 years ago A collection of research papers (with Python implementations) focusing on drug-drug interactions, synergy and polypharmacy

Backlinks from these awesome lists:

More related projects: