Awesome Python Chemistry

A curated list of awesome Python frameworks, libraries, software and resources related to Chemistry.

Inspired by awesome-python.

Table of contents

• Awesome Python Chemistry
  • General Chemistry
  • Simulations
  • Molecular Visualization
  • Database Wrappers

General Chemistry

Packages and tools for general chemistry.

• 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.
• 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).
• GoodVibes - A Python program to compute quasi-harmonic thermochemical data from Gaussian frequency calculations.
• ionize - Calculates the properties of individual ionic species in aqueous solution, as well as aqueous solutions containing arbitrary sets of ions.
• mendeleev - A package that provides a python API for accessing various properties of elements from the periodic table of elements.
• Open Babel - 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.
• 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.
• 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 - A library for building, manipulating, analyzing and automatic design of molecules, including a genetic algorithm.

Simulations

Packages for atomistic simulations and computational chemistry.

• amp - Is an open-source package designed to easily bring machine-learning to atomistic calculations.
• Atomic Silumation Environment (ASE) - 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 - Cactvs is a universal, scriptable cheminformatics toolkit, with a large collection of modules for property computation, chemistry data file I/O and other tasks.
• ccdc - An API for the Cambridge Structural Database System.
• cclib - A library for parsing output files various quantum chemical programs.
• cinfony - A common API to several cheminformatics toolkits (Open Babel, RDKit, the CDK, Indigo, JChem, OPSIN and cheminformatics webservices).
• chainer-chemistry - A Library for Deep Learning in Biology and Chemistry.
• chemlab - Is a library that can help the user with chemistry-relevant calculations.
• chemml - A machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data.
• deepchem - Deep-learning models for Drug Discovery and Quantum Chemistry.
• 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.
• 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.
• Indigo - Universal cheminformatics libraries, utilities and database search tools.
• MAML - Aims to provide useful high-level interfaces that make ML for materials science as easy as possible.
• 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.
• OPEM - Open source PEM (Proton Exchange Membrane) fuel cell simulation tool.
• pGrAdd - 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 - 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 - 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.
• 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
• pysic - A calculator incorporating various empirical pair and many-body potentials.
• Pyscf - A quantum chemistry package written in Python.
• pyvib2 - A program for analyzing vibrational motion and vibrational spectra.
• RDKit - Open-Source Cheminformatics Software.
• ReNView - A program to visualize reaction networks.
• stk - A library for building, manipulating, analyzing and automatic design of molecules.
• QUIP - A collection of software tools to carry out molecular dynamics simulations.
• tsase - The library which depends on ASE to tackle transition state calculations.

Molecular Visualization

Packages for viewing molecular structures.

• 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.
• nglview - A Jupyter 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.
• 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.

Database Wrappers

Providing a python layer for accessing chemical databases

• ChemSpiPy - ChemSpider 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.
• pubchempy - PubChemPy provides a way to interact with PubChem in Python.

See Also

• awesome-cheminformatics Another list focuses on Cheminformatics, including tools not only in Python.