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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: 3 days ago
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  • Simulations

    • 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.
    • 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).
    • 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.
    • 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.
    • 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.
    • RDKit - Open-Source Cheminformatics Software.
    • 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.

  • 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).
    • datamol - Molecular Manipulation Made Easy. A light wrapper build on top of RDKit.
    • 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.
    • Open Babel - A chemical toolbox designed to speak the many languages of chemical data.
    • 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.
    • AQME - Ensemble of automated QM workflows that can be run through jupyter notebooks, command lines and yaml files.
    • 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).
    • GoodVibes - A Python program to compute quasi-harmonic thermochemical data from Gaussian frequency calculations.

  • Machine Learning

    • amp - Is an open-source package designed to easily bring machine-learning to atomistic calculations.
    • deepchem - Deep-learning models for Drug Discovery and Quantum Chemistry.

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

  • 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.
      • 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.

  • 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.

  • 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.

  • See Also

  • Table of contents

Programming Languages
Python 4
Categories
Simulations 22 General Chemistry 19 Molecular Visualization 8 Database Wrappers 4 See Also 3 Machine Learning 2 Learning Resources 1 Table of contents 1 Miscellaneous Awesome 1
Sub Categories
Force Fields 17
Keywords
cheminformatics 3 awesome 2 awesome-list 2 chemistry 2 python 2 quantum-chemistry 2 bioinformatics 1 lists 1 resources 1 unicorns 1 automation 1 jupyter-notebooks 1 reproducibility 1 workflows 1 astrazeneca 1 chemical-reactions 1 monte-carlo-tree-search 1 neural-networks 1 reaction-informatics 1 chemical-formulas 1 chemicals 1 chemistry-database 1 chemistry-formulas 1 python-library 1 python-module 1 gaussian 1 orca 1 thermochemistry 1 vibrational-frequencies 1 zero-point-energy 1