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awesome-python-chemistry


https://github.com/2lambda123/awesome-python-chemistry

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  • Table of contents

  • General Chemistry

    • 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).
    • 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.
    • LModeA-nano - Calculates the intrinsic chemical bond strength based on local vibrational mode theory in solids and molecules.
    • 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.
    • symfit - a curve-fitting library ideally suited to chemistry problems, including fitting experimental kinetics data.
    • GoodVibes - A Python program to compute quasi-harmonic thermochemical data from Gaussian frequency calculations.

  • Molecular Visualization

    • Force Fields

      • PyMOL - A user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.
      • ase-gui - The graphical user-interface allows users to visualize, manipulate, and render molecular systems and atoms objects.
      • 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.

  • 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).
    • 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.
    • 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.
    • 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.
    • phonopy - An open source package for phonon calculations at harmonic and quasi-harmonic levels.
    • RDKit - Open-Source Cheminformatics Software.
    • tsase - The library which depends on ASE to tackle transition state calculations.

  • 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.

  • Database Wrappers

    • Force Fields

      • ccdc - An API for the Cambridge Structural Database System.

  • 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

Programming Languages
Python 2
Categories
Simulations 14 General Chemistry 12 Molecular Visualization 5 See Also 2 Learning Resources 1 Database Wrappers 1 Table of contents 1 Miscellaneous Awesome 1
Sub Categories
Force Fields 10
Keywords
awesome 2 awesome-list 2 chemistry 2 cheminformatics 2 lists 1 resources 1 unicorns 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 1 python-library 1 python-module 1 bioinformatics 1