Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

awesome-python-chemistry

A curated list of Python packages related to chemistry
https://github.com/lmmentel/awesome-python-chemistry

Last synced: 3 days ago
JSON representation

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.
- ReNView - Usage-Instructions) - A program to visualize reaction networks.
- 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
- Force Fields
  - awesome-cheminformatics
  - awesome-molecular-docking
  - jarvis - field, density functional theory, machine learning calculations and experiments.
Table of contents
- Awesome Python Chemistry ![Awesome - python-chemistry-)

Programming Languages

Python 3

Ecosyste.ms: Awesome

awesome-python-chemistry

Simulations

General Chemistry

Machine Learning

Molecular Visualization

Force Fields

Database Wrappers

Force Fields

Learning Resources

Force Fields

Miscellaneous Awesome

Force Fields

See Also

Force Fields

Table of contents