Open Chemistry: 18 Open-source Chemistry Libraries and Frameworks
As we at MEDevel.com are hunting for open-source medical and healthcare apps, as well as education and software development. Chemistry is not an exception. So here is our list for the open-source chemistry library and frameworks.
1- Open Chemistry
Open Chemistry has a collection of open-source chemistry specific projects
- Avogadro; a desktop app for editing and visualizing molecular data
- MoleQueue provides desktop integration of high-performance computing (HPC) resources, along with local execution of standalone code. It is a small, Qt-based, system-tray resident application that makes computing resources easier to access from graphical applications.
- Tomviz offers a desktop application for the processing, visualization, and analysis of 3D tomographic data.
- Here is the Open Chemistry Collection at GitHub.
2- Open Molecules
Open Molecules contains some set of open-source projects such as
- DataWarrior; an open-source data visualization and analysis program with embedded chemical intelligence.
- Osiris Property Explorer was originally released in 2000 by Actelion Pharmaceuticals Ltd.
- Torsion Explorer is an easy-to-use tool to learn about molecule conformations.
- www.webreactions.net. Since
3- Chemistry Development Kit
CDK or Chemistry Development Kit is an open source modular Java libraries for Chem-informatics.
Features and functionalities
- Molecule and reaction valence bond representation.
- Read and write file formats: SMILES, SDF, InChI, Mol2, CML, and others.
- Efficient molecule processing algorithms: Ring Finding, Kekulisation, Aromaticity.
- Coordinate generation and rendering.
- Canonical identifiers for fast exact searching.
- Substructure and SMARTS pattern searching.
- ECFP, Daylight, MACCS, and other fingerprint methods for similarity searching.
- QSAR descriptor calculations
4- PSI4
PSI4 is an open-source library for quantum chemistry that is released under the LGPL3 License and available for C++ and Python.
5- ChemSpider
ChemSpider is a free chemical structure database providing fast text and structure search access to over 100 million structures from hundreds of data sources.
6- ChemDoodle
ChemDoodle is a free open-source JavaScript library for fast, professional, HTML5 scientific interfaces.
The ChemDoodle Web Components (CWC) library is a pure JavaScript chemical graphics and cheminformatics library derived from the ChemDoodle® application and produced by iChemLabs.
ChemDoodle Web Components allow the wielder to present publication quality 2D and 3D graphics and animations for chemical structures, reactions and spectra.
7- NWChem
NWChem is a free open-source High-Performance Computational Chemistry.
NWChem is actively developed by a consortium of developers and maintained by the EMSL located at the Pacific Northwest National Laboratory (PNNL) in Washington State. Researchers interested in contributing to NWChem should review the Developers page. The code is distributed as open-source under the terms of the Educational Community License version 2.0 (ECL 2.0).
NWChem software can handle:
- Biomolecules, nanostructures, and solid-state
- From quantum to classical, and all combinations
- Ground and excited-states
- Gaussian basis functions or plane-waves
- Scaling from one to thousands of processors
- Properties and relativistic effects
8- Open Babel
Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
9- Centera
Cantera is an open-source suite of tools for problems involving chemical kinetics, thermodynamics, and transport processes.
10- PySCF
The Python-based Simulations of Chemistry Framework (PySCF) is an open-source collection of electronic structure modules powered by Python. The package provides a simple, lightweight, and efficient platform for quantum chemistry calculations and methodology development.
11- Blender Chemical
Blender is a free open-source 3D modeling and design software. Blender Chemical allows designs and students to draw chemicals in blender >2.8 using common inputs.
The project is an open-source that is released under the MIT license.
12- Webchem
webchem is an R package to retrieve chemical information from the web. This package interacts with a suite of web APIs to retrieve chemical information.
13- Thermo
Thermo is open-source software for engineers, scientists, technicians and anyone trying to understand the universe in more detail.
It facilitates the retrieval of constants of chemicals, the calculation of temperature and pressure dependent chemical properties (both thermodynamic and transport), and the calculation of the same for chemical mixtures (including phase equilibria) using various models.
Thermo is written in Python and can be installed using Conda or from source.
14- Fluids
Fluids library is open-source software for engineers and technicians working in the fields of chemical, mechanical, or civil engineering.
It includes modules for piping, fittings, pumps, tanks, compressible flow, open-channel flow, atmospheric properties, solar properties, particle size distributions, two phase flow, friction factors, control valves, orifice plates and other flow meters, ejectors, relief valves, and more.
15- Catalyst.jl
Catalyst.jl is a symbolic modeling package for analysis and high performance simulation of chemical reaction networks for the Julia programming language.
16- ChemML
ChemML is a machine learning and informatics program suite for the analysis, mining, and modeling of chemical and materials data.
17- Chemical Computing
This is an open-source project for explorations in chemical computing with Clojure.
18- ChemistryCSS
The chemistry CSS library for creating Chemical Structures and Equations with just HTML. Similar project to: MathCSS.
If you know of any other Chemistry Framework or library that we didn't mention here, let us know.
Resources
Photo by Karolina Grabowska.
