Open Source Chemistry Software

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An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).

The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java. The main home page of the CDK is now at: http://cdk.github.io

A univariate and multivariate analysis UI. This project is no longer under development. Please use as you wish.

Software developed for the analysis of Neutron Reflectivity data.

BinBase is a software for the automatic analysis of Massspec data from LECO GC-Tofs. All code and documentation has been moved to the google code site of this project: https://code.google.com/p/binbase/ And support is provided by the company coding and more, which can be reached under: contact@codingandmore.org

Fast search using a standard SQL on Oracle or PostgreSQL database. The package includes the database creator, loader and web application. It supports SMILES and SMARTS substructure searches, similarity search, stereochemistry.

ICED (Inline Chemical Equations Drawer) is the implementation of the web based chemical markup language, which can be used as a part of HTML layout. Its purpose is the visualization of chemical structural formulas, equations and other chemical info.

JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.

Open Source MS/MS algorithm with integrated target-decoy based FDR. Reference- http://pubs.acs.org/doi/abs/10.1021/pr200031z , Check out the wiki site for help and support - https://sourceforge.net/apps/mediawiki/masswiz/index.php?title=Main_Page

A plugin for the Eclipse IDE implementing NumericalChameleon: a powerful numerical convertor, supporting more than 2300 units in 78 categories (physics, radixes, exchange rates, unicode, etc). Fully integrated in the Eclipse IDE (refactoring, copy/paste)

ORE-CHEM is an open source implementation of software for managing online chemical repositories and services using the Object Reuse and Exchange specification. For more information on ORE, see http://www.openarchives.org/ore/.

Olex2 is visualisation software for small-molecule crystallography developed at Durham University/EPSRC. It provides comprehensive tools for crystallographic model manipulation for the end user and an extensible development framework for programmers. The project has been supported by Olexsys Ltd since 2010.

This is a general open source Quantum Mechanics/Molecular Mechanics project with academic origin. Its intention is to produce free software tools to study molecular systems through QM/MM, in open collaboration.

Quantities provides an interface to the use of numbers which are associated with a dimension and a unit (physical quantities) in computer calculations (quantity calculus) just like C++ built-in types.

SMSD is a Java based software library for calculating Maximum Common Subgraph (MCS) between small molecules. This will help us to find similarity/distance between two molecules. MCS is also used for screening drug like compounds by hitting molecules, which share common subgraph (substructure).

SuperG is a code library written in Python intended to quickly enable programmers in a scientific environment to manage data files created by dispersed scientific instrumentation.

yagdt (Yet Another Graph Drawing Tool) is a plugin-based graph drawing application & distributed graph storage engine.

Cca-forum unifies the Common Component Architecture tools and tutorial. It includes the CCA specifications, the Ccaffeine framework for HPC, and related tools. These support multilanguage scientific and parallel computing.

Chemfiles is a modern and high-quality library for reading and writing trajectory files created by computational chemistry simulations program. These trajectories contains atomic positions, velocities, names, topology and sometimes more. Running simulations produce enormous amounts of data, which has to be post-processed to extract physical information about the simulated system. Chemfiles provides an interface to access this information which is - unified: the same code will work with all the supported formats; - simple: the interface is easy to use and extensively documented. This is only a mirror of the main repository, development of chemfiles happens on Github, at https://github.com/chemfiles/chemfiles/

GLARE is a library and a software for product based optimization of reagent lists in the context of a chemical combinatorial library design. Large virtual combinatorial libraries containing 10^12 products have been optimized within a second.

MS Excel, OOo Calc, Matlab steam and water properties based on IAPWS IF-97 Standard. Provide accurate steam and water properties such as enthalpy from 0-100 bar and 0-2000°C. The perfect tool both for replacing paper tables and for advanced calculations