Chemistry Software

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Chemistry Software

  • Get the Edge; Toad Edge Get the Edge; Toad Edge Icon
    Get the Edge; Toad Edge Icon

    Your next-gen toolset for MySQL database environments

    If your organization takes advantage of the cost-effective, flexible MySQL open source database platform, then you need a toolset that supports your commitment to open source relational databases.  Toad Edge for MySQL has what you need and helps you ramp up on MySQL quickly, ensuring faster time to value.
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  • Jmol Icon

    Jmol

    An interactive viewer for three-dimensional chemical structures.

    Over 10,000,000 page views! Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other quantum chemistry programs. Files can be transferred directly from several databases, including RCSB, EDS, NCI, PubChem, and MaterialsProject. Multiple files can be loaded and compared. A rich scripting language and a well-developed web API allow easy customization of the user interface. Features include interactive animation and linear morphing. Jmol interfaces well with JSpecView for spectroscopy, JSME for 2D->3D conversion, POV-Ray for images, and CAD programs for 3D printing (VRML export).

  • JSmol Icon

    JSmol

    JavaScript-Based Molecular Viewer From Jmol

    JSmol is the extension of the Java-based molecular visualization applet Jmol (jmol.sourceforge.net) as an HTML5 JavaScript-only web app. It can be used in conjunction with the Java applet to provide an alternative to Java when the platform does not support that (iPhone/iPad) or does not support applets (Android). Used in conjunction with the Jmol JavaScript Object (http://wiki.jmol.org/index.php/Jmol_Javascript_Object), JSmol seamlessly offers alternatives to Java on these non-Applet platforms. JSmol can read all the files that Jmol reads. You can do all the scripting that Jmol does. You can create all the buttons and links and such that you are used to creating for Jmol. All of the rendering capability of the Jmol applet is there. JSmol has both a console and a popup menu. JSmol is integrated fully with JSME and JSpecView. A "lite" version of JSmol provides minimal functionality (balls and sticks only) for extremely small-bandwith apps. Released 1/12/2013

  • SASHIMI

    The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.

  • JSpecView Project Icon

    JSpecView Project

    Spectroscopy Viewer

    The JSpecView Project initially provided JAVA applets for the display of JCAMP-DX and AnIML/CML spectral files. The source and binary files are available via the Code (sourceforge SVN) and Files menu options. See the WIKI pages (Hosted Apps) for more detail. Since October 2013, JSmol now incorporates a HTML5/JavaScript version of this project

  • The Chemistry Development Kit Icon

    The Chemistry Development Kit

    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

    Downloads: 46 This Week Last Update: See Project
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    Identify and respond to threats before damage is done Icon

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  • ShelXle Icon

    ShelXle

    ShelXle is a Qt GUI for SHELXL

    ShelXle combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo-Fc) maps. See J. Appl. Cryst. (2011). 44, 1281–1284. for details.

  • AMBIT:Chemical Structure DB&Web Service  Icon

    AMBIT:Chemical Structure DB&Web Service

    Chemical structures database & machine learning with web services API

    AMBIT offers a cheminformatics data management for chemical substances, structures and nanomaterials. Flexible structure, similarity and study queries storage, descriptor calculation and predictive models building via REST web services.User interface for creating read across assessment and generating reports, aligned with regulatory and industrial requirements. Command line applications also available. Integration with third party tools and databases.

  • JChemPaint Applet and Swing Application Icon

    JChemPaint Applet and Swing Application

    The JChemPaint Applet and Swing Application are Java programs for drawing 2D chemical structures like those found in most chemistry textbooks. It is based on the Chemistry Development Kit (cdk.sf.net). Downloads, tracker, and source code repository can be found on http://jchempaint.github.com

  • Analytical Data Interchange

    This project provides open software for working with analytical instrumentation data using the ASTM "ANDI" standard.

    Downloads: 7 This Week Last Update: See Project
  • JCAMP-DX

    The JCAMP-DX project is the reference implemention of the IUPAC JCAMP-DX spectroscopy data standard.

    Downloads: 7 This Week Last Update: See Project
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  • xylib - library for reading x-y data

    xylib is a portable library for reading x-y data from powder diffraction, spectroscopy and other experimental methods. Supported formats: VAMAS, pdCIF, Bruker, Philips, Rigaku DAT, Sietronics CPI, DBWS/DMPLOT, Koalariet XDD and others.

  • AutoMap

    AutoMap is a tool for structural biology and drug design.

    AutoMap takes a series of poses obtained from molecular docking and applies the site, epitope and conformational mapping techniques to the poses to select likely ligand binding modes.

    Downloads: 5 This Week Last Update: See Project
  • ChemCpp software

    ChemCpp is a C++ toolbox for chemoinformatics focusing on the computation of kernel functions between chemical compounds. Together with Support Vector Machines, these kernel functions find natural applications for virtual screening of molecules.

    Downloads: 3 This Week Last Update: See Project
  • NanoHive Nanospace Simulator Icon

    NanoHive Nanospace Simulator

    NanoHive is a modular simulator used for modelling the physical world at a nanometer scale. The intended purpose of the simulator is to act as a tool for the study and development of nanotech entities. The project will also focus on the simulation of complex biological applications such as Targeted Drug Delivery by simulating nanowires, magnetic nanoparticles and others. Updates will follow from January 2017.

  • ChemNomParse

    A Java program to parse chemical names using IUPAC nomenclature. The output can be either a visualisation of the molecule, or in a form for other programs to use (e.g. CML).

    Downloads: 2 This Week Last Update: See Project
  • OPEN GENERAL SCIENTIFIC INTERFACES Icon

    OPEN GENERAL SCIENTIFIC INTERFACES

    OPEN GENERAL SCIENTIFIC INTERFACES homepage : http://www.opengsi.org

    Downloads: 2 This Week Last Update: See Project
  • iterate

    Iterate is an implementation of the Bravais-lattice-finding algorithm from: Andrews and Bernstein, Acta Cryst. (1988). A44, 1009-1018 Lattices and Reduced Cells as Points in 6-Space and Selection of Bravais Lattice Type by Projections.

    Downloads: 2 This Week Last Update: See Project
  • Downloads: 1 This Week Last Update: See Project
  • PLASMAKIN: a chemical kinetics package

    A library to compute the electron and chemical kinetics on plasmas

    PLASMAKIN is a package to handle physical and chemical data used in plasma physics modeling and to compute gas-phase and gas-surface kinetics data: particle production and loss rates, photon emission spectra and energy exchange rates.

    Downloads: 1 This Week Last Update: See Project
  • SciBearSpace

    Clinical Information Management

    Open Source Clinical Information Management System. From research to laboratory. Gathering / storing of analytical data within an SQL database.

    Downloads: 1 This Week Last Update: See Project
  • Structure

    Structure is a framework for two-dimensional molecular visualization written in Java and based on Octet.

    Downloads: 1 This Week Last Update: See Project
  • 4DiCeS

    4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.

    Downloads: 0 This Week Last Update: See Project
  • ARGonWin - Automatic Retrosynthesis

    ARGonWin - Automatic retrosynthesis generator on (X)Windows: COMPUTERASSISTED ORGANIC SYNTHESIS / Chemoinformatics package to propose a chemical synthesis for an organic compound given its structural formula. (C++ XWindows/MSWindows). Based on OpenBabel.

    Downloads: 0 This Week Last Update: See Project
  • Algorithms in Spectroscopy

    The aim of the project is to provide open source collection of algorithms in the field of spectroscopy: data handling and processing, modeling and artificial intelligence tools.

    Downloads: 0 This Week Last Update: See Project
  • Analytical Information Markup Language

    Open XML format for analytical chemistry and biology data.

    This project supports ASTM E13.15 "Analytical Data Magement" in its work defining AnIML, an XML standard for representing, managing and interchanging analytical chemistry and biology data.

    Downloads: 0 This Week Last Update: See Project
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