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Top : Java : Scientific : Chemistry

Highlights
Powerful Command-line File Transfer Programs
This article provides my pick of the best open source command line file transfer programs. The software featured here supports a number of different protocols. They offer shell-like command syntax, and are great for scripting purposes.

(Read more)
Majordomo
Majordomo controls a list of addresses for some mail transport system (like sendmail or smail) to handle. Majordomo itself performs no mail delivery (though it has scripts to format and archive messages). Features include: Supports various types of lists, including moderated, All list management activities are handled by email, so list owners don't need access to Majordomo server machine, Supports archival and remote retrieval of messages and digests, and is written in Perl. Read more

Links:

  • Bioclipse
    Bioclipse is a rich-client platform chemistry and biology workbench. It provides access to many open source bioinformatics and chemoinformatics toolkits and has plugins for the Chemistry Development Kit, JChemPaint, Jmol, and BioJava. Read more
  • Chemistry 4-D Draw
    (commercial) Chemistry 4-D Draw is an easy-to-use and powerful structure drawing program.
  • ChemNomParse
    an open source project to create a chemical nomenclature parser. The project aims to build molecules from an IUPAC chemical name and comes in two parts: The ChemNomParse library - which contains the core of the project and is now part of the CDK and Nomen - A complete program which demonstrates the library's abilities
  • CORINA
    (commercial) CORINA (COoRdINAtes), is a rule and data based system, that automatically generates three-dimensional atomic coordinates from the constitution of a molecule as expressed by a connection table or linear code.
  • DisMol
    DisMol is a molecular viewer applet written in Java, which allows molecular structures to be viewed on the web.
  • DL_MESO
    DL_MESO is a general purpose mesoscopic simulation package. DL_MESO consists of Lattice-Boltzmann Equation, Dissipative Particle Dynamics and Smoothed Particle Hydrodynamics.
  • DL_POLY
    DL_POLY is a general purpose serial and parallel molecular dynamics simulation package.
  • GriF
    The Grid Framework (GriF) is a SOA Grid Framework aimed at running on the EGI Grid multi-purpose scientific applications. The SOA-based organization of GriF consists of two JAVA servers (YR and YP) and a JAVA client (YC).
  • JChem
    JChem is a tool for developing applications that manipulate mixed chemical and corporate data.
  • JChemPaint
    JChemPaint is the editor and viewer for 2D chemical structures developed using the Chemistry Development Kit (CDK). It is implemented in several forms: a Java application and two varieties of Java applet.
  • JME Molecular Editor
    a free Java applet, which allows creation, editing, and display of molecules directly within a web page, and can generate molecular SMILES code
  • Jmol
    Jmol is an open-source Java viewer for three-dimensional chemical structures with features for chemicals, crystals, materials and biomolecules. Read more
  • JOELib
    a platform independent open source computational chemistry package written in Java
  • Marvin
    (commercial) Marvin is a Java based chemistry software consisting of Marvin Applets, Marvin Beans, MarvinSketch and MarvinView.
  • NMRShiftDB
    NMRShiftDB is a web database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (currently only for carbon) as well as for searching spectra, structures and other properties. Last not least, it features peer-reviewed submission of datasets by its users.
  • NMRViewJ
    (commercial) NMRView is a program for the visualization and analysis of NMR datasets.
  • SketchEl
    SketchEl is an interactive chemical molecule sketching tool, designed for quick and simple entry of structures. The feature set is limited to those necessary to enter a single chemical species, in a form that might be used in a cheminformatic database, representing each atom and bond as a part of a labelled graph.
  • WebMol
    WebMol was designed to display and analyze structural information contained in the Brookhaven Protein Data Bank (PDB).



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