Open Source Java Chemistry Software for Windows - Page 3

The CheckCML project is a collection of modules for the production and checking of chemical experimental data represented as CML. The core CheckCML library provides classes for the checking process; tools such as OscarData allow for the production of CML

Mathematics, Chemistry and Bio-informatics semantic knowledge editor and simulation environment. It should serve as interactive science learning program or science classroom notebook and workshop.

Chemical Evaluation Framework (CEF) is a molecular structure based software to assist in hazard assessment. Download requires Java 6 update 1. Source code is contained in jar files. Download contains GSH reactivity plugin.

Graphical editor using HTML5 canvas for input of chemical structures, molecule interactions, as well as protein sequence and 3D structural motifs. Facilitates searches in chemo-informatics, bioinformatics and structural biology .

The Chemical Manager application can be of great help to Organic Chemistry Departments. University research groups will benefit from using this application, since it was optimized for their needs. Currently, Technion Chemistry department is benefiting from it.

Java program for computations with values expressed in terms of physical or other units. Supports complicated mathematical expressions and user-defined functions. Invoked from scripts, line command, or as GUI. Extensive units data base.

ConvertMAS - molecule converter; use to convert Chemical File Formats. It works on mol, mol2 and sdf files. It converts single file to respective formats. It will split sdf file with multiple molecules into seperate single files of any desired format. Also ConvertMAS creates sdf files from joining of mol, mol2 and sdf files. This is stand alone application; hence no need of internet connectivity to get results. It will generate output files in less time. Various online tools are available for conversion of Chemical file formats; but ConvertMAS mainly works on mol, mol2 and sdf effectively.

DockoMatic is a GUI application that is intended to ease and automate the creation and management of AutoDock jobs for high throughput screening of ligand/receptor interactions.

The EDAM ENCHILADA - The Exploratory Data Analysis and Management Project's Environmental Chemistry Data Processing and Mining Application.

Diagram (JGraph) driven simulator. Bondgraphs > nonlinear differantial system > plot: implemented for economics and ecology. Network analysis: emergy propagation implemented. Would also fit for electronics, mechanics, cost, GWP, footprint analysis.

EPeriodic is the electronic periodic table. you can read the properties of each element in the table with a single click

Extended Bioaccumulation Framework (ExBAF) is a tool for assessing bioaccumulation in foodwebs. Supports several bioaccumulation models and provides tools for analysis and visualization.

Calculating 2D-Gray-scale bitmaps Calculation of a 3D-rotation-body form a detected area by using different image processing algorithms. Developed for the German Aerospace Center (DLR). Used Projects: Substance (GUI)

Gavrog stands for "Generation, Analysis and Visualization of Reticular Ornaments using Gavrog". It is a Java library together with a suite of interactive applications for the study of periodic net-like structures in space and their applications.

Gridder is a group of portlets that simplify the use and administration of grid services. Especially for job submission management. Gridder also extends and documents the functionality of the OGCE Bundle. It is plenty of useful documentation.

IQuant is an automated pipeline for quantitative proteomics based upon isobaric tags. It integrates post-processing tool of protein identification and advanced statistical algorithms to process the MS/MS signals generated from the peptides labeled by isobaric tags for quantification. IQuant can run from a graphical user interface (GUI) as well as a command-line interface and work with both Windows and Linux system. This website contains the IQuant software, an example data labeled by iTRAQ-8plex for testing and a user's manual. If you have any question about IQuant, please contact me: wenbo@genomics.cn. The source code of IQuant can be found here "https://sourceforge.net/p/iquant/code/".

J-ICE stands for Jmol interface for crystallographic and electronic properties. Is an extension of the powerful, platform independent molecular visualizer Jmol, towards crystallographic and electronic properties. More info will be given soon.

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

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 https://jchempaint.github.io

A set of utilities for working with the GAMESS Computational packages. Written in java to maximize cross platform use

2-D chemical structure drawing program

Chemical Equations with Cows

Java Native Interface wrapper for the IUPAC International Chemical Identifier (InChI)

The JPAT API is a Java API designed to provide developers with tools for calculating the results of protease digestion of proteins and ms/ms fragmentation of peptides. JPAT also contains GUI components for displaying the results. JPAT is a nice way to get

JPhysChem - a mathematical modeling toolbox designed to provide an abstract layer and a comprehensive graphical front-end for general model building and specific modeling and data processing in the field of mass spectrometry and physical chemistry.