Projects tagged ‘chemistry’

Kalzium is an application which will show you some information about the periodic system of the elements. Therefore you could use it as an information database. It also includes an equation solver and 3D viewer for molecules.

Jmol is a Java molecular viewer for three-dimensional chemical structures. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame files and computed normal modes from quantum programs.

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.

The Chemistry Development Kit (CDK) is a library of Java classes for chemo-, bioinformatics, computational chemistry, and chemometrics. It provides important algorithms like substructure search, SMILES, Gasteiger charges, QSAR descriptor calculation, 3D structure generation, 2D layout and rendering, many IO formats, atom typing, and more.

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.

The Bioclipse project is aimed at creating a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). Bioclipse, as any RCP application, is based on a plugin architecture that inherits ... [More] basic functionality and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc. [Less]

JChemPaint is a program for drawing 2D chemical structures like those found in most chemistry textbooks.

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.

QuteMol is an open source (GPL), interactive, high quality molecular visualization system. QuteMol exploits the current GPU capabilities through OpenGL shaders to offers an array of innovative visual effects. QuteMol visualization techniques are ... [More] aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins. * Real Time Ambient Occlusion * Depth Aware Silhouette Enhancement * Ball and Sticks, Space-Fill and Liquorice visualization modes * High resolution antialiased snapshots for creating publication quality renderings * Automatic generation of animated gifs of rotating molecules for web pages animations * Interactive rendering of large molecules and protein (>100k atoms) * Standard PDB input [Less]

cclib is an open source library, written in Python, for parsing and interpreting the results of computational chemistry packages. The goals of cclib are: * to facilitate the implementation of algorithms that are not specific to a particular ... [More] computational chemistry package * to provide a simple and standard interface to the results of computational chemistry calculations, particularly those results that are useful for algorithms or visualisation * to maximise interoperability with other open source computational chemistry and cheminformatic software libraries [Less]

PyMOlyze is a graphical program to analyze the results of quantum chemistry (HF/DFT) calculations. Features include various population analyses, fragment analysis, monitoring structures during an optimization, and a simple, but powerful, XYZ editor.

Open source steam property routines for C++. Implements the IAPWS-IF97 and IAPWS-95 steam tables from the International Association for the Properties of Water and Steam. Includes two-way property solvers and test suite. Can be used from Python.

A project in progress that will speed up the G2-network by using the similarity in files instead of the complete file.

The BinBase Database system was created to provide an accurate and fast solution for the analysis of thousand of Chromatograms and to create a library of compounds. Better known as Bins. The system is so designed that it can be easily extended and ... [More] adapted for your specific problems. You also have the possibilities to use it in different runtime configurations like: * using it as standalone system * using it with a cluster * using it with setupX as meta information provider * using with a custom meta information provider BinBase core part is now available in the svn. Websites are down to server error and we are working on it! [Less]

JaCuda is a small project which provides several mathematical function useful for a chemist or somebody working with mass specs. These functions will be executed using a cuda compatible gpu or if none is available it will fall back to the c++ ... [More] implementation. If this is also not possible we will invoke the function defined in the programming language. Which would be java/groovy for now and later python. --this project is abounded for the benefit of pycuda-- [Less]

The Massively Parallel Quantum Chemistry program, MPQC, computes properties of atoms and molecules from first principles using the time independent Schroedinger equation.

a small team of package maintainers that share interest in chemical applications and their packaging for Debian and Ubuntu

To have an atomic cluster simulation project that is reliable and easy to use.

This is the development support site for the FDS-SMV Public Domain Project. Funded by the US Department of Commerce, National Institute of Standards and Technology (NIST). See disclaimer below... IMPORTANT NOTE: This is NOT, the Primary Website ... [More] for FDS and Smokeview Information. You can find the primary website at http://fire.nist.gov/fds What is FDS and Smokeview?Fire Dynamics Simulator (FDS) is a computational fluid dynamics (CFD) model of fire-driven fluid flow. The software solves numerically a form of the Navier-Stokes equations appropriate for low-speed, thermally-driven flow, with an emphasis on smoke and heat transport from fires. Smokeview (SMV) is an OpenGL based visualization program that is used to display the results of an FDS simulation. Note: You can subscribe to the SVN Commit Log at http://groups.google.com/group/fds-smv-svn, and Issue Tracker Changes at http://groups.google.com/group/fds-smv-issues these groups are Announcement Only and allow users to watch Issue Tracker and Subversion activity through email. DisclaimerFDS and Smokeview software are developed at the National Institute of Standards and Technology (NIST) by employees of the Federal Government in the course of their official duties. Pursuant to Title 17, Section 105 of the United States Code. This software is not subject to copyright protection and is in the public domain. NIST assumes no responsibility whatsoever for use by other parties of its source code, documentation or compiled executables, and makes no guarantees, expressed or implied, about its quality, reliability, or any other characteristic. These World Wide Web pages in general and the FDS and Smokeview software in particular are provided as a public service by the National Institute of Standards and Technology (NIST). With the exception of material marked as copyrighted, information presented on these pages is considered public domain and may be distributed or copied. Use of appropriate byline/photo/image credits is requested. The US Department of Commerce makes no warranty, expressed or implied, to users of the Fire Dynamics Simulator (FDS), and accepts no responsibility for its use. Users of FDS assume sole responsibility under Federal law for determining the appropriateness of its use in any particular application; for any conclusions drawn from the results of its use; and for any actions taken or not taken as a result of analysis performed using these tools. Users are warned that FDS is intended for use only by those competent in the fields of fluid dynamics, thermodynamics, combustion, and heat transfer, and is intended only to supplement the informed judgment of the qualified user. The software package is a computer model that may or may not have predictive capability when applied to a specific set of factual circumstances. Lack of accurate predictions by the model could lead to erroneous conclusions with regard to fire safety. All results should be evaluated by an informed user. Any mention of computer hardware or commercial software does not constitute endorsement by NIST, nor does it indicate that the products are necessarily those best suited for the intended purpose. [Less]

molsKetch is a molecular drawing tool for 2D molecular structures. Its goal is to help you draw molecules quick and easily. Of course you're creation can be exported afterwards in high quality in a number of vector and bitmap formats.

Estimates toxic hazard of chemical compounds based on a decision tree approach. Provides a plugin framework to incorporate different approaches to the estimation. Platform independent (written in Java).

What is CHARMMingCHARMMING is a public domain web portal to the CHARMM molecular simulation program, which must be licensed separately. It includes functionality for uploading structures, visualizing them, and performing minimization, solvation, and ... [More] classical molecular dynamics. MPORTANT NOTEAlthough you can set up CHARMMing for your own research group, CHARMM's license prohibits you from making it available to anyone who does not have a license. You are responsible for ensuring that access to your CHARMMing server is limited only to those people who are part of a research group that possesses a CHARMM license. Getting CHARMMingYou can find released versions of CHARMMing on the project's download page. The latest released version is 0.5.1. You can also get the latest released installer version from Subversion with svn co http://charmming.googlecode.com/svn/installer/INSTALLER_0_5 . DocumentationComplete install documentation Change log for version 0.5 Quick start guide [Less]

Collaborative Computing Project for NMR (CCPN)

Ruby accessor to the Blue Obelisk Data Repository (BODR).

A collection of cheminformatics and machine-learning software written in C++ and Python.

MADNESS provides a high-level environment for the solution of integral and differential equations in many dimensions using adaptive, fast methods with guaranteed precision based on multi-resolution analysis and novel separated representations. There ... [More] are three main components to MADNESS. At the lowest level is a new petascale parallel programming environment that increases programmer productivity and code performance/scalability while maintaining backward compatibility with current programming tools such as MPI and Global Arrays. The numerical capabilities built upon the parallel tools provide a high-level environment for composing and solving numerical problems in many (1-6+) dimensions. Finally, built upon the numerical tools are new applications with initial focus upon chemistry, atomic and molecular physics, material science, and nuclear structure. The developers gratefully acknowledge the support of the Department of Energy, Office of Science, Office of Basic Energy Sciences and Office of Advanced Scientific Computing Research, under contract DE-AC05-00OR22725 with Oak Ridge National Laboratory. This is the central source of funding for MADNESS and associated applications. The developers gratefully acknowledge the support of the National Science Foundation under grant 0509410 to the University of Tennessee in collaboration with The Ohio State University (P. Sadayappan). The MADNESS parallel runtime and parallel tree-algorithms include concepts and software developed under this project. The developers gratefully acknowledge the support of the Defense Advanced Research Projects Agency (DARPA) under subcontract from Argonne National Laboratory as part of the High-Productivity Computer Systems (HPCS) language evaluation project. Please look in the wiki for more information and project activity. Anonymous, read-only source checkout: svn checkout http://m-a-d-n-e-s-s.googlecode.com/svn/local/trunk m-a-d-n-e-s-s-read-onlyDevelopers, please see the wiki Subversion page for instructions. [Less]

PD - Molecular Simulation Software

The Periodic Tables Package is an advanced suite of applications for both Windows and Linux that allow chemists and students alike to use the Periodic Table on their computers.