Chemistry
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Avogadro Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture.
1,765 weekly downloads -
Jmol 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.
1,555 weekly downloads -
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.
226 weekly downloads -
ASCEND modelling environment ASCEND is a modelling environment and solver for large or small systems of non-linear equations, for use in engineering, thermodynamics, chemistry, physics, mathematics and biology. Solvers for both steady and dynamic (NLA & DAE) problems, are provid
209 weekly downloads -
APBS APBS is a software package for the numerical solution of the Poisson-Boltzmann equation, a popular continuum model for describing electrostatic interactions between molecular solutes over a wide range of length scales. <http://www.poissonboltzmann.org/>.
171 weekly downloads -
Gabedit Gabedit is a Graphical User Interface for FireFly (PC-Gamess), Gamess-US, Gaussian, Molcas, Molpro, MPQC, NWChem, OpenMopac, Orca, and Q-Chem computational chemistry packages.
193 weekly downloads -
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 our open mzXML format.
205 weekly downloads -
Bioclipse An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).
167 weekly downloads -
Insensitive NMR spin dynamics simulation
453 weekly downloads -
GaussSum GaussSum parses the output of ADF, GAMESS, GAMESS-UK, and Gaussian to extract useful information: progress of geometry optimisation, UV/IR/Raman spectra, MO contributions and more.
126 weekly downloads -
SketchEl Chemical structure sketching tool, for use with various cheminformatics applications. Convenient to use and moderately sophisticated. Suitable for viewing, creating and editing MDL MOL files.
124 weekly downloads -
XDrawChem XDrawChem is a drawing application designed for drawing and analyzing chemical structures and reactions.
168 weekly downloads -
Bika Open Source LIS/LIMS Lab workflow and web content management. 1-Stop solution
62 weekly downloads -
RMG - Reaction Mechanism Generator RMG is an automatic chemical reaction mechanism generator that constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react (currently limited to C, H, O, and S atoms).
72 weekly downloads -
Toxic Hazard Estimation A GUI application which estimates toxic hazard of chemical compounds. The latest version includes the following toxicity prediction modules: -Cramer rules (oral toxicity) -Toxicity mode of action via Verhaar scheme -Skin irritation prediction -Eye irritation prediction -Benigni / Bossa rulebase for mutagenicity and carcinogenicity prediction -START biodegradation and persistence prediction -Structure Alerts for identification of Michael Acceptors -Structure Alerts for skin sensitisation -Kroes TTC Decision tree -SMARTCyp - Cytochrome P450-Mediated Drug Metabolism and metabolites prediction -Structure Alerts for the in vivo micronucleus assay in rodents (ISSMIC) -Structural Alerts for Functional Group Identification (ISSFUNC) Toxtree provides a plugin framework to incorporate different approaches to the estimation. Platform independent (written in Java), with the use of The Chemistry Development Kit.
100 weekly downloads -
GSim - tool for NMR spectroscopy GSim - free software tool for visualisation and processing of experimental and simulated nuclear magnetic resonance (NMR) spectra.
44 weekly downloads -
DWSIM - Open Source Process Simulator DWSIM is an open source, CAPE-OPEN compliant chemical process simulator for Windows, Linux and Mac OS X. Written in Visual Basic .NET, DWSIM features a comprehensive set of unit operations, advanced thermodynamic models, support for reacting systems, petroleum characterization tools and a fully-featured graphical interface.
245 weekly downloads -
NumericalChameleon The NC is a free, open source, platform-independent software to convert units. It converts numbers with a precision of up to 1000 significant figures. It supports more than 3200 units in 82 categories, and it has been localized in 7 languages.
117 weekly downloads -
STochastic Engine for Pathway Simulation Stochastic simulator for signaling pathways occuring in biological cells. Handles reaction-diffusion processes in 3D tetrahedral meshes.
31 weekly downloads -
LAMMPS LAMMPS is a classical molecular dynamics simulator designed for parallel machines. It can model atomic, polymeric, biological, metallic, or mesoscale systems using a variety of force fields and boundary conditions and is easy to modify or extend.
52 weekly downloads -
PyCIFRW Python module for manipulation of Crystallographic Information Framework (CIF) files
174 weekly downloads -
osra OSRA is a utility designed to convert graphical representations of chemical structures and reactions, as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES or SD file format- a computer recognizable molecular structure You can find links to the binary executables here: https://sourceforge.net/apps/mediawiki/osra/index.php?title=Download
92 weekly downloads -
OpenChrom OpenChrom is a tool for gas chromatography and mass spectrometry. The focus is to handle data files from different GC/MS systems and vendors. Its functionality and algorithms can be extended using a flexible plugin approach, based on Eclipse RCP.
160 weekly downloads -
open enventory Web-based Electronic Laboratory Notebook (ELN) with integrated Chemical Inventory by the group of Prof. Goossen (TU Kaiserslautern, Germany), based on PHP/MySQL. Allows (sub-)structure search, reaction planning, management of spectra and literature.
45 weekly downloads -
RDKit Open-Source Cheminformatics and Machine Learning
82 weekly downloads
