Molecule

Chemistry::Mol is a molecule object toolkit. SYNOPSIS use Chemistry::Mol; $mol = Chemistry::Mol->new(id => "mol_id", name => "my molecule"); $c = $mol->new_atom(symbol => "C", coords => [0,0,0]); $o = $mol->new_atom(symbol => "O", coords => [0,0,1.23]); $mol->new_bond(atoms => [$c, $o],... Platforms: *nix

aufbau is a simple, Command-Line-based tool that was specifically designed to create electron configurations for an atom, molecule or ion. It is built so it follows the "Aufbau" principle. The input has to be a number between 1 and 53. Platforms: Windows, Windows Vista, 7

Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. * The JmolApplet is a web browser applet that can be integrated into web pages. * The Jmol application... Platforms: *nix

XDrawChem is a two-dimensional molecule drawing program. It is similar in functionality to other molecule drawing programs such as ChemDraw (TM, CambridgeSoft). It can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry... Platforms: Windows, Mac, *nix, C/C++, BSD Solaris

The program parses Gaussian 98/03 single-point output and draws HFC tensors as ellipsoids on top of the length-based connected molecule. Platforms: Matlab

Explore an active area of research in optical physics: producing designer pulse shapes to achieve specific purposes, such as breaking apart a molecule. Carefully create the perfect shaped pulse to break apart a molecule by individually manipulating the colors of light that make up a pulse. Platforms: Mac

Molar Mass is a Dashboard widget that calculates the molar mass of a molecule based on the formula entered in the input field. The calculator has an option to show the calculations."Molar mass" is a chemistry related term, that refers to the mass of one mole of a chemical compound. Platforms: Mac

SketchEl is an interactive chemical molecule sketching tool, and molecular spreadsheet data entry application. The feature set provided by the molecular sketcher is largely limited to the minimum features required to conveniently edit diagram representations of small molecule structures.... Platforms: Windows

ShelXle is an instrument that manages to combine 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... Platforms: Windows

Solubility provides a GUI allowing users to develop regression models to predict the aqueous solubility of a molecule. Users can choose or create descriptors and/or atomic typing parameters, train the model, and apply it to large databases. 100% Java. Platforms: Windows, Mac, Linux

Gabedit is a Graphical User Interface to Gamess-US, Gaussian, Molcas, Molpro, MPQC and Q-Chem computational chemistry packages.Gabedit includes graphical facilities for generating keywords and options, molecule specifications and their input sections for even the most advanced calculation... Platforms: *nix, C/C++, BSD

Hidden Markov models are used to describe the "stepping" behavior of molecular motors, as measured by single-molecule fluorescence techniques. Our HMM implementation is more versatile than the one described by Milescu, et al. Biophys. J. 91:3135-3150 and can be used as a "blind" step detector or... Platforms: Matlab

The file drawpdb.m is about 40 lines of code that makes a simple compact viewer of small molecules. A number of .pdb files are also included. Platforms: Matlab

PDBRead is a function that will read a Protein Data Bank file into a MATLAB structure.PDB_struct = PDBRead(filename) reads the file corresponding to filename and stores the information contained in this file in the PDB_struct. e.g. PDB_struct = PDBRead('PDBSilk.txt')The file that is being read by... Platforms: Matlab

SMIProm: Single Molecule Image Processing Program.I use this program to get intensity profiles of single molecule images and fit it using the curve fitting toolbox.basically you can use the program to:-->Select an ROI from an image-->Find the intensity profile along a line in the image--> Fit the... Platforms: Matlab

Starting from atoms, see how many molecules you can build. Collect your molecules and see them in 3D! Platforms: Mac

ChemAzTech is an OpenSource (GPL licence) Web chemistry software connected to a MySQL database (L.A.M.P. software) which is storing molecules. You can manage a chemical laboratory database, with product's properties. Features MyChem + JChemPaint applet allow to the user to search by... Platforms: *nix

Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture. Cross-Platform: Molecular... Platforms: *nix

The Xtal System is a comprehensive suite of small molecule structural solution, refinement and analysis software, supporting both X-ray, neutron and electron diffraction data. It runs on both Unix and MS Win32 platforms and uses tcl/tk graphics. Platforms: *nix

The brand new AbszOrb 3.0 is a game, it's a program, it's a screensaver - it's three mints in one. The new version of AbszOrb has been completely revamped. You can now texture orbs, arrange them in your universe, and fly freely throughout the whole universe or particle system. The new version...