Atoms Molecules Ions

GDIS is a scientific visualization program for the display, manipulation, and analysis of isolated molecules and periodic structures. It is in development, but is nonetheless quite functional. It has the following features: * Support for many common file formats (CIF, PDB, XTL, XYZ, and many...

An editor for small organic molecules, written in C using gtk+. It can read and write SMILES and cml and can save to dia's file format. It is suitable for creating chemical molecule diagrams for lower level chemistry/ochem lab reports.

In this submission we present the code of the Replacement Method (RM) [1-4] and Enhanced Replacement Method (ERM)[5], that were proposed some time ago by our group. Both methods produce linear regression QSPR-QSAR models that are quite close the FS (full search) ones with much less computational...


Platforms: Matlab

function [Xcoord,Ycoord,Zcoord] = fcc_cluster(L,M,a)generates coordinates of atoms inside fcc-cluster (face-centered-cubic)with cuboctatruncated shape (hovewer one can change from {111} to {110} truncation)it's arguments: L,M - parameters of cluster (L - size of the cluster,number of unit cells...


Platforms: Matlab

function [Xcoord,Ycoord,Zcoord] = bcc_cluster(L,M,a)generates coordinates of atoms inside bcc-cluster (base-centered-cubic)with cuboctatruncated shape (hovewer one can change from {111} to {110} truncation)it's arguments: L,M - parameters of cluster (L - size of the cluster,number of unit cells...


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

NanoVis (beta version) allows to visualize any atomistic structure by reading a user defined file. The supported formats are "gen" and "xyz". There are two display modes: normal and "spacefill". In the zip file, with the .m file, there are two examples of structure and a file containing the atoms...


Platforms: Matlab

initializePhysicalConstants.m loads important physical constants into the structure CONSTS. The CONSTS structure will contain both values (accessible by CONSTS.var_name), and descriptive information (CONSTS.desc.var_name.[Name, Units, Value]).EXAMPLE USAGE: % What are the units of the unversal...


Platforms: Matlab

How do you know if a chemical equation is balanced? What can you change to balance an equation? Play a game to test your ideas! Sample Learning Goals * Balance a chemical equation. * Recognize that atoms are conserved in a chemical reaction. * Describe the difference between coefficients and...


Platforms: Mac

Gene Studio is a free tool for modelling of DNA manipulation. It will allow to work with vectors, to design primers, to clone molecules and provide user friendly intewrface.


Platforms: Mac

Are all atoms of a given element the same? How can you tell one isotope from another? Learn about isotopes, and about how to calculate the average atomic mass of an element. Sample Learning Goals: * Define "isotope" using mass number, atomic number, number of protons, neutrons and electrons...


Platforms: Mac

EasyChem is designed to draw chemical molecules in an intuitive way, with a very high quality (designed for book-publishing). Exporting is done to various formats (PostScript, Fig, LaTeX, etc.) to help you integrate your drawing in any software you use.


Platforms: *nix

This is a GTK/OpenGL based program for displaying isolated molecules, periodic systems, and crystalline habits. It also acts as a GUI to packages such as GAMESS, GULP, and POVRay to provide energy minimizations and publication quality rendering.


Platforms: *nix

123Tag is an easy-to-use and powerful Tag editor and file renamer for MP3,MP4,WMA and many other audio formats, useful to manage and catalog all your music files. 123Tag helps you also to find and catalog  the huge amount of music files that usually are stored and disperded on your PC,...


Platforms: Windows, Windows 7, Windows Server, Other

This great free screen saver will soothe your eyes and mind during long workhours. Colourful atoms floating in space around your desktop, getting fused and nuked all the time. You can also download arcade game and take part in all this fun yourself - it's better than Star Wars. Small...


Platforms: Windows

For the set of chemical elements (Ba, Sr, Ca and so on) there is a function enabling to print capital and small letters without switching by "Shift" and "Caps Lock" keys. Figures specifying the number of atoms in chemical formula (H2SO4) are automatically made subscripts, and atom's oxidation...


Platforms: Windows

Language::Basic::Expression is a Perl package to handle string, numeric, and boolean expressions. SYNOPSIS See Language::Basic for the overview of how the Language::Basic module works. This pod page is more technical. # Given an LB::Token::Group, create an expression I parse it my $exp =...


Platforms: *nix

The Elektra Project provides an alternative back-end for text configuration files. Instead of each program to have its own text configuration files, with a variety of formats, Elektra tries to provide a universal, hierarchical, fast and consistent namespace and infrastructure to access...


Platforms: *nix

MassSpec::ViewSpectrum::RealVsHypPeptide is a Perl module to view a real mass spectrum on the same graph as a hypothetical spectrum generated by fragmenting a peptide in silico. SYNOPSIS use MassSpec::ViewSpectrum::RealVsHypPeptide; open GRAPHIC, ">mygraphic.png" or die "Unable to open...


Platforms: *nix

LMarbles is an Atomix clone with a slight change in concept. Instead of assembling molecules you create figures out of marbles. Nevertheless, the basic game play is the same: If a marble starts to move it will not stop until it hits a wall or another marble. To make it more interesting there...


Platforms: *nix