Free general chemistry software for linux

Gnome Chemistry Utils software provides C++ classes and Gtk+-2 widgets related to chemistry. They are used in both Gnome Crystal and GChemPaint.

To compile and use the Gnome Chemistry Utils, you need libglade-2, and GtkGLExt, and their own dependencies. Everything except GtkGLExt is available from the Gnome repository or one of its mirrors.

The GtkChem3DViewer widget also needs Gnome-vfs and OpenBabel to be built.

GChemistry Utils are distributed under the LGPL license.

Gnome Chemistry Utils are in an early development stage.

Three widgets:

- a periodic table,
- a crystal structure viewer,
- a 3D molecular structure viewer.

The last widget is also accesible as a Bonobo control.

The Gnome Chemistry Utils are the basis for the development of both GChemPaint and Gnome Crystal

General Package/Module Interface (GPMI) is a lightweight library that assists with modularizing applications.
It includes prewritten script interpreter modules in addition to timers, events, and package dependencies.
Enhancements:
- This version features many bugfixes and memory leak cleanups.
- It is now possible to compile the code on Windows using mingw.

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], order => 3);

print $mol->print;

This package, along with Chemistry::Atom and Chemistry::Bond, includes basic objects and methods to describe molecules.
The core methods try not to enforce a particular convention. This means that only a minimal set of attributes is provided by default, and some attributes have very loosely defined meaning.

This is because each program and file type has different idea of what each concept (such as bond and atom type) means. Bonds are defined as a list of atoms (typically two) with an arbitrary type. Atoms are defined by a symbol and a Z, and may have 3D and internal coordinates (2D coming soon).

Kemistry is a collection of chemical applications for the K Desktop Environment (release 3.x).

Originally the applications were distributed in a single source package, but currently every application is distributed in a standalone package. The available applications are

* KMolCalc - molecular weight and elemental composition calculator
* KemBabel - a file conversion program based on Open Babel

GENESIS (short for GEneral NEural SImulation System) is a general purpose simulation platform that was developed to support the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, simulations of large networks, and systems-level models.

GENESIS has provided the basis for laboratory courses in neural simulation at Caltech, the Marine Biological Laboratory, the Crete, Trieste, Bangalore, and Obidos short courses in Computational Neuroscience, and at least 49 universities of which we are aware.

Most current GENESIS applications involve realistic simulations of biological neural systems. Although the software can also model more abstract networks, other simulators are more suitable for backpropagation and similar connectionist modeling.

Installation

1. Pick the place where you want to install the "genesis" directory tree. If you are making a system-wide installation as "root" user, /usr/local is a good choice. For a personal installation, without root privileges, you can use your home directory ("~"). Change to this directory and extract the genesis directory from the archive file genesis2.2.1-linux-bin.tar.gz. For example,

cd /usr/local
tar xvzf /mnt/cdrom/genesis2.2.1-linux-bin.tar.gz

or from wherever you have it (e.g.~/downloads/genesis2.2.1-linux-bin.tar.gz).

2. Change to the "genesis" directory and run the setup script that creates the ".simrc" GENESIS initialization file". Then copy .simrc to your home directory.

cd genesis
./binsetup
cp .simrc ~

3. Finallly, add the genesis directory to your search path, so that "genesis" can be found from any directory that you are in. If your login shell is bash, you can do this by editing the .bashrc file in your home directory to add the line

PATH=$PATH:/usr/local/genesis

at the end of the file. If you are using tcsh or csh as your command shell, add

set path=($path /usr/local/genesis)

to your .tcsh or .csh file.

At this point, you are ready to try running GENESIS. Change into the directory genesis/Scripts and try some of the tutorials suggested in the README file.

The goal of the General Applet Interface Library is to give programmers a simple yet powerful applet interface. This library supports wmapplet/dockapps, GNOME 2 panel applets, and ROX panel applets.
This library supports at the moment Dockapps, Gnome 2 Panel Applets and Rox panel applets. In the future support for XFCE 4 and KDE is planned to be added. The applet program doesnt have to care about if the applet will be used on the Gnome panel or in the dock. The library handles that.
Over 50% of the code in a Dockapp and a Gnome 2 Panel applet does actully only one thing, setting up the applet window. With GAI, you can reduce it to just a few lines of code.
Enhancements:
- Updated the example applets.
- The preference dialog is now nicely resized.
- Fixed some minor memory leaks in the preference dialog.
- API change: The function connected to gai_signal_on_preferences() shall now take: (gboolean changed, gpointer data) as argument. changed is true if the user changed
- anything in the preference window. False if the user did nothing.
- Added two new preference window items. GAI_LISTSTORE and GAI_EDITLISTSTORE. The first shows just a list, no altering is possible. The second provide a list that can be increased and reduced by the user. (NOT YET FINISHED!)
- Cleaned up parts of the preference generator. Several minor memory leaks fixed.
- Update gai.spec. Some Fedora Core changes by Michael Schwendt mschwendt@users.sf.net, and Michel Alexandre Salim salimma@users.sf.net
- Allowing applet to be bigger than 1000 pixels (2560 is now max).
- Ashley V wants to have Shermans
- aquarium real big Destroying (clicking on the window manager "X" icon) the preference window now works fine.
- Destroying About box is now handled correctly.
- Rewrote large part of the right mouse click menu handleling code. Now you can remove, change, insert and add menu items during run time. gai_menu_insert(...), gai_menu_change(...) and gai_menu_remove(...) is new. gai_menu_add now returns an integer that is the ID of the menu item.
- Fixed broken libdir link in gai.pc
- Make sure GdkColor is never null when given to applet.
- Documentation updates.
- Various minor fixes found on the fedora extras by Michael Schwendt and Thorsten Leemhuis fedora@leemhuis.info. Please mail me fixes directly!!
- GtkFileChooser dialog is now used instead of GtkFileSelector when GTK+ 2.4 or later is detected.
- If gtk+ 2.4 or later, use varously updated widgets instead of older ones.
- Merged big nls patch by Olaf Leidinger Thanks!
- NLS is finally supported for GAI. Not yet there for applets
- The BonoboUIVerb array canary was missing and that caused the GNOME to crash. Patch by Jean-Yves Lefort

MIBA Consulting General System Library is a collection of cross-platform C++ class libraries. Provides thread, IPC, file, network, SNMP (net-snmp) and Database (MySQL) interfaces. Comes with the usual array of utility classes - smart pointers, singletons, registries, serialization etc.

Installation:

The dist (or debug) directory contains everything you need apart from the NSPR library (and NETSNMP and STLPORT iostream library if you choose to use these), and two header files from NSPR. To get a complete kit use

make install INSTALL_PATH=path

where path is where you want the kit installed. If you have doxygen the documentation will be created by the install target, or you can make it independently with "make doc". In either case the documentation will get copied to the install path too.

BrowserLauncher2 is a library that facilitates opening a browser from a Java application and directing the browser to a supplied URL.

In most cases, the browser opened will be the users default browser.

BrowserLauncher2 is free software and it is being released under the GNU Lesser General Public License.