Free chemistry development kit software for linux

Chemistry Development Kit classes are Java utitility classes for ChemoInformatics and Computational chemistry, written in Java. They are developed constantly developed parallel to other projects that make use of them.
They are a complete re-write of the CompChem classes that were the basis of JChemPaint, a Java Editor for 2D chemical structures, and of JMDraw, a Java package for the graphical layout of 2D chemical structures.
The CDK project was started in September 2000 to replace the CompChem libraries used by JChemPaint, Jmol and SENECA. It no longer is in its initial stage, but is slowly getting a solid state.
The people involved in setting up the project are Christoph Steinbeck then at the Chemoinformatics Group at the Max Planck Institute of Chemical Ecology in Jena, as well as Egon Willighagen from the University of Nijmegen, The Netherlands, who is also involved with JChemPaint and many other Java Chemoinformatics programs, and Dan Gezelter from Notre Dame University, South Bend, USA, the initiator of Jmol, a 3D viewer and analyzer for molecules .
Now, the rewrite of these CompChem/CDK library classes do somehow effect all of our projects. All of our code relies to some extend on the so-called CompChem classes for computational chemistry.
Christoph Steinbeck started this chemistry library when he started programming SENECA, a system for Computer Assisted Structure Elucidation. It turned out that some of the code had design flaws that prevented others, like the authors of (Jmol) to use it.
Enhancements:
- This release consists of mostly some bugfixes, but also solves a few Java 1.4.2 compile problems and adds more functionality to the SMARTS parser.

GNU MIX Development Kit offers an emulation of MIX and MIXAL. The current version of MDK includes the following applications:
- mixasm A MIXAL compiler, which translates your source files into binary ones, executable by the MIX virtual machine.
- mixvm A MIX virtual machine which is able to run and debug compiled MIXAL programs, using a command line interface with readlines line editting capabilities.
- gmixvm A MIX virtual machine with a GTK+ GUI which allows you running and debugging your MIXAL programs through a nice graphical interface (see screenshots).
- mixguile A Guile interpreter with an embedded MIX virtual machine, manipulable through a library of Scheme functions.
- mixal-mode.el An Emacs major mode for MIXAL source files editing, providing syntax highlighting, documentation lookup and invocation of mixvm within Emacs.
- mixvm.el An elisp program which allows you to run mixvm within an Emacs GUD window, simultaneously viewing your MIXAL source file in another buffer.
Using the GNU MDK tools, youll be able to:
- write, compile and execute MIXAL programs,
- set breakpoints and run your programs step by step,
- set conditional breakpoints (register change, memory change, etc.),
- collect execution timing statistics,
- trace executed instructions,
- inspect and modify the MIX registers, flags and memory contents at any step,
- simulate MIX input-output devices using the standard output and your file system.
In addition, the MIX virtual machine simulators include an embedded Guile interpreter and, therefore, their functionality can be extended using Scheme.
Enhancements:
- The Gmixvm interface has been improved with respect to the external programs dialog and about box.
- Compilation warnings in PPC and 64-bit platforms were fixed.
- Minor bugs were fixed.

Heirloom Development Tools package provides yacc, lex, m4, make, and SCCS as portable derivatives of the utilities released by Sun as part of OpenSolaris. The OpenSolaris utilities were in turn derived from the original Unix versions, and are assumed be conforming implementations of the POSIX standard.

Software developed on original Unix systems has quite often used internals of yacc and lex. The tools in this package provide a convenient way to make such software compile on free Unix platforms such as Linux or BSD. In particular, they serve as a stable base for compiling other components of the Heirloom Project.

CDK4AVR stands for Cross Development Kit for Atmels AVR RISC processor serie and should support your development with a comprehensive Assembler and C development environment for even this processor familie under Linux. It will present only free of fee tools, so you can use it without risks. Further you will find some useful OS projects and related sample code all arround AVRs inside of the example packages.
CDK4AVR collects all programms and development tools in one directory (/opt/cdk4avr) and will try to present an easy to admin installation.
My intention for CDK4AVR is / was to provide a full featurd tool chain distribution of all the free accessible resources, because the most stuff is scattered to the wide of the whole Internet and only compileable by wizards or professions.
Installation:
Each package will be provided as RPM only. It is not necessary to install all packages,but you have to install the base package cdk-avr-base every time you want to use another package. Here is an example for a typical GNU development environment:
[user@host]$ rpm -hiv cdk-avr-base-0.3-20031111.i386.rpm
[user@host]$ rpm -hiv cdk-avr-binutils-2.14-20030906.i386.rpm
[user@host]$ rpm -hiv cdk-avr-gcc-3.3.2-20031021.i386.rpm
[user@host]$ rpm -hiv cdk-avr-gcc-c++-3.3.2-20031021.i386.rpm
[user@host]$ rpm -hiv cdk-avr-gcc-colorgcc-3.3.2-20031021.i386.rpm
[user@host]$ rpm -hiv cdk-avr-libc-1.0.2-20040229.noarch.rpm
[user@host]$ rpm -hiv cdk-avr-gdb-6.0-20031019.i386.rpm
[user@host]$ rpm -hiv cdk-avr-simulavr-0.1.2.20040304cvs-20040304.i386.rpm
[user@host]$ rpm -hiv cdk-avr-avarice-2.2-20040229.i386.rpm
[user@host]$ rpm -hiv cdk-avr-uisp-20040207cvs-20040304.i386.rpm
[user@host]$ rpm -hiv cdk-avr-avrdude-4.3.0-20040229.i386.rpm
Base package -- is needed every time you will use any CDK4AVR package.
NOTE: Users of base packages with version 0.2 and prior have to update to latest version. There was a damaged (t)csh startup script. As a result of an buggy %preun script in previous packages you have to update in two cycles:
[user@host]$ rpm -hUv cdk-nios-base-0.3-20031111.i386.rpm
[user@host]$ rpm -hUv --force cdk-nios-base-0.3-20031111.i386.rpm
Enhancements:
- There are minor feature enhancements in AVR-Ada 0.4.1.
- As a result, the packeges for binutils and gcc/gnat were rebuilt.
- There are new packages for the AVR-Ada run time system and related examples.

NCurses Development Kit for C++ provides a set of widgets for text user interface like menubars, popup menus, various dialog boxes, and controls (push buttons, check buttons etc.). Using this library you can easy create a powefull console program with compicated interface. А powerfull event engine allows you to create a various dynamic widgets.

There are two big branches of this library avaliable - main (head) and the ALT:

Main - original NDK++ library. This library is an extention of libncurses++ library. Event system is working like MFC.

ALT - full rewrite and redesign of the previous code. It not a superset of libncurses++ library, it uses only ncurses and panel libraries. It also uses a new event engine.

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).

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

RogueScanner project is an open-source vulnerability management tool that is used to gain greater network visibility to enable you to quickly identify and remove rogue wireless devices that may provide a back door to access your critical data and infrastructure.
Considering that rogue access points and peers represent a major threat to data integrity, RogueScanner is a valuable tool that you can start using today at no cost.
More than 300 companies manufacture access points, and there are more than 10,000 different models of network infrastructure.
Companies thus face a major challenge in maintaining a system to track and identify all potential rogue wireless devices and in continually scanning the network to identify them. To address this challenge, Network Chemistry has made an open-source product available to help organizations begin to immediately scan their networks.
RogueScanner is available for use at no charge by organizations looking for a tool focused on device identification and rogue detection. RogueScanner leverages the Collaborative Device Classification system to automatically lookup and identify the device type and its identity in real time.
Enhancements:
- Many scanning and classification improvements.
- Support has been added for parsing routes under from IOS CLI.
- Support has been added for dumping Cisco device CDP cache via both SNMP and CLI (IOS and CatOS).
- Support has been added for sniffing CDP broadcasts off the wire.
- CDP information is now submitted to the classification server and used for classification.
- FTP (21/TCP) has been added to the list of ports that are probed if open.