Free branches of 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

Chemistry::SQL is an access database functions module.

SYNOPSIS

use strict;
use Chemistry::SQL;
use Chemistry::Artificial::SQL;

my $db_name = $ARGV[0];
my $file = $ARGV[1];

my $db1 = Chemistry::SQL::new(db_host=>"127.0.0.1",db_user=>"root",db_port=>"3306",db_pwd=>"",
db_name=>$db_name,db_driver=>"mysql");
if ($db1->db_exist)
{ $db1->connect_db;
$db1->del_tables;
$db1->create_tables_mysql;
$db1->inscomp_from_file("$file");
}
else
{
$db1->create_db;
$db1->connect_db;
$db1->create_tables_mysql;
$db1->inscomp_from_file("$file");
}
# Reaction Insertion

my $qart = Chemistry::Artificial::SQL::new($db1);
my $qr =$qart->q_reaccion(C=CC=C.C=C>>C1=CCCCC1,smiles);
$db1->reactionsert($qr,"","0");

This package provides the necessary functions to interact with the database. The methods implemented in this module are oriented to give users control of the database without knowing how to use SQL queries.

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

CCFlauncher is the meta-tool for starting and joining a CCF collaborative computing session. With CCFlauncher you can invite your colleagues/friends to join you in a shared X windows virtual desktop with multiparty audio conferencing, white board, and file sharing in just a few mouse clicks. In this setting, participants interact with each other, simultaneously access and operate computer applications, refer to global data repositories or archives, collectively create and manipulate documents or other artifacts, perform computational transformations, and conduct a number of other activities via telepresence. Research issues addressed in this project include problem solving environments and methodologies for laboratory and instrument-based scientific disciplines, and computer science issues in heterogeneous distributed systems. New approaches are being investigated and developed for fast multiway communication, robust geographically distributed data management methodologies, high-performance computational transforms inlined within collaboration sessions, and related auxiliary issues such as active documents, security, archival storage, and experiment management and control.

The main goal of CCF is to enable the construction of efficient and flexible collaborations. Although we expect that CCF will be useful in a number of scenarios, a guiding principle in its design was to identify and meet the needs of natural science investigators with a diverse set of computing, instrument interfacing, and collaboration requirements. Thus, the primary target domain for CCF is collaborative research in chemistry, physics, and biochemistry, and closely related areas. Research methodology in laboratory and instrument based sciences is increasingly dependent upon computation, interaction, visualization, and data storage/retrieval. The CCF project is investigating and developing innovative enabling technologies to support collaborative, distributed, computer-based problem solving in the natural sciences. The goal is to evolve a virtual environment for distributed computing that integrally supports human AV communication, high performance heterogeneous computing, and distributed data management facilities. Computational transforms, instrument interfacing, data referral, visualization, and collaborative work in chemistry, physics, and biomedical fields will guide the development of methodologies and software tools to facilitate collaborative research.

GChemPaint is a 2D chemical structures editor for the Gnome desktop.

GChemPaint should enable embedding some chemistry in files from other programs using Bonobo.

Brabosphere is an OpenSource program for the 3D visualisation of molecular systems and their properties. Brabospheres name is derived from the quantum mechanical program package BRABO (developed at the Structural Chemistry Group of the University of Antwerp) for which it acts as a graphical frontend.
It can also be used for the analysis and visualisation of the data resulting from this type of calculations. In that respect, results from some other quantum mechanical applications will also be accepted.
For quick viewing of molecular structures, the program CrdView is being developed, acting as a replacement for Xmol and allowing command line conversion between a multitude of coordinate file formats.
Main features:
- Molecule builder:
- Atoms can be added and positioned using absolute or relative cartesian coordinates and internal coordinates.
- They can, of course, also be deleted
- Atoms or groups of atoms can be moved using mouse/keyboard or by giving the exact values.
- Groups of atoms can be rotated around their center of mass.
- Bonds, valence angles and torsion angles can be altered using the mouse/keyboard. Calculating torsion potentials has never been easier!
- The following properties can be visualised in the 3D windows:
- Element type and index
- Mulliken or stockholders charges
- Atomic forces
- An unlimited number of 3D density isosurfaces with different colors and transparency settings
- Calculations are saved in the Chemical Markup Language (CML) format, the XML-based chemistry format of the future.
- The following types of BRABO calculations can be set up:
- Single point energy
- Energy and forces
- Geometry optimization
- The calculation settings can be changed in extreme detail with an interface allowing the addition of new keywords and options. Generated input files can be reviewed before execution.
- An easy interface is provided for showing all output files created by a calculation.
- 2D electron density map files created by BRABOs Potdicht program can be visualized in high quality in a variety of ways. Regions can be analyzed for extrema in the density.
- 3D hydrogen-like orbitals can be calculated analytically for all elements and visualized using isodensity and scatter plots.
- MDI: Brabosphere can open an unlimited number of calculations and present them in the native Multiple Document Interface of each platform. One can switch between the Windows MDI mode, the UNIX Toplevel mode and the tabpage mode, even while the application is running.

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.

kfile_chemical is a set of kfile plugins for chemistry documents. It has support for XYZ, PDB, MDL mol/sd, Mol2, CML, ShelX, SMILES and CIF files.
kfile_chemical is currently in alpha stage: 1.0 will be alpha too; it will be feature complete, i.e. proving plugins kfile plugins for all files mentioned at the official chemical mime page (and a few more).
Version 2.0 will be beta, and feature a more organized set of extracted pieces of information.
Version 3.0 will be beta too, and mime magic, which is a method to detect the mime type not from the file extension, but from the content.
Verion 4.0 will be the first stable release and is aimed to be ready with Kubuntu 6.04 and KDE 4.0.
Enhancements:
- This release adds support for chemical-mime-data, thus synchronizing with the main MIME type library for chemical data.
- It also fixes QChar / QString conversion, the FSF address, and the contact email address.