Free chemistry articles software for linux

Chemistry::Artificial::Graphics is a graphic plot for artificial with database support.

SYNOPSIS

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

my $dbname = $ARGV[0];
my $chaname = $ARGV[1];
my $file = $ARGV[2];
my $mode = $ARGV[3];

if (scalar(@ARGV)!=4)
{ print "Error in parameter number n";
print "perl chaplot.pl DB_NAME
CHA_NAME FILE_NAME MODE (svg | svg_static | text)n";
exit;
}
my $db1 =
Chemistry::SQL->new(db_host=>"127.0.0.1",db_user=>"root",db_port=>"3306",sb_pwd=>"",db_name=>"$dbname",db_driver=>"mysql");
$db1->connect_db;
my $pcha = Chemistry::Artificial::Graphics->new(db => $db1, width=> "800",height=>"600",radius=> "10",distanceh=>"200",file=> $file,
mode=> $mode);
$pcha->ch_plot("$chaname");

This package, along with Chemistry::SQL, includes all the necessary to generate graphics of the artificial chemistry in database.

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).

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.

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.

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.

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

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

News::Archive is a Usenet news archiving package for downloading and later accessing news articles in bulk.

It can load articles laid out in INN format, retrieve them from a running news server, or just take articles one-by-one. News::Archive module is compatible with News::Web and Net::NNTP::Server, so the articles can be shared either via the Web or via NNTP.

SYNOPSIS

use News::Archive;
my $archive = new News::Archive
( basedir => /home/tskirvin/kiboze );

# Get a news article
my $article = News::Article->new(*STDIN);
my $msgid = article->header(message-id);

die "Already processed $msgidn"
if ($archive->article( $messageid ));

# Get the list of groups were supposed to be saving the article into
my @groups = split(s*,s*, $article->header(newsgroups) );
map { s/s+//g } @groups;

# Make sure were subscribed to these groups
foreach (@groups) { $archive->subscribe($_) }

# Actually save the article.
my $ret = $archive->save_article(
[ @{$article->rawheaders}, , @{$article->body} ], @groups );
$ret ? print "Accepted article $messageidn"
: print "Couldnt save article $messageidn";

News::Archive keeps several files to keep track of its archives:

active file

Keeps track of all newsgroups we are "subscribed" to and all of the information that changes regularly - the number of articles we have archived, the current first and last article numbers, etc.

Watched over with News::Active.

history database

A simple database keeping track of articles by Message-ID. Makes access by ID easy, and ensures that we dont save the same article twice. The database chosen to maintain these is user-determined.

newsgroup file

Keeps track of more static information about the newsgroups we are subscribed to - descriptions, creation dates, etc.

Watched over with News::GroupInfo.

archive directory

Directory structure of all articles, with each article saved as a single textfile within a directory structure laid out at one section of the group name per directory, such as "rec/games/mecha". Crossposts are hardlinked to other directory structures.

Articles are actually divided into sub-directories containing up to 500 articles, to avoid Unix directory size performance limitations. Individual files are thus stored in a file such as "rec/games/mecha/1.500/1".

Each newsgroup also contains overview information, watched over with
News::Overview. This overview file goes in the top of the structure,
such as "rec/games/mecha/.overview".

You may note that these files are very similar to how INN does its work. This is intentional - this package is meant to act in many ways like a lighter-weight INN.

Usage:

Global Variables

The following variables are set within News::Archive, and are global throughout all invocations.

$News::Active::DEBUG
Default value for "debug()" in new objects.

$News::Active::HOSTNAME
Default value for "hostname()" in new objects. Obtained using
"Sys::Hostname::hostname()".

$News::Active::HASH
The number of articles to keep in each directory. Default is 500;
change this at your own peril, since things may get screwed up later
if you change it after archiving any articles!