Free chemistry answers software for linux

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.

Chemtool project is a small program for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11.
Chemtool relies on transfig by Brian Smith for postscript printing and exporting files in PicTeX and EPS formats. Its companion program, XFig, is recommended for enhancing the output of chemtool, and for creation of 2D diagrams and schematics in general.
Both are included with most distributions of Linux, and are available through a number of websites including www.xfig.org. If you want to import chemtool drawings into word processing programs other than LaTeX, you will probably want to add a preview bitmap to them, as neither StarOffice/OpenOffice nor that software from Redmond seem to be able to display postscript inserts on screen without them.
For this purpose, using either ps2epsi, which comes with ghostscript, or epstool, a part of gsview is recommended. Since chemtool-1.6, this option is supported directly (through the equivalent function offered by recent versions of transfig).
Chemtool was originally written by Thomas Volk, then a student of chemistry and biology at the university of Ulm, Germany. His version, which was described in an article in the german periodical LinuxMagazin, was using plain X11.
The bond types available in chemtool are:
- a single bond
- a double bond (with one line shorter than the other)
- a double bond (having the shorter line on the opposite side)
- a centered double bond
- a triple bond (with the flanking lines shorter than the center)
- a wedge-shaped bond
- a dashed wedge-shaped bond
- a wavy line
- a dashed wide line
- a half arrow
- an arrow
- a wide bond
- a circle
- a dotted line
- a single bond that cuts out a segment from any bond it crosses
- a triple bond (with equal line lengths)
- a quadruple bond
Enhancements:
- PNG export, kprinter support, and a few new template structures were added.
- Screen rendering of complex labels was improved.
- Several problems with text input in UTF8-enabled locales were fixed.
- Arrowhead size in EPS output and the appearance of arrowheads, superscripts, and national characters in SVG output were fixed.

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Ghemical is a computational chemistry software package released under the GNU GPL. It means that full source code of the package is available, and users are free to study and modify the package. Ghemical is written in C++.
Ghemical project has a graphical user interface (which is based on GNOME), and it supports both quantum-mechanics (semi-empirical and ab initio) models and molecular mechanics models (there is an experimental Tripos 5.2-like force field for organic molecules). Also a tool for reduced protein models [1] is included. Geometry optimization, molecular dynamics and a large set of visualization tools are currently available.
Ghemical relies on external code to provide the quantum-mechanical calculations. Semi-empirical methods MNDO, MINDO/3, AM1 and PM3 come from the MOPAC7 package (Public Domain), and are included in the source distribution.
The MPQC package (GNU GPL) is used to provide ab initio methods: the methods based on Hartree-Fock theory are currently supported with basis sets ranging from STO-3G to 6-31G**.
The MPQC code is not included in the source distribution. In order to use the MPQC-based ab initio methods in Ghemical, you must first compile and install the MPQC program for your system, and then compile Ghemical using some specific settings that link the programs together; see the INSTALL file for more information. Ghemical also contains the OpenBabel package for import and export of many different file formats (as well as other tasks).
Installation
Once you have downloaded the latest release, you should extract all files from your archive file using "tar -zxvvf ghemical-1.00.tgz" or equivalently "gunzip ghemical-1.00.tgz; tar -xvvf ghemical-1.00.tar". After that please read the "INSTALL"-file you just extracted to get additional information.
Enhancements:
- bug fixes

Net::DNS::TestNS is a Perl extension for simulating simple Nameservers.

SYNOPSIS

use Net::DNS::TestNS;

ABSTRACT

Class for setting up "simple DNS" servers.

Class to setup a number of nameservers that respond to specific DNS queries (QNAME,QTYPE) by prespecified answers. This class is to be used in test suites where you want to have servers to show predefined behavior.

If the server will do a lookup based on QNAME,QTYPE and return the specified data. If there is no QNAME, QTYPE match the server will return a SERVFAIL.

A log will be written to STDERR it contains time, IP/PORT, QNAME, QTYPE, RCODE