Free chemistry software for linux

GenChemLab is an OpenGL-based application intended to simulate several common general chemistry exercises. It is meant to be used to help students prepare for actual lab experience. It could also be used in cases where laboratory facilites are not accessible, for instance in K-12 schools or home schooling.

At present, supported experiments include titration, calorimetry, freezing point depression, vapor pressure, and spectrophotometry.

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.

Whats New in This Release:

+ Reserved VLANs (1000 < VLAN < 1025) on Cisco devices are not queried.
+ Capture packets to trace.pcap and perform a hexdump of them in the log file
if DEBUG_PACKET is set (debug=0x01 or better).
+ Promiscuous mode testing is disabled unless ENABLE_SCAN_PROMISC is defined.
+ The switch/network scanning interval was bumped up to 24 hours.
+ Attribute data in the EvidenceMap wasnt being printed out correctly (always showed
up as "true") when issuing "device detail" commands in the CLI.
+ Ignore MACs in the bridge table that arent "learned" when querying switches.
+ *TAnalysisManager::LookupOrCreateDevice() will now refuse to create devices outside
"home_net" ranges, thus the IPs wont be scanned even if they are passively observed
on the local network.
+ Ignore our MAC address if a switch reports it to us.
+ Log timestamps are now in GMT.
+ Prevent duplicates in the "udp_ports" evidence by using AddEvidence() instead of
inserting into the EvidenceMap directly.
+ Manually invoke Rubys garbage collector after scanning a switch/router.
+ Added "packet queue size" CLI command to show how many packets are in the
AnalysisManagers packet queue.
+ If a device fails to be classified the classification will be retried automatically
in one minute.
+ All communication with the classification server is performed in a separate thread.
+ Keep ARP scanning from starving other threads for CPU time by introducing a delay
in addition to any that is added by bandwidth throttling.
+ Replaced internal ARP and routing table on WIN32 systems with functions from the
IPHelper API.
+ Added "device list size" command to show how many devices have been found.
+ Add read community strings from configured infrastructure devices to the list
of strings used when probing unknown devices.
+ Discard deferred scans if another scan of the same type is already deferred for
a device.
+ Added reporting of DHCP data.
+ If no scans are pending against a device, but a new port is found open then
submit the devices evidence.
+ Devices are re-scanned whenever a re-occuring ARP/Ping scan is launched.
+ Added "deferred list" CLI command to show scans that have been deferred.
+ Added "sniffer status" CLI command to report the number of packets that
have been received and dropped.
+ If we discover the IP of a device that we only knew about the MAC address for,
then issue scans against it.
+ If we see the MAC address associated with an IP change, then re-scan it since
its likely to be a different device.

Molecular Workbench project is a piece of free, open-source modeling software specifically designed for use in education. Powered by a set of real-time molecular simulation engines that compute and visualize the motion of particles interacting through force fields, in both 2D and 3D, it provides a simulation platform for teaching and learning science.
Many abstract concepts in physics, chemistry and biology can be dynamically visualized, and virtual experiments based on molecular simulations can be designed, limited only to your imagination.
The MW software consists of:
- a set of model builders, simulators and their associated scripting environments.
- a word processor for creating hypertext.
- an authoring system for constructing your own graphical user interfaces for your own simulations.
- an embedded-assessment system that allows you to design your own questions and collects student data.
- a special browser for you to deliver and for the users to access stuff created using the above sub-systems.
- Web services for collaboration among authors, students and teachers.
All these sub-systems are seamlessly integrated behind an easy-to-use graphical user interface. The customizability of models through the authoring system allows you to design user interfaces appropriate to your audience, without having to get them involved in the complexity of the modeling engines.

XDrawChem is a two-dimensional molecule drawing program for Unix operating systems. XDrawChem is similar in functionality to other molecule drawing programs such as ChemDraw (TM, CambridgeSoft).
It can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry applications, and it can create images in popular formats like PNG and EPS. XDrawChem has been tested on Linux, SGI IRIX 6.5, Sun Solaris, Mac OS X, and Windows.
Main features:
- 100% compatible Windows 95/98/NT version
- Fixed length, fixed angle drawing.
- Automatic alignment of figures. Detects structures, text, and arrows and places them automatically.
- Can automatically draw rings and other structures - has all standard amino acids and nucleic acids in built-in library.
- Can retrieve structures from a network database based on CAS number, formula, or name.
- Can draw symbols such as partial charge, radicals, etc.
- Can read MDL Molfiles, CML [Chemical Markup Language, defined in J. Chem. Inf. Comput. Sci.39(1999), 928-942], ChemDraw(TM) binary format, ChemDraw(TM) XML text format.
- Can write MDL Molfiles, CML, ChemDraw(TM) XML text format.
- Can also read and write any format supported by the current release of OpenBabel.
- Can export pictures in PNG, Windows bitmap (*.bmp), Encapsulated PostScript (EPS), and Scalable Vector Graphics (SVG).
- Can generate 3-D structures with the help of the external program BUILD3D.
- Online help, including tool tips.
- 13C-NMR prediction, based on Bremser W, Mag. Res. Chem.23(4):271-275
- 1H-NMR prediction, based on additive rules and functional group lookup methods, described in Pretsch, Clerc, Seibl, Simon, "Tables of Spectral Data for Structure Determination of Organic Compounds", 2ed., 1989, Springer-Verlag
- Simple IR prediction.
- Simple pKa estimation.
- Octanol-water partition coefficient estimation.
- Reaction analysis: gas-phase enthalpy change estimate, 1H NMR and 13C NMR comparison.
- Integration with OpenBabel, allowing XDrawChem to read and write over 20 different chemical file formats.

PyDespike is a program to graphically process (ie. despike) Raman and other spectroscopic data. Removing spikes in data due to artificial background fluctuations can be a tedious and time-consuming process, and since no other software with these requirements was known to exist, PyDespike was created to make Raman data processing more efficient.

PyDespike is the brain child of Michael Vance (Department of Chemistry, Stanford University) and much thanks is given to him for supporting the development of a scientifically useful project and providing valuable feedback to the graphical interface of PyDespike in its beta stages.

It was written using python and the python extensions to Qt and Qwt (PyQt and PyQwt), and thus, is cross-platform. PyDespike application has only been tested on Gentoo Linux and Windows XP, but there is no reason for it not to be supported on any platform with python, PyQwt, and PyQt.

SimSoup is a graphical Artificial Chemistry simulator for Linux and Windows.
The program enables a Chemistry to be defined in terms of Molecule Types and the possible Interactions between them. A simulation run involves setting up a number of Molecules of various Molecule Types in a Reactor, and then allowing Interactions to take place over a period of time. Interactions taking place in the Reactor are shown on a graphical display.
The motivation for development of the program is to enable investigations into the behaviour of networks, particularly in relation to metabolism first theories of the origin of life, although the basic design of SimSoup supports modelling of any network in which interactions can take place between nodes.
Currently, SimSoup development has reached prototype stage.
Enhancements:
- A Chemistry including Molecule Types and Interaction Types
- A Reactor in which Interactions take place between Molecules
- Graphical views of the Chemistry and Reactor. Interactions taking place in the Reactor are displayed in real time
- Display of Simulation Statistics in real time. Statistics can be displayed in two formats:-
- Data Series Plots: These show the real-time behaviour of a range of variables that are monitored as the simulation runs. The Data Series to be displayed are selectable from a list
- Manhattan Plot: This shows the amount of variability in the composition of the material in the Reactor.
- Simulation Control facilities, including the ability to use Predefined Scenarios to control the operation of the simulation, and a facility enabling Action Requests to be setup to customise Predefined Scenarios or create user defined scenarios.
- A (partly hidden) System Monitor screen - mainly for diagnostic purposes
SimSoup has an object oriented design.The main benefit of this is that it allows concepts such as Molecule and Interaction Type to be represented as self contained units in the program. This makes understanding the code easier, and therefore improves maintainability of the code.
I use techniques such as inheritance and polymorphism sparingly, but they are used in the case of the Interaction Types listed above. All eight Interaction Types are variants derived from a base Interaction class. As a result of this approach, implementation of the six Interaction Types not yet completed should be relatively straightforward.
SimSoup is a cross platform C++ program for Linux and Windows. It has been compiled and linked using the Borland products Kylix 3 Open Edition (Linux) and C++ Builder 6 Personal (Windows). The KDE product KDevelop has been used for code navigation and editing. The code makes considerable use of the C++ Standard Template Library (STL). I believe that the benefits of using this library more than justify the effort required to learn the STL basics.
This source code distribution includes the Kylix code only. The cross platform code enables SimSoup to be compiled and linked using both Kylix and C++ Builder. If possible, a future distribution will include the cross platform code enabling out of the box compilation using C++ Builder on Windows as well as Kylix.
The user interface is relatively basic, but I have tried to make it as intuitive as possible. Its worth looking at Help | Quick Start for notes on editing Interaction Types in the Chemistry view.
Installation
Your system needs to have X installed. SimSoup runs on both KDE and Gnome, but also runs fine on lighter window managers such as WindowMaker.
Extract from the file SimSoup-0.1-i386-pc-linux-tar.gz to a directory of your choice. Now copy the file libborqt-6.9.0-qt2.3.so to a library directory on your system. On SuSE 8.1 the directory /usr/lib can be used.
If for some reason the above does not work, or you want to try SimSoup without copying the file to a system directory, then you can get started by copying the file libborqt-6.9.0-qt2.3.so to any directory of your choice (eg /home/chris/libs) and then typing the following at a bash prompt
LD_LIBRARY_PATH=/home/chris/libs
export LD_LIBRARY_PATH
You can now run SimSoup. Using the -ns command line option (./SimSoup -ns) will run the program without the startup message.

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.

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.