Software Map

frowns is a chemoinformatics toolkit geared toward rapid development
of chemistry-related algorithms.

PyVib2 permits the automatic correlation of
vibrational motions of molecules, thereby allowing
an understanding of Raman, Raman optical activity
(ROA), infrared vibrational absorption (IR), and
vibrational circular dichroism (VCD) spectra. The
versatile representation of vibrational motions,
the visualization techniques of Raman/ROA and
IR/VCD generation in molecules, and the production
of publication quality spectra are features of
PyVib2. Output files of Raman/ROA and IR/VCD
calculations, produced with the DALTON and
Gaussian quantum chemistry packages, can be
directly opened. Files in the MOLDEN and XMol XYZ
format can be imported and exported. A variety of
formats (JPEG, TIFF, PNG, PNM, PS, PDF, animated
GIF, and FLI) are available to the user for saving
results. All the functionality is accessible via
the pyviblib class library.

QuteMol is an interactive, high-quality molecular
visualization system. QuteMol exploits the
capabilites of current GPUs through OpenGL shaders
to offer an array of innovative visual effects.
QuteMol visualization techniques are aimed at
improving clarity and an easier understanding of
the 3D shape and structure of large molecules or
complex proteins.

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 supports modeling of any
network in which interactions can take place
between nodes. Currently, development has reached
the prototype stage.

Mychem is an extension that provides a set of
functions that permit you to handle chemical data
within a MySQL database.

kfile_chemical is a set of kfile plugins for the
KDE desktop that extract metadata from chemistry
documents. This metadata can be used by desktop
search engines like Kat. It supports PDB, MDL
mol/sd, CML, ShelX, and CIF files.

PyMOlyze is a graphical program for analyzing the
results of quantum chemistry (DFT) calculations.
The following analyses are available for
user-defined molecular fragments: Mulliken
Population Analysis (MPA), C-squared Population
Analysis (SCPA), Overlap Population Analysis, and Mayer's Bond orders. Supported QM packages include Gaussian, ADF, GAMESS (US), GAMESS (UK), and PCGAMESS.

lazar (Lazy-Structure-Activity Relationships) is a
tool for the prediction of toxic activities of
chemical structures. lazar derives predictions
from databases with experimental toxicity data. It
searches in these databases for compounds with
similar structures and calculates the prediction
from their measured activities.

chemicalInventory is an intelligent tool for
managing chemical inventories. You can find
chemicals via substructure or text searches,
manage container and shelf locations, check
containers in and out, or transfer containers
between users.

Bist stands for "bidimensional structures" and is
a chemical drawing tool. It is focused on organic
chemistry, but it may be useful for chemists or
teachers as well. Bist support many of the
formalisms used to describe molecular structures
like single bond, double bond, stereospecific
bond, charges, resonance arrows, lone pairs, and
so on. It can export both PostScript and PNG
formats.

Bioclipse is a rich-client platform chemistry and
biology workbench. It provides access to many open
source bioinformatics and chemoinformatics
toolkits and has plugins for the Chemistry
Development Kit, JChemPaint, Jmol, and BioJava.