Software Map

Indigo is a universal organic chemistry toolkit. It contains tools for end users, as well as a documented API for developers. It is based on a cheminformatics library that incorporates a number of unique algorithms developed by GGA Software Services, as well as some standard algorithms well known in the cheminformatics world. The API allows developers to integrate Indigo into their C/Java/C#/Python projects.
Two Indigo-based Java GUI applications are provided: Legio (combinatorial chemistry) and chemdiff (visual comparison of two SDF or SMILES files). Three Indigo-based command line utilities written in plain C are provided: indigo-depict (molecule and reaction rendering utility), indigo-cano (canonical SMILES generator), and indigo-deco (R-Group deconvolution utility).

GKrellF@H is a GKrellM 1.2.x plugin to monitor the
Folding@Home client. It can be configured to
display the name of the molecule being folded, the
download time of the work unit, and the progress
through the work unit. It supports starting and
stopping the Folding@Home client and will
optionally run a command when a work unit
completes.

Brabosphere is a program for the 3D visualization of molecular systems
and their properties. Its name is derived from the quantum mechanical
program package BRABO, for which it acts as a graphical frontend. It can
also be used for the analysis and visualization of the data resulting
from this type of calculation, so results from some other quantum
mechanical applications will also be accepted.

PyDespike is a graphical cross-platform program
for despiking Raman and other spectroscopic data.
It supports multiple data scans per file, graph
zooming, and an easy, graphical mechanism for
removing anomalous spikes due to background noise
in Raman data.

OpenChrom provides mass spectrometric analysis of chromatographic data, in a way similar to ChemStation from Agilent Technologies. It handles data files from different LC/MS, GC/MS systems and vendors, such as (*.D) chromatograms from Agilent Technologies, Finnigan ITS40 (*.ms), NetCDF (*.cdf), MzXML (*.mzxml), and other formats. It is flexible and can be extended by plugins.

ccwatcher monitors the progress of computational chemistry calculations as they run. It has both a GUI and a command line interface to which it parses important output and plots SCF energies. It supports most computational chemistry programs via cclib.

Modama is a software project for processing and
analyzing 2D detector data (images) provided by
any available detectors, mainly SAX and WAX.

PhosphoFind locates and quantifies phosphorylated
peptides and proteins from a set of four MALDI
mass spectra run in linear positive, linear
negative, reflectron positive, and reflectron
negative modes.

ProteomeCommons.org Java Analysis Framework is a
framework for referencing common mass spectrometry
data such as atoms and residues. This framework
provides a programmer with an easy-to-use library
for writing programs that rely on common mass
spectrometry data. The framework also contains
utilities such as an isotope calculator and a
reference for residue abbreviations.

The Biomolecule Toolkit is an Open Source library
for the structural modeling of biological
macromolecules. The toolkit provides a C++
interface for common tasks in computational
structural biology, to facilitate the development
of molecular modeling, design, and analysis tools.

jsPro is a set of libraries that extend the core
Javascript classes and provide a number of
new classes. The aim is to provide a rich set of
object-based functionality to the Javascript
language.

XMDS is a code generator that integrates equations. You write them down in human readable form in an XML file, and it goes away and writes and compiles a C++ program that integrates those equations as fast as it can possibly be done in your architecture.

Chemkit is a C++ library for molecular modelling, cheminformatics, and molecular visualization.