Projects

Kalzium

claimed by KDE

Kalzium is an application which will show you some information about the periodic system of the elements. Therefore you could use it as an information database. It also includes an equation solver and 3D viewer for molecules.

The Chemistry Development Kit

The Chemistry Development Kit (CDK) is a library of Java classes for chemo-, bioinformatics, computational chemistry, and chemometrics. It provides important algorithms like substructure search, SMILES, Gasteiger charges, QSAR descriptor calculation, 3D structure generation, 2D layout and rendering, many IO formats, atom typing, and more.

Bioclipse

The Bioclipse project is aimed at creating a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). Bioclipse, as any RCP application, is based on a plugin architecture that inherits basic functionality and visual interfaces from ... [More] Eclipse, such as help system, software updates, preferences, cross-platform deployment etc. [Less]

Blue Obelisk

The Internet has brought together a group of chemists/programmers/informaticians who are driven by wanting to do things better, but are frustrated with the Closed systems that chemists currently have to work with. They share a belief in the concepts of Open Source, Open Standards and Open Data ... [More] (but not necessarily Open Access). And they express this in code, data, algorithms, specifications, tutorials, demonstrations, articles and anything that helps get the message across. [Less]

JaCuda

JaCuda is a small project which provides several mathematical function useful for a chemist or somebody working with mass specs. These functions will be executed using a cuda compatible gpu or if none is available it will fall back to the c++ implementation. If this is also not possible we will ... [More] invoke the function defined in the programming language. Which would be java/groovy for now and later python. --this project is abounded for the benefit of pycuda-- [Less]

cinfony

CinfonyCinfony presents a common API to several cheminformatics toolkits. It uses the Python programming language, and builds on top of OpenBabel, RDKit and the CDK. DocumentationThe Cinfony paper Install on Windows or Linux A complete description of Cinfony API documentation. This ... [More] documentation can also be accessed using the help command, e.g. help(cdk). Further information on Pybel and using the OpenBabel Python bindings is available on the OpenBabel wiki ExampleHere's a short example to get the juices flowing. Let's read a molecule with OpenBabel, use Webel to find out its IUPAC name, draw it with RDKit and calculate descriptor values with the CDK: C:\> cinfony # Set environment variables C:\> python Python 2.6.4 (r264:75708, Oct 26 2009, 08:23:19) [MSC v.1500 32 bit (Intel)] on win32 Type "help", "copyright", "credits" or "license" for more information. >>> from cinfony import rdk, cdk, obabel, webel >>> obabelmol = obabel.readstring("smi", "CCC") >>> print webel.Molecule(obabelmol).write("iupac") "PROPANE" >>> rdkmol = rdk.Molecule(obabelmol) >>> rdkmol.draw(show=False, filename="propane.png") >>> print cdk.Molecule(rdkmol).calcdesc() {'chi0C': 2.7071067811865475, 'BCUT.4': 4.4795252101839402, 'BCUT.5': 5.14569107 34650307, 'BCUT.2': -0.17199466342172476, 'BCUT.3': 0.048131793579068549, 'BCUT. 0': 11.889999999999995, 'BCUT.1': 12.110018178813911, 'rotatableBondsCount': 2, 'mde.9': 0.0, 'mde.8': 0.0, 'mde.3': 0.0, 'mde.2': 0.0, ... } [Less]

chemojava

ChemoJava is a project based on the Chemistry Development Kit (LGPL). It aggregates chemoinformatics functionality which itself is license GPL, but using the CDK APIs. It is not aimed at replacing the CDK, but complementing it with unique functionality, possibly from originally other projects, which is not available from the CDK itself.

sqlmol

中文介绍 The long-term goal of this project is to provide chemical molecule handling functions in SQL, for all common RDBMS platforms. Currently it is implemented in T-SQL and tested under MS SQL Server express 2008. Currently featuresThe paper Chemical Substructure Search in SQL (Adel ... [More] Golovin and Kim Henrick) shows a method to store chemical molecule graph in Relational Database Management Systems (RDBMS) and query by substrucure without cartridge installed on the database. That means the whole chemical registry system and the structure query is processed on pure SQL environment. SQLMOL currently provides SQL functions as a SMILES parser to transform the SMILES string into bond table. That helps Transforming and importing molecule graph data into RDBMS as atoms and bonds table. Parsing substructure query with SMILES and building SQL query string. Please see the Brief Introduction and Demos. And a demo web interface in ASP.NET A installation guide is also provied. THIS PROJECT IS STILL IN BETA, there're still Known Issues. Welcome contact me, zh.charlie@gmail.com [Less]

pharmaforge

The PharmaForge.NET Framework is an open source .NET (C#) framework for software developers within the pharmaceutical and life science industries. A large portion of the software products developed for the pharmaceutical industry are commercial. However, over the last few years there has been a ... [More] significant number of open source software projects created. Most of these open source software projects have been developed with a variety of programming languages using the traditional open source tools. Though, very few open source projects in the pharmaceutic world have been developed using Microsoft's .NET Framework. This project's goal is to give the life sciences .NET developer an opportunity to participate in the open source community. The framework may contain libraries for the following areas within the Pharmaceutical industry: Cheminformatics Chemometrics Bioinformatics Lab Automation Molecular Modeling Please note that this is the very beginning stage for this project. If you have interest software development in just about any area within the pharmaceutical industry and would like to contribute or become a member of this project please contact me through our PharmaForge Discussion Group. [Less]

qsardb

QSAR DataBank (or QsarDB for short, or QDB for the shortest) is an emerging proposal for the electronic organization and archiving of QSAR/QSPR model information. The QsarDB specification is available at http://www.qsardb.org