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Pybel 1.3 Released

2008-07-11T08:08:09Z

The version 1.3 of Pybel has been released on 2008-07-04.

Changes. The main changes are :
Additions to Pybel Molecules to take advantage of new features of the OpenBabel toolkit: make3D() for generation of 3D structures, localopt() for geometry optimisation using forcefields, addh() and removeh() for adding and removing hydrogens
The draw() method of a Molecule allows 2D structure diagram generation and depiction using an interface to OASA
Breadth-first iteration over molecules with depth information (OBMolAtomBFSIter)
Integration with cinfony , enabling data to exchanged between OpenBabel and other open source cheminformatics toolkits

Pybel. Pybel is a Python module that allow you to access the Open Babel library in your Python script. OpenBabel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.

Download. The download and the installation process of Pybel is detailed on the Open Babel website.

Open Babel 2.2.0 Released

2008-07-10T20:01:35Z

The version 2.2.0 of Open Babel has been released on 2008-07-04.

Changes. The main changes are:
Improved force fields and coordinate generation
Improved conformer searching
Enhanced plugins including molecular descriptors, filters, and command-line transformations
Many formats are improved or added, including CIF, mmCIF, Gaussian cube, PQR, OpenDX cubes, and more
An improved developer API

Open Babel. Open Babel is a community-driven scientific project including both cross-platform programs and a developer library designed to support molecular modeling, chemistry, and many related areas, including interconversion of file formats and data.

Download. The download and the installation process of Open Babel is detailed on the Open Babel website.

ChemiSQL: an Umbrella for Open Source Chemical Database Cartridges

2008-05-05T22:00:00Z

Jerome Pansanel, Ernst-Georg Schmidt and Christoph Steinbeck have founded the ChemiSQL project on SourceForge. ChemiSQL is supposed to be an umbrella project to ensure an as-similar-as-possible API for our three open source database cartridges for MySQL (Mychem, Jerome), Postgres (Pgchem, Ernst-Georg) and Oracle (Orchem, Christoph). Mychem and Orchem are SF projects whereas pgchem is hosted at http://pgfoundry.org/projects/pgchem/.

Both Pgchem and Mychem are based on OpenBabel - the existing bits of Orchem use the Chemistry Development Kit (CDK).

The discussions on API and backend are about to start on chemdb-discuss. Don't miss the chance to subscribe !

Mychem v0.5.5 Released

2008-04-11T07:07:19Z

The version 0.5.5 of Mychem has been released on 2008-04-08.

Changes. The main changes are:
2 functions added in the conversion module
A function added in the modification module
9 functions added in the property module
Bug fixes
Optimization of the Tanimoto function
Updated documentation
Fingerprint are stored as binary string

Mychem. Mychem is a chemoinformatics extension to MySQL. It add many functions for handling data (conversion, property computation, ...). You can read the following article for further information.

Download. You can download the last release of Mychem on SourceForge. A complete documentation is also available on this site.

Chemical Structures v2.1 Released

2008-01-04T13:42:13Z

The version 2.1 of Chemical Structure has been released on 2008-01-03.

Changes. The main changes are:
New style for the html pages
Many french translations added
Some spanish translations available
33 new structures (including many carbohydrates)
The structure file are named with the usual name of the structure
Bug fixes
MicroFormat support
More documentation in Python modules
All webpages are xhtml1.0-strict compliant

Chemical Structures. The Chemical Structures project aims to provide a complete set of molecular structures. The version 2.1 contains over 550 structures of organic compounds. In addition to structural data, each file contains complementary informations, like molecular weight, boiling point, melting point or InChI code. Chemical Structures is part of the Blue Obelisk Data Repository.

Download. The last version can be downloaded on this page: https://sourceforge.net/project/showfiles.php?group_id=169897

AutoDock 4.0 is released under GNU GPL

2007-11-19T15:12:02Z

News. AutoDock, the most cited docking software, is released under GNU GPL. This change occurs in version 4, released on May 7, 2007.

AutoDock. AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

AutoDock actually consists of two main programs:
AutoDock performs the docking of the ligand to a set of grids describing the target protein
AutoGrid pre-calculates these grids

In addition to using them for docking, the atomic affinity grids can be visualised. This can help, for example, to guide organic synthetic chemists design better binders.

A graphical user interface called AutoDockTools (ADT) is also available. It can be used to setup the docking experiment. Some parts of ADT are not released under GNU GPL.

Avogadro 0.2.0 Released

2007-10-29T10:03:45Z

News. The version 0.2.0 of Avogadro has been released on 2007-10-23. It's the second development release of the Avogadro project. You are encouraged to contact the development team with any questions, comments or concerns. In particular, if you would like to contribute, or find out how to use Avogadro to fit your needs, do not hesitate to contact the team !

Changes. This release includes numerous enhancements and fixes from 0.1, including lots of summer projects by students. Among the major improvements:
Enhanced rendering options: crystallographic cells, transparency, atom labels, custom rendering options
New editing tools: full periodic table, animated rotations, automatic geometry optimization, easy modification of bond lengths and angles
Improved plugin architecture, including a "painter" framework which enables POV-Ray export.
Initial internationalization support, including German and French translations.
Many, many more...

Avogadro. Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers a flexible rendering and a powerful plugin architecture.

pgchem::tigress 7.1 released

2007-08-20T07:35:29Z

The version 7.1 of pgchem::tigress has been released on 2007-08-14.

News. pgchem::tigress 7.1 is now available for download on pgfoundry.org.

Changes. Main changes include:

Cleanup of function names.
Lots of fixes.
Use of Open Babel 2.1.1.
Use of SSE for parallel fingerprint screening on x86 if available.

Open Babel: Version 2.1.1 Released

2007-07-21T11:54:57Z

The version 2.1.1 of Open Babel has been released on 2007-07-07.

News. This release represents a stable bug-fix release and is highly recommended for all users, even those who have not had problems with 2.1.0. It includes fixes for several important crashes, and many, many bug fixes and improvements.

Changes. The full release notes are availabe on:

http://openbabel.sourceforge.net/wiki/Open_Babel_2.1.1

The main changes are:
Improved scripting support, including dictionary-support for OBGenericData in pybel, casting from OBUnitCell, etc. Improved access to OBRings from OBMol.GetSSSR():
Added support for descriptors (e.g., PSA, logP) from scripting interfaces;
Added support for reading all PDB records (beyond current atom and bond connections). Records not handled directly by Open Babel are added as key/value pairs through OBPairData;
Added a new configure flag —with-pkglibdir to allow Linux package distributors to define version-specific directories for file format plugins;
Many bug fixes.

OpenBabel. Open Babel is a cross-platform program and library designed to interconvert between many file formats used in chemistry. A large range of format are supported (either in importing, exporting or the both). The command-line utility that comes with Open Babel is able to translate between various chemical file formats. The library includes the file-translation code and utilities, who permit other free chemistry software to integrate these functionalities.

PyMOL: v1.0 released

2007-07-19T08:22:46Z

The version 1.0 of PyMOL has been released on 2007-06-21.

News. PyMOL 1.0 executables are available for download by current PyMOL Subscribers. The open-source code for 1.0 is freely available from the b10 branche of the subversion repository:

svn co https://pymol.svn.sourceforge.net/svnroot/pymol/branches/b10/pymol pymol-1.0

A new version 1.x branch will be pending soon.

Changes. The main changes are:
better performances
updated numerous command entries
updated documentation
additional menus
various improvements to the sequence viewer
improved alignment functions
refactored cmd.py module
enhanced multithread support
better argument handling from the command line
many bug fixes

For more informations, see the entire ChangeLog.

PyMOL. PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is a free software available under the Python License.