Alchem.org

Mychem 0.7.0 released

2009-10-14T17:22:14Z

The version 0.7.0 of Mychem has been released on 2009-09-30.

Changes. This release represents a major bug-fix release and is a stable upgrade, strongly recommended for all users of Mychem. While there may not be many new functions, several crashes and other bugs have been fixed since 0.6.0. The main changes are:
Added the mol2_to_molecule() function
Added the molecule_to_mol2() function
Added the inchi_version() function
Added the pdb_to_molecule() function
Added the molecule_to_serializedOBMol() function
Added the serialized OBMol type
The code has been entirely rewritten
The documentation has been updated
Several bug fixes and small feature improvements

Mychem. Mychem is a chemoinformatics extension to MySQL. It add many functions for handling data (conversion, property computation, ...). You can find more informations on the Mychem Home Page.

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

Bioclipse 2.0 released

2009-07-15T08:24:51Z

The version 2.0 of Bioclipse has been released on 2009-07-09.

Changes and Features. This release is a major release and they are many changes. Some major components include a brand new chemical editor for SWT (JChemPaint), interactive 3D visualization of molecules (Jmol), a Molecules Table capable of reading large files, and a powerful backbone in cheminformatics provided by the Chemistry Development Kit (CDK) library.

Bioclipse. Bioclipse is a free, open source workbench for the life sciences that provides advanced functionality mainly in cheminformatics (bioinformatics is planned for version 2.1 later this summer).

Bioclipse is a Rich Client for the life sciences that provides the means to run and integrate algorithms and tools in disconnected state, while still taking advantage of remote services if a network connection is available. Built on the famous Eclipse framework, Bioclipse delivers a state-of-the-art plugin architecture which makes it possible to extend it in any direction.

There is much ongoing work with Bioclipse and new features are constantly added. Please visit the Bioclipse Wiki in order to get the latest information regarding the development.

Download. Bioclipse is available for download from Sourceforge.

Open Babel 2.2.2 released

2009-07-14T22:00:00Z

The version 2.2.2 of Open Babel has been released on 2009-07-10.

Changes. This release represents a major bug-fix release and is a stable upgrade, strongly recommended for all users of Open Babel. While there may not be many new features, many crashes and other bugs have been fixed. The main changes and fixes are:
Upgraded to the new InChI 1.02 release to produce standardized InChI and InChIKey output.
Fixed many stereochemistry errors when reading/writing SMILES. This is part of a larger project which will be finished in the 2.3 release.
Fixed compilation and installation on Cygwin and MinGW platforms.
Significantly improved aromaticity and Kekule bond assignment.
Improved 2D -> 3D coordinate generation
Improved coordinate generation using the —gen3d command-line operation
Improved performance for coordinate generation.
New —fillUC command-line operation for babel.
Fixes to pH-dependent hydrogen addition.
Added support for reading vibrational data from Molden, Molpro, and NWChem output files.
Updated atomic radii from recent theoretical calculations.
Fixed bug when reading gzip-compressed Mol2 or XML files.
Close files after an error. Fixes a bug with Pybel where files would remain open.
Many more bug fixes and small feature improvements.
New file formats (Molpro and VASP coordinates file).

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. Open Babel is available for download from SourceForge.

Chemical Structures 2.2.0 released

2009-07-09T22:00:00Z

The version 2.2.0 of Chemical Structure has been released on 2009-07-08.

Changes. This release is a stable upgrade and provides several enhancement. The main changes and fixes are:
Traditional Chinese translation added
New compound categories:
- Natural products
- Peptides
New structures added:
- 4-Aminobutanoic acid
- Tetrahydropyran
- Pyrrol-2-one
- 1,5-Dihydro-2H-pyrrol-2-one
- Norepinephrine
- Coelenterazine
- D-Luciferin.
- R-Adrenaline
- Aspartame
New version of Jmol included (v11.6.25)
The license and contributions notices have been added to the HTML pages
The build system has been updated. The out-of-source build is now supported.
Compounds and directories are now sorted by alphabetic order
Several bug fixes

Chemical Structures. The Chemical Structures Project provides a set of molecular structures. Each structure is stored in a CML file, that contains the 3D coordinates and some properties of the chemical compound. The project provides also a HTML interface for accessing the data. Two types of archive are available to download:
a source archive, that contains only CML files and tools for building the HTML files
a binary archive, that contains the HTML files and the structure as CML and MOL files.

Download. The last version of Chemical Structures can be downloaded from SourceForge.

Open Babel 2.2.1 released

2009-03-22T13:30:16Z

The version 2.2.1 of Open Babel has been released on 2009-03-02.

Changes. This release represents a major bug-fix release and is a stable upgrade, strongly recommended for all users of Open Babel. The main changes and fixes are:
Improved scripting interfaces, including Python 3 support and improved Java and C# support.
Added support for MACCS fingerprints. Thanks to the RDKit project.
Many fixes and enhancements to the force field code. In particular, the UFF force field implementation should handle many more molecules.
Improved 3D coordinate generation, particularly with ring fragments. You can give this a try with the obgen utility.
Fixed a variety of PDB import errors with atom types.
Added support for reading charges and radii from PQR file formats.
Added support for reading and writing unit cells in PDB formats.
New "output" file format for taking generic ".out", ".log", and ".dat" files and reading with appropriate file type based on contents. Currently works extremely well for quantum chemistry packages.
Added improved error handling and reporting when unable to load file formats.
Improved CIF file format support.
Many, many, many additional bug fixes and small enhancements.

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

Mychem v0.6.0 Released

2009-01-04T15:19:00Z

The version 0.6.0 of Mychem has been released on 2008-12-30.

Changes. The main changes are:
2 functions added in the conversion module
3 functions added in the molmatch module
Bug fixes
Updated documentation
Default molecule type is MDL Molfile
Works with Open Babel v2.1.1 and v2.2.0

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.

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

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

2008-04-10T22:00:00Z

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

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