The version 0.7.0 of Mychem has been released

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

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

The version 2.2.0 of Chemical Structures is released!

The Chemical Structures Project
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.

For a better overview, look at the online version!

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

As this project is Free Software, it can be freely downloaded from the SourceForge repository!

chem-bla-ics: Bioclipse-JChemPaint

Les équipes de développement CDK à l'université d'Uppsala et à l'EBI ont travaillé intensivement à la ré-écriture de JChemPaint. La nouvelle version est maintenant stable et devrait être prochainement annoncée officiellement. Ci-dessous, le lien vers l'annonce sur le blog d'Egon Willighagen, l'un des fondateurs du projet CDK :
chem-bla-ics: Bioclipse-JChemPaint

Mychem v0.6.0 is Released !

The version 0.6.0 of Mychem has been released on 2008-12-30. The main changes are:

• New functions:
  
  
  
  • bit_fp_or
  
  
  • bit_fp_count
  
  
  • bit_fp_and
  
  
  • molecule_to_inchi
  
  
  • inchi_to_molecule


• Bug fixes


• Updated documentation


• Molecule type is now MDL Molfile


• Works with Open Babel v2.1.1 and v2.2.0.

Two versions of Mychem are now available:

• Mychem² - Designed for Open Babel v2.1.1.


• Mychem³ - Designed for Open Babel v2.2.0.

Major fix in Mychem

A major bug has been fixed into Mychem. Fredrik Wallner has posted the main patch.
In some case, the return value of Mychem functions was blank and no error were raised.
Fredrik Wallner has founded that setting a character at the end of the string to '\0' fixes this issue.

The old code:
const char *inputMol = args->args[0];

The new code:
char *inputMol = (char *) malloc(sizeof(char)*(args->lengths[0]+1));
strncpy(inputMol, args->args[0], args->lengths[0]);
inputMol[args->lengths[0]] = 0;

This indicates that the character string given by MySQL as parameter does not contains the '\0' character at the end.

Many thanks to Fredrik Wallner !

The road is now open to go to the next release (0.6.0)

Mychem works on Windows XP

After some works on the source files and tuning Microsoft Visual Express C++, I'm proud to announce that Mychem is working on Microsoft Windows XP.

The Microsoft Windows version of Mychem will be released soon. The Mychem documentation will also contain a section about the compilation and the installation of Mychem on Windows XP.

New release of Mychem

The version 0.5.5 of Mychem has been released on 2008-04-08. The main changes are:

• New functions:
  
  
  
  • strip_salts
  
  
  • molecule_to_canonical_smiles
  
  
  • is_2D
  
  
  • is_3D
  
  
  • is_chiral
  
  
  • number_of_rings
  
  
  • number_of_acceptors
  
  
  • number_of_donors
  
  
  • molpsa
  
  
  • molmr
  
  
  • mollogp
  
  
  
  


• Bug fixes


• Updated documentation

The Tanimoto function has been enhanced by two methods. The first was to store the
fingerprint as binary string. The second was to implement directly the tanimoto algorithm. Now, the Tanimoto coefficient computation of more than 70.000 entries takes less than 0.4 second on my laptop.

At least, a short article has been published about Pgchem and Mychem on Alchem.org.