Mychem 0.8.1: more than just a bug fix

Mychem 0.8.1 has been released on 2010-09-07.

This version fix an important bug. All functions using serialized obmol type were impacted. The problem has been resolved by using the solution published by the pgchem project.

Mychem is now fully usable with MySQL 5.0 and 5.1. It should also be working with MySQL 4.1, but it has not been tested.

The bug list is now empty. I'm waiting for new providers!

chem-bla-ics: Warren DeLano and the future of PyMOL

chem-bla-ics: Warren DeLano and the future of PyMOL

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)