[Rdkit-devel] Beta of Q2 2013 release

[Greg L. <gre...@gm...>]

Dear all,

Today I tagged the beta for the 2013.06 release in git:
*https://github.com/rdkit/rdkit/releases/tag/Release_2013_06_1beta1*

Thanks to the magic of github, this automatically creates a download link:
https://github.com/rdkit/rdkit/archive/Release_2013_06_1beta1.tar.gz

If no show-stopper bugs appear, I will do the release itself next week.
Note: because I will be traveling for the next couple of weeks, the windows
binaries for the upcoming release will likely be delayed.

Excerpts from the partially updated release notes are below.

Best Regards,
-greg

******  Release_2013.06.1 *******
(Changes relative to Release_2013.03.2)

Administrivia note:
In the course of this release cycle, development was moved over
entirely to github. The sourceforge svn repository no longer contains
an up-to-date version of the code.

Acknowledgements:
Andrew Dalke, JP Ebejer, Nikolas Fechner, Roger Sayle, Riccardo Vianello,
Yingfeng Wang, Dan Warner

Bug Fixes:
 - The docs for Descriptors.MolWt are now correct (GitHub #38)
 - Molecules coming from InChi now have the correct molecular
   weight. (GitHub #40)
 - RemoveAtoms() no longer leads to problems in canonical SMILES
   generation when chiral ring atoms are present. (GitHub #42)
 - Atom invariants higher than the number of atoms in the molecule can
   now be provided to the atom pairs and topological torsions
   fingerprinters. (GitHub #43)
 - A typo with the handling of log levels was fixed in the python
   wrapper code for InChI generation. (GitHub #44)
 - Stereochemistry no longer affects canonical SMILES generation if
   non-stereo SMILES is being generated. (GitHub #45)
 - The ExactMolWt of [H+] is no longer zero. (GitHub #56)
 - The MPL canvas now has an addCanvasDashedWedge() method. (GitHub
   #57)
 - RWMol::insertMol() now copies atom coordinates (if
   present). (GitHub #59)
 - The "h" primitive in SMARTS strings now uses the method
   getTotalNumHs(false) instead of getImplicitValence().
   (GitHub #60)
 - bzip2 files now work better with the SDWriter class. (GitHub #63)

New Features:
 - Sanitization can now be disabled when calling GetMolFrags() from
   Python (GitHub #39)
 - Bond.GetBondTypeAsDouble() has been added to the python
   wrapper. (GitHub #48)
 - The fmcs code now includes a threshold argument allowing the MCS
   that hits a certain fraction of the input molecules (instead of all
   of them) to be found. The code has also been synced with the most
   recent version of Andrew Dalke's version.
 - Atoms now have a getTotalValence() (GetTotalValence() from Python)
   method. (GitHub #61)

New Database Cartridge Features:

New Java Wrapper Features:
 - {Get,Set}Prop() methods are now available for both Atoms and
   Bonds. (GitHub #32)


Deprecated modules (to be removed in next release):

Removed modules:

Other:
 - the handling of flex/bison output files as dependencies has been
 improved (GitHub #33)