[Rdkit-devel] 2011.06 (Q2 2011) RDKit release

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

Dear all,

I'm very happy to announce that the next version of the RDKit --
2011.06 (a.k.a Q2 2011) -- is released.

The release notes are below.

The source release is on the sourceforge downloads page:
http://sourceforge.net/projects/rdkit/files/rdkit/Q2_2011/
The files can also be downloaded from the google project page:
http://code.google.com/p/rdkit/downloads/list
The binaries for Windows and Python 2.7 are uploaded already,
I will do the Python 2.6 binaries in the next couple of days.

Thanks to the everyone who submitted bug reports and suggestions for
this release!

Please let me know if you find any problems with the release or have
suggestions for the next one.

-greg



******  Release_2011.06.1 *******
(Changes relative to Release_2011.03.2)

Acknowledgements:
 - Eddie Cao, Andrew Dalke, James Davidson, JP Ebejer, Gianluca
   Sforna, Riccardo Vianello, Bernd Wiswedel

Bug Fixes:
 - A problem with similarity values between SparseIntVects that
   contain negative values was fixed. (Issue 3295215)
 - An edge case in SmilesMolSupplier.GetItemText() was fixed. (Issue
   3299878)
 - The drawing code now uses dashed lines for aromatic bonds without
   kekulization. (Issue 3304375)
 - AllChem.ConstrainedEmbed works again. (Issue 3305420)
 - atomic RGP values from mol files are accessible from python (Issue
   3313539)
 - M RGP blocks are now written to mol files. (Issue 3313540)
 - Atom.GetSymbol() for R atoms read from mol files is now
   correct. (Issue 3316600)
 - The handling of isotope specifications is more robust.
 - A thread-safety problem in SmilesWrite::GetAtomSmiles() was fixed.
 - some of the MACCS keys definitions have been corrected
 - Atoms with radical counts > 2 are no longer always written to CTABs
   with a RAD value of 3. (Issue 3359739)

New Features:
 - The smiles, smarts, and reaction smarts parsers all now take an additional
   argument, "replacements", that carries out string substitutions pre-parsing.
 - There is now optional support for generating InChI codes and keys
   for molecules.
 - the atom pair and topological torsion fingerprint generators now
   take an optional "ignoreAtoms" argument
 - a function to calculate exact molecular weight was added.
 - new java wrappers are now available in $RDBASE/Code/JavaWrappers
 - the methods getMostCommonIsotope() and getMostCommonIsotopeMass()
   have been added to the PeriodicTable class.

New Database Cartridge Features:
 - Support for generating InChIs and InChI keys
   (if the RDKit InChI support is enabled).

Deprecated modules (to be removed in next release):
 - The original SWIG wrappers in $RDBASE/Code/Demos/SWIG are deprecated

Removed modules:

Other:
 - The quality of the drawings produced by both the python molecule drawing
   code and $RDBASE/Code/Demos/RDKit/Draw is better.
 - the python molecule drawing code will now use superscripts and
   subscripts appropriately when using the aggdraw or cairo canvases
   (cairo canvas requires pango for this to work).
 - $RDBASE/Code/Demos/RDKit/Draw now includes an example using cairo
 - A lot of compiler warnings were cleaned up.
 - The error reporting in the SMILES, SMARTS, and SLN parsers was improved.
 - the code for calculating molecular formula is now in C++
   (Descriptors::calcMolFormula())