I'm very happy to announce that the next version of the RDKit --
2012.12 (a.k.a Q4 2012) -- is released.

The release notes are below.

The source release is on the sourceforge downloads page:
The files can also be downloaded from the google project page:
The binaries for Windows, 32bit Python 2.7, have also been uploaded.
If there's demand, I can also provide 32bit Python 2.6 binaries or
64bit Python 2.7 binaries.

The online version of the documentation at rdkit.org has been updated.

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.


******  Release_2012.12.1 *******
(Changes relative to Release_2012.09.1)

Andrew Dalke, James Davidson, Robert Feinstein, Nikolas Fechner,
Nicholas Firth, Markus Hartenfeller, Jameed Hussain, Thorsten Meinl,
Sereina Riniker, Roger Sayle, Gianluca Sforna, Pat Walters, Bernd

Bug Fixes:
 - Using parentheses for zero-level grouping now works in reaction
   SMARTS. This allows intramolecular reactions to be expressed.
 - SMILES generated for molecules with ring stereochemistry
   (e.g. N[C@H]1CC[C@H](CC1)C(O)=O) are now canonical. (issue 40)
 - SKP lines in a CTAB property block are now properly handled. (issue
 - The molecular drawing code now shows dotted lines for Any bonds.
   (issue 260)
 - ROMol::debugMol() (ROMol.DebugMol() in Python) now reports isotope
   information. (issue 261)
 - The molecular drawing code now correctly highlights wedged bonds.
   (issue 262)
 - RWMol::addAtom() now adds atoms to conformers.
   (issue 264)
 - TDT files with atomic coordinates now have those coordinates in the
   correct order. (issue 265)
 - A ring-finding error/crash has been fixed. (issue 266)
 - Dummy atoms now have a default valence of 0 and no maximim
   valence. (issue 267)
 - The Python code no longer throws string exceptions. (issue 268)
 - Invalid/unrecognized atom symbols in CTABs are no longer
   accepted. (issue 269)
 - Chem.RDKFingerprint now accepts atom invariants with values larger
   than the number of atoms. (issue 270)
 - The code should now all work when the locale (LANG) is set to
   values other than "C" or one of the English locales. (issue 271)
 - Two-coordinate Hs are no longer removed by
   MolOps::removeHs(). (issue 272)
 - R groups read from CTABs are now marked using setIsotope() instead
   of setMass(). (issue 273)
 - Hs present in the molecule graph no longer incorrectly impact
   substructure matches. (issue 274)
 - Murcko decomposition of molecules with chiral ring atoms now
   works. (issue 275)
 - Methane now shows up in molecular drawings. (issue 276)
 - '&' in SLN properties is now correctly handled. (issue 277)
 - Molecules with string-valued molAtomMapNumber atomic properties can
   now be serialized. (issue 280)
 - SMARTS strings containing a dot in a recursive piece are now
   properly parsed. (issue 281)
 - The SMILES and SLN parsers no longer leak memory when sanitization
   of the result molecule fails. (issue 282)
 - The cairo canvas drawing code now works with PIL v1.1.6 as well as
   more recent versions.

New Features:
 - RDKit ExplicitBitVects and DiscreteValueVects can now be directly
   converted into numpy arrays.
 - Rogot-Goldberg similarity has been added.
 - C++: BitVects and SparseIntVects now support a size() method.
 - C++: DiscreteValueVects now support operator[].
 - An initial version of a SWIG wrapper for C# has been added.
 - Support for easily adding recursive queries to molecules and
   reactions has been added. More documentation is required for this
 - To allow more control over the reaction, it is possible to flag reactant
   atoms as being protected by setting the "_protected" property on those
   atoms. Flagged atoms will not be altered in the reaction.
 - Atoms and Bonds now support a ClearProp() method from python.
 - The new Python module rdkit.ML.Scoring.Scoring includes a number of
   standard tools for evaluating virtual screening experiments: ROC
   curve generation, AUC, RIE, BEDROC, and Enrichment.
 - The function RDKit::Descriptors::getCrippenAtomContribs()
   (rdkit.Chem.rdMolDescriptors._CalcCrippenContribs() from Python)
   can now optionally return atom-type information as ints or text.

New Database Cartridge Features:
- The Chi and Kappa descriptors are now available

New Java Wrapper Features:
- The Chi and Kappa descriptors are now available

Deprecated modules (to be removed in next release):

Removed modules:
- The old SWIG wrapper code in $RDBASE/Code/Demos/SWIG has been
  removed. The SWIG wrappers are now in $RDBASE/Code/JavaWrappers

- The C++ code for drawing molecules previously found in
  $RDBASE/Code/Demos/RDKit/Draw has been moved to
- Calculation of the Chi and Kappa descriptors has been moved into
- To make builds easier, the thread-safety of the recursive-smarts
  matcher has been made optional. The build option is
- There are two new entries in the Contrib directory:
  * Contrib/PBF : An implementation of the Plane of Best Fit
    contributed by Nicholas Firth.
  * Contrib/mmpa : An implementation of GSK's matched molecular pairs
    algorithm contributed by Jameed Hussain
- A new "Cookbook" has been added to the documentation to provide
  a collection of recipes for how to do useful tasks.

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