RDKit Files

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

Acknowledgements:
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
Wiswedel 

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
   255)
 - 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
   feature.
 - 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

Other:
- The C++ code for drawing molecules previously found in
  $RDBASE/Code/Demos/RDKit/Draw has been moved to
  $RDBASE/Code/GraphMol/MolDrawing
- Calculation of the Chi and Kappa descriptors has been moved into
  C++.
- To make builds easier, the thread-safety of the recursive-smarts
  matcher has been made optional. The build option is
  RDK_BUILD_THREADSAFE_SSS. 
- 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.