I'm very happy to announce that the next version of the RDKit --
2012.09 (a.k.a Q3 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, Python 2.6 and Python 2.7, have also been uploaded.

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_2012.09.1 *******
(Changes relative to Release_2012.06.1)

!!!!!! IMPORTANT !!!!!!
 - Some of the bug fixes affect the generation of SMILES. Canonical
   SMILES generated with this version of the RDKit will be different
   from previous versions.
 - The fix to Issue 252 (see below) will lead to changes in calculated
   logP and MR values for some compounds.
 - The fix to Issue 254 (see below) will lead to changes in some
   descriptors and geometries for sulfur-containing compounds.
 - The fix to Issue 256 (see below) has changed the name of the
   optional argument to mol.GetNumAtoms from onlyHeavy to
   onlyExplicit. For compatibility reasons, Python code that uses
   explicitly uses onlyHeavy will still work, but it will generate
   warnings. This compatibility will be removed in a future release.

Gianpaolo Bravi, David Cosgrove, Andrew Dalke, Fabian Dey, James
Davidson, JP Ebejer, Gabriele Menna, Stephan Reiling, Roger Sayle,
James Swetnam

Bug Fixes:
- The molecules that come from mergeQueryHs() now reset the RingInfo
  structure. (issue 245)
- The output from MurckoScaffold.MakeScaffoldGeneric no longer
  includes stereochemistry or explicit Hs. (issue 246)
- D and T atoms in CTABs now have their isotope information
  set. (issue 247)
- Some problems with ring finding in large, complex molecules have
  been fixed. (issue 249)
- The "rootedAtAtom" argument for FindAllSubgraphsOfLengthN is now
  handled properly. (issue 250)
- Bonds now have a SetProp() method available in Python. (issue 251)
- A number of problems with the Crippen atom parameters have been
  fixed. (issue 252)
- Ring closure digits are no longer repeated on the same atom in
  SMILES generated by the RDKit. (issue 253)
- Non-ring sulfur atoms adjacent to aromatic atoms are no longer set
  to be SP2 hybridized. This allows them to be stereogenic. (issue
- The combineMols() function now clears computed properties on the
  result molecule.
- A couple of problems with the pickling functions on big endian
  hardware were fixed.
- The molecule drawing code now uses isotope information
- Superscript/Subscript handling in the agg canvas has been improved.
- SKP lines in CTABS are now propertly handled. (Issue 255)
- The name of the optional argument to mol.GetNumAtoms has been
  changed from onlyHeavy to onlyExplicit. The method counts the number
  of atoms in the molecular graph, not the number of heavy
  atoms. These numbers happen to usually be the same (which is why
  this has taken so long to show up), but there are exceptions if Hs
  or dummy atoms are in the graph. (Issue 256)
- Unknown bonds in SMILES are now output using '~' instead of '?'. The
  SMILES parser now recognizes '~' as an "any bond" query. (Issue 257)
- Lines containing only white space in SDF property blocks are no
  longer treated as field separators.
- Transition metals and lanthanides no longer have default valences

New Features:
- The RDKit now has a maximum common substructure (MCS) implementation
  contributed by Andrew Dalke. This is currently implemented in Python
  and is available as: from rdkit.Chem import MCS Documentation is
  available as a docstring for the function MCS.FindMCS and in the
  GettingStarted document.
- A few new functions have been added to rdkit.Chem.Draw:
  MolsToImage(), MolsToGridImage(), ReactionToImage()
- CalcMolFormula() now provides the option to include isotope
- The RDKit and Layered fingerprinters both now accept "fromAtoms"
  arguments that can be used to limit which atoms contribute to the
- Version information is now available in the Java wrapper.
- The descriptor NumRadicalElectrons is now available.
- The PyMol interface now supports a GetPNG() method which returns the
  current contents of the viewer window as an PIL Image object.
- Molecules (ROMol in C++, rdkit.Chem.Mol in Python) now have a
  getNumHeavyAtoms() method.
- Component-level grouping (parens) can be used in reaction SMARTS.

New Database Cartridge Features:
- support for molecule <-> pickle conversion via the functions
  mol_to_pkl, mol_from_pkl, and is_valid_mol_pkl.
- support for bit vector <-> binary text conversion via the functions
  bfp_to_binary_text, bfp_from_binary_text

New Java Wrapper Features:

Deprecated modules (to be removed in next release):

Removed modules:

- During this release cycle, the sourceforge project was updated to
  their new hosting system. This explains the change in bug/issue
- the SMILES parser is now substantially faster.
- The molecular drawings generated by Code/Demo/RDKit/Draw/MolDrawing.h
  have been improved.
- There is now demo code availble for using the C++ drawing code
  within Qt applications. (contributed by David Cosgrove)
- The directory $RDBASE/Regress now contains sample data and
  scripts for benchmarking the database cartridge.
- Fused-ring aromaticity is now only considered in rings of up to size
- It is no longer necessary to have flex and bison installed in order
  to build the RDKit.

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