RDKit Files

******  Release_2012.06.1 *******
(Changes relative to Release_2012.03.1)

!!!!!! 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.
 - Due to changes in the cartridge indexes on molecule and bitvector
   fingerprint columns will need to be rebuilt.

Acknowledgements:
Andrew Dalke, JP Ebejer, Igor Filippov, Peter Gedeck, Jan Holst
Jensen, Adrian Jasiński, George Papadatos, Andrey Paramonov, Adrian
Schreyer, James Swetnam

Bug Fixes: 
 - Radicals are now indicated in molecular depictions. (Issue 3516995)
 - Calling .next() on an SDMolSupplier at eof no longer results in an
   infinite loop. (Issue 3524949)
 - Chirality perception no longer fails in large molecules.
   (Issue 3524984)
 - problem creating molblock for atom with four chiral nbrs
   (Issue 3525000)
 - A second sanitization leads to a different molecule.
   (Issue 3525076)
 - can't parse Rf atom in SMILES
   (Issue 3525668)
 - generates [HH2-] but can't parse it
   (Issue 3525669)
 - improper (re)perception of 1H-phosphole
   (Issue 3525671)
 - ForwardSDMolSupplier not skipping forward on some errors
   (Issue 3525673)
 - SMILES/SMARTS parsers don't recognize 0 atom maps
   (Issue 3525776)
 - R group handling in SMILES
   (Issue 3525799)
 - Canonical smiles failure in symmetric heterocycles
   (Issue 3526810)
 - Canonical smiles failure with "extreme" isotopes
   (Issue 3526814)
 - Canonical smiles failure with many symmetric fragments
   (Issue 3526815)
 - Canonical smiles failure with dependent double bonds
   (Issue 3526831)
 - Build Fails Due to Missing include in Code/RDBoost/Wrap.h
   (Issue 3527061)
 - Incorrect template parameter use in std::make_pair
   (Issue 3528136)
 - Canonicalization failure in cycle
   (Issue 3528556)
 - incorrect values reported in ML analysis
   (Issue 3528817)
 - Cartridge does not work on 32bit ubuntu 12.04
   (Issue 3531232)
 - Murcko Decomposition generates unuseable molecule.
   (Issue 3537675)
 - A few memory leaks were fixed in the Java Wrappers
 - The exact mass of molecules with non-standard isotopes is now
   calculated correctly.
 - The default (Euclidean) distance metric should now work with Butina
   clustering.
 - Some bugs in the depictor were fixed.
 - AvalonTools bug with coordinate generation for mols with no
   conformers fixed. 

New Features:
 - ChemicalFeatures now support an optional id
 - Isotope handling has been greatly improved. Atoms now have a
   getIsotope() (GetIsotope() in Python) method that returns zero if
   no isotope has been set, the isotope number otherwise.
 - The function MolFragmentToSmiles can be used to generate canonical
   SMILES for pieces of molecules.
 - The function getHashedMorganFingerprint (GetHashedMorganFingerprint
   in Python) has been added.

New Database Cartridge Features: 
 - The functions mol_from_smiles(), mol_from_smarts(), and
   mol_from_ctab() now return a null value instead of generating an
   error when the molecule processing fails. This allows molecule
   tables to be constructed faster.
 - The functions mol_to_smiles() and mol_to_smarts() have been added.
 - Creating gist indices on bit-vector fingerprint columns is faster.
 - The indexing fingerprint for molecular substructures has been changed.
   The new fingerprint is a bit slower to generate, but is
   considerably better at screening. More information here:
   http://code.google.com/p/rdkit/wiki/ImprovingTheSubstructureFingerprint

New Java Wrapper Features:

Deprecated modules (to be removed in next release):
 - Support for older (pre9.1) postgresql versions.

Removed modules:
 - rdkit.Excel
 - the code in $RDBASE/Code/PgSQL/RDLib
 - rdkit.Chem.AvailDescriptors : the same functionality is now available
   in a more useable manner from rdkit.Chem.Descriptors

Other:
 - Similarity calculations on ExplicitBitVectors should now be much faster
 - Use of [Xa], [Xb], etc. for dummy atoms in SMILES is no longer
   possible. Use the "*" notation and either isotopes (i.e. [1*],
   [2*]) or atom maps (i.e. [*:1], [*:2]) instead.
 - Initial work was done towards make the RDKit work on big endian
   hardware (mainly changes to the way pickles are handled)
 - Canonical SMILES generation is now substantially faster.