RDKit Files

******  Release_2011.12.1 *******
(Changes relative to Release_2011.09.1)

!!!!!! IMPORTANT !!!!!!
 - The functions for creating bit vector fingerprints using atom pairs
   and topological torsions have been changed. The new default
   behavior will return different fingerprints than previous RDKit
   versions. This affects usage from c++, python, and within the
   postgresql cartridge. See the "Other" section below for more
   details. 
 - Due to a bug fix in the parameter set, the MolLogP and MolMR
   descriptor calculators now return different values for some
   molecules. See the "Bug Fixes" section below for more details.
 - To make storage more efficient, the size of the fingerprint
   used to store morgan fingerprints in the database cartridge
   has been changed from 1024 bits to 512 bits. If you update
   the cartridge version all morgan and featmorgan fingerprints
   and indices will need to be re-generated.

Acknowledgements:
Andrew Dalke, JP Ebejer, Roger Sayle, Adrian Schreyer, Gianluca
Sforna, Riccardo Vianello, Toby Wright

Bug Fixes: 
- molecules with polymeric S group information are now rejected by the
  Mol file parser. (Issue 3432136)
- A bad atom type definition and a bad smarts definition were fixed in
  $RDBASE/Data/Crippen.txt. This affects the values returned by the
  logp and MR calculators. (Issue 3433771)
- Unused atom-map numbers in reaction products now produce warnings
  instead of errors. (Issue 3434271)
- rdMolDescriptors.GetHashedAtomPairFingerprint() now works. (Issue
  3441641)
- ReplaceSubstructs() now copies input molecule conformations to the
  output molecule. (Issue 3453144)
- three-coordinate S and Se are now stereogenic (i.e. the
  stereochemistry of O=[S@](C)F is no longer ignored). (Issue 3453172) 

New Features:
- Integration with the new IPython graphical canvas has been
  added. For details see this wiki page: 
http://code.google.com/p/rdkit/wiki/IPythonIntegration
- Input and output from Andrew Dalke's FPS format
  (http://code.google.com/p/chem-fingerprints/wiki/FPS) for
  fingerprints. 
- The descriptor CalcNumAmideBonds() was added.

New Database Cartridge Features: 
- Support for PostgreSQL v9.1
- Integration with PostgreSQL's KNN-GIST functionality. (Thanks to
  Adrian Schreyer) 
- the functions all_values_gt(sfp,N) and all_values_lt(sfp,N) were
  added.

New Java Wrapper Features:
- A function for doing diversity picking using fingerprint similarity.
- support for the Avalon Toolkit (see below)

Deprecated modules (to be removed in next release):
- rdkit.Excel
- rdkit.ML.Descriptors.DescriptorsCOM
- rdkit.ML.Composite.CompositeCOM

Removed modules:
- rdkit.WebUtils
- rdkit.Reports
- rdkit.mixins

Other:
- Improvements to the SMARTS parser (Roger Sayle)
- The atom-pair and topological-torsion fingerprinting functions that
  return bit vectors now simulate counts by setting multiple bits in
  the fingerprint per atom-pair/torsion. The number of bits used is
  controlled by the nBitsPerEntry argument, which now defaults to 4.
  The new default behavior does a much better job of reproducing the
  similarities calculated using count-based fingerprints: 95% of
  calculated similarities are within 0.09 of the count-based value
  compared with 0.22 or 0.17 for torsions and atom-pairs previously.
  To get the old behavior, set nBitsPerEntry to 1.
- Optional support has been added for the Avalon Toolkit
(https://sourceforge.net/projects/avalontoolkit/) to provide an
alternate smiles canonicalization, fingerprint, and 2D coordination
generation algorithm.
- The SLN support can now be switched off using the cmake variable
RDK_BUILD_SLN_SUPPORT.
- There are now instructions for building the RDKit and the SWIG
wrappers in 64bit mode on windows.