RDKit Files

******  Release_2013.03.2 *******
(Changes relative to Release_2013.03.1)

Acknowledgements:
Manuel Schwarze

Bug Fixes:
 - The hashed topological torsion fingerprints generated are now the
   same as in previous rdkit versions. (GitHub issue 25)

******  Release_2013.03.1 *******
(Changes relative to Release_2012.12.1)

!!!!!! IMPORTANT !!!!!!

 - The algorithm for hashing subgraphs used in the RDKit fingerprinter
   has 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.

Acknowledgements:
Paul Czodrowski, Andrew Dalke, Jan Domanski, Jean-Paul Ebejer, Nikolas
Fechner, Jameed Hussain, Stephan Reiling, Sereina Riniker, Roger
Sayle, Riccardo Vianello 

Bug Fixes: 
 - removeBond now updates bond indices (sf.net issue 284)
 - dummy labels are no longer lost when atoms are copied (sf.net issue
   285) 
 - more specific BRICS queries now match before less specific ones
   (sf.net issue 287, github issue 1) 
 - molAtomMapNumber can now be set from Python (sf.net issue 288)
 - the legend centering for molecular image grids has been improved
   (sf.net issue 289) 
 - make install now includes all headers (github issue 2)
 - InChIs generaged after clearing computed properties are now correct
   (github issue 3)
 - Reacting atoms that don't change connectivity no longer lose
   stereochemistry (github issue 4)  
 - Aromatic Si is now accepted (github issue 5)  
 - removeAtom (and deleteSubstructs) now correctly updates stereoAtoms
   (github issue 8)  
 - [cartridge] pg_dump no longer fails when molecules cannot be
    converted to SMILES (github issue 9)  
 - a canonicalization bug in MolFragmentToSmiles was fixed (github issue 12)  
 - atom labels at the edge of the drawing are no longer cut off (github issue 13)  
 - a bug in query-atom -- query-atom matching was fixed (github issue 15)  
 - calling ChemicalReaction.RunReactants from Python with None
   molecules no longer leads to a seg fault. (github issue 16)  
 - AllChem.ReactionFromSmarts now generates an error message when called
   with an empty string.
 - Writing CTABs now includes information about atom aliases.
 - An error in the example fdef file
   $RDBASE/Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef
   has been fixed. (github issue 17)
 - Quantize.FindVarMultQuantBounds() no longer generates a seg fault
   when called with bad arguments. (github issue 18)
 - The length of SDMolSuppliers constructed from empty files is no
   longer reported as 1. (github issue 19)
 - Partial charge calculations now work for B, Si, Be, Mg, and Al.
   (github issue 20)
 - Two logging problems were fixed (github issues 21 and 24)
 - Molecules that have had kappa descriptors generated can now be
   written to SD files (github issue 23)

New Features:
 - The handling of chirality in reactions has been reworked and
   improved. Please see the RDKit Book for an explanation.
 - Atom-pair and topological-torsion fingerprints now support the
   inclusion of chirality in the atom invariants.
 - A number of new compositional descriptors have been added:
   calcFractionCSP3, calcNum{Aromatic,Aliphatic,Saturated}Rings,
   calcNum{Aromatic,Aliphatic,Saturated}Heterocycles,
   calcNum{Aromatic,Aliphatic,Saturated}Carbocycles
 - An implementation of the molecular quantum number (MQN) descriptors
   has been added.
 - RDKFingerprintMol now takes an optional atomBits argument which is
   used to return information about which bits atoms are involved in.
 - LayeredFingerprintMol no longer takes the arguments tgtDensity and
   minSize. They were not being used.
 - LayeredFingerprintMol2 has been renamed to PatternFingerprintMol
 - The substructure matcher can now properly take stereochemistry into
   account if the useChirality flag is provided.
 - The module rdkit.Chem.Draw.mplCanvas has been added back to svn.
 - A new module integrating the RDKit with Pandas (rdkit.Chem.PandasTools)
   has been added.

New Database Cartridge Features: 
 - The new compositional descriptors are available:
   calcFractionCSP3, calcNum{Aromatic,Aliphatic,Saturated}Rings,
   calcNum{Aromatic,Aliphatic,Saturated}Heterocycles,
   calcNum{Aromatic,Aliphatic,Saturated}Carbocycles
 - MACCS fingerprints are available
 - the substruct_count function is now available
 - substructure indexing has improved. NOTE: indexes on molecule
    columns will need to be rebuilt.

New Java Wrapper Features:
 - The new compositional descriptors are available:
   calcFractionCSP3, calcNum{Aromatic,Aliphatic,Saturated}Rings,
   calcNum{Aromatic,Aliphatic,Saturated}Heterocycles,
   calcNum{Aromatic,Aliphatic,Saturated}Carbocycles
 - The molecular quantum number (MQN) descriptors are available
 - MACCS fingerprints are available
 - BRICS decomposition is available.

Deprecated modules (to be removed in next release):

Removed modules:

Other:
 - RDKit fingerprint generation is now faster. The hashing algorithm
   used in the RDKit fingerprinter has changed.
 - Force-field calculations are substantially faster (sf.net issue 290)
 - The core of the BRICS implementation has been moved into C++.
 - The MACCS fingerprint implementation has been moved into
   C++. (contribution from Roger Sayle)
 - New documentation has been added: Cartridge.rst, Overview.rst,
   Install.rst