******  Release_2014.03.1 *******
(Changes relative to Release_2013.09.2)

!!!!!! IMPORTANT !!!!!!
 - Due to a bug fix in the rotatable bonds definition, the default
   rotatable bond calculation returns different values than before.
   This also affects MQN descriptor #18.

Acknowledgements:
Paul Czodrowski, James Davidson, Markus Elfring, Nikolas Fechner, Jan Holst Jensen, Christos Kannas, Sereina Riniker, Roger Sayle, Paolo Tosco, Samo Turk, Riccardo Vianello, Maciej Wójcikowski, Toby Wright 

Bug Fixes:
- Dict::DataType declaration causing problems with C++11 std::lib
 (github issue 144)
- Pre-condition Violation in AllChem.Compute2DCoords
 (github issue 146)
- GetSimilarityMapForFingerprint() fails when similarity is zero
 (github issue 148)
- PatternFingerprint failure for substructure matching
 (github issue 151)
- query atoms don't match ring queries
 (github issue 153)
- Incorrect SMILES generated after calling MMFF parameterization
 (github issue 162)
- Problems with Xe from SDF
 (github issue 164)
- Radicals not being used in atom--atom matches
 (github issue 165)
- Cannot skip sanitization while reading PDB
 (github issue 166)
- Distance Geometry embedding not thread safe
 (github issue 167)
- O3A::align() and O3A::trans() now return "true" RMSD value
 (github pull 173)
- RangeError when pre-incrementing or decrementing AtomIterators
 (github issue 180)
- ctabs do not contain wedged bonds for chiral s
 (github issue 186)
- ctabs do not contain "A" when appropriate
 (github issue 187)
- Problems round-tripping Al2Cl6 via CTAB
 (github issue 189)
- Don't merge Hs onto dummies
 (github issue 190)
- Wavy bonds to Hs in CTABs should affect the stereochemistry of attached double bonds
 (github issue 191)
- Rendering binary compounds as ClH, FH, BrH or IH rather than putting H first.
 (github issue 199)
- Fixed data race condition in Code/GraphMol/MolAlign/testMolAlign.cpp
 (github pull 202)
- Re-prepared SDF/SMILES files of the MMFF validation suite + a fix
 (github pull 205)
- Problems round-tripping P with non-default valence.
 (github issue 206)
- Added a stricter definition of rotatable bonds as a new function in the ...
 (github pull 211)
- Code/GraphMol/AddHs patch proposal
 (github pull 212)
- Fix: Changed getNumReactantTemplates to GetNumReactantTemplates.
 (github pull 219)
- aromatic B ("b") causes errors from SMARTS parser
 (github issue 220)
- Segmentation fault for MMFF optimization with dummy atoms
 (github issue 224)
- isMoleculeReactantOfReaction() and isMoleculeProductOfReaction() not useable from SWIG wrappers
 (github issue 228)
- cartridge: mol_from_ctab() ignores argument about keeping conformers
 (github issue 229)
- Reaction not correctly preserving chirality on unmapped atoms.
 (github issue 233)
- AllChem.AssignBondOrdersFromTemplate() fails with nitro groups
 (github issue 235)
- Fix molecule dataframe rendering in pandas 0.13.x
 (github pull 236)
- Dummy labels copied improperly into products
 (github issue 243)
- Two bugfixes in MMFF code
 (github pull 248)
- seg fault when trying to construct pharmacophore with no conformation
 (github issue 252)
- EmbedMolecule() should not create a conformer for molecules that have zero atoms
 (github issue 256)
- cartridge: dice similarity calculation does not use USE_BUILTIN_POPCOUNT flag
 (github issue 259)
- cartridge: similarity calculations wrong for maccs fps when USE_BUILTIN_POPCOUNT flag is set
 (github issue 260)

New Features:
- Expose gasteiger charge calculation to SWIG
 (github issue 152)
- Added additional functionality to PandasTools
 (github pull 155)
- Add MMFFHasAllMoleculeParams() to SWIG interface
 (github issue 157)
- O3A code should throw an exception if the parameterization is not complete.
 (github issue 158)
- Support zero order bonds
 (github issue 168)
- Add attachmentPoint argument to ReplaceSubstructs
 (github issue 171)
- Forcefield constraints (distances, angles, torsions, positions)
 (github pull 172)
- Add kekulize flag to SDWriter
 (github issue 174)
- Support operator= for RWMol
 (github issue 175)
- Get GetAromaticAtoms() and GetQueryAtoms() working from python
 (github issue 181)
- Support richer QueryAtom options in Python
 (github issue 183)
- Support writing V3000 mol blocks
 (github issue 184)
- Allow disabling the building of tests
 (github issue 185)
- Expand DbCLI to allow updating databases 
 (github issue 197)
- Code refactoring and enhancement to allow for O3A alignment according to atom-based Crippen logP contribs
 (github pull 201)
- call MolOps::assignStereochemistry() with flagPossibleStereoCenters true from within the molecule parsers.
 (github issue 210)
- Support passing of file-like PandasTools.LoadSDF
 (github pull 221)
- Reaction SMARTS parser should support agents
 (github issue 222)
- Add function to MolOps to allow a molecule to be split into fragments based on a query function
  This is useable from python as Chem.SplitMolByPDBResidues() and Chem.SplitMolByPDBChainId()
 (github issue 234)
- Adding option useCounts for Morgan fingerprints
 (github pull 238)
- support SimpleEnum functionality for adding recursive queries to reactions
 (github issue 242)
- Additional functions for bit vectors
 (github pull 244)
- Support of RDK fingerprints added to SimilarityMaps
 (github pull 246)
- add get3DDistance
- support 3D distances in the atom pair fingerprints
 (github issue 251)
- added MolOps::get3DDistanceMat() (Chem.Get3DDistanceMatrix() from python)

 
New Database Cartridge Features: 
- Support configuration of fingerprint sizes in cartridge.
 (github issue 216)
- Add mol_to_ctab(mol, bool default true) to Postgres cartridge.
 (github pull 230)
- Adds sum formula function to PG cartridge.
 (github pull 232)

New Java Wrapper Features:

Deprecated modules (to be removed in next release):

Removed modules:
- The CMIM integration (previously available to python in the rdkit.ML.FeatureSelect package)
  has been removed due to license incompatibility.

Contrib updates:
- Added Contribution to train ChEMBL-based models
 (github pull 213)
- ConformerParser functionality
 (github pull 245)

Other:
- The Open3DAlign code is considerably faster.
- The SMILES parsing code is faster.
- Fix Bison 3.x incompabtility
 (github pull 226)
- Add Travis support
 (github pull 227)
- port of rdkit.ML  bindings from Python/C API to boost::python
 (github pull 237)
- The code now builds more easily using the Anaconda python distribution's 
  conda package manager
 (github pull 247)

******  Release_2013.09.2 *******
(Changes relative to Release_2013.09.1)

Acknowledgements:
Andrew Dalke, JP Ebejer, Daniel Moser, Sereina Riniker, Roger Sayle, Manuel Schwarze, Julia Weber

Bug Fixes:
- cannot pickle unsanitized molecules
  (github issue 149)
- Problems reading PDB files when locale is DE
  (github issue 170)
- calling RWMol::clear() leaves property dict empty
  (github issue 176)
- zero atom molecule generates exception in MolToSmiles when 
  rootedAtAtom is provided
  (github issue 182)
- bond orders not being set when PDB files are read
  (github issue 194)
- GenMACCSKeys() raises an exception with an empty molecule
  (github issue 195)
- left-justified SDF bond topology of "0" raises an unexpected
  exception
  (github issue 196)

******  Release_2013.09.1 *******
(Changes relative to Release_2013.06.1)

Acknowledgements:
James Davidson, JP Ebejer, Nikolas Fechner, Grégori Gerebtzoff, Michal Nowotka, Sereina Riniker, Roger
Sayle, Gianluca Sforna, Matthew Szymkiewicz, Paolo Tosco, Dan Warner, 

!!!!!! IMPORTANT !!!!!!
 - Due to a bug fix in the parameter set, the MolLogP and MolMR
   descriptor calculators now return different values for molecules
   with pyrrole (or pyrrole-like) Ns.

Bug Fixes:
 - The pymol ShowMol method can now handle molecules with more than
   999 atoms (they are sent via PDB)
 - Various stability improvements to the Pandas integration.
   (github issues 129 and 51)
 - Some RDKit methods require python lists and don't allow passing
   numpy arrays or pandas series directly
   (github issue 119)
 - mol2 parser not setting E/Z flags on double bonds
   (github issue 114)
 - Incorrect angle terms in UFF
   (github issue 105)
 - Problems with stereochemistry flags and PathToSubmol()
   (github issue 103)
 - Bad Crippen atom type for pyrrole H
   (github issue 92)
 - PandasTools tests fail with Pandas v0.12
   (github issue 91)
 - Isotope information not affecting chirality
   (github issue 90)
 - properties are not read from SDF files with V3000 mol blocks.
   (github issue 88)
 - assignStereochemistry does not remove bond wedging that shouldn't be there.
   (github issue 87)
 - Drawing code modifies wedge bonds in reactions
   (github issue 86)
 - Stereochemistry not perceived when parsing CTABs unless sanitization is done.
   (github issue 82)
 - 2D rendering issue for epoxide ( CAS  70951-83-6)
   (github issue 78)
 - PandasTools doctests should be failing, but are not
   (github issue 75)
 - Better handling of radicals to/from mol files
   (github issue 73)
 - Benzothiazolium structure can be parsed from ctab, but the SMILES generated cannot be processed.
   (github issue 72)
 - Chem.MolFromInch hangs on CID 23691477 and CID 23691480
   (github issue 68)
 - Chem.MolFromInchi on CHEMBL104337 leads to segmentation fault 
   (github issue 67)
 - "Could not embed molecule." (The Anthony Conundrum)
   (github issue 55)

New Features:
 - Add fragmentOnBonds() to python wrapper
   (github issue 142)
 - Allow renumbering atoms in a molecule.
   (github issue 140)
 - MMFF94 and MMFF94S support
 - implementation of the Open3DAlign rigid alignment algorithm
 - Support for reading and writing PDB files
 - The python function AllChem.AssignBondOrdersFromTemplate() can be
   used to assign bond orders from a reference molecule to the bonds
   in another molecule. This is helpful for getting bond orders
   correct for PDB ligands.
   (github issue 135)
 - Bond lengths, angles, and torsions can now be queries and adjusted.
   (github issue 132)
 - Implementation of similarity maps
   (github issue 94)
 - Python implementation of the Fraggle similarity algorithm.
   See Jameed Hussain's presentation from the 2013 UGM for details:
   https://github.com/rdkit/UGM_2013/blob/master/Presentations/Hussain.Fraggle.pdf?raw=true
 - SparseIntVects now support -=, +=, /=, and *= with ints from C++
   and Python
 - support \\ in SMILES
   (github issue 136)
 - Support a similarity threshold in DbCLI
   (github issue 134)
 - Support construction molecules from other molecules in the python wrapper
   (github issue 133)
 - support tversky similarity in DbCLI
   (github issue 130)
 - support tversky similarity in cartridge
   (github issue 121)
 - support reading and writing reactionComponentType and reactionComponentNumber from ctabs
   (github issue 118)
 - Add in-place forms of addHs(), removeHs(), and mergeQueryHs()
   (github issue 117)
 - modify MolOps::cleanUp() to support this azide formulation: C-N=N#N
   (github issue 116)
 - Dihedral rotation exposed in python
   (github issue 113)
 - Support for cairocffi (cairo drop-in replacement that plays nicely with virtualenv) 
   (github issue 80) 
 - Grey color for Hydrogens
   (github issue 97)
 - Improvements to the Dict interface in C++
   (github issue 74)
 - customizable drawing options
   (github issue 71)
 - Add method for setting the chiral flag in mol blocks
   (github issue 64)
 - New descriptors added (Python only for now):
   MaxPartialCharge(),MinPartialCharge(),MaxAbsPartialCharge(),MinAbsPartialCharge(),
   MaxEStateIndex(),MinEStateIndex(),MaxAbsEStateIndex(),MinAbsEStateIndex()

New Database Cartridge Features: 

New Java Wrapper Features:
 - MMFF support
 - PDB reading and writing
 - Open3DAlign support


Deprecated modules (to be removed in next release):

Removed modules:

Contrib updates:
 - The MMPA implementation has been updated
   See Jameed Hussain's tutorial from the 2013 UGM for details:
   https://github.com/rdkit/UGM_2013/tree/master/Tutorials/mmpa_tutorial
   [Jameed Hussain]
 - An implementation of Ertl and Schuffenhauer's Synthetic
   Accessibility score is available in Contrib/SA_Score
   [Peter Ertl, Greg Landrum]
 - Command line scripts for the Fraggle similarity algorithm
   See Jameed Hussain's presentation from the 2013 UGM for details:
   https://github.com/rdkit/UGM_2013/blob/master/Presentations/Hussain.Fraggle.pdf?raw=true
   [Jameed Hussain]

Other:
 - Some of the changes to UFF deviate from the published force
   field. Specifics of the changes, and the reasoning behind them, are
   in Paolo Tosco's 2013 RDKit UGM presentation: 
   https://github.com/rdkit/UGM_2013/blob/master/Presentations/Tosco.RDKit_UGM2013.pdf?raw=true
 - Reaction drawing has been improved. Support for reaction drawing
   has been added to the IPython notebook.


******  Release_2013.06.1 *******
(Changes relative to Release_2013.03.2)

Administrivia note:
In the course of this release cycle, development was moved over
entirely to github. The sourceforge svn repository no longer contains
an up-to-date version of the code.

Acknowledgements:
Andrew Dalke, JP Ebejer, Nikolas Fechner, Roger Sayle, Riccardo Vianello,
Yingfeng Wang, Dan Warner 

Bug Fixes:
 - The docs for Descriptors.MolWt are now correct (GitHub #38)
 - Molecules coming from InChi now have the correct molecular
   weight. (GitHub #40)
 - RemoveAtoms() no longer leads to problems in canonical SMILES
   generation when chiral ring atoms are present. (GitHub #42)
 - Atom invariants higher than the number of atoms in the molecule can
   now be provided to the atom pairs and topological torsions
   fingerprinters. (GitHub #43)
 - A typo with the handling of log levels was fixed in the python
   wrapper code for InChI generation. (GitHub #44)
 - Stereochemistry no longer affects canonical SMILES generation if
   non-stereo SMILES is being generated. (GitHub #45)
 - The ExactMolWt of [H+] is no longer zero. (GitHub #56)
 - The MPL canvas now has an addCanvasDashedWedge() method. (GitHub
   #57) 
 - RWMol::insertMol() now copies atom coordinates (if
   present). (GitHub #59)
 - The "h" primitive in SMARTS strings now uses the method
   getTotalNumHs(false) instead of getImplicitValence().
   (GitHub #60)
 - bzip2 files now work better with the SDWriter class. (GitHub #63)
 - a crashing bug in InChI generation was fixed. (GitHub #67)

New Features:
 - Sanitization can now be disabled when calling GetMolFrags() from
   Python (GitHub #39)
 - Bond.GetBondTypeAsDouble() has been added to the python
   wrapper. (GitHub #48)
 - The fmcs code now includes a threshold argument allowing the MCS
   that hits a certain fraction of the input molecules (instead of all
   of them) to be found. The code has also been synced with the most
   recent version of Andrew Dalke's version.
 - Atoms now have a getTotalValence() (GetTotalValence() from Python)
   method. (GitHub #61)
 - R labels from Mol files now can go from 0-99
 - chiral flags in CTABs are now handled on both reading and writing.
   The property "_MolFileChiralFlag" is used.


New Database Cartridge Features: 

New Java Wrapper Features:
 - {Get,Set}Prop() methods are now available for both Atoms and
   Bonds. (GitHub #32)


Deprecated modules (to be removed in next release):

Removed modules:
 - rdkit.utils.pydoc_local

Other:
 - the handling of flex/bison output files as dependencies has been
   improved (GitHub #33)
 - the molecule drawing code should now also work with pillow (a fork of
   PIL)
 - the PANDAS integration has been improved.  
 

******  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 

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

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

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.

  
******  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.

Acknowledgements:
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
  254) 
- 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
  assigned. 

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
  information.
- The RDKit and Layered fingerprinters both now accept "fromAtoms"
  arguments that can be used to limit which atoms contribute to the
  fingerprint. 
- 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:

Other:
- During this release cycle, the sourceforge project was updated to
  their new hosting system. This explains the change in bug/issue
  ids. 
- 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
  24.
- It is no longer necessary to have flex and bison installed in order
  to build the RDKit.


******  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.

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.

******  Release_2012.03.1 *******
(Changes relative to Release_2011.12.1)

!!!!!! IMPORTANT !!!!!!
 - The atom-atom match behavior for non-query atoms has been changed.
    This affects the results of doing substructure matches using
    query molecules that are not constructed from SMARTS.

Acknowledgements:
JP Ebejer, Paul Emsley, Roger Sayle, Adrian Schreyer, Gianluca Sforna,
Riccardo Vianello 

Bug Fixes: 
- the older form of group evaluations in Mol blocks is now correctly
  parsed. (Issue 3477283)
- some problems with handling aromatic boron were fixed. (Issue 3480481)
- the SD writer no longer adds an extra $$$$ when molecule parsing
  fails (Issue 3480790)
- molecules in SD files that don't contain atoms are now parsed
  without warnings and their properties are read in. (Issue 3482695)
- it's now possible to embed molecules despite failures in the triangle
  bounds checking (Issue 3483968)
- Isotope information in Mol blocks is now written to M ISO lines
  instead of going in the atom block. (Issue 3494552)
- Better 2D coordinates are now generated for neighbors of atoms with 
  unspecified hybridization. (Issue 3487469)
- Dummy atoms and query atoms are now assigned UNSPECIFIED hybridization
  instead of SP. (Issue 3487473)
- Error reporting for SMARTS involving recursion has been improved.
  (Issue 3495296)
- Some problems of queries and generating SMARTS for queries were resolved.
  (Issues 3496759, 3496799, 3496800)
- It's now possible to do database queries with SMARTS that use the index.
  (Issue 3493156).
- A series of problems related to thread safety were fixed.
- Tracking the lifetime of owning molecules across the C++/Python
  border is now being handled better (Issue 3510149)
- A bug with ring-finding in some complex fused ring systems was fixed.
  (Issue 3514824)
- The AllChem module now imports successfully even if the SLN parser
hasn't been built.

New Features:
- The molecular sanitization is now configurable using an optional
  command-line argument.
- It's now possible to get information from the sanitization routine
  about which operation failed.
- Suppliers support GetLastItemText()
- ComputeDihedralAngle() and ComputeSignedDihedralAngle() were added
  to the rdkit.Geometry module.
- computeSignedDihedralAngle() was added to the C++ API
- ChemicalReactions now support a GetReactingAtoms() method
- the Mol file and Mol block parsers, as well as the SD suppliers,
  now support an optional "strictParsing" argument.
  When this is set to False, problems in the structure of the
  input file are ignored when possible 
- EditableMols return the index of the atom/bond added by AddAtom/AddBond
- rdkit.Chem.Draw.MolToImage() now supports an optional "legend" argument
- The MolToSmiles function now supports an optional "allBondsExplicit" argument. 

New Database Cartridge Features: 
- the functions mol_from_smiles() and mol_from_smarts() were added

New Java Wrapper Features:
- the diversity picker now supports an optional random-number seed

Deprecated modules (to be removed in next release):
- rdkit.Excel

Removed modules:
- rdkit.ML.Descriptors.DescriptorsCOM 
- rdkit.ML.Composite.CompositeCOM

Other:
- Assigning/cleaning up stereochemistry is now considerably
faster. This makes standard molecule construction faster.


******  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.

******  Release_2011.09.1 *******
(Changes relative to Release_2011.06.1)

!!!!!! IMPORTANT !!!!!!
 - A bug in the definition of the Lipinski HBD descriptor was fixed in
   this release. The descriptor Lipinski.NHOHCount will return
   different values for molecules containing Ns or Os with more than
   one attached H.

Acknowledgements:
Eddie Cao, Richard Cooper, Paul Czodrowski, James Davidson, George
Papadatos, Riccardo Vianello  

Bug Fixes: 
 - A problem with interpretation of stereochemistry from mol files was
   fixed (Issue 3374639)
 - Sterochemistry information for exocyclic double bonds in mol blocks
   is no longer lost. (Issue 3375647)
 - linear double bonds from mol files now have their stereochemistry
   set correctly(Issue 3375684)
 - Chirality for phosphates and sulfates is not longer automatically
   removed. (Issue 3376319)
 - A bug with the reading of query information from mol files was
   fixed. (Issue 3392107)
 - Sterochemistry is now cleaned up after processing mol2
   files. (Issue 3399798) 
 - mergeQueryHs now correctly handles atoms with multiple Hs (Issue
   3415204) 
 - mergeQueryHs now correctly handles atoms without initial query
   information (Issue 3415206)
 - the calcLipinskiHBD() (equivalent to Lipinski.NHOHCount) descriptor
   now correctly handles Ns or Os with multiple Hs. (Issue 3415534)
 - Morgan fingerprints generated using the fromAtoms argument now have
   all bits from those atoms set.(Issue 3415636)
 - A problem with the way MolSuppliers handle the EOF condition when
   built with the most recent versions of g++ was fixed.
 - Translation of RDKit stereochemistry information into InChI
   stereochemistry information is improved.

New Features:

New Database Cartridge Features: 
 - molecules can now be built from mol blocks using the function
   mol_from_ctab(). The corresponding is_valid_ctab() function was
   also added.
 - the radius argument is now optional for the functions morganbv_fp,
   morgan_fp, featmorganbv_fp, and featmorgan_fp. The default radius
   for all four functions is 2.

Deprecated modules (to be removed in next release):

Removed modules:

Other:
 - The documentation in $RDBASE/Docs/Book has been migrated to use
   Sphinx instead of OpenOffice.
 - The optional InChI support can now be built using a system
   installation of the InChI library.

 

******  Release_2011.06.1 *******
(Changes relative to Release_2011.03.2)

Acknowledgements:
 - Eddie Cao, Andrew Dalke, James Davidson, JP Ebejer, Gianluca
   Sforna, Riccardo Vianello, Bernd Wiswedel

Bug Fixes: 
 - A problem with similarity values between SparseIntVects that
   contain negative values was fixed. (Issue 3295215)
 - An edge case in SmilesMolSupplier.GetItemText() was fixed. (Issue
   3299878)
 - The drawing code now uses dashed lines for aromatic bonds without
   kekulization. (Issue 3304375)
 - AllChem.ConstrainedEmbed works again. (Issue 3305420)  
 - atomic RGP values from mol files are accessible from python (Issue
   3313539)
 - M RGP blocks are now written to mol files. (Issue 3313540)
 - Atom.GetSymbol() for R atoms read from mol files is now
   correct. (Issue 3316600)
 - The handling of isotope specifications is more robust.
 - A thread-safety problem in SmilesWrite::GetAtomSmiles() was fixed.
 - some of the MACCS keys definitions have been corrected
 - Atoms with radical counts > 2 are no longer always written to CTABs
   with a RAD value of 3. (Issue 3359739)

New Features:
 - The smiles, smarts, and reaction smarts parsers all now take an additional
   argument, "replacements", that carries out string substitutions pre-parsing.
 - There is now optional support for generating InChI codes and keys
   for molecules.
 - the atom pair and topological torsion fingerprint generators now
   take an optional "ignoreAtoms" argument
 - a function to calculate exact molecular weight was added.
 - new java wrappers are now available in $RDBASE/Code/JavaWrappers
 - the methods getMostCommonIsotope() and getMostCommonIsotopeMass()
   have been added to the PeriodicTable class.

New Database Cartridge Features: 
 - Support for generating InChIs and InChI keys
   (if the RDKit InChI support is enabled). 

Deprecated modules (to be removed in next release):
 - The original SWIG wrappers in $RDBASE/Code/Demos/SWIG are deprecated

Removed modules:

Other:
 - The quality of the drawings produced by both the python molecule drawing
   code and $RDBASE/Code/Demos/RDKit/Draw is better.
 - the python molecule drawing code will now use superscripts and
   subscripts appropriately when using the aggdraw or cairo canvases
   (cairo canvas requires pango for this to work). 
 - $RDBASE/Code/Demos/RDKit/Draw now includes an example using cairo
 - A lot of compiler warnings were cleaned up.
 - The error reporting in the SMILES, SMARTS, and SLN parsers was improved.
 - the code for calculating molecular formula is now in C++
   (Descriptors::calcMolFormula()) 

 
******  Release_2011.03.2 *******
(Changes relative to Release_2011.03.1)

Bug Fixes:
 - A problem in the refactored drawing code that caused the
   rdkit.Chem.Draw functionality to not work at all was fixed.


******  Release_2011.03.1 *******
(Changes relative to Release_2010.12.1)

Acknowledgements:
 - Eddie Cao, James Davidson, Kirk DeLisle, Peter Gedeck, George
   Magoon, TJ O'Donnell, Gianluca Sforna, Nik Stiefl, Bernd Wiswedel

Bug Fixes: 
 - The performance of SSSR finding for molecules with multiple highly-fused
   ring systems has been improved. (Issue 3185548)
 - Isotope information is now correctly saved when molecules are
   serialized (pickled). (Issue 3205280)
 - Generating SMILES for a molecule no longer changes the
   molecule. This fixes a round-trip bug with certain highly symmetric
   molecules read from SD files. (Issue 3228150)
 - Another bounds-matrix generation bug for highly (con)strained
   systems was fixed. (Issue 3238580)
 - Conformation information is now better handled by deleteSubstructs(),
   replaceSubstructs(), and replaceCore().

New Features:
 - the rdkit.Chem.Draw package has been significantly refactored.
 - Code for doing Murcko decomposition of molecules has been
   added. From Python this is in the module:
   rdkit.Chem.Scaffolds.MurckoScaffold
   It's available in C++ in the GraphMol/ChemTransforms area.
 - rdkit.Chem.AllChem.TransformMol() now takes optional arguments
   allowing the conformation to be transformed to be specified and
   other existing conformations to be preserved.
 - Calculations for most of the descriptors in rdkit.Chem.Lipinski and
   rdkit.Chem.MolSurf have been moved into C++. The python API is the
   same, but the calculations should be somewhat faster.
 - Extensive feature additions to the SWIG-based java wrapper.
 - The Chem.ReplaceCore() function is now better suited for use
   in R-group decomposition.
 - The Morgan fingerprinting code can now return information about
   which atoms set particular bits.
 - The function pathToSubmol() now copies coordinate information
   from conformations (if present). The function is also now available
   from Python
 - The path and subgraph finding code now takes an optional
   rootedAtAtom argument to allow only paths/subgraphs that start at a
   particular atom to be generated.
 - The function findAtomEnvironmentOfRadiusN has been added to allow
   circular atom environments to be located in molecules.
 - MolOps::assignStereochemistry now can also flag potential
   stereocenters that are not specified.

New Database Cartridge Features: 
 - the descriptor-calculation functions mol_numrotatablebonds(),
   mol_numheteroatoms(), mol_numrings(), and mol_tpsa() have been
   added.
 
Deprecated modules (to be removed in next release):

Removed modules:

Other:
 - In C++, the functions CalcCrippenDescriptors and CalcAMW have been
   renamed calcCrippenDescriptors and calcAMW to make them consistent
   with the other descriptor calculators.
 - The molecule serialization (pickling) format has been changed. The
   new format is more compact.
 


******  Release_2010.12.1 *******
(Changes relative to Release_2010.09.1)

!!!!!! IMPORTANT !!!!!!
 - Due to changes made to the fingerprinting code, RDKit and layered
   fingerprints generated with this release are not compatible with
   those from previous releases. For users of the database cartridge:
   you will need to re-generate RDKit fingerprint columns and any
   indices on molecule tables.

Acknowledgements:
 - Eddie Cao, Andrew Dalke, James Davidson, Kirk DeLisle, Peter Gedeck,
   TJ O'Donnell, Gianluca Sforna, Nik Stiefl, Riccardo Vianello 
   
Bug Fixes: 
 - The depiction code no longer crashes with single-atom templates
   (issue 3122141) 
 - Aromatic bonds in the beginning of a SMILES branch are now
   correctly parsed (issue 3127883)
 - A crash when generating 2d constrained coordinates was fixed (issue
   3135833) 
 - Stereochemistry no longer removed from double bonds in large
   rings. (issue 3139534) 
 - Atom mapping information no longer in reaction products (issue
   3140490)  
 - Smiles parse failure with repeated ring labels and dot disconnects
   fixed (issue 3145697)
 - a bug causing the molecule drawing code to not use the cairo canvas
   when it's installed was fixed
 - the SMILES generated for charged, aromatic Se or Te has been fixed
   (issue 3152751)
 - PropertyMols constructed from pickles and then written to SD files
   will now include the properties in the SD file.
 - SMILES can now be generated correctly for very large molecules
   where more than 50 rings are open at once. (issue 3154028)

New Features:
 - All molecular descriptor calculators are now pulled in by the
   rdkit.Chem.Descriptors module. So you can do things like:
   Descriptors.MolLogP(mol) or Descriptors.fr_amide(mol)
 - Atom-map numbers in SMILES are now supported. They can be accessed
   as the atomic "molAtomMapNumber" property. (issue 3140494)
 - It's now possible to tell the RDKit to generate non-canonical
   SMILES via an optional argument to MolToSmiles. This is faster than
   generating canonical SMILES, but is primarity intended for
   debugging/testing. (issue 3140495)
 - The function GenerateDepictionMatching2DStructure() has been added
   to the rdkit.Chem.AllChem module to make generating
   template-aligned depictions easier.
 - Generating FCFP-like fingerprints is now more straightforward via
   the useFeatures optional argument to GetMorganFingerprint()
 - Extensive changes were made to the layered fingerprinting code to
   allow better coverage of queries.
 - Functionality for stripping common salts from molecules has been
   added in rdkit.Chem.SaltRemover. The salts themselves are defined
   in $RDBASE/Data/Salts.txt
 - Functionality for recognizing common functional groups has been
   added in rdkit.Chem.FunctionalGroups. The functional groups
   themselves are defined in
   $RDBASE/Data/Functional_Group_Hierarchy.txt 

New Database Cartridge Features: 
 - The cartridge now supports SMARTS queries.
 - The functions is_valid_{smiles,smarts}() are now available
   (issue 3097359).
 - The operator @= is now supported for testing molecule equality.
   (issue 3120707)
 - The functions featmorgan_fp() and featmorganbv_fp() are now
   available for generating FCFP-like fingerprints.

Deprecated modules (to be removed in next release):
 - rdkit.Chem.AvailDescriptors : the same functionality is now available
   in a more useable manner from rdkit.Chem.Descriptors (see above).

Removed modules:

Other:
 - RDKit support has been added to the Knime data mining and reporting
   tool. More information is available from the knime.org community
   site: http://tech.knime.org/community/rdkit
   Thanks to Thorsten, Bernd, Michael, and the rest of the crew at
   knime.com for making this possible.
 - RPMs to allow easy installation of the RDKit on Fedora/CentOS/RHEL 
   and similar systems are now available. Thanks to Gianluca Sforna
   for doing this work.
 - The database cartridge now statically links the RDKit libraries.
   This should make installation easier.
 - The RDKit fingerprinter now by default sets 2 bits per hashed
   subgraph instead of 4. The old behavior can be regained by setting
   nBitsPerHash to 4.

******  Release_2010.09.1 *******
(Changes relative to Release_Q22010_1)

!!!!!! IMPORTANT !!!!!!
 - Due to changes made to the layered fingerprinting code,
   fingerprints generated with this release are not compatible with
   fingerprints from earlier releases.
 - The default arguments to the Morgan fingerprinting code will yield
   fingerprints that are not backwards compatible.

Acknowledgements:
 - Andrew Dalke, James Davidson, Paul Emsley, Peter Gedeck,
   Uwe Hoffmann, Christian Kramer, Markus Kossner, TJ O'Donnell,
   Gianluca Sforna, Nik Stiefl, Riccardo Vianello 
   
Bug Fixes: 
 - A typo in the parameters for the Crippen clogp calculator was
   fixed. (issue 3057201)
 - some problems in the layered fingerprinting code were fixed. (issue
   3030388)
 - a bug in the ring-finding code that could lead to incorrect results
   or crashes in large molecules was fixed.  
 - the Murtagh clustering code should now execute correctly on recent
   versions of the MacOS.
 - some problems with the cairo canvas were fixed
 - a problem with matching non-default isotope SSS queries for molecules
   read in from CTABs was fixed (issue 3073163).
 - a problem with calculating AMW for molecules with non-default isotopes
   was fixed.

New Features:
 - a PostgreSQL cartridge for similarity and substructure searching
   has been added to the RDKit distribution.
 - The Morgan fingerprinting code accepts additional arguments that
   control whether or not bond order and chirality are taken into
   account. By default chirality is ignored and the bond order is
   used. Another change with the MorganFPs is that ring information is
   now included by default. 
 - 2D coordinates can now be generated for chemical reactions.
 - The functions IsMoleculeReactantOfReaction and
   IsMoleculeProductOfReaction have been added to the C++
   interface. From python these are methods of the ChemicalReaction
   class: 
   rxn.IsMoleculeReactant and rxn.IsMoleculeProduct
 - The default bond length for depiction can now be changed.
 - FCFP-like fingerprints can now be generated with the Morgan
   fingerprinting code by starting with feature invariants.
 - The close() method has been added to MolWriters.
 - Morgan, atom-pair, and topological-torsion fingerprints can now
   also be calculated as bit vectors.
 - RDKit and layered fingerprints can now be generated using only
   linear paths.
 - the function findAllPathsOfLengthMtoN() was added

Deprecated modules (to be removed in next release):
 
Removed modules:
 - rdkit/qtGui
 - rdkit/RDToDo
 - Projects/SDView

Other:
 - As of this release a new version numbering scheme is being used:
   YYYY.MM.minor. An example, this release was done in Sept. of 2010
   so it's v2010.09.1.
 - the RDBASE environment variable is no longer required. It will be
   used if set, but the code should work without it
 - The directory Contrib/M_Kossner contains two new contributions from
   Markus Kossner.
 - A change was made to the subgraph matching code that speeds up
   substructure searches involving repeated recursive queries.
 - the deprecated registerQuery argument has been removed from the
   substructure matching functions.
 - the empty header files AtomProps.h and BondProps.h have been
   removed.
 - in order to simplify the build process the test databases are now
   in svn
 - some python functions to calculate descriptors (i.e. pyMolWt,
   pyMolLogP, etc.) that have C++ equivalents have been removed to
   clean up the interface
 - the PIL canvas should no longer generate warnings
 - Thanks to the help of Gianluca Sforna and Riccardo Vianello, it is
   now much easier to package and distribute the RDKit.
 - the bjam-based build system has been removed.

******  Release_Q22010_1 *******
(Changes relative to Release_Q12010_1)

!!!!!! IMPORTANT !!!!!!
 - There are a couple of refactoring changes that affect people using
   the RDKit from C++. Please look in the Other section below for a list.
 - If you are building the RDKit yourself, changes made in this
   release require that you use a reasonably up-to-date version of
   flex to build it. Please look in the Other section below for more
   information.

Acknowledgements:
 - Andrew Dalke, James Davidson, Kirk DeLisle, Thomas Heller, Peter Gedeck,
   Greg Magoon, Noel O'Boyle, Nik Stiefl,  
   
Bug Fixes: 
 - The depictor no longer generates NaNs for some molecules on
   windows (issue 2995724)
 - [X] query features work correctly with chiral atoms. (issue
   3000399)
 - mols will no longer be deleted by python when atoms/bonds returned
   from mol.Get{Atom,Bond}WithIdx() are still active. (issue 3007178)
 - a problem with force-field construction for five-coordinate atoms
   was fixed. (issue 3009337)
 - double bonds to terminal atoms are no longer marked as "any" bonds
   when writing mol blocks. (issue 3009756)
 - a problem with stereochemistry of double bonds linking rings was
   fixed. (issue 3009836)
 - a problem with R/S assignment was fixed. (issue 3009911)
 - error and warning messages are now properly displayed when cmake
   builds are used on windows.
 - a canonicalization problem with double bonds incident onto aromatic
   rings was fixed. (issue 3018558)
 - a problem with embedding fused small ring systems was fixed.
   (issue 3019283)
    
New Features:
 - RXN files can now be written. (issue 3011399)
 - reaction smarts can now be written.
 - v3000 RXN files can now be read. (issue 3009807)
 - better support for query information in mol blocks is present.
   (issue 2942501)
 - Depictions of reactions can now be generated.
 - Morgan fingerprints can now be calculated as bit vectors (as
   opposed to count vectors.
 - the method GetFeatureDefs() has been added to
   MolChemicalFeatureFactory
 - repeated recursive SMARTS queries in a single SMARTS will now be
   recognized and matched much faster.
 - the SMILES and SMARTS parsers can now be run safely in
   multi-threaded code. 

Deprecated modules (to be removed in next release):
 - rdkit/qtGui
 - Projects/SDView
 
Removed modules:
 - SVD code: External/svdlibc External/svdpackc rdkit/PySVD
 - rdkit/Chem/CDXMLWriter.py

Other:
 - The large scale changes in the handling of stereochemistry were
   made for this release. These should make the code more robust.
 - If you are building the RDKit yourself, changes made in this
   release require that you use a reasonably up-to-date version of
   flex to build it. This is likely to be a problem on Redhat, and
   redhat-derived systems. Specifically: if your version of flex is
   something like 2.5.4 (as opposed to something like 2.5.33, 2.5.34,
   etc.), you will need to get a newer version from
   http://flex.sourceforge.net in order to build the RDKit.

 - Changes only affecting C++ programmers:
   - The code for calculating topological-torsion and atom-pair
     fingerprints has been moved from $RDBASE/Code/GraphMol/Descriptors
     to $RDBASE/Code/GraphMol/Fingerprints.
   - The naming convention for methods of ExplicitBitVect and
     SparseBitVect have been changed to make it more consistent with
     the rest of the RDKit.
   - the bjam-based build system should be considered
     deprecated. This is the last release it will be actively
     maintained. 


******  Release_Q12010_1 *******
(Changes relative to Release_Q42009_1)

Acknowledgements:
 - Andrew Dalke, Jean-Marc Nuzillard, Noel O'Boyle, Gianluca Sforna, 
   Nik Stiefl, Anna Vulpetti
   
Bug Fixes
 - Substantial improvements were made to the SLN parser
 - A bad depiction case was fixed. (issue 2948402)
 - Hs added to planar carbons are no longer in the same plane as the
   other atoms. (issue 2951221)
 - Elements early in the periodic table (e.g. Mg, Na, etc.) no longer
   have their radical counts incorrectly assigned. (issue 2952255)
 - Some improvements were made to the v3k mol file parser. (issue
   2952272)
 - Double bonds with unspecified stereochemistry are now correctly
   flagged when output to mol files. (issue 2963522)
 - A segmentation fault that occured when kekulizing modified
   molecules has been fixed. (issue 2983794)
    
New Features
 - The MaxMin diversity picker can now be given a seed for the random
   number generator to ensure reproducible results. 

Other
 - the vflib source, which is no longer used, was removed from the
   External source tree. It's still available in svn at rev1323 or via
   this tarball:
   http://rdkit.svn.sourceforge.net/viewvc/rdkit/trunk/External/vflib-2.0.tar.gz?view=tar&pathrev=1323
 - the directory Contrib has been added to the RDKit distribution to
   house contributions that don't necessarily fit anywhere else. The
   first contribution here is a collection of scripts required to
   implement local-environment fingerprints contributed by Anna
   Vulpetti.
 - Some optimization work was done on the molecule initialization code:
   reading in molecules is now somewhat faster.
 - Some optimization work was done on the RDK and Layered fingerprinting code.

******  Release_Q42009_1 *******
(Changes relative to Release_Q32009_1)

!!!!!! IMPORTANT !!!!!!
  - A bug fix in the SMARTS parser has changed the way atom-map
    numbers in Reaction SMARTS are parsed.
      Earlier versions of the RDKit required that atom maps be
      specified at the beginning of a complex atom query:
        [CH3:1,NH2]>>[*:1]O
      The corrected version only accepts this form:
        [CH3,NH2:1]>>[*:1]O
    This change may break existing SMARTS patterns.
  - A switch to using cmake as the build system instead of bjam has
    made the RDKit much easier to build.

Acknowledgements
  - Andrew Dalke, Kirk DeLisle, David Hall, Markus Kossner, Adrian
    Schreyer, Nikolaus Stiefl, Jeremy Yang
   
Bug Fixes
  - the SMARTS parser now correctly requires tha atom-map numbers be
    at the end of a complex atom query.
    (issue 1804420)
  - a bug in the way SMARTS matches are uniquified has been fixed
    (issue 2884178)
    
New Features
  - The new SMARTS atomic query feature "x" (number of ring bonds) is
    now supported.
  - The proof-of-concept for a SWIG-based wrapper around the RDKit has
    been expanded a bit in functionality. Samples are now included for
    Java, C#, and Python.
  - Information about the current RDKit and boost versions is now
    available from C++ (file RDGeneral/versions.h) and Python 
    (rdBase.rdkitVersion and rdBase.boostVersion)
  - The KNN code now supports weighted nearest-neighbors calculations
    with a radius cutoff.

Other
  - The lapack dependency has been completely removed from the RDKit.
  - The supported build system for the RDKit is now cmake
    (http://www.cmake.org) instead of bjam. See the file INSTALL for
    the new installation instructions. Files for bjam are still
    included in the distribution but are deprecated and will be
    removed in a future version.


******  Release_Q32009_1 *******
(Changes relative to Release_Q22009_1)

!!!!!! IMPORTANT !!!!!!
  - Due to bug fixes in the boost random-number generator, RDK
    fingerprints generated with boost 1.40 are not backwards
    compatible with those from earlier versions.

Acknowledgements
  - Uwe Hoffmann, Nik Stiefl, Greg Magoon, Ari Gold-Parker,
    Akihiro Yokota, Kei Taneishi, Riccardo Vianello, Markus Kossner

Bug Fixes
  - the canonOrient argument to the depiction code now works 
    (issue 2821647)
  - typo in the depictor 2D embedding code fixed  
    (issue 2822883)
  - single aromatic atoms in chains now (correctly) fail sanitization
    (issue 2830244)
  - problem with embedding and fused rings fixed
    (issue 2835784)
  - crash when reading some large molecules fixed
    (issue 2840217)
  - trailing newline in TemplateExpand.py fixed
    (issue 2867325)
  - fingerprint incompatibility on 64bit machines fixed
    (issue 2875658)
  - PropertyMol properties are now written to SD files
    (issue 2880943)

New Features
  - to the extent possible, reactions now transfer coordinates from
    reactant molecules to product molecules (issue 2832951)
Other
  - the function DaylightFingerprintMol() has been removed
  - the outdated support for Interbase has been removed
  - the Compute2DCoords() function in Python now canonicalizes the
    orientation of the molecule by default.
  - the distance-geometry code should now generate less bad amide
    conformations. (issue 2819563)
  - the quality of distance-geometry embeddings for substituted- and
    fused-ring systems should be better.  

******  Release_Q22009_1 *******
(Changes relative to Release_Q12009_2)

Acknowledgements
  - Uwe Hoffmann, Marshall Levesque, Armin Widmer

Bug Fixes
  - handling of crossed bonds in mol files fixed (issue 2804599) 
  - serialization bug fixed (issue 2788233) 
  - pi systems with 2 electrons now flagged as aromatic (issue 2787221) 
  - Chirality swap on AddHs (issue 2762917) 
  - core leak in UFFOptimizeMolecule fixed (issue 2757824) 
   
New Features
  - cairo support in the mol drawing code (from Uwe Hoffmann) (issue 2720611)
  - Tversky and Tanimoto similarities now supported for SparseIntVects
  - AllProbeBitsMatch supported for BitVect-BitVect comparisons
  - ChemicalReactions support serialization (pickling) (issue 2799770)
  - GetAtomPairFingerprint() supports minLength and maxLength arguments
  - GetHashedTopologicalTorsionFingerprint() added
  - preliminary support added for v3K mol files
  - ForwardSDMolSupplier added
  - CompressedSDMolSupplier added (not supported on windows)
  - UFFHasAllMoleculeParams() added
  - substructure searching code now uses an RDKit implementation of
    the vf2 algorithm. It's much faster.
  - Atom.GetPropNames() and Bond.GetPropNames() now available from
    python
  - BRICS code now supports FindBRICSBonds() and BreakBRICSBonds()
  - atom labels Q, A, and * in CTABs are more correctly supported 
    (issue 2797708)
  - rdkit.Chem.PropertyMol added (issue 2742959)
  - support has been added for enabling and disabling logs
    (issue 2738020)

Other
  - A demo has been added for using the MPI with the RDKit
    ($RDBASE/Code/Demos/RDKit/MPI).
  - Embedding code is now better at handling chiral structures and
    should produce results for molecules with atoms that don't have
    UFF parameters. 
  - the UFF code is more robust w.r.t. missing parameters
  - GetHashedAtomPairFingerprint() returns SparseIntVect instead of
    ExplicitBitVect
  - the CTAB parser (used for mol files and SD files) is faster
  - extensive changes to the layered fingerprinting code;
    fingerprinting queries is now possible
  - molecule discriminator code moved into $RDBASE/Code/GraphMol/Subgraphs
  - the SDView4 prototype has been expanded
  - $RDBASE/Regress has been added to contain regression and
    benchmarking data and scripts.
  - support for sqlalchemy has been added to $RDBASE/rdkit/Chem/MolDb
  - $RDBASE/Projects/DbCLI/SDSearch.py has been removed; use the
    CreateDb.py and SearchDb.py scripts in the same directory instead.
  - the BRICS code has been refactored  

******  Release_Q12009_2 *******
(Changes relative to Release_Q42008_1)

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

 - The directory structure of the distribution has been changed in
   order to make installation of the RDKit python modules more
   straightforward. Specifically the directory $RDBASE/Python has been
   renamed to $RDBASE/rdkit and the Python code now expects that
   $RDBASE is in your PYTHONPATH. When importing RDKit Python modules,
   one should now do: "from rdkit import Chem" instead of "import
   Chem". Old code will continue to work if you also add $RDBASE/rdkit
   to your PYTHONPATH, but it is strongly suggested that you update
   your scripts to reflect the new organization.
 - For C++ programmers: There is a non-backwards compatible change in
   the way atoms and bonds are stored on molecules. See the *Other*
   section for details.
   
Acknowledgements
 - Kirk DeLisle, Noel O'Boyle, Andrew Dalke, Peter Gedeck, Armin Widmer
 
Bug Fixes
 - Incorrect coordinates from mol2 files (issue 2727976)
 - Incorrect handling of 0s as ring closure digits (issues 2525792,
 and 2690982)
 - Incorrect handling of atoms with explicit Hs in reactions (issue 2540021)
 - SmilesMolSupplier.GetItemText() crashes (issue 2632960)
 - Incorrect handling of dot separations in reaction SMARTS (issue 2690530)
 - Bad charge lines in mol blocks for large molecules (issue 2692246)
 - Order dependence in AssignAtomChiralTagsFromStructure (issue 2705543)
 - Order dependence in the 2D pharmacophore code
 - the LayeredFingerprints now handle non-aromatic single ring bonds
   between aromatic atoms correctly.
   

New Features
 - BRICS implementation
 - Morgan/circular fingerprints implementation 
 - The 2D pharmacophore code now uses standard RDKit fdef files.
 - Atom parity information in CTABs now written and read. If present
   on reading, atom parity flags are stored in the atomic property
   "molParity".
 - An optional "fromAtoms" argument has been added to the atom pairs
   and topological torsion fingerprints. If this is provided, only atom
   pairs including the specified atoms, or torsions that either start
   or end at the specified atoms, will be included in the fingerprint.
 - Kekulization is now optional when generating CTABs. Since the MDL
   spec suggests that aromatic bonds not be used, this is primarily
   intended for debugging purposes.
 - the removeStereochemistry() (RemoveStereoChemistry() from Python)
   function has been added to remove all stereochemical information
   from a molecule.

Other
 - The Qt3-based GUI functionality in $RDBASE/rdkit/qtGui and
   $RDBASE/Projects/SDView is deprecated. It should still work, but it
   will be removed in a future release. Please do not build anything
   new on this (very old and creaky) framework.
 - The function DaylightFingerprintMol() is now deprecated, use
   RDKFingerprintMol() instead.
 - For C++ programmers: The ROMol methods getAtomPMap() and
   getBondPMap() have been removed. The molecules themselves now support
   an operator[]() method that can be used to convert graph iterators
   (e.g. ROMol:edge_iterator, ROMol::vertex_iterator,
   ROMol::adjacency_iterator) to the corresponding Atoms and Bonds.
   New API for looping over an atom's bonds:
        ... molPtr is a const ROMol * ...
        ... atomPtr is a const Atom * ...
        ROMol::OEDGE_ITER beg,end;
        boost::tie(beg,end) = molPtr->getAtomBonds(atomPtr);
        while(beg!=end){
          const BOND_SPTR bond=(*molPtr)[*beg];
          ... do something with the Bond ...
          ++beg;
        }
  New API for looping over a molecule's atoms:
        ... mol is an ROMol ...
        ROMol::VERTEX_ITER atBegin,atEnd;
        boost::tie(atBegin,atEnd) = mol.getVertices();  
        while(atBegin!=atEnd){
          ATOM_SPTR at2=mol[*atBegin];
          ... do something with the Atom ...
          ++atBegin;
        }

******  Release_Q42008_1 *******
(Changes relative to Release_Q32008_1)

!!!!!! IMPORTANT !!!!!!
 - A fix in the handling of stereochemistry in rings means that the
   SMILES generated with this release are different from those in
   previous releases. Note that the canonicalization algorithm does
   not work in cases of pure ring stereochemistry : the SMILES should
   be correct, but it is not canonical. Rings containing chiral
   centers should be fine.

Acknowledgements:
 - Kirk DeLisle, Markus Kossner, Greg Magoon, Nik Stiefl 

Bug Fixes
 - core leaks in learning code (issue 2152622)
 - H-bond acceptor definitions (issue 2183240)
 - handling of aromatic dummies (issue 2196817)
 - errors in variable quantization (issue 2202974)
 - errors in information theory functions on 64 bit machines (issue 2202977)
 - kekulization problems (issue 2202977)
 - infinite loop in getShortestPaths() for disconnected structures (issue 2219400)
 - error in depictor for double bonds with stereochemistry connected
   to rings (issue 2303566)
 - aromaticity flags not copied to null atoms in reaction products
   (issue 2308128)
 - aromaticity perception in large molecule hangs (issue 2313979)
 - invariant error in canonicalization (issue 2316677)
 - mol file parser handling of bogus bond orders (issue 2337369)
 - UFF optimization not terminating when atoms are on top of each
   other (issue 2378119)
 - incorrect valence errors with 4 coordinate B- (issue 2381580)
 - incorrect parsing of atom-list queries with high-numbered atoms
   (issue 2413431)
 - MolOps::mergeQueryHs() crashing with non-query molecules. (issue
   2414779) 

New Features
 - SLN parser (request 2136703).
 - Mol2 parser : Corina atom types (request 2136705).
 - Building under mingw (request 2292153).
 - Null bonds in reaction products are replaced with the corresponding
   bond from the reactants (request 2308123).

Other
 - a bunch of deprecation warnings from numpy have been cleaned up
   (issue 2318431)
 - updated documentation
 - some optimization work on the fingerprinter

******  Release_Q32008_1 *******
(Changes relative to Release_May2008_1)

Acknowledgements:
 - Noel O'Boyle, Igor Filippov, Evgueni Kolossov, Greg Magoon

Bug Fixes
 - A memory leak in the ToBase64 and FromBase64 wrapper functions was
   fixed. 
 - The UFF atom typer has been made more permissive: it now will pick
   "close" atom types for things it does not recognize. (issue
   2094445)
 - The handling of molecules containing radicals has been greatly
   improved (issues 2091839, 2091890, 2093420)
 - Iterative (or secondary, or dependent) chirality is now supported,
   see this page for more information:
   http://code.google.com/p/rdkit/wiki/IterativeChirality
   (issue 1931470)
 - Isotope handling has been changed, this allows correct matching of
   SMARTS with specified isotopes. (issue 1968930)
 - Some problems with the MACCS key definitions have been
   fixed. (issue 2027446)
 - Molecules with multiple fragments can now be correctly
   embedded. (issue 1989539)
 - Adding multiple bonds between the same atoms in a molecule now
   produces an error. (issue 1993296)
 - The chemical reaction code now handles chiral atoms correctly in
   when applying reactions with no stereochem information
   provided. (issue 2050085)
 - A problem with single-atom cores in TemplateExpand.py has been
   fixed. (issue 2091304)  
 - A problem causing bicyclobutane containing molecules to not be
   embeddable has been fixed. (issue 2091864)
 - The default parameters for embedding are now molecule-size
   dependent. This should help with the embedding of large, and
   crowded molecules. (issue 2091974)
 - The codebase can now be built with boost 1.36. (issue 2071168)
 - A problem with serialization of bond directions was fixed. 
   (issue 2113433)

New Features
 - The RDKit can now be built under Darwin (Mac OS/X).
 - Tversky similarity can now be calculated. (request 2015633)
 - Many of the core datastructures now support equality comparison
   (operator==). (request 1997439)
 - Chirality information can now be assigned based on the 3D
   coordinates of a molecule using
   MolOps::assignChiralTypesFrom3D(). (request 1973062) 
 - MolOps::getMolFrags() can now return a list of split molecules
   instead of just a list of atom ids. (request 1992648)
 - ROMol::getPropNames() now supports the includePrivate and
   includeComputed options. (request 2047386)


Other
 - the pointers returned from Base64Encode/Decode are now allocated
   using new instead of malloc or calloc. the memory should be
   released with delete[]. 
 - the generation of invariants for chirality testing is now quite a
   bit faster; this results in faster parsing of molecules. 
 - The use of C include files instead of their C++ replacements has
   been dramatically reduced. 
 - The new (as of May2008) hashing algorithm for fingerprints is now
   the default in the python fingerprinting code 
   (Chem.Fingerprints.FingerprintMols).
 - The functions MolOps::assignAtomChiralCodes() and
   MolOps::assignBondStereoCodes() are deprecated. Use
   MolOps::assignStereochemistry() instead.
 - The RDKit no longer uses the old numeric python library. It now
   uses numpy, which is actively supported.
 - By default Lapack++ is no longer used. The replacement is the boost
   numeric bindings: http://mathema.tician.de/software/boost-bindings.
   

******  Release_May2008_1 *******
(Changes relative to Release_Jan2008_1)
 
!!!!!! IMPORTANT !!!!!!
 - A fix to the values of the parameters for the Crippen LogP
   calculator means that the values calculated with this version are
   not backwards compatible. Old values should be recalculated.
 - topological fingerprints generated with this version *may* not be
   compatible with those from earlier versions. Please read the note
   below in the "Other" section.
 - Please read the point about dummy atoms in the "New Features"
   section. It explains a change that affects backwards compatibility
   when dealing with dummy atoms.
  

Acknowledgements:
 - Some of the bugs fixed in this release were found and reported by
   Adrian Schreyer, Noel O'Boyle, and Markus Kossner.

Bug Fixes
 - A core leak in MolAlign::getAlignmentTransform was fixed (issue
   1899787) 
 - Mol suppliers now reset the EOF flag on their stream after they run
   off the end (issue 1904170) 
 - A problem causing the string "Sc" to not parse correctly in
   recursive SMARTS was fixed (issue 1912895) 
 - Combined recursive smarts queries are now output correctly.
   (issue 1914154)
 - A bug in the handling of chirality in reactions was fixed (issue
   1920627) 
 - Looping directly over a supplier no longer causes a crash (issue
   1928819) 
 - a core leak in the smiles parser was fixed (issue 1929199)
 - Se and Te are now potential aromatic atoms (per the proposed
   OpenSmiles standard). (issue 1932365)
 - isotope information (and other atomic modifiers) are now correctly
   propagated by chemical reactions (issue 1934052)
 - triple bonds no longer contribute 2 electrons to the count for
   aromaticity (issue 1940646)
 - Two bugs connected with square brackets in SMILES were fixed
   (issues 1942220 and 1942657)
 - atoms with coordination numbers higher than 4 now have tetrahedral
   stereochemistry removed (issue 1942656)
 - Bond.SetStereo() is no longer exposed to Python (issue 1944575)
 - A few typos in the parameter data for the Crippen logp calculator
   were fixed. Values calculated with this version should be assumed
   to not be backwards compatible with older versions (issue 1950302)
 - Isotope queries are now added correctly (if perhaps not optimally)
   to SMARTS.
 - some drawing-related bugs have been cleared up. 
 - A bug in Chem.WedgeMolBonds (used in the drawing code) that was
   causing incorrect stereochemistry in drawn structures was
   fixed. (issue 1965035)
 - A bug causing errors or crashes on Windows with [r<n>] queries was
   fixed. (issue 1968930)
 - A bug in the calculation of TPSA values in molecules that have Hs
   in the graph was fixed. (issue 1969745)

New Features
 - Support for supplying dummy atoms as "[Du]", "[X]", "[Xa]", etc. is
   now considered deprecated. In this release a warning will be
   generated for these forms and in the next release the old form will
   generate errors. Note that the output of dummy atoms has also
   changed: the default output format is now "*", this means that the
   canonical SMILES for molecules containing dummies are no longer
   compatible with the canonical SMILES from previous releases.
   (feature request 186217)
 - Atom and bond query information is now serializable; i.e. query
   molecules can now be pickled and not lose the query
   information. (feature request 1756596)
 - Query features from mol files are now fully supported. (feature
   request 1756962) 
 - Conformations now support a dimensionality flag. Dimensionality
   information is now read from mol blocks and TDT files. (feature request
   1906758)
 - Bulk Dice similarity functions have been added for IntSparseIntVect
   and LongSparseIntVect (feature request 1936450)
 - Exceptions are no longer thrown during molecule parsing. Failure in
   molecule parsing is indicated by returning None. Failure to *open* a
   file when reading a molecule throws BadFileExceptions (feature
   requests 1932875 and 1938303)
 - The various similarity functions for BitVects and SparseIntVects
   now take an optional returnDistance argument. If this is provided,
   the functions return the corresponding distance instead of
   similarity.
 - Some additional query information from Mol files is now translated
   when generating SMARTS. Additional queries now translated:
     - number of ring bonds
     - unsaturation queries
     - atom lists are handled better as well
   (feature request 1902466)
 - A new algorithm for generating the bits for topological
   fingerprints has been added. The new approach is a bit quicker and
   more robust than the old, but is not backwards compatible.
   Similarity trends are more or less conserved.
 - The molecule drawing code in Chem.Draw.MolDrawing has been modified
   so that it creates better drawings. A new option for drawing that
   uses the aggdraw graphics library has been added.
 - The RingInfo class supports two new methods: AtomRings() and
   BondRings() that return tuples of tuples with indices of the atoms
   or bonds that make up the molecule's rings.

Other
 - Changes in the underlying boost random-number generator in version
   1.35 of the boost library may have broken backwards compatibility
   of 2D fingerprints generated using the old fingerprinter. It is
   strongly suggested that you regenerate any stored fingerprints (and
   switch to the new fingerprinter if possible). There is an explicit
   test for this in $RDBASE/Code/GraphMol/Fingerprints/test1.cpp
 - The unofficial and very obsolete version of John Torjo's v1
   boost::logging library that was included with the RDKit
   distribution is no longer used. The logging library has been
   replaced with the much less powerful and flexible approach of just
   sending things to stdout or stderr. If and when the logging library
   is accepted into Boost, it will be integrated.
 - The DbCLI tools (in $RDBASE/Projects/DbCLI) generate topological
   fingerprints using both the old and new algorithms (unless the
   --noOldFingerprints option is provided). The default search
   uses the newer fingerprint.
 - The directory $RDBASE/Data/SmartsLib contains a library of sample
   SMARTS contributed by Richard Lewis.

   
******  Release_Jan2008_1 *******
(Changes relative to Release_Aug2007_1)
 
!!!!!! IMPORTANT !!!!!!
 - Bug fixes in the canonicalization algorithm have made it so that
   the canonical SMILES from this version are not compatible with
   those from older versions of the RDKit.
 - Please read the point about dummy atoms in the "New Features"
   section. It explains a forthcoming change that will affect
   backwards compatibility when dealing with dummy atoms.
 - The build system has been completely changed. Makefiles and Visual
   Studio project files have been removed. See the "Other" section for
   more info.
   
Acknowledgements:
 - Adrian Schreyer uncovered and reported a number of the bugs fixed
   in this release.

Bug Fixes
 - the Recap code no longer generates illegal fragments for
   highly-branched atoms. (issue 1801871)
 - the Recap code no longer breaks cyclic bonds to N
   (issue 1804418)
 - A bug in the kekulization of aromatic nitrogens has been fixed
   (issue 1811276)
 - Bugs in the Atom Type definitions for polar carbons and positive
   nitrogens in BaseFeatures.fdef have been fixed. (issue 1836242)
 - A crash in the sanitization of molecules that only have degree 4
   atoms has been fixed; it now generates an exception. The underlying
   problem with ring-finding in these systems is still present. (issue
   1836576)
 - Mol files for molecules that have more than 99 atoms or bonds are
   no longer incorrectly generated. (issue 1836615)
 - Problems with the sping PIL and PDF canvases have been cleared
   up. The PIL canvas still generates a lot of warnings, but the
   output is correct.
 - The query "rN" is now properly interpreted to be "atom whose
   smallest ring is of size N" in SMARTS queries. It was previously
   interpreted as "atom is in a ring of size N". (issue 1811276)
   This change required that the default feature definitions for
   aromaticity and lumped hydrophobes be updated.
 - The MolSuppliers (SDMolSupplier, TDTMolSupplier, SmilesMolSupplier) 
   no longer fail when reading the last element. (issue 1874882)
 - A memory leak in the constructor of RWMols was fixed.
 - A problem causing rapid memory growth with Recap analysis was fixed. 
   (issue 1880161)
 - The Recap reactions are no longer applied to charged Ns or Os
   (issue 1881803)
 - Charges, H counts, and isotope information can now be set in
   reactions. (issue 1882749)
 - The stereo codes from double bonds (used for tracking cis/trans)
   are now corrected when MolOps::removeHs is called. (issue 1894348)
 - Various small code cleanups and edge case fixes were done as a
   result of things discovered while getting the VC8 build working.
   
New Features
 - The SparseIntVect class (used by the atom pairs and topological
   torsions) is now implemented in C++.
 - The package $RDKit/Python/Chem/MolDb has been added to help deal
   with molecular databases. (this was intended for the August release
   and overlooked)
 - The module $RDKit/Python/Chem/FastSDMolSupplier has been added to
   provide a fast (at the expense of memory consumption) class for
   working with SD files. (this was intended for the August release
   and overlooked)
 - A new directory $RDKit/Projects has been created to hold things
   that don't really fit in the existing directory structure.
 - The new project $RDKit/Projects/DbCLI has been added. This contains
   command-line scripts for populating molecular database and
   searching them using substructure or similarity.
 - The code for calculating some descriptors has been moved into C++
   in the new module Chem.rdMolDescriptors. The C++ implementation is
   considerably faster than the Python one and should be 100%
   backwards compatible.
 - The MaxMinPicker (in Code/SimDivPickers) supports two new options:
   1) the user can provide a set of initial picks and the algorithm
      will pick new items that are diverse w.r.t. to those
   2) the user can provide a function to calculate the distance matrix
      instead of calculating it in advance. This saves the N^2 step of
      calculating the distance matrix.
 - A new piece of code demo'ing the use of the RDKit to add chemical
   functionality to SQLite is in Code/Demos/sqlite. This will
   eventually move from Demos into Code/sqlite once some more
   functionality has been added and more testing is done.
 - The distance geometry embedding code now supports using random
   initial coordinates for atoms instead of using the eigenvalues of
   the distance matrix. The default behavior is still to use the
   eigenvalues of the distance matrix.
 - The function Recap.RecapDecompose now takes an optional argument
   where the user can specify the minimum size (in number of atoms)
   of a legal fragment. (feature request 180196)
 - Dummy atoms can be expressed using asterixes, per the Daylight spec.
   Dummy atoms are also now legal members of aromatic systems (e.g.
   c1cccc*1 is a legal molecule). Support for supplying dummy atoms
   as "[Du]", "[X]", "[Xa]", etc. is now considered deprecated. In
   the next release a warning will be generated for these forms and
   in the release after that the old form will generate errors. Note
   that the output of dummy atoms will also change: in the next release
   the default output format will be "*".
   (feature request 186217)
 - A proof of concept for doing a SWIG wrapper of RDKit functionality
   has been added in: $RDBASE/Code/Demos/SWIG/java_example. This isn't
   even remotely production-quality; it's intended to demonstrate that
   the wrapping works and isn't overly difficult.

Other
 - The full set of tests is now easier to setup and run on new
   machines. (issue 1757265) 
 - A new build system, using Boost.Build, has been put into place on
   both the windows and linux sides. The new system does much better
   dependency checking and handles machine-specific stuff a lot
   better. The new system has been tested using Visual Studio 2003,
   Visual Studio Express 2005, Ubuntu 7.10, and RHEL5.
 - The "Getting Started in Python" document has been expanded.
 - There's now an epydoc config file for building the python
   documentation ($RDBASE/Python/epydoc.config).

******  Release_Aug2007_1 *******
(Changes relative to Release_April2007_1)

Bug Fixes
 - operators and SparseIntVects. (issue 1716736)
 - the Mol file parser now calculates cis/trans labels for double
   bonds where the two ends had the same substituents. (issue 1718794)
 - iterator interface to DiscreteValueVects and UniformGrid3D. (issue
   1719831)
 - improper removal of stereochemistry from ring atoms (issue
   1719053)
 - stereochemistry specifications and ring bonds.  (issue 1725068)
 - handling of aromatic bonds in template molecules for chemical
   reactions. (issue 1748846)
 - handling of unrecognized atom types in the descriptor calculation
   code. (issue 1749494)
 - ChemicalReactionException now exposed to Python. (issue 1749513)
 - some small problems in topological torsions and atom pairs

New Features
 - The Atom Pairs and Topological Torsions code can now provide
   "explanations" of the codes. See $RDBASE/Python/Chem/AtomPairs for
   details.
 - The PointND class has been exposed to Python
 - The "Butina" clustering algorithm [JCICS 39:747-50 (1999)] is now
   available in $RDBase/Python/Ml/Cluster/Butina.py 
 - A preliminary implementation of the subshape alignment algorithm is
   available. 
 - The free version of MS Visual C++ is now supported.   
 - There is better support for queries in MDL mol files. (issue 1756962)
   Specifically: ring and chain bond queries; the not modifier for
   atom lists; R group labels. 
 - An EditableMol class is now exposed to Python to allow molecules to
   be easily edited. (issue 1764162)
 - The RingInfo class is now exposed to Python.
 - The replaceSidechains and and replaceCore functions have been added
   in the ChemTransforms library and are exposed to Python as
   Chem.ReplaceSidechains and Chem.ReplaceCore.
 - pickle support added to classes: PointND
 - atoms and bonds now support the HasQuery() and GetSmarts() methods
   from Python.   
   
Other
 - Similarity scores can now be calculated from Python in bulk
   (i.e. calculating the similarity between one vector and a list of
   others). This can be substantially faster than calling the
   individual routines multiple times. The relevant functions are
   BulkTanimotoSimilarity, BulkDiceSimilarity, etc.
 - The calculation of AtomPairs and TopologicalTorsions fingerprints
   is now a lot more efficient.
 - Optimization of the Dice metric implementation for SparseIntVects
 - The Visual Studio build files have been moved to the directories
   $RDBASE/Code/Build.VC71 and $RDBASE/Code/Build.VC80. This allows
   simultaneous support of both versions of the system and cleans up
   the source trees a bit.
 - Boost version 1.34 is now supported (testing has been done on 1.34 and 1.34.1).
 - Updates to the "Getting Started" documentation.
 
******  Release_April2007_1 *******
(Changes relative to Release_Jan2007_1)

Bug Fixes
 - handing of isotope information in SMILES has been fixed
 - "implicit" hydrogens are now added to charged atoms explicitly when
   writing SMILES. (issue 1670149)
 - the 2D->3D code no longer generates non-planar conjugated 4-rings
   (e.g. C1=CC=C1). (issue 1653802) 
 - removing explicit hydrogens no longer produces incorrect smiles 
   (issue 1694023)
 - bit indices and signature lengths in the AtomPairs code no longer
   being calculated incorrectly. *NOTE* this changes the bits that are
   set, so if you have existing signatures, they will need to be
   regenerated.
 - Fixed a bug causing MolSuppliers to generate incorrect length
   information when a combination of random access and iterator
   interfaces are used. (issue 1702647)
 - Fixed a bug leading to incorrect line numbers in error messages
   from the SDMolSuppler. (issue 1695221)

New Features
 - chemical reactions are now supported
 - there is a new entry point into the 2D depictor code,
   compute2DCoordsMimicDistMat(), that attempts to generate 2D
   depictions that are similar to the structure described by the
   distance matrix. There's also a shorthand approach for calling this
   to mimic a 3D structure available as:
   AllChem.GenerateDepictionMatching3DStructure()
 - DiscreteValueVect and UniformGrid3D now support the binary 
   operators |, &, +, and -.
 - a reader/writer for TPL files has been added.
 - support has been added for MolCatalogs: hierarchical catalogs that
   can store complete molecules.
 - the protrude distance metric for shapes has been added
 - pickle support added to classes: UniformGrid, DiscreteValueVect,
   Point 
 - added the class DataStructs/SparseIntVect to improve performance
   and clarity of the AtomPairs code

Other
 - the non-GUI code now supports python2.5; the GUI code may work with
   python2.5, but that has not been tested
 - the Mol and SD file parsers have been sped up quite a bit.
 - the "Crippen" descriptors are now calculated somewhat faster.
 - in-code documentation updates
 - new documentation for beginners in $RDBASE/Docs/Book

******  Release_Jan2007_1 *******
(Changes relative to Release_Oct2006_1)

Bug Fixes
  - zero-atom molecules now trigger an exception
  - dummy atoms are no longer labelled 'Xe'
  - core leak in the mol file writer fixed
  - mol files with multiple charge lines are now correctly parsed
  - a workaround was installed to prevent crashes in the regression
    tests on Windows when using the newest VC++ v7 series compiler.
    (http://sourceforge.net/tracker/index.php?func=detail&aid=1607290&group_id=160139&atid=814650)
  - chirality perception (which requires partial sanitization) is no
    longer done by the MolFileParser when sanitization is switched
    off.
  - Two potential memory corruption problems were fixed (rev's 150 and
    151).

New Features
  - optional use of chirality in substructure searches
  - MolWriters can now all take a stream as an argument
  - Chiral terms can now be included in the DistanceGeometry
    embedding.

Other
  - $RDBASE/Code/Demos/RDKit/BinaryIO is a demonstration of using
    boost IOStreams and the ROMol pickling mechanism to generate
    highly compressed, random-access files of molecules.
  - the Point code has been refactored