<commit_before>******  Release_Q12009_1 *******
(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.


Acknowledgements:

Bug Fixes

New Features

Other


******  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:
 - <NAME>, <NAME>, <NAME>, <NAME> 

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:
 - <NAME>, <NAME>, <NAME>, <NAME>

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
   <NAME>, <NAME>, and <NAME>.

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 <NAME>'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 <NAME>.

   
******  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:
 - <NAME> 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
<commit_msg>start updating the release notes<commit_after>******  Release_Q12009_1 *******
(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
 - <NAME>, <NAME>, <NAME>
 
Bug Fixes
 - 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)

New Features
 - BRICS implementation
 - Morgan/circular fingerprints implementation 

Other
 - 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:
 - <NAME>, <NAME>, <NAME>, <NAME> 

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:
 - <NAME>, <NAME>, <NAME>, <NAME>

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
   <NAME>, <NAME>, and <NAME>.

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 <NAME>'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 <NAME>.

   
******  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:
 - <NAME> 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

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