Dear all,

I'm pleased to announce that the next version of the RDKit -- 2014.03
(a.k.a Q1 2014) -- is released. This is a "bit" late, but it turned out
that it takes longer to get a 6-month release together than it did a
3-month release. Who ever would have anticipated that? ;-)

The release notes are below.

The release and binary files are on the github release page:
as well as the sourceforge downloads page:

I have uploaded 32-bit and 64-bit Windows binaries for Python 2.7 and, in
response to a couple of requests, 32-bit and 64-bit Windows binaries for

The online version of the documentation at has been updated.

Thanks to the everyone who submitted bug reports and suggestions for this

Please let me know if you find any problems with the release or have
suggestions for the next one, which is scheduled for September 2014.

Best Regards,

******  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.

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
 (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
 (github issue 259)
- cartridge: similarity calculations wrong for maccs fps when
 (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
 (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
 (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)

- 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)
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