Dear all,

I'm pleased to announce that the next version of the RDKit -- 2014.09
(a.k.a. Q3 2014) -- is released.

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 will be updated in the
next day or so.

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 March 2015.

Best Regards,

******  Release_2014.09.1 *******
(Changes relative to Release_2014.03.1)

Andrew Dalke, James Davidson, Jan Domanski, Patrick Fuller, Seiji
Matsuoka, Noel O'Boyle, Sereina Riniker, Alexander Savelyev, Roger
Sayle, Nadine Schneider, Matt Swain, Paolo Tosco, Riccardo Vianello,
Richard West

Bug Fixes:
- Bond query information not written to CTAB
 (github issue #266)
- Bond topology queries not written to CTABs
 (github issue #268)
- Combined bond query + topology query not correctly parsed from CTAB
 (github issue #269)
- SWIG wrapped suppliers leak memory on .next()
 (github issue #270)
- SWIG wrappers don't build with SWIG 3.0.x
 (github issue #277)
- core leak from DataStructs.ConvertToNumpyArray
 (github issue #281)
- MolTransforms not exposed to Java wrapper
 (github issue #285)
- Seg fault in ReactionFromRxnBlock
 (github issue #290)
- BitInfo from GetHashedMorganFingerprint() has non-folded values
 (github issue #295)
- bad inchi for chiral S when the molecule is sanitized
 (github issue #296)
- Cannot generate smiles for ChEBI 50252
 (github issue #298)
- Either molecule-molecule substruct matching is wrong *OR* the docs for
Atom::Match incorrect
 (github issue #304)
- fluorine F-F  gives segmentation fault with MMFF forcefield
 (github issue #308)
- cartridge: MACCS similarity wrong when using the builtin popcount and the
 (github issue #311)
- Substructure Search via SMARTS implicit hydrogens
 (github issue #313)
- SMARTS output for [x] is wrong
 (github issue #314)
- Bonds not being set up properly in renumberAtoms
 (github issue #317)
- Python 2 code in python 3 branch
 (github issue #326)
- Linking error with ICC 15.0 on Linux
 (github issue #327)
- Using explicit hydrogens in the SMILES lead to the same AP FP for two
different molecules
 (github issue #334)
- memory leaks when smiles/smarts parsers fail
 (github issue #335)
- No double bond stereo perception from CTABs when sanitization is turned
 (github issue #337)
- missing MACCS key 44 might be found
 (github issue #352)
- Hydrogens in mol blocks have a valence value set
 (github issue #357)
- Computed props on non-sanitized molecule interfering with substructure
 (github issue #360)
- Fixed a weakness in the angular restraint code
 (github pull #261 from ptosco)
- A few fixes to improve MMFF/UFF robustness
 (github pull #274 from ptosco)
- Static webGL rendering fix
 (github pull #287 from patrickfuller)
- Revert #include ordering in SmilesMolSupplier.cpp
 (github pull #297 from mcs07)
- Add missing include for RDDepict::compute2DCoords
 (github pull #301 from baoilleach)
- Herschbach-Laurie fallback implemented to fix GitHub 308
 (github pull #312 from ptosco)
- Issue #320 Making GetBestRMS more idiot-proof
 (github pull #322 from jandom)
- Update URLs to InChI API after website redesign.
 (github pull #341 from rwest)

New Features:
- Should be able to do intramolecular bond breaking in reactions.
 (github issue #58)
- Support reactions in cartridge
 (github issue #223)
- Documentation of Inchi methods
 (github issue #240)
- add DescribeQuery() to Bond python wrapper
 (github issue #267)
- support avalon fingerprint in cartridge
 (github issue #286)
- support partial fragmentation with fragmentOnSomeBonds
 (github issue #288)
- Add calcNumHeterocycles() descriptor
 (github issue #351)
- C++ implementation of FMCS algorithm
- Reordering feature for Butina clustering
 (github pull #302 from sriniker)
- Changes and new functions for the calculation of RMS values between
conformers of a molecule
 (github pull #306 from sriniker)
- Extended chemical reaction functionality and add chemical reactions to
 (github pull #315 from NadineSchneider)
- Custom color to highlight atoms in Mol2Image
 (github pull #316 from jandom)
- Several different fingerprint algorithms for chemical reactions are now
- add Chem.Draw.MolToQPixmap
 (github pull #355 from mojaie)

New Database Cartridge Features:
- *NOTE:* the configuration variable rdkit.ss_fp_size has been renamed to
- Chemical reactions and several operations on them are now supported
- Avalon fingerprints now supported (when support has been compiled in)

New Java Wrapper Features:
- FMCS implementation exposed
- Fingerprints for chemical reactions
- Possible core leak in some of the MolSuppliers was fixed

Deprecated modules (to be removed in next release):
- Projects/SDView4
- rdkit/utils/
- rdkit/Logger

Removed modules:

Contrib updates:

- The RDKit now supports both python3 and python2.
- There is now conda integration for the RDKit.
- SMILES generation is substantially faster
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