Dear all,

In preparation for this week's RDKit UGM, I have tagged a beta of the next
RDKit release here:

The relevant section of the release notes is below.

I will try to get windows binaries up before the UGM starts on Wednesday.

Unless major problems are found, I plan to do the actual release in about a


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

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

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)
- 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)

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

New Database Cartridge Features:
- 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):

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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