Dear all,

I'm pleased to announce that the next version of the RDKit -- 2015.09
(a.k.a. Q3 2015) -- is released. The new RDKit release theme is: Better
late than never. :-)

Note that this is a patch release (the version number ends in _2). We
discovered a couple of problems in the original release before I actually
announced it and decided we should fix those before announcing the release.

The release notes are below.

The release and binary files are on the github release page:
Unless there's serious demand for it, I do not plan to duplicate these on
the sourceforge download page.

I will be uploading 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

Gianluca's binary RPMs for Fedora 20, 21 and RHEL/Centos 6, 7 will be
available from
this repository:

Conda builds will start to appear in the RDKit channel at ( over the next few days.

We have updated the homebrew recipe and will update the conda build script
to reflect the new version.

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 March 2016.

Best Regards,

# Release_2015.09.2
(Changes relative to Release_2015.09.1)

## Acknowledgements:
Brian Kelley, Paolo Tosco, Riccardo Vianello

## Bug Fixes:
  - Fixed a post-decrement which causes a crash when compiling under
Windows with MSVC 9
  (from ptosco)
  - Fixes a memory leak in fragmentMol
  (github #669 from bp-kelley)
  - MMPA compile error with Microsoft Visual C++ Compiler for Python 2.7
  (github #655 from rvianello)

# Release_2015.09.1
(Changes relative to Release_2015.03.1)

## Acknowledgements:

Pierre Bhoorasingh, Gungor Budak, Andrew Dalke, JP Ebejer, Peter Ertl,
Jan Holst Jensen, Brian Kelley, Joos Kiener, Noel O'Boyle, Axel Pahl,
Sereina Riniker, Alexander Savelyev, Roger Sayle, Nadine Schneider,
Andrew Stretton, Paolo Tosco, Samo Turk, JL Varjo, Riccardo Vanello,
Maciek Wojcikowski

## Highlights:

  - Addition of parsers/writers for sequence notation, FASTA, and basic HELM
  - Improved conformation generation based on experimental torsional
  - Much better filtering of generated conformations to ensure they
    match the chirality of the input structure
  - New method for enumerating molecular resonance structures
  - Addition of a molecular FilterCatalog data structure

## Bug Fixes:
  - Draw.MolToImage(mol) does not work for Python 3, because cairo for
Python 3 has not yet implemented Surface.create_for_data
 (github issue #460 from apahl)
  - SDWriter.close() fails when the underlying stream has an error
 (github issue #498 from greglandrum)
  - Hexafluorophosphate cannot be handled
 (github issue #510 from greglandrum)
  - Labels of highlighted atoms are invisible
 (github issue #519 from NadineSchneider)
  - MolDraw2D: Fix in highlighting atoms
 (github pull #521 from NadineSchneider)
  - Cartridge: index failing for molecular equality in some circumstances
 (github issue #525 from greglandrum)
  - Bad ring finding in a complex fused ring
 (github issue #526 from greglandrum)
  - Fixed crash upon closing a gzip/bzip2 stream opened in binary mode for
use with SDWriter under Python3
 (github pull #531 from ptosco)
  - Regression: _smilesAtomOutputOrder incorrect for dot disconnected
 (github issue #532 from baoilleach)
  - Fix #532 - smilesAtomOutputOrder incorrect
 (github pull #535 from baoilleach)
  - Fix Python3 encoding for FilterCatalog/Entry serialization
 (github pull #537 from bp-kelley)
  - Catalog::setCatalogParams needs to be virtual now
 (github pull #538 from bp-kelley)
  - Bonds in allyl cation are not conjugated
 (github issue #539 from greglandrum)
  - Fixes GitHub issue 539
 (github pull #540 from ptosco)
  - SaltBuilder._initPatterns incorrectly handles SMARTS errors
 (github issue #541 from adalke)
  - merging query Hs failing on recursive SMARTS
 (github issue #544 from greglandrum)
  - Crash in O3A alignment when running multi-threaded
 (github issue #546 from greglandrum)
  - changed xmlrpc import to have Python2/Python3 compatibility
 (github pull #547 from apahl)
  - fix MMPA bugs for some tests
 (github pull #548 from AlexanderSavelyev)
  - TFD fix for single bonds adjacent to triple bonds
 (github pull #550 from sriniker)
  - Canonicalization paper Aug2015
 (github pull #552 from NadineSchneider)
  - Chirality not affected by atom-map index
 (github issue #553 from adalke)
  - Implicit Hs should not appear in depictions for query atoms.
 (github issue #556 from greglandrum)
  - Fix issue with invalid reactions throwing NameError
 (github pull #559 from bp-kelley)
  - InChI radicals not properly converted
 (github issue #562 from pierrelb)
  - MMPA code not python3 compatible
 (github issue #564 from greglandrum)
  - mmpa: fix bug with num_of_cuts > 2 case
 (github pull #566 from AlexanderSavelyev)
  - Incorrect stereochemistry after embedding
 (github issue #568 from greglandrum)
  - changed FrameToGridImage() so that the dataframe index can be used as
 (github pull #570 from apahl)
  - MolDraw2DCairo.GetDrawingText() doesn't work with Python3
 (github issue #571 from greglandrum)
  - addBond return value
 (github issue #572 from JLVarjo)
  - Process aborts during ForwardSDMolSupplier gc when the file object is
 (github issue #579 from adalke)
  - Fix/update pains filter catalog
 (github pull #581 from bp-kelley)
  - Importing PandasTools on Windows fails due to Salts.txt
 (github issue #583 from baoilleach)
  - renumberAtoms() not setting conformer dimensionality properly
 (github issue #584 from greglandrum)
  - stereo atoms property on double bonds not being updated properly with
 (github issue #608 from greglandrum)
  - UFF Atom type not properly assigned to lanthanides
 (github issue #613 from greglandrum)
  - segfault from MolToInchi when bad bond stereochem info is present
 (github issue #614 from greglandrum)
  - MQN12 (heavy atom count) seems to be always 0.
 (github issue #623 from kienerj)
  - fmcs: fix issue with initial seed for PR 580
 (github pull #624 from AlexanderSavelyev)
  - fmcs: fixes #631 with chiralirty
 (github pull #634 from AlexanderSavelyev)
  - Fixes sprintf not found on some gcc compiles
 (github pull #635 from bp-kelley)
  - Fix AppVeyor and Travis UnitTests
 (github pull #636 from bp-kelley)
  - Fixes #629 - python GetSubstructureMatch thread safety
 (github pull #637 from bp-kelley)
  - Fix regressions occurring when building with msvc9
 (github pull #638 from rvianello)
  - Fix/python gil release on rdkit threadsafe sss only
 (github pull #639 from bp-kelley)
  - ctest not running some of the python tests.
 (github issue #643 from greglandrum)
  - Issue643
 (github pull #646 from greglandrum)
  - Fix/various bug fixes filtercatalog and bad operator
 (github pull #648 from bp-kelley)
  - unlocking or destroying a locked mutex in the substructure matcher
 (github issue #653 from greglandrum)
  - MMPA compile error with Microsoft Visual C++ Compiler for Python 2.7
 (github issue #655 from rvianello)
  - new canon: fix in special symmetry invariant
 (github pull #663 from NadineSchneider)

## New Features and Enhancements:
  - enable popcount by default for cartridge
 (github issue #428 from greglandrum)
  - Added the RSMD calculation over N molecules in the cookbook.
 (github pull #495 from malteseunderdog)
  - Modified force field constraint tests to be more robust
 (github pull #503 from ptosco)
  - Fix mol drawing on Python3 (issue #460)
 (github pull #504 from apahl)
  - mmpa first version was added
 (github pull #505 from AlexanderSavelyev)
  - Forcefield tests now use RDKit::feq() instead of RDKit::round()
 (github pull #506 from ptosco)
  - SDMolSupplier(), setData() and strictParsing
 (github pull #507 from ptosco)
  - Improvements to LoadSDF and WriteSDF
 (github pull #513 from samoturk)
  - updates to mmpa. reduce number of smiles parsing
 (github pull #515 from AlexanderSavelyev)
  - Some enhancements for the new canonicalization
 (github pull #520 from NadineSchneider)
  - mmpa: remove boost_regex dependency at all. Add new test references
 (github pull #527 from AlexanderSavelyev)
  - Support getting atoms involved in Pharm2D bits
 (github issue #530 from greglandrum)
  - Optimized MMFF::MMFFOptimizeMoleculeConfs()
 (github pull #534 from ptosco)
  - RDKit learns how to filter PAINS/BRENK/ZINC/NIH via FilterCatalog
 (github pull #536 from bp-kelley)
  - Expose Conformer's copy constructor to Python
 (github issue #545 from greglandrum)
  - changed xmlrpc import to have Python2/Python3 compatibility
 (github pull #547 from apahl)
  - Update PAINS smarts to validated set.  Always use mergeQueryHs when
reading Smarts
 (github pull #549 from bp-kelley)
  - Add a curated set of PAINS filters to the RDKit
 (github issue #555 from greglandrum)
  - Update pains from wehi_pains.csv
 (github pull #560 from bp-kelley)
  - Change MMPA to use CanonicalRankAtoms instead of _CIPRank
 (github issue #561 from adalke)
  - Add adjustQuery() function to make substructure queries more specific.
 (github issue #567 from greglandrum)
  - changed to enable import from different location
 (github pull #569 from apahl)
  - add export_values() to enums in the python wrapper where it's sensible
to do so
 (github issue #573 from greglandrum)
  - Support Sheridan's BT and BP fingerprints
 (github issue #574 from greglandrum)
  - Locale dependent float for _GasteigerCharge
 (github issue #577 from adalke)
  - fmcs: implement adding an initial seed structure
 (github pull #580 from AlexanderSavelyev)
  - Where possible convert docs from RST to MD
 (github issue #585 from greglandrum)
  - [UGM2015] Autodetection of numThreads
 (github issue #586 from mwojcikowski)
  - Generating SVG Images with Transparent Background
 (github issue #587 from gungorbudak)
  - updates to PandasTools.LoadSDF
 (github pull #599 from adalke)
  - Can control mol depiction size with PandasTools.molSize = (200,200).
 (github pull #600 from samoturk)
  - pandas performance and functionality improvements
 (github pull #601 from adalke)
  - Adding documentation for installation with conda.
 (github pull #602 from strets123)
  - Automatic atom reordering in TorsionFingerprints
 (github pull #603 from sriniker)
  - remove bare excepts
 (github pull #606 from adalke)
  - Added option to use SVG rendering in pandas data frames
 (github pull #609 from samoturk)
  - Handle inserting molecules with conformers into molecules without
 (github issue #610 from greglandrum)
  - If wedged bonds are already present, write them to mol blocks
 (github issue #611 from greglandrum)
  - Dev/filter catalog java wrapper
 (github pull #612 from bp-kelley)
  - Support extended reduced graphs
 (github issue #615 from greglandrum)
  - port NumSpiroCenters and NumBridgeheadAtoms descriptors to C++
 (github issue #617 from greglandrum)
  - Add parser/writer for peptide sequences
 (github issue #620 from greglandrum)
  - Add parser/writer for FASTA
 (github issue #621 from greglandrum)
  - Add parser/writer for HELM
 (github issue #622 from greglandrum)
  - Migrate std::string APIs to const std::string &
 (github pull #627 from bp-kelley)
  - Chirality tests
 (github pull #628 from sriniker)
  - Improvements of TFD
 (github pull #630 from sriniker)
  - Added ResonanceMolSupplier
 (github pull #632 from ptosco)
  - Image tostring/fromstring methods replaced by tobytes/frombytes
 (github pull #644 from rvianello)
  - ET(K)DG implementation
 (github pull #647 from sriniker)
  - Build multithreading support by default when boost::threads is present
 (github issue #649 from greglandrum)
  - Minimal SWIG Java wrappers for ResonanceMolSupplier
 (github pull #657 from ptosco)

## New Database Cartridge Features:
  - Support for PostgreSQL v8.x has been removed
  - NumSpiroCenters and NumBridgeheadAtoms added

## New Java Wrapper Features:
  - Support for FilterCatalogs
  - Support for ResonanceMolSuppliers

## Deprecated code (to be removed in next release):

## Removed code:
  - rdkit/DataStructs/ : a C++ version is used, this was only
present for historical reasons
  - rdkit/DataStructs/ : a C++ version is used, this was
only present for historical reasons

## Contrib updates:
  - Addition of Peter Ertl's Natural Product Likeness score.

## Other:
  - Much of the documentation has been translated from RST to MD
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