The URL in the email below is incorrect (copy-paste bug!), it should be:
https://github.com/rdkit/rdkit/releases/tag/Release_2015_03_1beta1
Apologies for the mistake.
-greg
On Fri, Apr 17, 2015 at 4:32 AM, Greg Landrum <greg.land...@gmail.com>
wrote:
> Dear all,
>
> I have tagged a beta of the next RDKit release here:
> https://github.com/rdkit/rdkit/releases/tag/2014_09_1beta1
>
> The relevant section of the release notes is below.
>
> I will try to get windows binaries up in the next few days.
>
> Unless major problems are found, I plan to do the actual release in about
> two weeks.
>
> Best,
> -greg
>
> ****** Release_2015.03.1 *******
> (Changes relative to Release_2014.09.2)
>
> !!!!!! IMPORTANT !!!!!!
>
> - This release has a new algorithm for canonical atom ordering. This
> means that canonical SMILES generated with the new version will be
> different from those generated with previous versions.
>
> Acknowledgements:
> David Cosgrove, Andrew Dalke, JP Ebejer, Niko Fechner, Igor Filippov,
> Patrick Fuller, David Hall, J Bach Hardie, Jan Holst Jensen, Brian
> Kelley, Rich Lewis, John May, Sereina Riniker, Alexander Savelyev,
> Roger Sayle, Nadine Schneider, Paolo Tosco, Samo Turk, JL Varjo,
> Riccardo Vianello
>
> Highlights:
>
> - A new algorithm for generating canonical atom orders. The new
> algorithm is faster and more robust than the old one.
> - C++-based molecule drawing code, allows consistent molecule
> renderings from C++, Java, and Python. This will become the
> default renderer in the next release.
> - General performance improvements and reduction of memory usage.
> - Torsion Fingerprints for comparing 3D conformations to each other
> - MCS code now available from the PostgreSQL cartridge
>
> Bug Fixes:
>
> - fmcs: use the zero bond type instead of other
> (github issue #368 from AlexanderSavelyev)
> - bug fixed in TorsionFingerprints.GetTFDMatrix
> (github issue #376 from sriniker)
> - rdkit.Chem.MolDb.Loader_sa does not work with python3.4
> (github issue #390)
> - ChemReactions: Bugfix/Memleak-fix in runReactants
> (github issue #394 from NadineSchneider)
> - TorsionConstraint bug fix
> (github issue #395 from ptosco)
> - Fixed LoadSDF to keep 3D info
> (github pull #401 from samoturk)
> - Incorrect expected absolute stereochemistries in a test
> (github issue #407)
> - GetSubstructMatches() consumes all available memory
> (github issue #409)
> - Bugfix in the chirality handling of chemical reactions
> (github pull #410 from NadineSchneider)
> - fixed two minor bugs in MMFF code
> (github issue #416 from ptosco)
> - Varied sanitise rejection with hydrogen representation
> (github issue #418)
> - Fixed two trivial bugs
> (github issue #419 from ptosco)
> - RDKit learns how to roundtrip MOLFile values.
> (github issue #420 from bp-kelley)
> - cairoCanvas.py python3 compatibility
> (github issue #426 from bach-hardie)
> - Chem.FragmentOnSomeBonds() should update implicit H count on aromatic
> heteroatoms when addDummies is False
> (github issue #429)
> - Chem.FragmentOnSomeBonds() crashes if the bond list is empty
> (github issue #430)
> - Increase limit for smallest ring size
> (github issue #431 from cowsandmilk)
> - Problems caused by heteroatoms with radicals in aromatic rings.
> (github issue #432)
> - Metals in mol2 blocks handled incorrectly
> (github issue #438)
> - Fixed a few tests failing when the Windows git client is used
> (github pull #439 from ptosco)
> - Fixed tests failing on Windows when retrieving sources through the
> Windows git client
> (github pull #440 from ptosco)
> - Conformers not copied correctly in renumberAtoms
> (github issue #441)
> - Radicals are not correctly assigned when reading from SMILES
> (github issue #447)
> - moving RDBoost/Exceptions.h to RDGeneral
> (github pull #458 from rvianello)
> - Add code to accept blank SMILES input.
> (github issue #468 from janholstjensen)
> - Accept empty SMILES and SMARTS
> (github issue #470)
> - Fix MolFile Atom Line List Writer
> (github issue #471 from bp-kelley)
> - Moved 3D ipython renderer to dependency
> (github pull #472 from patrickfuller)
> - Windows build/test failure fixes
> (github issue #473 from ptosco)
>
> New Features:
>
> - Isomeric fix in PandasTools
> (github issue #369 from samoturk)
> - added SaveXlsxFromFrame - first version
> (github issue #371 from samoturk)
> - New feature: Torsion fingerprints
> (github issue #372 from sriniker)
> - Add function to extract a molecule with a single (particular)
> conformer from a multiconf mol
> (github issue #384)
> - Added C++ and Python helpers to retrieve force-field parameters
> (github issue #387 from ptosco)
> - Support providing all options to SWIG-wrapped FMCS
> (github issue #397)
> - Add function to request if calling UpdatePropertyCache is necessary
> (github issue #399)
> - Add function to test if UpdatePropertyCache is necessary
> (github issue #400 from NadineSchneider)
> - Substructure highlighting in pandas dataframe (fixes #362)
> (github issue #403 from nhfechner)
> - Added SDF Export to PandasTools and adjusted SDF Import
> (github issue #404 from nhfechner)
> - support count-based avalon fingerprint
> (github issue #408)
> - New C++ drawing code
> (github issue #412 from greglandrum)
> - RDKit learns how to compute code coverage for tests
> (github issue #413 from bp-kelley)
> - Dictionary access is saniztized and optimized.
> (github issue #414 from bp-kelley)
> - expose MolOps::rankAtoms() and MolOps::rankAtomsInFragment() to python
> (github issue #421)
> - Dev/expose rank atoms to python
> (github issue #422 from bp-kelley)
> - rdkit learns how to wrap a proper RWMol in python
> (github issue #423 from bp-kelley)
> - Docs: document "magic" property values that are used throughout the
> code
> (github issue #425)
> - MolDraw2D: expose class to Python
> (github issue #433)
> - RDKit learns how to query properties on Atoms
> (github issue #442 from bp-kelley)
> - Issue445: provide helper functions for multithreaded evaluation of
> some expensive functions
> (github issue #448 from greglandrum)
> - RDKit learns how to release the GIL in python
> (github pull #449 from bp-kelley)
> - Dev/property queries
> (github pull #450 from bp-kelley)
> - Support a confId argument to the atom pair fingerprinting code
> (github issue #453)
> - Save the atom bookmarks so we can deconvolute reaction products.
> (github pull #454 from bp-kelley)
> - Cartridge: Support converting no structs to InChI
> (github issue #455)
> - RDKit learns how to expose ChemicalReaction copy constructor to python
> (github pull #456 from bp-kelley)
> - chirality flag was implemented for fmcs() function. NOTE: as of the
> beta release,
> there is a known order-dependency bug in this functionality.
> (github pull #466 from AlexanderSavelyev)
> - Support copy and deepcopy properly for at least Mol and RWMol
> (github issue #467)
> - Cartridge: add qmol_from_smiles() and qmol_from_ctab()
> (github issue #469)
> - restore java and python wrappers. New parameter (matchChiralTag)
> (github issue #477 from AlexanderSavelyev)
>
> New Database Cartridge Features:
>
> - The MCS code is now available within the cartridge
> - The functions qmol_from_smiles() and qmol_from_ctab()
>
> New Java Wrapper Features:
>
> - The new molecule rendering code is accessible from the SWIG wrappers.
>
> Deprecated code (to be removed in next release):
>
> - C++: The functionality in $RDBASE/Code/GraphMol/MolDrawing has been
> superseded by the new drawing code in $RDBASE/Code/GraphMol and will
> be removed in the next release.
> - Python:
> - rdkit/Dbase/Pubmed
> - rdkit/Chem/fmcs (this has been superseded by the C++ implementation)
> - Cartridge: support for v8.x of PostgreSQL (v8.4 is no longer
> supported by the PostgreSQL project team as of July 2014)
>
> Removed code:
>
> - the method Atom::setMass() has been removed. Please use setIsotope()
> instead.
> - the methods involving an atom's dativeFlag have been removed.
>
> Contrib updates:
>
> Other:
> - Python 2.6 support is deprecated. Starting with the next RDKit
> release, we will only support python 2.7 and python 3.4 and
> higher. Python 2.6 has not been supported since October 2013. If you
> believe that you are stuck with python 2.6 because of the version of
> RHEL you are running, please read this post to learn about your
> options:
>
> http://www.curiousefficiency.org/posts/2015/04/stop-supporting-python26.html
> - The RDKit molecule objects (ROMol and RWMol) now require about 15%
> less memory to store
>
>
------------------------------------------------------------------------------
BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
Develop your own process in accordance with the BPMN 2 standard
Learn Process modeling best practices with Bonita BPM through live exercises
http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
_______________________________________________
Rdkit-devel mailing list
Rdkit-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-devel