Re: [Rdkit-devel] Beta of Q1 2015 release now up

[Greg L. <gre...@gm...>]

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 <gre...@gm...>
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
>
>