Re: [Rdkit-devel] 2012.12 (Q4 2012) RDkit release

[Yiqun C. <cao...@gm...>]

Hi,

If you use Homebrew to install rdkit, the formula has been updated to use the new release. To update, run these two commands

brew update edc/homebrew-rdkit
brew upgrade rdkit

You should see something like this:

==> Upgrading 6 outdated packages, with result:
cmake 2.8.10.1, wget 1.14, pcre 8.32, swig 2.0.9, boost 1.52.0, rdkit 2012.12.1

If it does not work, try untap and retap:

brew untap edc/homebrew-rdkit
brew tap edc/homebrew-rdkit
brew uninstall rdkit
brew install rdkit

Regards,
Eddie

On Jan 21, 2013, at 9:00 PM, Greg Landrum <gre...@gm...> wrote:

> I'm very happy to announce that the next version of the RDKit --
> 2012.12 (a.k.a Q4 2012) -- is released.
> 
> The release notes are below.
> 
> The source release is on the sourceforge downloads page:
> http://sourceforge.net/projects/rdkit/files/rdkit/Q4_2012/
> The files can also be downloaded from the google project page:
> http://code.google.com/p/rdkit/downloads/list
> The binaries for Windows, 32bit Python 2.7, have also been uploaded.
> If there's demand, I can also provide 32bit Python 2.6 binaries or
> 64bit Python 2.7 binaries.
> 
> The online version of the documentation at rdkit.org has been updated.
> 
> Thanks to the everyone who submitted bug reports and suggestions for
> this release!
> 
> Please let me know if you find any problems with the release or have
> suggestions for the next one.
> 
> -greg
> 
> ******  Release_2012.12.1 *******
> (Changes relative to Release_2012.09.1)
> 
> Acknowledgements:
> Andrew Dalke, James Davidson, Robert Feinstein, Nikolas Fechner,
> Nicholas Firth, Markus Hartenfeller, Jameed Hussain, Thorsten Meinl,
> Sereina Riniker, Roger Sayle, Gianluca Sforna, Pat Walters, Bernd
> Wiswedel
> 
> Bug Fixes:
> - Using parentheses for zero-level grouping now works in reaction
>   SMARTS. This allows intramolecular reactions to be expressed.
> - SMILES generated for molecules with ring stereochemistry
>   (e.g. N[C@H]1CC[C@H](CC1)C(O)=O) are now canonical. (issue 40)
> - SKP lines in a CTAB property block are now properly handled. (issue
>   255)
> - The molecular drawing code now shows dotted lines for Any bonds.
>   (issue 260)
> - ROMol::debugMol() (ROMol.DebugMol() in Python) now reports isotope
>   information. (issue 261)
> - The molecular drawing code now correctly highlights wedged bonds.
>   (issue 262)
> - RWMol::addAtom() now adds atoms to conformers.
>   (issue 264)
> - TDT files with atomic coordinates now have those coordinates in the
>   correct order. (issue 265)
> - A ring-finding error/crash has been fixed. (issue 266)
> - Dummy atoms now have a default valence of 0 and no maximim
>   valence. (issue 267)
> - The Python code no longer throws string exceptions. (issue 268)
> - Invalid/unrecognized atom symbols in CTABs are no longer
>   accepted. (issue 269)
> - Chem.RDKFingerprint now accepts atom invariants with values larger
>   than the number of atoms. (issue 270)
> - The code should now all work when the locale (LANG) is set to
>   values other than "C" or one of the English locales. (issue 271)
> - Two-coordinate Hs are no longer removed by
>   MolOps::removeHs(). (issue 272)
> - R groups read from CTABs are now marked using setIsotope() instead
>   of setMass(). (issue 273)
> - Hs present in the molecule graph no longer incorrectly impact
>   substructure matches. (issue 274)
> - Murcko decomposition of molecules with chiral ring atoms now
>   works. (issue 275)
> - Methane now shows up in molecular drawings. (issue 276)
> - '&' in SLN properties is now correctly handled. (issue 277)
> - Molecules with string-valued molAtomMapNumber atomic properties can
>   now be serialized. (issue 280)
> - SMARTS strings containing a dot in a recursive piece are now
>   properly parsed. (issue 281)
> - The SMILES and SLN parsers no longer leak memory when sanitization
>   of the result molecule fails. (issue 282)
> - The cairo canvas drawing code now works with PIL v1.1.6 as well as
>   more recent versions.
> 
> New Features:
> - RDKit ExplicitBitVects and DiscreteValueVects can now be directly
>   converted into numpy arrays.
> - Rogot-Goldberg similarity has been added.
> - C++: BitVects and SparseIntVects now support a size() method.
> - C++: DiscreteValueVects now support operator[].
> - An initial version of a SWIG wrapper for C# has been added.
> - Support for easily adding recursive queries to molecules and
>   reactions has been added. More documentation is required for this
>   feature.
> - To allow more control over the reaction, it is possible to flag reactant
>   atoms as being protected by setting the "_protected" property on those
>   atoms. Flagged atoms will not be altered in the reaction.
> - Atoms and Bonds now support a ClearProp() method from python.
> - The new Python module rdkit.ML.Scoring.Scoring includes a number of
>   standard tools for evaluating virtual screening experiments: ROC
>   curve generation, AUC, RIE, BEDROC, and Enrichment.
> - The function RDKit::Descriptors::getCrippenAtomContribs()
>   (rdkit.Chem.rdMolDescriptors._CalcCrippenContribs() from Python)
>   can now optionally return atom-type information as ints or text.
> 
> 
> New Database Cartridge Features:
> - The Chi and Kappa descriptors are now available
> 
> New Java Wrapper Features:
> - The Chi and Kappa descriptors are now available
> 
> Deprecated modules (to be removed in next release):
> 
> Removed modules:
> - The old SWIG wrapper code in $RDBASE/Code/Demos/SWIG has been
>  removed. The SWIG wrappers are now in $RDBASE/Code/JavaWrappers
> 
> Other:
> - The C++ code for drawing molecules previously found in
>  $RDBASE/Code/Demos/RDKit/Draw has been moved to
>  $RDBASE/Code/GraphMol/MolDrawing
> - Calculation of the Chi and Kappa descriptors has been moved into
>  C++.
> - To make builds easier, the thread-safety of the recursive-smarts
>  matcher has been made optional. The build option is
>  RDK_BUILD_THREADSAFE_SSS.
> - There are two new entries in the Contrib directory:
>  * Contrib/PBF : An implementation of the Plane of Best Fit
>    contributed by Nicholas Firth.
>  * Contrib/mmpa : An implementation of GSK's matched molecular pairs
>    algorithm contributed by Jameed Hussain
> - A new "Cookbook" has been added to the documentation to provide
>  a collection of recipes for how to do useful tasks.
> 
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