Re: [Rdkit-devel] 2012.12 (Q4 2012) RDkit release
Open-Source Cheminformatics and Machine Learning
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glandrum
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From: Yiqun C. <cao...@gm...> - 2013-01-25 05:42:14
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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 Upgrading 6 outdated packages, with result: cmake 2.8.10.1, wget 1.14, pcre 8.32, swig 2.0.9, boost 1.52.0, rdkit 2012.12.1 If it does not work, try untap and retap: brew untap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. > > ------------------------------------------------------------------------------ > Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, > MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current > with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft > MVPs and experts. ON SALE this month only -- learn more at: > http://p.sf.net/sfu/learnnow-d2d > _______________________________________________ > Rdkit-devel mailing list > Rdk...@li... > https://lists.sourceforge.net/lists/listinfo/rdkit-devel |