Re: [Rdkit-devel] 2012.12 (Q4 2012) RDkit release
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 Upgrading 6 outdated packages, with result: cmake 2.8.10.1, wget 1.14, pcre 8.32, swig 2.0.9, boost 1.52.0, rdkit 2012.12.1 If it does not work, try untap and retap: brew untap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 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::getCripp
Re: [Rdkit-devel] 2012.12 (Q4 2012) RDkit release
Thanks Gianluca! On Tue, Jan 22, 2013 at 10:26 AM, Gianluca Sforna wrote: > On Tue, Jan 22, 2013 at 6:00 AM, Greg Landrum wrote: >> I'm very happy to announce that the next version of the RDKit -- >> 2012.12 (a.k.a Q4 2012) -- is released. > > Thanks to Greg, I can offer again binary RPMs for Enterprise Linux 6 > (RHEL, CentOS, etc) and Fedora 18, both at 64bit. > > grab them from: http://giallu.fedorapeople.org/rdkit-2012.12/ > > > -- > Gianluca Sforna > > http://morefedora.blogspot.com > http://identi.ca/giallu - http://twitter.com/giallu -- 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 Rdkit-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-devel
Re: [Rdkit-devel] 2012.12 (Q4 2012) RDkit release
On Tue, Jan 22, 2013 at 6:00 AM, Greg Landrum wrote: > I'm very happy to announce that the next version of the RDKit -- > 2012.12 (a.k.a Q4 2012) -- is released. Thanks to Greg, I can offer again binary RPMs for Enterprise Linux 6 (RHEL, CentOS, etc) and Fedora 18, both at 64bit. grab them from: http://giallu.fedorapeople.org/rdkit-2012.12/ -- Gianluca Sforna http://morefedora.blogspot.com http://identi.ca/giallu - http://twitter.com/giallu -- 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 Rdkit-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-devel
[Rdkit-devel] 2012.12 (Q4 2012) RDkit release
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 C
