Today I tagged the beta for the 2012.09 release in svn: http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_2012_09_1beta1/
and uploaded a source distribution to the google code site: http://code.google.com/p/rdkit/downloads/detail?name=RDKit_2012_09_1beta1.tgz The google code page also has binaries for python2.6 and python2.7 on win32. As usual: if no show-stopper bugs appear, I will do the release itself in about a week. Excerpts from the release notes are below. Best Regards, -greg ****** Release_2012.09.1 ******* (Changes relative to Release_2012.06.1) !!!!!! IMPORTANT !!!!!! - Some of the bug fixes affect the generation of SMILES. Canonical SMILES generated with this version of the RDKit will be different from previous versions. - The fix to Issue 252 (see below) will lead to changes in calculated logP and MR values for some compounds. - The fix to Issue 254 (see below) will lead to changes in some descriptors and geometries for sulfur-containing compounds. Acknowledgements: Gianpaolo Bravi, David Cosgrove, Andrew Dalke, Fabian Dey, James Davidson, JP Ebejer, Gabriele Menna, Stephan Reiling, James Swetnam Bug Fixes: - The molecules that come from mergeQueryHs() now reset the RingInfo structure. (issue 245) - The output from MurckoScaffold.MakeScaffoldGeneric no longer includes stereochemistry or explicit Hs. (issue 246) - D and T atoms in CTABs now have their isotope information set. (issue 247) - Some problems with ring finding in large, complex molecules have been fixed. (issue 249) - The "rootedAtAtom" argument for FindAllSubgraphsOfLengthN is now handled properly. (issue 250) - Bonds now have a SetProp() method available in Python. (issue 251) - A number of problems with the Crippen atom parameters have been fixed. (issue 252) - Ring closure digits are no longer repeated on the same atom in SMILES generated by the RDKit. (issue 253) - Non-ring sulfur atoms adjacent to aromatic atoms are no longer set to be SP2 hybridized. This allows them to be stereogenic. (issue 254) - The combineMols() function now clears computed properties on the result molecule. - A couple of problems with the pickling functions on big endian hardware were fixed. - The molecule drawing code now uses isotope information - Superscript/Subscript handling in the agg canvas has been improved. New Features: - The RDKit now has a maximum common substructure (MCS) implementation contributed by Andrew Dalke. This is currently implemented in Python and is available as: from rdkit.Chem import MCS Documentation is available as a docstring for the function MCS.FindMCS and in the GettingStarted document. - A few new functions have been added to rdkit.Chem.Draw: MolsToImage(), MolsToGridImage(), ReactionToImage() - CalcMolFormula() now provides the option to include isotope information. - The RDKit and Layered fingerprinters both now accept "fromAtoms" arguments that can be used to limit which atoms contribute to the fingerprint. - Version information is now available in the Java wrapper. - The descriptor NumRadicalElectrons is now available. - The PyMol interface now supports a GetPNG() method which returns the current contents of the viewer window as an PIL Image object. New Database Cartridge Features: - support for molecule <-> pickle conversion via the functions mol_to_pkl, mol_from_pkl, and is_valid_mol_pkl. - support for bit vector <-> binary text conversion via the functions bfp_to_binary_text, bfp_from_binary_text New Java Wrapper Features: Deprecated modules (to be removed in next release): Removed modules: Other: - During this release cycle, the sourceforge project was updated to their new hosting system. This explains the change in bug/issue ids. - the SMILES parser is now substantially faster. - The molecular drawings generated by Code/Demo/RDKit/Draw/MolDrawing.h have been improved. - There is now demo code availble for using the C++ drawing code within Qt applications. (contributed by David Cosgrove) - The directory $RDBASE/Regress now contains sample data and scripts for benchmarking the database cartridge. - Fused-ring aromaticity is now only considered in rings of up to size 24. ------------------------------------------------------------------------------ Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://ad.doubleclick.net/clk;258768047;13503038;j? http://info.appdynamics.com/FreeJavaPerformanceDownload.html _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
