I'm pleased to announce that the next version of the RDKit -- 2013.03 (a.k.a Q1 2013) -- is released.
The release notes are below. The source release is on the sourceforge downloads page: http://sourceforge.net/projects/rdkit/files/rdkit/Q1_2013/ The files can also be downloaded from the google project page: http://code.google.com/p/rdkit/downloads/list I will be uploading 32-bit and 64-bit Windows binaries for Python 2.7 later today. 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_2013.03.1 ******* (Changes relative to Release_2012.12.1) !!!!!! IMPORTANT !!!!!! - The algorithm for hashing subgraphs used in the RDKit fingerprinter has changed. The new default behavior will return different fingerprints than previous RDKit versions. This affects usage from c++, python, and within the postgresql cartridge. See the "Other" section below for more details. Acknowledgements: Paul Czodrowski, Andrew Dalke, Jan Domanski, Jean-Paul Ebejer, Nikolas Fechner, Jameed Hussain, Stephan Reiling, Sereina Riniker, Roger Sayle, Riccardo Vianello Bug Fixes: - removeBond now updates bond indices (sf.net issue 284) - dummy labels are no longer lost when atoms are copied (sf.net issue 285) - more specific BRICS queries now match before less specific ones (sf.net issue 287, github issue 1) - molAtomMapNumber can now be set from Python (sf.net issue 288) - the legend centering for molecular image grids has been improved (sf.net issue 289) - make install now includes all headers (github issue 2) - InChIs generaged after clearing computed properties are now correct (github issue 3) - Reacting atoms that don't change connectivity no longer lose stereochemistry (github issue 4) - Aromatic Si is now accepted (github issue 5) - removeAtom (and deleteSubstructs) now correctly updates stereoAtoms (github issue 8) - [cartridge] pg_dump no longer fails when molecules cannot be converted to SMILES (github issue 9) - a canonicalization bug in MolFragmentToSmiles was fixed (github issue 12) - atom labels at the edge of the drawing are no longer cut off (github issue 13) - a bug in query-atom -- query-atom matching was fixed (github issue 15) - calling ChemicalReaction.RunReactants from Python with None molecules no longer leads to a seg fault. (github issue 16) - AllChem.ReactionFromSmarts now generates an error message when called with an empty string. - Writing CTABs now includes information about atom aliases. - An error in the example fdef file $RDBASE/Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef has been fixed. (github issue 17) - Quantize.FindVarMultQuantBounds() no longer generates a seg fault when called with bad arguments. (github issue 18) - The length of SDMolSuppliers constructed from empty files is no longer reported as 1. (github issue 19) - Partial charge calculations now work for B, Si, Be, Mg, and Al. (github issue 20) - Two logging problems were fixed (github issues 21 and 24) - Molecules that have had kappa descriptors generated can now be written to SD files (github issue 23) New Features: - The handling of chirality in reactions has been reworked and improved. Please see the RDKit Book for an explanation. - Atom-pair and topological-torsion fingerprints now support the inclusion of chirality in the atom invariants. - A number of new compositional descriptors have been added: calcFractionCSP3, calcNum{Aromatic,Aliphatic,Saturated}Rings, calcNum{Aromatic,Aliphatic,Saturated}Heterocycles, calcNum{Aromatic,Aliphatic,Saturated}Carbocycles - An implementation of the molecular quantum number (MQN) descriptors has been added. - RDKFingerprintMol now takes an optional atomBits argument which is used to return information about which bits atoms are involved in. - LayeredFingerprintMol no longer takes the arguments tgtDensity and minSize. They were not being used. - LayeredFingerprintMol2 has been renamed to PatternFingerprintMol - The substructure matcher can now properly take stereochemistry into account if the useChirality flag is provided. - The module rdkit.Chem.Draw.mplCanvas has been added back to svn. - A new module integrating the RDKit with Pandas (rdkit.Chem.PandasTools) has been added. New Database Cartridge Features: - The new compositional descriptors are available: calcFractionCSP3, calcNum{Aromatic,Aliphatic,Saturated}Rings, calcNum{Aromatic,Aliphatic,Saturated}Heterocycles, calcNum{Aromatic,Aliphatic,Saturated}Carbocycles - MACCS fingerprints are available - the substruct_count function is now available - substructure indexing has improved. NOTE: indexes on molecule columns will need to be rebuilt. New Java Wrapper Features: - The new compositional descriptors are available: calcFractionCSP3, calcNum{Aromatic,Aliphatic,Saturated}Rings, calcNum{Aromatic,Aliphatic,Saturated}Heterocycles, calcNum{Aromatic,Aliphatic,Saturated}Carbocycles - The molecular quantum number (MQN) descriptors are available - MACCS fingerprints are available - BRICS decomposition is available. Deprecated modules (to be removed in next release): Removed modules: Other: - RDKit fingerprint generation is now faster. The hashing algorithm used in the RDKit fingerprinter has changed. - Force-field calculations are substantially faster (sf.net issue 290) - The core of the BRICS implementation has been moved into C++. - The MACCS fingerprint implementation has been moved into C++. (contribution from Roger Sayle) - New documentation has been added: Cartridge.rst, Overview.rst, Install.rst ------------------------------------------------------------------------------ Try New Relic Now & We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, & servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr _______________________________________________ Rdkit-devel mailing list Rdkit-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-devel
