Dear all, Today I tagged the beta for the 2013.03 release in svn: https://sourceforge.net/p/rdkit/code/HEAD/tree/tags/Release_2013_03_1beta1/
and uploaded a source distribution to the google code site: https://rdkit.googlecode.com/files/RDKit_2013_03_1beta1.tgz There's still some documentation work to do, but I wanted to get the changes out there for the community to test. If no show-stopper bugs appear, I will do the release itself at the end of next week. Excerpts from the updated release notes are below. Best Regards, -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: Jan Domanski, Jean-Paul Ebejer, Nikolas Fechner, Jameed Hussain, Stephan Reiling, Sereina Riniker, Roger Sayle 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) 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. 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 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 ------------------------------------------------------------------------------ Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter _______________________________________________ Rdkit-devel mailing list Rdkit-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-devel
