Dear all, I'm pleased to announce that the next version of the RDKit - 2019.03 - is released. The release notes are below.
The release files are on the github release page: https://github.com/rdkit/rdkit/releases/tag/Release_2019_03_1 Binaries have been uploaded to anaconda.org (https://anaconda.org/rdkit). The available conda binaries for this release are: Linux 64bit: python 3.6, 3.7 Mac OS 64bit: python 3.6, 3.7 Windows 64bit: python 3.6, 3.7 I believe that conda-forge will also switch to the new version in the near future. Please note that the RDKit no longer supports Python 2.7. More details on this here: https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg08354.html I plan to put conda builds of the PostgreSQL cartridge up in the near future. The online version of the documentation at rdkit.org ( http://rdkit.org/docs/index.html) has been updated. Some things that will be finished over the next couple of days: - The conda build scripts will be updated to reflect the new version - The homebrew script Thanks to everyone who submitted code, 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, which is scheduled for October 2019. Best Regards, -greg # Release_2019.03.1 (Changes relative to Release_2018.09.1) ## REALLY IMPORTANT ANNOUNCEMENT - As of this realease (2019.03.1) the RDKit no longer supports Python 2. Please read this rdkit-discuss post to learn what your options are if you need to keep using Python 2: https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg08354.html ## Backwards incompatible changes - The fix for github #2245 means that the default behavior of the MaxMinPicker is now truly random. If you would like to reproduce the previous behavior, provide a seed value of 42. - The uncharging method in the MolStandardizer now attempts to generate canonical results for a given molecule. This may result in different output for some molecules. ## Highlights: - There's now a Japanese translation of large parts of the RDKit documentation - SGroup data can now be read from and written to Mol/SDF files - The enhanced stereo handling has been improved: the information is now accessible from Python, EnumerateStereoisomers takes advantage of it, and it can be read from and written to CXSmiles ## Acknowledgements: Michael Banck, Francois Berenger, Thomas Blaschke, Brian Cole, Andrew Dalke, Bakary N'tji Diallo, Guillaume Godin, Anne Hersey, Jan Holst Jensen, Sunhwan Jo, Brian Kelley, Petr Kubat, Karl Leswing, Susan Leung, John Mayfield, Adam Moyer, Dan Nealschneider, Noel O'Boyle, Stephen Roughley, Takayuki Serizawa, Gianluca Sforna, Ricardo Rodriguez Schmidt, Gianluca Sforna, Matt Swain, Paolo Tosco, Ricardo Vianello, 'John-Videogames', 'magattaca', 'msteijaert', 'paconius', 'sirbiscuit' ## Bug Fixes: - PgSQL: fix boolean definitions for Postgresql 11 (github pull #2129 from pkubatrh) - update fingerprint tutorial notebook (github pull #2130 from greglandrum) - Fix typo in RecapHierarchyNode destructor (github pull #2137 from iwatobipen) - SMARTS roundtrip failure (github issue #2142 from mcs07) - Error thrown in rdMolStandardize.ChargeParent (github issue #2144 from paconius) - SMILES parsing inconsistency based on input order (github issue #2148 from coleb) - MolDraw2D: line width not in python wrapper (github issue #2149 from greglandrum) - Missing Python API Documentation (github issue #2158 from greglandrum) - PgSQL: mol_to_svg() changes input molecule. (github issue #2174 from janholstjensen) - Remove Unicode From AcidBasePair Name (github pull #2185 from lilleswing) - Inconsistent treatment of `[as]` in SMILES and SMARTS (github issue #2197 from greglandrum) - RGroupDecomposition fixes, keep userLabels more robust onlyMatchAtRGroups (github pull #2202 from bp-kelley) - Fix TautomerTransform in operator= (github pull #2203 from bp-kelley) - testEnumeration hangs/takes where long on 32bit architectures (github issue #2209 from mbanck) - Silencing some Python 3 warning messages (github pull #2223 from coleb) - removeHs shouldn't remove atom lists (github issue #2224 from rvianello) - failure round-tripping mol block with Q atom (github issue #2225 from rvianello) - problem round-tripping mol files that include bond topology info (github issue #2229 from rvianello) - aromatic main-group atoms written to SMARTS incorrectly (github issue #2237 from greglandrum) - findPotentialStereoBonds() stopping too early (github issue #2244 from greglandrum) - MinMax Diversity picker seeding shows deterministic / non-random behaviour (github issue #2245 from sroughley) - Fix to serialize binary strings (github pull #2264 from bp-kelley) - Recognize N in three-membered rings as potentially chiral (github issue #2268 from greglandrum) - Failure when parsing mol block with M PXA (github issue #2277 from greglandrum) - query-query matching failing for atoms constructed from SMARTS (github issue #2299 from greglandrum) - SMILES parsing fails for dative ring closures (github issue #2303 from greglandrum) - Missing Dict.h overload: std::string Dict::getVal<std::string> (github issue #2308 from greglandrum) - fix a problem with the random pickers test (github pull #2310 from greglandrum) - Some tests still failing on less common platforms. (github issue #2311 from giallu) - AddHs() using 3D coordinates with 2D conformations (github pull #2328 from greglandrum) - change to make the SWIG builds work on windows (github pull #2340 from greglandrum) - uncharger behaves differently on molecules constructed from mol blocks and SMILES (github issue #2346 from greglandrum) - Memory Error When Writing ToBinary With "AllProps" (github issue #2352 from atom-moyer) - Seg fault on init if RDBASE is not set (github issue #2368 from greglandrum) - PandasTools.FrameToGridImage() fails with SVG output (github issue #2380 from greglandrum) - ClusterMols.GetDistanceMatrix throws a type error in Python 3 (github issue #2387 from John-Videogames) - Uncharging logic reversed: protonate non-acids first (github issue #2392 from Anne Hersey) ## New Features and Enhancements: - Allow access to Enhanced Stereochemistry information from Python (github issue #2108 from d-b-w) - Adopt EnumerateStereoisomers to use extended stereo (github issue #2109 from greglandrum) - Enable ctest -T memcheck (github pull #2113 from ricrogz) - Support for parsing/writing SGroups in SD Mol files (github pull #2138 from ricrogz) - Rename the #define _DEBUG to MMPA_DEBUG in mmpa.cpp (github pull #2140 from baoilleach) - MolDraw2D: line width should be controlled by MolDrawOptions (github issue #2151 from greglandrum) - Some refactoring of the distance geometry code (github pull #2153 from greglandrum) - Less warnings (github pull #2155 from UnixJunkie) - ShapeTverskyIndex python function (github pull #2156 from susanhleung) - Skip compound if smiles conversion fails (github pull #2168 from msteijaert) - Fix #2176: InChI functions should return NULL on un-InChI-able input molecules. (github pull #2177 from janholstjensen) - Update installation instructions for Linux (github pull #2181 from sirbiscuit) - Update CMake rules to find external coorgen & maeparser libs (github pull #2184 from ricrogz) - Update to use the travis Xenial environment (github pull #2200 from greglandrum) - Do not allow PandasTools to overwrite pandas settings (github pull #2206 from sirbiscuit) - re-enable (and update) the file parser tests (github pull #2208 from greglandrum) - Added documentation files written in Japanese into Book directory (github pull #2210 from magattaca) - Add C++ convenience function for drawing ROMols (github issue #2220 from greglandrum) - Change boost int types to std types (github pull #2233 from bp-kelley) - Added exports for SGroup functions (github pull #2242 from ricrogz) - Use coordMap when starting embedding from random coords (github issue #2246 from greglandrum) - Improve interactivity of output SVG (github pull #2253 from greglandrum) - Add options for substructure searching (github pull #2254 from greglandrum) - keep extra information about bonds from Mol files (github pull #2260 from greglandrum) - Allow converting mol blocks directly to InChI (github pull #2262 from greglandrum) - Patch/pains updates (github pull #2272 from johnmay) - add warning for 2D conformations flagged as 3D (github pull #2273 from greglandrum) - Store extra CXSMILES data as a property (github pull #2281 from ricrogz) - Parse enhanced stereo information from CXSMILES (github pull #2282 from ricrogz) - Robustify parsing of CTABs and SGROUPs (github pull #2283 from greglandrum) - Write enhanced stereo to cxsmiles (github pull #2290 from greglandrum) - Allow custom type-handlers in the RDProps interface (github pull #2293 from bp-kelley) - Add serialization to SubstructLibrary (github pull #2295 from bp-kelley) - support reading/writing atom props from SD files (github pull #2297 from greglandrum) - Add test for issue #2285, fix molbundle test (github pull #2301 from bp-kelley) - Update maeparser & coordgen libraries (github pull #2302 from ricrogz) - Mem errors clean up (github pull #2305 from ricrogz) - Add definition of MolFragmentToCXSmiles (github pull #2307 from greglandrum) - Doc update (github pull #2312 from greglandrum) - Adds gzstream stream, exposes to swig (github pull #2314 from bp-kelley) - Remove a bunch of Python2-related warts (github pull #2315 from greglandrum) - some much-needed optimization work on the new property lists (github pull #2317 from greglandrum) - Build warnings revisited (github pull #2318 from ricrogz) - change bogus "3D" to "2D" in a test file (github pull #2319 from greglandrum) - Allow copying atoms in Python (github pull #2322 from d-b-w) - fixes an r-group symmetrization problem (github pull #2324 from greglandrum) - simple docstring fix (github pull #2326 from sunhwan) - allow using system's catch2 for tests (github pull #2327 from giallu) - Python wrap DetectAtomStereoChemistry from MolFileStereochem.h (github issue #2329 from d-b-w) - switch to using cmake to handle the C++ spec (github pull #2334 from greglandrum) - WIP: optional integration with YAeHMOP (github pull #2335 from greglandrum) - Exposes substructlibrary to swig (github pull #2337 from bp-kelley) - Add a skip_all_if_match option to the FragmentRemover (github pull #2338 from greglandrum) - Dev/general csharp fixes (github pull #2341 from bp-kelley) - Add a read-only Python wrapper for SGroups (github pull #2343 from greglandrum) - Expose RGroupDecomposition to SWIG (github pull #2345 from greglandrum) - update debian build script to python3 (github pull #2350 from UnixJunkie) - add GetStereoIsomerCount() function to EnumerateStereoisomers (github pull #2354 from greglandrum) - Update coordgenlibs to v1.2.2 (github pull #2355 from ricrogz) - Small fixes to get DLLs to build on Windows (github pull #2356 from ptosco) - Boost deprecation warning (github pull #2357 from d-b-w) - Removes an extra debugging cerr statment (github pull #2360 from d-b-w) - Preserve enhanced stereo in reactions (github pull #2366 from d-b-w) - improvements to the Uncharge functionality (github pull #2374 from greglandrum) - Add ExplicitBitVect prop and query (github pull #2384 from bp-kelley) - Allow components of the MolStandardize code to be initialized from streams (github pull #2385 from greglandrum)
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