Hi, I'm using the 2019-03.1 conda build of the new version of rdkit-postgresql on macOS Mohave 10.14.4.
just FYI, I got the following error when trying to create the cartridge extension in a postgresql chembl_25 instance in the conda build - chembl_25=# create extension if not exists rdkit; ERROR: could not load library "/Users/drew/anaconda3/envs/rdkit-psql-2019/lib/rdkit.so": dlopen(/Users/drew/anaconda3/envs/rdkit-psql-2019/lib/rdkit.so, 10): Library not loaded: @rpath/libboost_system.dylib Referenced from: /Users/drew/anaconda3/envs/rdkit-psql-2019/lib/rdkit.so Reason: image not found I couldn't see "libboost_system.dylib" in my conda environment /lib directory, so I installed anaconda boost and it fixed the problem - (from within the conda environment) conda install -c anaconda boost chembl_25=# create extension if not exists rdkit; CREATE EXTENSION chembl_25=# I then followed the other commands in the rdkit docs to create some fingerprints and build the similarity search index - all seems to be working ok. Cheers, Drew On Tue, 9 Apr 2019 at 04:42, Greg Landrum <greg.land...@gmail.com> wrote: > 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) > > _______________________________________________ > Rdkit-announce mailing list > rdkit-annou...@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-announce >
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