Re: [Rdkit-discuss] 2019.03.1 RDKit Release
I appreciate this release and updated all Chembience components to RDKit 2019.03: https://github.com/chembience/chembience/releases/tag/0.2.10 Best, Markus On Tue, Apr 9, 2019 at 5:43 AM Greg Landrum 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
[Rdkit-discuss] 2019.03.1 RDKit Release
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
