2020_03_1 (Q1 2020) Release

Release_2020.03.1

(Changes relative to Release_2019.09.1)

Backwards incompatible changes

• Searches for equal molecules (i.e. mol1 @= mol2) in the PostgreSQL cartridge
  now use the do_chiral_sss option. So if do_chiral_sss is false (the
  default), the molecules CC(F)Cl and C[C@H](F)Cl will be considered to be equal.
  Previously these molecules were always considered to be different.
• Attempting to create a MolSupplier from a filename pointing to an empty file,
  a file that does not exist or sometihing that is not a standard file (i.e.
  something like a directory) now generates an exception.
• The cmake option RDK_OPTIMIZE_NATIVE has been renamed to RDK_OPTIMIZE_POPCNT

Highlights:

• The drawings generated by the MolDraw2D objects are now significantly improved
  and can include simple atom and bond annotations (#2931 and #3010)
• An initial implementation of a modified scaffold network algorithm is now
  available (#2911)
• A few new descriptor/fingerprint types are available - BCUTs (#2957), Morse
  atom fingerprints (#1773), Coulomb matrices (#2993), and MHFP and SECFP
  fingerprints (#2643)
• There is a new, and greatly improved, version of the RDKit Cookbook (#2884)
• There is a new version (v3) of the ETKDG conformer generator along with
  optional new terms for handling small rings and macrocyles (http://doi.org/dqnh) (#2999)

Acknowledgements:

Marcel Baltruschat, Jason Biggs, Eliane Briand, Ben Cornett, David Cosgrove,
Andrew Dalke, Tim Dudgeon, Zhenting Gao, Guillaume Godin, Manan Goel, Gareth
Jones, Zachary Kaplan, Eisuke Kawashima, Steven Kearnes, Brian Kelley, Maxim
Koltsov, Franziska Kruger, Mieszko Manijak, Dan Nealschneider, Daniil
Polykovskiy, Daniel Probst, Sereina Riniker, Matthew Robinson, Steve Roughley,
Kevin Ryan, Vincent F. Scalfani, Ricardo Rodriguez Schmidt, Rim Shayakhmetov,
Aryan Shrey, Nik Stiefl, Matt Swain, Paolo Tosco, Wiep van der Toorn, Riccardo
Vianello, Shuzhe Wang, Piotr Wawrzyniak, Hsiao Yi, 'jasad1',
'luancarvalhomartins'

Bug Fixes:

• Mol rendering within DataFrames in a Jupyter Notebook is broken with Pandas 0.25.1
  (github issue #2673 from mrcblt)
• Removed RDKIT_SIMDIVPICKERS_EXPORT
  (github pull #2740 from ptosco)
• • enable building RDKitRingDecomposerLib.dll under Windows
    (github pull #2742 from ptosco)
• Do a windows DLL build as part of the Azure DevOps setup
  (github pull #2743 from greglandrum)
• Fix data race in sascorer.py
  (github pull #2744 from skearnes)
• Uncharger not properly setting explicit/implicit H count
  (github issue #2749 from greglandrum)
• MSVC compile error: MolHash scoped enum cannot be redeclared as unscoped
  (github issue #2752 from mcs07)
• Molecules whose Y size is very small won't display as SVG
  (github issue #2762 from ptosco)
• Make the cartridge tests work with PostgreSQL 12
  (github pull #2767 from greglandrum)
• Salt stripper should consider bond matches as well as atom matches
  (github pull #2768 from greglandrum)
• Bismuth should count as an early element
  (github issue #2775 from greglandrum)
• addHs() fails on atoms with "bad" valences
  (github issue #2782 from greglandrum)
• Element symbol lookup for some transuranics returns incorrect results
  (github issue #2784 from LeanAndMean)
• [cartridge] molecular equality should use do_chiral_sss setting
  (github issue #2790 from greglandrum)
• uncharger removes Hs from carbocations instead of adding them
  (github issue #2792 from greglandrum)
• Fix build without boost serialization library
  (github pull #2796 from maksbotan)
• Using SetBoundsMat significantly slows down conformer generation process.
  (github issue #2800 from hjuinj)
• rdkit.Ched.rdFMCS.FindMCS generates invalid smarts
  (github issue #2801 from luancarvalhomartins)
• Remove confId from *FFOptimizeMoleculeConfs Python docs
  (github issue #2805 from ptosco)
• Hybridization queries on dummy atoms not written properly to SMARTS
  (github issue #2814 from greglandrum)
• Charge range queries not properly written to SMARTS
  (github issue #2815 from greglandrum)
• RDKit segfaults in MMFFOptimizeMoleculeConfs()
  (github issue #2820 from ptosco)
• Trusted Smiles holder doesn't handle ring queries
  (github issue #2830 from bp-kelley)
• Fix windows substructure crash
  (github pull #2836 from greglandrum)
• Fix YAeHMOP build
  (github pull #2838 from ptosco)
• testGithub2245 in testPickers.cpp occasionally fails
  (github issue #2839 from ptosco)
• add define for RDK_USE_BOOST_SERIALIZATION
  (github pull #2859 from greglandrum)
• fix start/end atoms when wedging bonds
  (github pull #2861 from greglandrum)
• Fixes the size of the reduced charge matrix from eHT calculations
  (github pull #2864 from greglandrum)
• Dev/pvs studio cleanups2
  (github pull #2877 from greglandrum)
• segfault in MaeMolSupplier
  (github issue #2881 from greglandrum)
• update maven url in build system
  (github pull #2889 from greglandrum)
• EnumerateStereoisomers cannot handle STEREOANY bonds
  (github issue #2890 from ricrogz)
• Update one of the cartridge tests that got missed
  (github pull #2894 from greglandrum)
• acepentalene aromaticity perception
  (github issue #2895 from adalke)
• New Similarity Maps drawing code Java Wrappers non-functional
  (github issue #2896 from sroughley)
• Fix to allow multistructure images in Java/C# and use MCS for c# wrapper
  (github pull #2898 from jones-gareth)
• Remove bogus URFLib library
  (github pull #2900 from greglandrum)
• java wrapper build cleanups
  (github pull #2901 from greglandrum)
• SMARTS parser fails on high-numbered ring closures in branches
  (github issue #2909 from greglandrum)
• patch to make PandasTools tests pass with pandas v0.22
  (github pull #2913 from greglandrum)
• fix doctest problem with Pandas v1.0
  (github pull #2918 from greglandrum)
• Build with -D RDK_BUILD_COORDGEN_SUPPORT=OFF includes a test case that depends on MaeMolSupplier
  (github issue #2929 from rvianello)
• MinimalLib: get_stereo_tags() should also return unspecified centers
  (github issue #2936 from greglandrum)
• Fix regression introduced by e245349
  (github pull #2945 from cornett)
• Avoid data race warning in SmilesParse.cpp
  (github pull #2946 from skearnes)
• Empty molecule has non-zero LabuteASA
  (github issue #2948 from jasondbiggs)
• Fix a problem with aromatic heteroatom tautomer enumeration
  (github pull #2952 from greglandrum)
• Molecule properties not retained with MolStandardize.rdMolStandardize.Cleanup()
  (github issue #2965 from ZacharyKaplan)
• Fix build without boost serialization.
  (github pull #2972 from ricrogz)
• RDKFuncs.chargeParent() core dumps when standardization is skipped
  (bithub issue #2970 from tdudgeon)
• fix a typo in the scaffold network wrappers and add some tests
  (github pull #2982 from greglandrum)
• Tautomer enumeration should remove stereo in all tautomers
  (github issue #2990 from greglandrum)
• Segmentation fault on EmbedMolecule
  (github issue #3019 from shayakhmetov)
• Removed dllexport from a function that lives in the anonymous namespace
  (github pull #3027 from ptosco)

New Features and Enhancements:

• Morse atom fingerprint
  (github pull #1773 from thegodone)
• Allow serializing coordinates as doubles
  (github issue #2510 from danpol)
• Rework MaeMolSupplier, fix #2617
  (github pull #2620 from ricrogz)
• Implementation of MHFP and SECFP Fingerprints
  (github pull #2643 from daenuprobst)
• MatchFusedRings does not imply CompleteRingsOnly anymore
  (github pull #2748 from ptosco)
• Improvements to JS wrappers
  (github pull #2751 from greglandrum)
• Fix installed header directory structure
  (github pull #2754 from ricrogz)
• Add doRandom to the header docs
  (github pull #2756 from bp-kelley)
• Add queryMol data member to MCSResult
  (github pull #2759 from ptosco)
• Add functions to enable/disable the substructure matching monkey patching in IPythonConsole.py
  (github issue #2786 from greglandrum)
• Add a function to assign chiral tags from sss atom parity
  (github issue #2823 from ptosco)
• Support MRV_IMPLICIT_H S groups when reading Mol blocks
  (github issue #2829 from greglandrum)
• Unset executable flag
  (github pull #2833 from e-kwsm)
• Remove O(N) behavior of getNumBonds
  (github pull #2847 from bp-kelley)
• Feature proposal: add remove_stereochemistry=False flag for RemoveHs()
  (github issue #2848 from shayakhmetov)
• Expose SubstructLibrary serialization stream
  (github pull #2853 from bp-kelley)
• Fix typo
  (github pull #2862 from e-kwsm)
• Rename RDK_OPTIMIZE_NATIVE to RDK_OPTIMIZE_POPCNT
  (github pull #2865 from ElianeBriand)
• Update Draw.MolToImage() and Draw.MolToFile() to use the new drawing code
  (github pull #2866 from greglandrum)
• Improve PostgreSQL cartridge install documentation
  (github pull #2870 from yellowBirdy)
• Fixes #2858
  (github pull #2871 from greglandrum)
• Add a cartridge test to the azure devops config
  (github pull #2873 from greglandrum)
• Add a new Cookbook v2 to the RDKit docs
  (github pull #2884 from vfscalfani)
• Add MolVS tautomer canonicalization
  (github pull #2886 from greglandrum)
• add a convenience function for RGD--Pandas integration
  (github pull #2887 from greglandrum)
• run clang-tidy with readability-braces-around-statements
  (github pull #2899 from greglandrum)
• Allow RDProps::clearProp to succeed even if the prop doesn't exist
  (github issue #2910 from greglandrum)
• Add a scaffold network implementation
  (github pull #2911 from greglandrum)
• cleanup of the SMILES/SMARTS parsing and writing code
  (github pull #2912 from greglandrum)
• Add _ctab, _mol2, _pdb to allow direct mol construction from strings
  (github issue...

2020_03_1b1 (Q1 2020) Release

Release_2020.03.1

(Changes relative to Release_2019.09.1)

Backwards incompatible changes

• Searches for equal molecules (i.e. mol1 @= mol2) in the PostgreSQL cartridge
  now use the do_chiral_sss option. So if do_chiral_sss is false (the
  default), the molecules CC(F)Cl and C[C@H](F)Cl will be considered to be equal.
  Previously these molecules were always considered to be different.
• Attempting to create a MolSupplier from a filename pointing to an empty file,
  a file that does not exist or sometihing that is not a standard file (i.e.
  something like a directory) now generates an exception.
• The cmake option RDK_OPTIMIZE_NATIVE has been renamed to RDK_OPTIMIZE_POPCNT

Highlights:

• The drawings generated by the MolDraw2D objects are now significantly improved
  and can include simple atom and bond annotations (#2931 and #3010)
• An initial implementation of a modified scaffold network algorithm is now
  available (#2911)
• A few new descriptor/fingerprint types are available - BCUTs (#2957), Morse
  atom fingerprints (#1773), Coulomb matrices (#2993), and MHFP and SECFP
  fingerprints (#2643)

Acknowledgements:

Marcel Baltruschat, Jason Biggs, Eliane Briand, Ben Cornett, David Cosgrove,
Zhenting Gao, Guillaume Godin, Gareth Jones, Zachary Kaplan, Eisuke Kawashima,
Steven Kearnes, Brian Kelley, Maxim Koltsov, Mieszko Manijak, Dan Nealschneider,
Daniil Polykovskiy, Daniel Probst, Steve Roughley, Kevin Ryan, Vincent F.
Scalfani, Ricardo Rodriguez Schmidt, Rim Shayakhmetov, Aryan Shrey, Matt Swain,
Paolo Tosco, Wiep van der Toorn, Riccardo Vianello, Shuzhe Wang, Piotr
Wawrzyniak, Hsiao Yi, 'luancarvalhomartins'

Bug Fixes:

• Mol rendering within DataFrames in a Jupyter Notebook is broken with Pandas 0.25.1
  (github issue #2673 from mrcblt)
• Removed RDKIT_SIMDIVPICKERS_EXPORT
  (github pull #2740 from ptosco)
• • enable building RDKitRingDecomposerLib.dll under Windows
    (github pull #2742 from ptosco)
• Do a windows DLL build as part of the Azure DevOps setup
  (github pull #2743 from greglandrum)
• Fix data race in sascorer.py
  (github pull #2744 from skearnes)
• Uncharger not properly setting explicit/implicit H count
  (github issue #2749 from greglandrum)
• MSVC compile error: MolHash scoped enum cannot be redeclared as unscoped
  (github issue #2752 from mcs07)
• Molecules whose Y size is very small won't display as SVG
  (github issue #2762 from ptosco)
• Make the cartridge tests work with PostgreSQL 12
  (github pull #2767 from greglandrum)
• Salt stripper should consider bond matches as well as atom matches
  (github pull #2768 from greglandrum)
• Bismuth should count as an early element
  (github issue #2775 from greglandrum)
• addHs() fails on atoms with "bad" valences
  (github issue #2782 from greglandrum)
• Element symbol lookup for some transuranics returns incorrect results
  (github issue #2784 from LeanAndMean)
• [cartridge] molecular equality should use do_chiral_sss setting
  (github issue #2790 from greglandrum)
• uncharger removes Hs from carbocations instead of adding them
  (github issue #2792 from greglandrum)
• Fix build without boost serialization library
  (github pull #2796 from maksbotan)
• Using SetBoundsMat significantly slows down conformer generation process.
  (github issue #2800 from hjuinj)
• rdkit.Ched.rdFMCS.FindMCS generates invalid smarts
  (github issue #2801 from luancarvalhomartins)
• Remove confId from *FFOptimizeMoleculeConfs Python docs
  (github issue #2805 from ptosco)
• Hybridization queries on dummy atoms not written properly to SMARTS
  (github issue #2814 from greglandrum)
• Charge range queries not properly written to SMARTS
  (github issue #2815 from greglandrum)
• RDKit segfaults in MMFFOptimizeMoleculeConfs()
  (github issue #2820 from ptosco)
• Trusted Smiles holder doesn't handle ring queries
  (github issue #2830 from bp-kelley)
• Fix windows substructure crash
  (github pull #2836 from greglandrum)
• Fix YAeHMOP build
  (github pull #2838 from ptosco)
• testGithub2245 in testPickers.cpp occasionally fails
  (github issue #2839 from ptosco)
• add define for RDK_USE_BOOST_SERIALIZATION
  (github pull #2859 from greglandrum)
• fix start/end atoms when wedging bonds
  (github pull #2861 from greglandrum)
• Fixes the size of the reduced charge matrix from eHT calculations
  (github pull #2864 from greglandrum)
• Dev/pvs studio cleanups2
  (github pull #2877 from greglandrum)
• segfault in MaeMolSupplier
  (github issue #2881 from greglandrum)
• update maven url in build system
  (github pull #2889 from greglandrum)
• EnumerateStereoisomers cannot handle STEREOANY bonds
  (github issue #2890 from ricrogz)
• Update one of the cartridge tests that got missed
  (github pull #2894 from greglandrum)
• New Similarity Maps drawing code Java Wrappers non-functional
  (github issue #2896 from sroughley)
• Fix to allow multistructure images in Java/C# and use MCS for c# wrapper
  (github pull #2898 from jones-gareth)
• Remove bogus URFLib library
  (github pull #2900 from greglandrum)
• java wrapper build cleanups
  (github pull #2901 from greglandrum)
• SMARTS parser fails on high-numbered ring closures in branches
  (github issue #2909 from greglandrum)
• patch to make PandasTools tests pass with pandas v0.22
  (github pull #2913 from greglandrum)
• fix doctest problem with Pandas v1.0
  (github pull #2918 from greglandrum)
• Build with -D RDK_BUILD_COORDGEN_SUPPORT=OFF includes a test case that depends on MaeMolSupplier
  (github issue #2929 from rvianello)
• MinimalLib: get_stereo_tags() should also return unspecified centers
  (github issue #2936 from greglandrum)
• Fix regression introduced by e245349
  (github pull #2945 from cornett)
• Avoid data race warning in SmilesParse.cpp
  (github pull #2946 from skearnes)
• Empty molecule has non-zero LabuteASA
  (github issue #2948 from jasondbiggs)
• Fix a problem with aromatic heteroatom tautomer enumeration
  (github pull #2952 from greglandrum)
• Molecule properties not retained with MolStandardize.rdMolStandardize.Cleanup()
  (github issue #2965 from ZacharyKaplan)
• Fix build without boost serialization.
  (github pull #2972 from ricrogz)
• fix a typo in the scaffold network wrappers and add some tests
  (github pull #2982 from greglandrum)
• Tautomer enumeration should remove stereo in all tautomers
  (github issue #2990 from greglandrum)
• Removed dllexport from a function that lives in the anonymous namespace
  (github pull #3027 from ptosco)

New Features and Enhancements:

• Morse atom fingerprint
  (github pull #1773 from thegodone)
• Allow serializing coordinates as doubles
  (github issue #2510 from danpol)
• Rework MaeMolSupplier, fix #2617
  (github pull #2620 from ricrogz)
• Implementation of MHFP and SECFP Fingerprints
  (github pull #2643 from daenuprobst)
• MatchFusedRings does not imply CompleteRingsOnly anymore
  (github pull #2748 from ptosco)
• Improvements to JS wrappers
  (github pull #2751 from greglandrum)
• Fix installed header directory structure
  (github pull #2754 from ricrogz)
• Add doRandom to the header docs
  (github pull #2756 from bp-kelley)
• Add queryMol data member to MCSResult
  (github pull #2759 from ptosco)
• Add functions to enable/disable the substructure matching monkey patching in IPythonConsole.py
  (github issue #2786 from greglandrum)
• Add a function to assign chiral tags from sss atom parity
  (github issue #2823 from ptosco)
• Support MRV_IMPLICIT_H S groups when reading Mol blocks
  (github issue #2829 from greglandrum)
• Unset executable flag
  (github pull #2833 from e-kwsm)
• Remove O(N) behavior of getNumBonds
  (github pull #2847 from bp-kelley)
• Feature proposal: add remove_stereochemistry=False flag for RemoveHs()
  (github issue #2848 from shayakhmetov)
• Expose SubstructLibrary serialization stream
  (github pull #2853 from bp-kelley)
• Fix typo
  (github pull #2862 from e-kwsm)
• Rename RDK_OPTIMIZE_NATIVE to RDK_OPTIMIZE_POPCNT
  (github pull #2865 from ElianeBriand)
• Update Draw.MolToImage() and Draw.MolToFile() to use the new drawing code
  (github pull #2866 from greglandrum)
• Improve PostgreSQL cartridge install documentation
  (github pull #2870 from yellowBirdy)
• Fixes #2858
  (github pull #2871 from greglandrum)
• Add a cartridge test to the azure devops config
  (github pull #2873 from greglandrum)
• Add a new Cookbook v2 to the RDKit docs
  (github pull #2884 from vfscalfani)
• Add MolVS tautomer canonicalization
  (github pull #2886 from greglandrum)
• add a convenience function for RGD--Pandas integration
  (github pull #2887 from greglandrum)
• run clang-tidy with readability-braces-around-statements
  (github pull #2899 from greglandrum)
• Allow RDProps::clearProp to succeed even if the prop doesn't exist
  (github issue #2910 from greglandrum)
• Add a scaffold network implementation
  (github pull #2911 from greglandrum)
• cleanup of the SMILES/SMARTS parsing and writing code
  (github pull #2912 from greglandrum)
• Add _ctab, _mol2, _pdb to allow direct mol construction from strings
  (github issue #2916 from greglandrum)
• Parse and handle the stereoCare or STBOX flags in CTABs
  (github pull #2917 from greglandrum)
• RDKit exceptions do not override the default what() method
  (github issue #2920 from ricrogz)
• Allow custom post-match filters for substructure matching
  (github pull #2927 from greglandrum)
• Proposed improvements to 2D Drawing Code
  (github issue #2931 from DavidACosgrove)
• Include running the documentation tests as part of the CI runs
  (github pull #2932 from greglandrum)
• Add support for phosphine and arsine chirality
  (github issue #2949 from wopozka)
• A cou...

2019_09_3 (Q3 2019) Release

Release_2019.09.3

(Changes relative to Release_2019.09.2)

Acknowledgements:

Marcel Baltruschat, Brian Kelley, Matt Swain, Paolo Tosco, 'hjuinj'

Bug Fixes:

• Mol rendering within DataFrames in a Jupyter Notebook is broken with Pandas 0.25.1
  (github #2673 from mrcblt)
• MSVC compile error: MolHash scoped enum cannot be redeclared as unscoped
  (github #2752 from mcs07)
• Using SetBoundsMat significantly slows down conformer generation process.
  (github #2800 from hjuinj)
• Remove confId from *FFOptimizeMoleculeConfs Python docs
  (github #2805 from ptosco)
• RDKit segfaults in MMFFOptimizeMoleculeConfs()
  (github #2820 from ptosco)
• Trusted Smiles holder doesn't handle ring queries
  (github #2830 from bp-kelley)
• Fix windows substructure crash
  (github #2836 from greglandrum)
• Fix YAeHMOP build
  (github #2838 from ptosco)
• testGithub2245 in testPickers.cpp occasionally fails
  (github #2839 from ptosco)
• add define for RDK_USE_BOOST_SERIALIZATION
  (github #2859 from greglandrum)
• fix start/end atoms when wedging bonds
  (github #2861 from greglandrum)
• Fixes the size of the reduced charge matrix from eHT calculations
  (github #2864 from greglandrum)

2019_09_2 (Q3 2019) Release

Release_2019.09.2

(Changes relative to Release_2019.09.1)

Acknowledgements:

Stephen Kearnes, Brian Kelley, Maxim Koltsov, Luan Carvalho Martins, Kevin Ryan, Paolo Tosco

Bug Fixes:

• Removed RDKIT_SIMDIVPICKERS_EXPORT
  (github #2740 from ptosco)
• enable building RDKitRingDecomposerLib.dll under Windows
  (github #2742 from ptosco)
• Do a windows DLL build as part of the Azure DevOps setup
  (github #2743 from greglandrum)
• Fix data race in sascorer.py
  (github #2744 from skearnes)
• Uncharger not properly setting explicit/implicit H count
  (github #2749 from greglandrum)
• Molecules whose Y size is very small won't display as SVG
  (github #2762 from ptosco)
• Make the cartridge tests work with PostgreSQL 12
  (github #2767 from greglandrum)
• Salt stripper should consider bond matches as well as atom matches
  (github #2768 from greglandrum)
• Bismuth should count as an early element
  (github #2775 from greglandrum)
• addHs() fails on atoms with "bad" valences
  (github #2782 from greglandrum)
• Element symbol lookup for some transuranics returns incorrect results
  (github #2784 from LeanAndMean)
• uncharger removes Hs from carbocations instead of adding them
  (github #2792 from greglandrum)
• Fix build without boost serialization library
  (github #2796 from maksbotan)
• rdkit.Ched.rdFMCS.FindMCS generates invalid smarts
  (github #2801 from luancarvalhomartins)
• Hybridization queries on dummy atoms not written properly to SMARTS
  (github #2814 from greglandrum)
• Charge range queries not properly written to SMARTS
  (github #2815 from greglandrum)

2019_09_1 (Q3 2019) Release

Release_2019.09.1

(Changes relative to Release_2019.03.1)

Important

• The atomic van der Waals radii used by the RDKit were corrected/updated in #2154.
  This leads to different results when generating conformations, molecular volumes,
  and molecular shapes.

Backwards incompatible changes

• See the note about atomic van der Waals radii above.
• As part of the enhancements to the MolDraw2D class, we changed the type of
  DrawColour from a tuple to be an actual struct. We also added a 4th element to
  capture alpha values. This should have no affect on Python code (the alpha
  value is optional when providing color tuples), but will require changes to C++
  and Java/C# code that is using DrawColour.
• When reading Mol blocks, atoms with the symbol "R" are now converted into
  queries that match any atom when doing a substructure search (analogous to "*"
  in SMARTS). The previous behavior was to only match other dummy atoms
• When loading SDF files using PandasTools.LoadSDF(), we now default to
  producing isomeric smiles in pandas tables. To reproduce the original
  behavior, use isomericSmiles=False in the call to the function.
• The SMARTS generated by the RDKit no longer contains redundant wildcard
  queries. This means the SMARTS strings generated by this release will generally
  be different from that in previous releases, although the results produced by
  the queries should not change.
• The RGroupDecomposition code now removes Hs from output R groups by default.
  To restore the old behavior create an RGroupDecompositionParameters object and
  set removeHydrogensPostMatch to false.
• The default values for some of the new fingerprint generators have been changed so
  that they more closely resemble the original fingerprinting code. In
  particular most fingerprinters no longer do count simulation by default and
  the RDKit fingerprint now sets two bits per feature by default.
• The SMARTS generated for MCS results using the ringMatchesRingOnly or
  completeRingsOnly options now includes ring-membership queries.

Highlights:

• The substructure matching code is now about 30% faster. This also improves the
  speed of reaction matching and the FMCS code. (#2500)
• A minimal JavaScript wrapper has been added as part of the core release. (#2444)
• It's now possible to get information about why molecule sanitization failed. (#2587)
• A flexible new molecular hashing scheme has been added. (#2636)

Acknowledgements:

Patricia Bento, Francois Berenger, Jason Biggs, David Cosgrove, Andrew Dalke,
Thomas Duigou, Eloy Felix, Guillaume Godin, Lester Hedges, Anne Hersey,
Christoph Hillisch, Christopher Ing, Jan Holst Jensen, Gareth Jones, Eisuke
Kawashima, Brian Kelley, Alan Kerstjens, Karl Leswing, Pat Lorton, John
Mayfield, Mike Mazanetz, Dan Nealschneider, Noel O'Boyle, Stephen Roughley,
Roger Sayle, Ricardo Rodriguez Schmidt, Paula Schmiel, Peter St. John, Marvin
Steijaert, Matt Swain, Amol Thakkar Paolo Tosco, Yi-Shu Tu, Ricardo Vianello,
Marc Wittke, '7FeiW', 'c56pony', 'sirbiscuit'

Bug Fixes:

• MCS returning partial rings with completeRingsOnly=True
  (github issue #945 from greglandrum)
• Alternating canonical SMILES for fused ring with N
  (github issue #1028 from greglandrum)
• Atom index out of range error
  (github issue #1868 from A-Thakkar)
• Incorrect cis/trans stereo symbol for conjugated ring
  (github issue #2023 from baoilleach)
• Hardcoded max length of SMARTs string cut of input query for FragCatlog
  (github issue #2163 from 7FeiW)
• VSA_EState {1, ..., 10} calculated by rdkit doesn't seem correct.
  (github issue #2372 from c56pony)
• MolStandardize: FragmentRemover should not sanitize fragments
  (github issue #2411 from greglandrum)
• MolStandardize: combinatorial explosion in Normalizer
  (github issue #2414 from greglandrum)
• MCS code doesn't return envelope MCS if CompleteRingsOnly is true
  (github issue #2420 from greglandrum)
• RemoveHs() does not remove all hydrogens.
  (github issue #2422 from paulaju)
• Incorrect assignment of explicit Hs to Al+3 read from mol block
  (github issue #2423 from greglandrum)
• Cannot set maxProducts > 1000 in RunReactants
  (github issue #2427 from tduigou)
• Chem.MolStandardize.standardize.Standardizer drops molecular properties
  (github pull #2431 from lilleswing)
• Canon::rankMolAtoms results in crossed double bonds in rings
  (github issue #2437 from greglandrum)
• make boost::iostreams optional
  (github pull #2440 from greglandrum)
• Fix/rgroup sdf isotope
  (github pull #2449 from bp-kelley)
• Uncharger incorrectly removing charge from boron anions
  (github issue #2452 from greglandrum)
• Add java builds to azure devops
  (github pull #2460 from greglandrum)
• Cart fixes
  (github pull #2462 from jones-gareth)
• Negative atom map values cause depickling to fail
  (github issue #2465 from greglandrum)
• Deserialization failures crash Java wrapper
  (github issue #2466 from greglandrum)
• rdkit.six fix and cleanup
  (github pull #2469 from rvianello)
• dummy atom queries are flagged as complex
  (github issue #2471 from greglandrum)
• 3D structure display broken in jupyter notebook
  (github issue #2473 from greglandrum)
• Inconsistent defaults for nonBondedThresh in MMFF optimization
  (github issue #2475 from greglandrum)
• Fix/rgroup multiple labels
  (github pull #2481 from bp-kelley)
• 2D Depiction clipped atom highlighting
  (github issue #2486 from DavidACosgrove)
• BRICSBuild now passes scrambleReagents to children
  (github pull #2488 from greglandrum)
• Pattern Fingerprint Issues
  (github issue #2501 from jones-gareth)
• CMake Error: Wrap directories being used when python build is turned off
  (github issue #2516 from jasondbiggs)
• • fixes ResonanceMolSupplier bug in perceiving conjugated groups
    (github pull #2517 from ptosco)
• Fix/mmff threadsafety issues
  (github pull #2518 from bp-kelley)
• update expected SVG output in cartridge tests
  (github pull #2520 from greglandrum)
• fix to SDWriter docs
  (github pull #2521 from pstjohn)
• Fix the azure pipelines builds
  (github pull #2522 from greglandrum)
• Code cleanups from PVS/Studio
  (github pull #2531 from greglandrum)
• getAtomNeighbors() and getAtomBonds() not in SWIG wrappers.
  (github issue #2532 from greglandrum)
• Default sanitizerxn doesn't aromatize if possible
  (github issue #2547 from bp-kelley)
• Add RDKIT_FILEPARSERS_EXPORT to finishMolProcessing
  (github pull #2551 from d-b-w)
• Chem.rdFMCS.FindMCS hangs for certain ligand pairs
  (github issue #2581 from lohedges)
• fix the inclusion path for the targets file (#2584)
  (github pull #2589 from rvianello)
• Fix inocuous typo/bug in Dative bond matching
  (github pull #2593 from ricrogz)
• E/Z and CIS/TRANS stereo bonds are incorrectly matched
  (github pull #2596 from ricrogz)
• Uncharger ignores dications
  (github issue #2602 from greglandrum)
• Possible Garbage Collection Bug in Pharmacophore Generation
  (github issue #2603 from cing)
• Uncharger incorrectly neutralizes cations when non-neutralizable anions are present.
  (github issue #2605 from greglandrum)
• Bad valence corrections on Pb, Sn
  (github issue #2606 from greglandrum)
• Pb and Sn should support valence 2
  (github issue #2607 from greglandrum)
• Uncharger incorrectly modifying a zwitterion
  (github issue #2610 from greglandrum)
• CanonicalRankAtomsInFragment breakTies doesn't
  (github issue #2611 from bp-kelley)
• Pattern fingerprint failing substructure condition in very large molecules
  (github issue #2614 from greglandrum)
• Memory leak with Chem.Atom() constructor
  (github issue #2639 from AlanKerstjens)
• Fixes: Atoms in non-standard valences not being properly written to mol blocks
  (github pull #2646 from greglandrum)
• C++ MCS code returns a null MCS between methylcyclopentane and methylcyclohexane
  (github issue #2662 from ptosco)
• CXSMILES writer has error if mol comes from v3000 molfile
  (github issue #2666 from d-b-w)
• MolToCXSmiles generates error for empty molecule
  (github issue #2667 from greglandrum)
• fix a problem with normalize, ringinfo, and fragments
  (github pull #2685 from greglandrum)
• Error when a squiggle bond is in an aromatic ring
  (github issue #2695 from greglandrum)
• Cannot combine multiple range queries on a single atom.
  (github issue #2709 from greglandrum)
• setBondStereoFromDirections() returning incorrect results.
  (github issue #2712 from greglandrum)
• update supplier documentation to reflect python 3 iterator syntax
  (github pull #2719 from greglandrum)
• removeHs messing up double bond stereo in partially sanitized molecules
  (github issue #2721 from greglandrum)
• seg fault in ReactionRunner
  (github issue #2722 from greglandrum)
• Intermittent test failures for JavaDistanceGeometryTests
  (github issue #2727 from greglandrum)
• Fixes a bug in TorsionConstraint
  (github pull #2732 from ptosco)
• Apply fix for #1592 to _MolsToGridSVG
  (github pull #2737 from yishutu)

New Features and Enhancements:

• Added rankAtoms to ROMol wrapper and added Java test case
  (github pull #1540 from sroughley)
• Use van der Waals radii from blue obelisk
  (github pull #2154 from UnixJunkie)
• add generateDepictionMatching2DStructure() to SWIG wrappers
  (github issue #2239 from greglandrum)
• Added OptimizeMoleculeConfs with pre-generated force-field
  (github pull #2401 from ptosco)
• FreeSASA improvements
  (github pull #2402 from ptosco)
• Speed up symmetrizeSSSR
  (github issue #2403 from d-b-w)
• Trim whitespace from mol fragment SMARTS and check SMARTS presence
  (github pull #2406 from ricrogz)
• Run clang-tidy over the entire codebase
  (github pull #2408 from greglandrum)
• Enable...

2019_09_1b1 (Q3 2019) Release

Release_2019.09.1

(Changes relative to Release_2019.03.1)

Important

• The atomic van der Waals radii used by the RDKit were corrected/updated in #2154.
  This leads to different results when generating conformations, molecular volumes,
  and molecular shapes.

Backwards incompatible changes

• See the note about atomic van der Waals radii above.
• As part of the enhancements to the MolDraw2D class, we changed the type of
  DrawColour from a tuple to be an actual struct. We also added a 4th element to
  capture alpha values. This should have no affect on Python code (the alpha
  value is optional when providing color tuples), but will require changes to C++
  and Java/C# code that is using DrawColour.
• When reading Mol blocks, atoms with the symbol "R" are now converted into
  queries that match any atom when doing a substructure search (analogous to "*"
  in SMARTS). The previous behavior was to only match other dummy atoms
• When loading SDF files using PandasTools.LoadSDF(), we now default to
  producing isomeric smiles in pandas tables. To reproduce the original
  behavior, use isomericSmiles=False in the call to the function.
• The SMARTS generated by the RDKit no longer contains redundant wildcard
  queries. This means the SMARTS strings generated by this release will generally
  be different from that in previous releases, although the results produced by
  the queries should not change.
• The RGroupDecomposition code now removes Hs from output R groups by default.
  To restore the old behavior create an RGroupDecompositionParameters object and
  set removeHydrogensPostMatch to false.
• The default values for some of the new fingerprint generators have been changed so
  that they more closely resemble the original fingerprinting code. In
  particular most fingerprinters no longer do count simulation by default and
  the RDKit fingerprint now sets two bits per feature by default.
• The SMARTS generated for MCS results using the ringMatchesRingOnly or
  completeRingsOnly options now includes ring-membership queries.

Highlights:

Acknowledgements:

Patricia Bento, Francois Berenger, Jason Biggs, David Cosgrove, Andrew Dalke,
Thomas Duigou, Eloy Felix, Guillaume Godin, Lester Hedges, Anne Hersey,
Christoph Hillisch, Christopher Ing, Jan Holst Jensen, Gareth Jones, Eisuke
Kawashima, Brian Kelley, Alan Kerstjens, Karl Leswing, Pat Lorton, John
Mayfield, Mike Mazanetz, Dan Nealschneider, Noel O'Boyle, Stephen Roughley,
Roger Sayle, Ricardo Rodriguez Schmidt, Paula Schmiel, Peter St. John, Matt
Swain, Amol Thakkar Paolo Tosco, Ricardo Vianello, Marc Wittke,
'7FeiW', 'c56pony', 'msteijaert', 'sirbiscuit'

Bug Fixes:

• MCS returning partial rings with completeRingsOnly=True
  (github issue #945 from greglandrum)
• Alternating canonical SMILES for fused ring with N
  (github issue #1028 from greglandrum)
• Atom index out of range error
  (github issue #1868 from A-Thakkar)
• Incorrect cis/trans stereo symbol for conjugated ring
  (github issue #2023 from baoilleach)
• Hardcoded max length of SMARTs string cut of input query for FragCatlog
  (github issue #2163 from 7FeiW)
• VSA_EState {1, ..., 10} calculated by rdkit doesn't seem correct.
  (github issue #2372 from c56pony)
• MolStandardize: FragmentRemover should not sanitize fragments
  (github issue #2411 from greglandrum)
• MolStandardize: combinatorial explosion in Normalizer
  (github issue #2414 from greglandrum)
• MCS code doesn't return envelope MCS if CompleteRingsOnly is true
  (github issue #2420 from greglandrum)
• RemoveHs() does not remove all hydrogens.
  (github issue #2422 from paulaju)
• Incorrect assignment of explicit Hs to Al+3 read from mol block
  (github issue #2423 from greglandrum)
• Cannot set maxProducts > 1000 in RunReactants
  (github issue #2427 from tduigou)
• Chem.MolStandardize.standardize.Standardizer drops molecular properties
  (github pull #2431 from lilleswing)
• Canon::rankMolAtoms results in crossed double bonds in rings
  (github issue #2437 from greglandrum)
• make boost::iostreams optional
  (github pull #2440 from greglandrum)
• Fix/rgroup sdf isotope
  (github pull #2449 from bp-kelley)
• Uncharger incorrectly removing charge from boron anions
  (github issue #2452 from greglandrum)
• Add java builds to azure devops
  (github pull #2460 from greglandrum)
• Cart fixes
  (github pull #2462 from jones-gareth)
• Negative atom map values cause depickling to fail
  (github issue #2465 from greglandrum)
• Deserialization failures crash Java wrapper
  (github issue #2466 from greglandrum)
• rdkit.six fix and cleanup
  (github pull #2469 from rvianello)
• dummy atom queries are flagged as complex
  (github issue #2471 from greglandrum)
• 3D structure display broken in jupyter notebook
  (github issue #2473 from greglandrum)
• Inconsistent defaults for nonBondedThresh in MMFF optimization
  (github issue #2475 from greglandrum)
• Fix/rgroup multiple labels
  (github pull #2481 from bp-kelley)
• 2D Depiction clipped atom highlighting
  (github issue #2486 from DavidACosgrove)
• BRICSBuild now passes scrambleReagents to children
  (github pull #2488 from greglandrum)
• Pattern Fingerprint Issues
  (github issue #2501 from jones-gareth)
• CMake Error: Wrap directories being used when python build is turned off
  (github issue #2516 from jasondbiggs)
• • fixes ResonanceMolSupplier bug in perceiving conjugated groups
    (github pull #2517 from ptosco)
• Fix/mmff threadsafety issues
  (github pull #2518 from bp-kelley)
• update expected SVG output in cartridge tests
  (github pull #2520 from greglandrum)
• fix to SDWriter docs
  (github pull #2521 from pstjohn)
• Fix the azure pipelines builds
  (github pull #2522 from greglandrum)
• Code cleanups from PVS/Studio
  (github pull #2531 from greglandrum)
• getAtomNeighbors() and getAtomBonds() not in SWIG wrappers.
  (github issue #2532 from greglandrum)
• Default sanitizerxn doesn't aromatize if possible
  (github issue #2547 from bp-kelley)
• Add RDKIT_FILEPARSERS_EXPORT to finishMolProcessing
  (github pull #2551 from d-b-w)
• Chem.rdFMCS.FindMCS hangs for certain ligand pairs
  (github issue #2581 from lohedges)
• fix the inclusion path for the targets file (#2584)
  (github pull #2589 from rvianello)
• Fix inocuous typo/bug in Dative bond matching
  (github pull #2593 from ricrogz)
• E/Z and CIS/TRANS stereo bonds are incorrectly matched
  (github pull #2596 from ricrogz)
• Uncharger ignores dications
  (github issue #2602 from greglandrum)
• Possible Garbage Collection Bug in Pharmacophore Generation
  (github issue #2603 from cing)
• Uncharger incorrectly neutralizes cations when non-neutralizable anions are present.
  (github issue #2605 from greglandrum)
• Bad valence corrections on Pb, Sn
  (github issue #2606 from greglandrum)
• Pb and Sn should support valence 2
  (github issue #2607 from greglandrum)
• Uncharger incorrectly modifying a zwitterion
  (github issue #2610 from greglandrum)
• CanonicalRankAtomsInFragment breakTies doesn't
  (github issue #2611 from bp-kelley)
• Pattern fingerprint failing substructure condition in very large molecules
  (github issue #2614 from greglandrum)
• Memory leak with Chem.Atom() constructor
  (github issue #2639 from AlanKerstjens)
• Fixes: Atoms in non-standard valences not being properly written to mol blocks
  (github pull #2646 from greglandrum)
• C++ MCS code returns a null MCS between methylcyclopentane and methylcyclohexane
  (github issue #2662 from ptosco)
• CXSMILES writer has error if mol comes from v3000 molfile
  (github issue #2666 from d-b-w)
• MolToCXSmiles generates error for empty molecule
  (github issue #2667 from greglandrum)
• fix a problem with normalize, ringinfo, and fragments
  (github pull #2685 from greglandrum)
• Error when a squiggle bond is in an aromatic ring
  (github issue #2695 from greglandrum)
• Cannot combine multiple range queries on a single atom.
  (github issue #2709 from greglandrum)
• setBondStereoFromDirections() returning incorrect results.
  (github issue #2712 from greglandrum)
• update supplier documentation to reflect python 3 iterator syntax
  (github pull #2719 from greglandrum)
• removeHs messing up double bond stereo in partially sanitized molecules
  (github issue #2721 from greglandrum)
• seg fault in ReactionRunner
  (github issue #2722 from greglandrum)

New Features and Enhancements:

• Added rankAtoms to ROMol wrapper and added Java test case
  (github pull #1540 from sroughley)
• Use van der Waals radii from blue obelisk
  (github pull #2154 from UnixJunkie)
• add generateDepictionMatching2DStructure() to SWIG wrappers
  (github issue #2239 from greglandrum)
• Added OptimizeMoleculeConfs with pre-generated force-field
  (github pull #2401 from ptosco)
• FreeSASA improvements
  (github pull #2402 from ptosco)
• Speed up symmetrizeSSSR
  (github issue #2403 from d-b-w)
• Trim whitespace from mol fragment SMARTS and check SMARTS presence
  (github pull #2406 from ricrogz)
• Run clang-tidy over the entire codebase
  (github pull #2408 from greglandrum)
• Enable Azure Pipelines builds for CI
  (github pull #2409 from ricrogz)
• Add RDProps interface to Conformers
  (github issue #2441 from greglandrum)
• Add minimal JavaScript wrapper
  (github pull #2444 from greglandrum)
• Fixes annoying warnings on MSVC
  (github pull #2454 from ptosco)
• add prepareMolsBeforeDrawing option for drawMols
  (github pull #2455 from greglandrum)
• computeGasteigerCharges quality of life improvement for python api
  (github issue #2480 from bp-kelley)
• Preserve bond direction in fragmentOnBonds
  (github pull #2484 from greglandrum)
• SanitizeRxn code and docstring cleanup
  (github pull ...

2019_03_4 (Q1 2019) Release

Release_2019.03.4

(Changes relative to Release_2019.03.3)

Acknowledgements:

Jason Biggs, Lester Hedges, Brian Kelley, Noel O'Boyle, Ricardo
Rodriguez Schmidt, Peter St. John, Amol Thakkar, Paolo Tosco, Riccardo
Vianello

Bug Fixes:

• Atom index out of range error
  (github #1868 from A-Thakkar)
• Incorrect cis/trans stereo symbol for conjugated ring
  (github #2023 from baoilleach)
• Thread safety cleanups in the MMFF code
  (github #2511 from greglandrum)
• CMake Error: Wrap directories being used when python build is turned off
  (github #2516 from jasondbiggs)
• • fixes ResonanceMolSupplier bug in perceiving conjugated groups
    (github #2517 from ptosco)
• update expected SVG output in cartridge tests
  (github #2520 from greglandrum)
• fix to SDWriter docs
  (github #2521 from pstjohn)
• getAtomNeighbors() and getAtomBonds() not in SWIG wrappers.
  (github #2532 from greglandrum)
• Default sanitizerxn doesn't aromatize if possible
  (github #2547 from bp-kelley)
• Chem.rdFMCS.FindMCS hangs for certain ligand pairs
  (github #2581 from lohedges)
• fix the inclusion path for the targets file (#2584)
  (github #2589 from rvianello)
• Fix inocuous typo/bug in Dative bond matching
  (github #2593 from ricrogz)

2019_03_3 (Q1 2019) Release

Release_2019.03.3

(Changes relative to Release_2019.03.2)

Acknowledgements:

David Cosgrove, Gareth Jones, Brian Kelley, Karl Leswing, Vincent Scalfani,
Riccardo Vianello

Bug Fixes:

• Chem.MolStandardize.standardize.Standardizer drops molecular properties
  (github #2431 from lilleswing)
• Fix/rgroup sdf isotope
  (github #2449 from bp-kelley)
• Uncharger incorrectly removing charge from boron anions
  (github #2452 from greglandrum)
• Add java builds to azure devops
  (github #2460 from greglandrum)
• Cart fixes
  (github #2462 from jones-gareth)
• Negative atom map values cause depickling to fail
  (github #2465 from greglandrum)
• Deserialization failures crash Java wrapper
  (github #2466 from greglandrum)
• rdkit.six fix and cleanup
  (github #2469 from rvianello)
• dummy atom queries are flagged as complex
  (github #2471 from greglandrum)
• 3D structure display broken in jupyter notebook
  (github #2473 from greglandrum)
• Inconsistent defaults for nonBondedThresh in MMFF optimization
  (github #2475 from greglandrum)
• Fix/rgroup multiple labels
  (github #2481 from bp-kelley)
• 2D Depiction clipped atom highlighting
  (github #2486 from DavidACosgrove)
• BRICSBuild now passes scrambleReagents to children
  (github #2488 from greglandrum)
• fixed the dead Conda installation document link
  (github #2495 from vfscalfani)
• Pattern Fingerprint Issues
  (github #2501 from jones-gareth)

2019_03_2 (Q1 2019) Release

Release_2019.03.2

(Changes relative to Release_2019.03.1)

Acknowledgements:

Thomas Duigou, Paula Junge, Eisuke Kawashima, Brian Kelley, 'c56pony'

Bug Fixes:

• MCS returning partial rings with completeRingsOnly=True
  (github #945 from greglandrum)
• VSA_EState {1, ..., 10} calculated by rdkit doesn't seem correct.
  (github #2372 from c56pony)
• MolStandardize: FragmentRemover should not sanitize fragments
  (github #2411 from greglandrum)
• MolStandardize: combinatorial explosion in Normalizer
  (github #2414 from greglandrum)
• MCS code doesn't return envelope MCS if CompleteRingsOnly is true
  (github #2420 from greglandrum)
• RemoveHs() does not remove all hydrogens.
  (github #2422 from paulaju)
• Incorrect assignment of explicit Hs to Al+3 read from mol block
  (github #2423 from greglandrum)
• Improve installation guide [ci skip]
  (github #2424 from e-kwsm)
• Cannot set maxProducts > 1000 in RunReactants
  (github #2427 from tduigou)
• Canon::rankMolAtoms results in crossed double bonds in rings
  (github #2437 from greglandrum)
• make boost::iostreams optional
  (github #2440 from greglandrum)
• Small corrections to build system to enable static linking for java builds

2019_03_1 (Q1 2019) Release

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::getValstd::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 GetS...