2023_03_3 (Q1 2023) Release

Release_2023.03.3

(Changes relative to Release_2023.03.2)

Acknowledgements

(Note: I'm no longer attempting to manually curate names. If you would like to
see your contribution acknowledged with your name, please set your name in
GitHub)

David Cosgrove, Eloy Félix, Gareth Jones, Eisuke Kawashima, Brian Kelley, Dan
Nealschneider, Ricardo Rodriguez-Schmidt, Paolo Tosco, Riccardo Vianello, Rachel
Walker, thomp-j,

Backwards incompatible changes

• The CDXML parser now returns mols with reasonable coordinates and in
  the same coordinate axes as the other RDKit file parsers.

Bug Fixes:

• refactor(python): replace deprecated unittest methods
  (github #6304 from e-kwsm)
• RDKit hangs indefinitely when parsing not so big molblock
  (github #6434 from eloyfelix)
• Molecules from CDXML Parser have inverted, unrealistic atomic coordinates
  (github #6461 from greglandrum)
• CDXML Parser does not preserve information about bond wedging
  (github #6462 from greglandrum)
• boost::bad_any_cast error when calling getProp on properties set by applyMolListPropsToAtoms<int64_t>
  (github #6465 from rachelnwalker)
• Allow systems like C/C=N/[H] to be stereogenic with the new chirality code
  (github #6473 from greglandrum)
• Fix RWMol::addAtom docstring
  (github #6477 from d-b-w)
• Fix a few broken docstrings
  (github #6480 from ptosco)
• pin numpy to 1.24.3
  (github #6483 from bp-kelley)
• CMAKE_INSTALL_PREFIX not honored for Python files installation on Windows
  (github #6485 from ricrogz)
• Fixed tests that weren't being run in testDepictor.py
  (github #6486 from rachelnwalker)
• Fixes rdkit-js/issues/347
  (github #6490 from ptosco)
• Make sure that molecules are shown as images by PandasTools also when DataFrames are truncated horizontally
  (github #6496 from ptosco)
• fixes #6499
  (github #6500 from ptosco)
• MolToMolBlock writes "either" stereo for double bonds which shouldn't be stereo
  (github #6502 from ricrogz)
• Double bonds are not correctly drawn on sulfoximines
  (github #6504 from ptosco)
• RegistrationHash.GetMolLayers() with v2 tautomer hash does not filter CX extensions
  (github #6505 from ricrogz)
• Drop the s_m_color_rgb property from MaeWriter
  (github #6511 from ricrogz)
• update avalontools version to incorporate bug fixes
  (github #6513 from ptosco)
• update windows DLL CI build config
  (github #6535 from greglandrum)
• Add MolEnumerator to C#
  (github #6542 from jones-gareth)
• MolDraw2D: placement of bond or atom labels gets confused when atoms overlap
  (github #6569 from greglandrum)
• Fix vulnerabilities found by fuzzer.
  (github #6579 from thomp-j)
• allow building the cartridge against PostgreSQL 16
  (github #6580 from ptosco)
• Add newline to ConstrainedEmbed docstring.
  (github #6596 from DavidACosgrove)
• Avoid leaking memory in case exceptions are thrown while generating FPs
  (github #6630 from ptosco)

2023_03_2 (Q1 2023) Release

Release_2023.03.2

(Changes relative to Release_2023.03.1)

Acknowledgements

(Note: I'm no longer attempting to manually curate names. If you would like to
see your contribution acknowledged with your name, please set your name in
GitHub)

David Cosgrove, Andrew Dalke, Eloy Félix, Gareth Jones, Juuso Lehtivarjo, Vedran
Miletić, Timothy Ngotiaoco, Ernst-Georg Schmid, Ricardo Rodriguez-Schmidt, Paolo
Tosco, Riccardo Vianello, Maciej Wójcikowski, wangyingxie, teltim, lhyuen

Bug Fixes:

• PF6- still can not get Bad Conformer Id after the #510 issue fix
  (github #5145 from wangyingxie)
• Crash when parsing InChI
  (github #6172 from eloyfelix)
• generateDepictionMatching2DStructure: bonds to R groups should be generic when matching
  (github #6306 from ptosco)
• MolToSmiles(canonical=False) creates the wrong _smilesBondOutputOrder property
  (github #6315 from adalke)
• MolToMolBlock ignores unspecified information for double bonds in rings
  (github #6316 from mwojcikowski)
• bump yaehmop version
  (github #6330 from greglandrum)
• rdMolDraw2D.MolDraw2DCairo produces Pre-condition Violation: no draw context when SetColour, DrawRect or DrawLine was called.
  (github #6336 from lhyuen)
• Added cstdint include
  (github #6338 from vedranmiletic)
• remove the dependency from python distutils in the top CMakeLists.txt file
  (github #6339 from rvianello)
• take drawOptions into account when exporting structure to xlsx format
  (github #6341 from ptosco)
• Fix swig memory leak
  (github #6346 from jones-gareth)
• Add inlines to ForceFieldHelpers header functions
  (github #6356 from JLVarjo)
• Bug relating to this PF6- still can not get Bad Conformer Id
  (github #6365 from teltim)
• straightenDepiction should not consider 0-degree rotations as multiples of 60
  (github #6367 from ptosco)
• expose two missing EmbedFailureCauses tags to python
  (github #6372 from greglandrum)
• Molfile Unsaturation Query Not Parsed Correctly
  (github #6395 from timothyngo)
• MolDraw2D: chiral tag overlapping atom label
  (github #6397 from greglandrum)
• expose some missing CXSmiles flags to python
  (github #6415 from greglandrum)
• V3000 structure segfaults when converting to SVG
  (github #6416 from ergo70)
• WedgeMolBonds won't wedge/dash a 2nd bond when input already has a wedge/dash around the same chiral atom
  (github #6423 from ricrogz)
• MolEnumerate should clear the reaction properties on its results
  (github #6432 from greglandrum)
• Removing Hs on a pyrrol-like structure throws kekulization error
  (github #6437 from ricrogz)

Release_2023.03.1

(Changes relative to Release_2022.09.1)

Acknowledgements

(Note: I'm no longer attempting to manually curate names. If you would like to
see your contribution acknowledged with your name, please set your name in
GitHub)

Michael Banck, Christopher Von Bargen, Jason Biggs, Jonathan Bisson, Jacob
Bloom, shang chien, David Cosgrove, Iren Azra Azra Coskun, Andrew Dalke, Eloy
Félix, Peter Gedeck, Desmond Gilmour, Mosè Giordano, Emanuele Guidotti, Tad
Hurst, Gareth Jones, Calvin Josenhans, Maria Kadukova, Brian Kelley, Joos
Kiener, Chris Kuenneth, Martin Larralde, Krzysztof Maziarz, Jeremy Monat, Michel
Moreau, Rocco Moretti, Lucas Morin, Dan Nealschneider, Noel O'Boyle, Vladas
Oleinikovas, Rachael Pirie, Ricardo Rodriguez-Schmidt, Vincent F. Scalfani,
Gregor Simm, Marco Stenta, Georgi Stoychev, Paolo Tosco, Kazuya Ujihara,
Riccardo Vianello, Franz Waibl, Rachel Walker, Patrick Walters,
'dangthatsright', 'mihalyszabo88', 'Deltaus', 'radchenkods',
'josh-collaborationspharma', 'jkh', 'yamasakih'

Highlights

• The 2D coordinate generation can now optionally use templates when working with complex ring systems. We will continue to improve this functionality in future releases.
• There's now a single function which allows you to calculate all available 2D descriptors for a molecule: Descriptors.CalcMolDescriptors()
• Support for working with organometallic molecules has improved: drawings of these structures are now better and there's new code for switching back and forth between dative and multi-center views of the bonding in systems like ferrocene.
• The fingerprint generator code has been improved and expanded with the idea of allowing user to switch entirely to the new code for the supported fingerprint types: Morgan, RDKit, topological torsion, and atom pairs.

Backwards incompatible changes

• The ring-finding functions will now run even if the molecule already has ring information. Older versions of the RDKit would return whatever ring information was present, even if it had been generated using a different algorithm.
• The ring-finding functions now no longer consider dative bonds as possible ring bonds by default. All of the ring-finding functions have a new optional argument includeDativeBonds which can be used to change this behavior
• Generating 2D coordinates no longer has the side effect of running ring finding on molecules.
• The canonical SMILES and CXSMILES generated for molecules with enhanced stereochemistry (stereo groups) is different than in previous releases. The enhanced stereochemistry information and the stereo groups themselves are now canonical. This does not affect molecules which do not have enhanced stereo and will not have any effect if you generate non-isomeric SMILES. This change also affects the output of the MolHash and RegistrationHash code when applied to molecules with enhanced stereo.
• The doIsomericSmiles parameter in Java and C# ROMol.MolToSmiles() now defaults to true (previously it was false), thus aligning to the C++ and Python behavior.
• Double bonds which are marked as crossed (i.e. bond.GetBondDir() == Bond.BondDir.EITHERDOUBLE) now have their BondStereo set to Bond.BondStereo.STEREOANY and the BondDir information removed by default when molecules are parsed or AssignStereochemistry() is called with the cleanIt argument set to True.
• The conformers generated for molecules with three-coordinate chiral centers will be somewhat different due to the fix for #5883.
• Molecules which come from Mol or SDF files will now always have the "_MolFileChiralFlag" property set to the value of the chiral flag in the CTAB. In previous versions the property was not set if the chiral flag was 0.

Bug Fixes:

• GetSubstructMatches uniquify and maxMatches don't work well together
  (github issue #888 from adalke)
• DrawRDKBits raised RDKit error when it applied to the compounds that contains imidazole.
  (github issue #2164 from yamasakih)
• MolFromMol2File: O.co2 atom type correctness check ignores phosphate groups
  (github issue #3246 from chmnk)
• Enhanced Stereo is lost when using GetMolFrags(m, asMols=True)
  (github issue #4845 from kienerj)
• Segfault with coordgen v3.0.0
  (github issue #4845 from lucasmorin222)
• Dative bond and alkali and alkaline earth metals
  (github issue #5120 from marcostenta)
• RGD Stereochemistry in decomposed structure is not copied to the matching core
  (github issue #5613 from jones-gareth)
• fp.ToList() fails for empty molecule
  (github issue #5677 from baoilleach)
• SMILES and SMARTS parse bonds in a different order
  (github issue #5683 from ricrogz)
• postgresql makefile needs to be updated to use c++17
  (github issue #5685 from mbanck)
• Exception raised when reading very large SMILES file
  (github issue #5692 from DavidACosgrove)
• Update warning message about aromaticity detection
  (github pull #5696 from d-b-w)
• stop building catch_main when tests are disabled
  (github pull #5697 from greglandrum)
• Make PandasTools.RGroupDecompositionToFrame re-entrant
  (github pull #5698 from greglandrum)
• PandasTools.RGroupDecompositionToFrame() should call ChangeMoleculeRendering()
  (github issue #5702 from greglandrum)
• MolDraw2D should automatically set bond highlight color when atom colors are changed
  (github issue #5704 from greglandrum)
• Use correct _WIN32 macro for checking Windows target
  (github pull #5710 from giordano)
• Environment not set properly in chirality tests for MinGW builds
  (github pull #5711 from ptosco)
• windows.h header should be lowercase
  (github pull #5712 from ptosco)
• Fixes bond index parsing for w/c/t/ctu labels in CXSMILES/CXSMARTS
  (github pull #5722 from ricrogz)
• Fix a deprecation warning in pythonTestDirRoot
  (github pull #5723 from ricrogz)
• allowNontetrahedralChiralty should be honored when reading/writing SMILES
  (github pull #5728 from greglandrum)
• CFFI/MinimalLib fixes
  (github pull #5729 from ptosco)
• Allow setting custom FREETYPE_LIBRARY/FREETYPE_INCLUDE_DIRS through CMake
  (github pull #5730 from ptosco)
• Missing update path for postgreSQL from 3.8 to 4.2
  (github issue #5734 from Deltaus)
• Avoid passing a NULL pointer to CanSmiles()
  (github pull #5750 from ptosco)
• CDXML reader incorrectly sets stereo on crossed double bonds
  (github issue #5752 from baoilleach)
• R atom label information lost in molfile if not backed by a M RGP entry
  (github issue #5763 from eloyfelix)
• Missing monomer labels when depicting MON SGroups
  (github issue #5767 from eloyfelix)
• Wrongly oriented SGroup bracket
  (github issue #5768 from eloyfelix)
• Adjust LocaleSwitcher on Windows when RDK_BUILD_THREADSAFE_SSS not set
  (github pull #5783 from roccomoretti)
• KekulizationException in tautomer canonicalization
  (github issue #5784 from d-b-w)
• ChemicalReactionToRxnBlock ignores separateAgents if forceV3000 is true
  (github issue #5785 from jacobbloom)
• extend the allowed valences of the alkali earths
  (github pull #5786 from greglandrum)
• Minimallib build (rdkit-js) not working for release 2022.09.2
  (github issue #5792 from MichelML)
• Remove dependency on MSVC runtime DLL in MinGW buil...

2023_03_1 (Q1 2023) Release

Release_2023.03.1

(Changes relative to Release_2022.09.1)

Acknowledgements

(Note: I'm no longer attempting to manually curate names. If you would like to
see your contribution acknowledged with your name, please set your name in
GitHub)

Michael Banck, Christopher Von Bargen, Jason Biggs, Jonathan Bisson, Jacob
Bloom, Shang Chien, David Cosgrove, Iren Azra Azra Coskun, Andrew Dalke, Eloy
Félix, Peter Gedeck, Desmond Gilmour, Mosè Giordano, Emanuele Guidotti, Tad
Hurst, Gareth Jones, Calvin Josenhans, Maria Kadukova, Brian Kelley, Joos
Kiener, Chris Kuenneth, Martin Larralde, Krzysztof Maziarz, Jeremy Monat, Michel
Moreau, Rocco Moretti, Lucas Morin, Dan Nealschneider, Noel O'Boyle, Vladas
Oleinikovas, Rachael Pirie, Ricardo Rodriguez-Schmidt, Vincent F. Scalfani,
Gregor Simm, Marco Stenta, Georgi Stoychev, Paolo Tosco, Kazuya Ujihara,
Riccardo Vianello, Franz Waibl, Rachel Walker, Patrick Walters,
'dangthatsright', 'mihalyszabo88', 'Deltaus', 'radchenkods',
'josh-collaborationspharma', 'jkh', 'yamasakih'

Highlights

• The 2D coordinate generation can now optionally use templates when working with complex ring systems. We will continue to improve this functionality in future releases.
• There's now a single function which allows you to calculate all available 2D descriptors for a molecule: Descriptors.CalcMolDescriptors()
• Support for working with organometallic molecules has improved: drawings of these structures are now better and there's new code for switching back and forth between dative and multi-center views of the bonding in systems like ferrocene.
• The fingerprint generator code has been improved and expanded with the idea of allowing user to switch entirely to the new code for the supported fingerprint types: Morgan, RDKit, topological torsion, and atom pairs.

Backwards incompatible changes

• The ring-finding functions will now run even if the molecule already has ring information. Older versions of the RDKit would return whatever ring information was present, even if it had been generated using a different algorithm.
• The ring-finding functions now no longer consider dative bonds as possible ring bonds by default. All of the ring-finding functions have a new optional argument includeDativeBonds which can be used to change this behavior
• Generating 2D coordinates no longer has the side effect of running ring finding on molecules.
• The canonical SMILES and CXSMILES generated for molecules with enhanced stereochemistry (stereo groups) is different than in previous releases. The enhanced stereochemistry information and the stereo groups themselves are now canonical. This does not affect molecules which do not have enhanced stereo and will not have any effect if you generate non-isomeric SMILES. This change also affects the output of the MolHash and RegistrationHash code when applied to molecules with enhanced stereo.
• The doIsomericSmiles parameter in Java and C# ROMol.MolToSmiles() now defaults to true (previously it was false), thus aligning to the C++ and Python behavior.
• Double bonds which are marked as crossed (i.e. bond.GetBondDir() == Bond.BondDir.EITHERDOUBLE) now have their BondStereo set to Bond.BondStereo.STEREOANY and the BondDir information removed by default when molecules are parsed or AssignStereochemistry() is called with the cleanIt argument set to True.
• The conformers generated for molecules with three-coordinate chiral centers will be somewhat different due to the fix for #5883.
• Molecules which come from Mol or SDF files will now always have the "_MolFileChiralFlag" property set to the value of the chiral flag in the CTAB. In previous versions the property was not set if the chiral flag was 0.

Bug Fixes:

• GetSubstructMatches uniquify and maxMatches don't work well together
  (github issue #888 from adalke)
• DrawRDKBits raised RDKit error when it applied to the compounds that contains imidazole.
  (github issue #2164 from yamasakih)
• MolFromMol2File: O.co2 atom type correctness check ignores phosphate groups
  (github issue #3246 from chmnk)
• Enhanced Stereo is lost when using GetMolFrags(m, asMols=True)
  (github issue #4845 from kienerj)
• Segfault with coordgen v3.0.0
  (github issue #4845 from lucasmorin222)
• Dative bond and alkali and alkaline earth metals
  (github issue #5120 from marcostenta)
• RGD Stereochemistry in decomposed structure is not copied to the matching core
  (github issue #5613 from jones-gareth)
• fp.ToList() fails for empty molecule
  (github issue #5677 from baoilleach)
• SMILES and SMARTS parse bonds in a different order
  (github issue #5683 from ricrogz)
• postgresql makefile needs to be updated to use c++17
  (github issue #5685 from mbanck)
• Exception raised when reading very large SMILES file
  (github issue #5692 from DavidACosgrove)
• Update warning message about aromaticity detection
  (github pull #5696 from d-b-w)
• stop building catch_main when tests are disabled
  (github pull #5697 from greglandrum)
• Make PandasTools.RGroupDecompositionToFrame re-entrant
  (github pull #5698 from greglandrum)
• PandasTools.RGroupDecompositionToFrame() should call ChangeMoleculeRendering()
  (github issue #5702 from greglandrum)
• MolDraw2D should automatically set bond highlight color when atom colors are changed
  (github issue #5704 from greglandrum)
• Use correct _WIN32 macro for checking Windows target
  (github pull #5710 from giordano)
• Environment not set properly in chirality tests for MinGW builds
  (github pull #5711 from ptosco)
• windows.h header should be lowercase
  (github pull #5712 from ptosco)
• Fixes bond index parsing for w/c/t/ctu labels in CXSMILES/CXSMARTS
  (github pull #5722 from ricrogz)
• Fix a deprecation warning in pythonTestDirRoot
  (github pull #5723 from ricrogz)
• allowNontetrahedralChiralty should be honored when reading/writing SMILES
  (github pull #5728 from greglandrum)
• CFFI/MinimalLib fixes
  (github pull #5729 from ptosco)
• Allow setting custom FREETYPE_LIBRARY/FREETYPE_INCLUDE_DIRS through CMake
  (github pull #5730 from ptosco)
• Missing update path for postgreSQL from 3.8 to 4.2
  (github issue #5734 from Deltaus)
• Avoid passing a NULL pointer to CanSmiles()
  (github pull #5750 from ptosco)
• CDXML reader incorrectly sets stereo on crossed double bonds
  (github issue #5752 from baoilleach)
• R atom label information lost in molfile if not backed by a M RGP entry
  (github issue #5763 from eloyfelix)
• Missing monomer labels when depicting MON SGroups
  (github issue #5767 from eloyfelix)
• Wrongly oriented SGroup bracket
  (github issue #5768 from eloyfelix)
• Adjust LocaleSwitcher on Windows when RDK_BUILD_THREADSAFE_SSS not set
  (github pull #5783 from roccomoretti)
• KekulizationException in tautomer canonicalization
  (github issue #5784 from d-b-w)
• ChemicalReactionToRxnBlock ignores separateAgents if forceV3000 is true
  (github issue #5785 from jacobbloom)
• extend the allowed valences of the alkali earths
  (github pull #5786 from greglandrum)
• Minimallib build (rdkit-js) not working for release 2022.09.2
  (github issue #5792 from MichelML)
• Remove dependency on MSVC runtime DLL in MinGW builds
  (github pull #5800 from ptosco)
• Update macOS target platform to 10.13
  (github pull #5802 from ptosco)
• R# atom label information lost in molfile if not handled by the RGP spec
  (github issue #5810 from eloyfelix)
• Stop using recommonmark in the documentation
  (github issue #5812 from greglandrum)
• Properties with new lines can create invalid SDFiles
  (github issue #5827 from bp-kelley)
• Allow building PgSQL RPM and DEB packages
  (github pull #5836 from ptosco)
• Additional output is incorrect when FP count simulation is active
  (github issue #5838 from ptosco)
• Explicit valence check SiPa13fails for certain SMILES
  (github issue #5849 from josh-collaborationspharma)
• Set emsdk path for freetype in emscripten builds
  (github pull #5857 from ptosco)
• DrawMorganBit fails by default
  (github issue #5863 from eguidotti)
• Fix #5810 in V2000 mol files.
  (github pull #5864 from eloyfelix)
• Chemical drawings should be automatically enabled on Colab
  (github pull #5868 from kuelumbus)
• use enhanced stereo when uniquifying in SimpleEnum
  (github pull #5874 from greglandrum)
• Conformer Generation Fails for three-coordinate Ns with specified stereo
  (github issue #5883 from gncs)
• Fix documentation example for KeyFromPropHolder
  (github pull #5886 from gedeck)
• Allow unrecognized atom types when strictParsing=False
  (github pull #5891 from greglandrum)
• DetermineBonds assigning methyl carbon as tetrahedral center
  (github issue #5894 from jasondbiggs)
• numpy.float is no longer supported and causes exceptions
  (github issue #5895 from PatWalters)
• moldraw2DTest1 failure when building on aarch64
  (github issue #5899 from vfscalfani)
• DetermineBondOrders running out of memory on medium-sized disconnected structure
  (github issue #5902 from jasondbiggs)
• clear MDL Rgroup labels from core atoms when we aren't using them
  (github pull #5904 from greglandrum)
• Conformer generator produces strange structure for substituted butadiene
  (github issue #5913 from gncs)
• MHFPEncoder::Distance doesn't compute a (Jaccard) distance
  (github issue #5919 from althonos)
• AvalonTools: Avoid that trailing garbage pollutes the fmemopen buffer
  (github pull #5928 from ptosco)
• "not" queries in molfiles get inverted
  (github issue #5930 from d-b-w)
• CalcTPSA() doesn't use options when caching
  (github issue #5941 from greglandrum)
• Bad drawing of end points for dative bonds
  (github issue #5943 from DavidACosgrove)
• Extremes of drawn ellipses not being calculated correctly.
  (github issue #5947 from ...

2023_03_1b1 (Q1 2023) Release

Release_2023.03.1b1

(Changes relative to Release_2022.09.1)

Acknowledgements

(Note: I'm no longer attempting to manually curate names. If you would like to
see your contribution acknowledged with your name, please set your name in
GitHub)

Michael Banck, Christopher Von Bargen, Jason Biggs, Jonathan Bisson, Jacob
Bloom, shang chien, David Cosgrove, Iren Azra Azra Coskun, Andrew Dalke, Eloy
Félix, Peter Gedeck, Desmond Gilmour, Mosè Giordano, Emanuele Guidotti, Tad
Hurst, Gareth Jones, Calvin Josenhans, Maria Kadukova, Brian Kelley, Joos
Kiener, Chris Kuenneth, Martin Larralde, Krzysztof Maziarz, Jeremy Monat, Michel
Moreau, Rocco Moretti, Lucas Morin, Dan Nealschneider, Noel O'Boyle, Vladas
Oleinikovas, Rachael Pirie, Ricardo Rodriguez-Schmidt, Vincent F. Scalfani,
Gregor Simm, Marco Stenta, Georgi Stoychev, Paolo Tosco, Kazuya Ujihara,
Riccardo Vianello, Franz Waibl, Rachel Walker, Patrick Walters,
'dangthatsright', 'mihalyszabo88', 'Deltaus', 'radchenkods',
'josh-collaborationspharma', 'jkh', 'yamasakih'

Highlights

Backwards incompatible changes

• The ring-finding functions will now run even if the molecule already has ring information. Older versions of the RDKit would return whatever ring information was present, even if it had been generated using a different algorithm.
• The ring-finding functions now no longer consider dative bonds as possible ring bonds by default. All of the ring-finding functions have a new optional argument includeDativeBonds which can be used to change this behavior
• Generating 2D coordinates no longer has the side effect of running ring finding on molecules.
• The canonical SMILES and CXSMILES generated for molecules with enhanced stereochemistry (stereo groups) is different than in previous releases. The enhanced stereochemistry information and the stereo groups themselves are now canonical. This does not affect molecules which do not have enhanced stereo and will not have any effect if you generate non-isomeric SMILES. This change also affects the output of the MolHash and RegistrationHash code when applied to molecules with enhanced stereo.
• The doIsomericSmiles parameter in Java and C# ROMol.MolToSmiles() now defaults to true (previously it was false), thus aligning to the C++ and Python behavior.
• Double bonds which are marked as crossed (i.e. bond.GetBondDir() == Bond.BondDir.EITHERDOUBLE) now have their BondStereo set to Bond.BondStereo.STEREOANY and the BondDir information removed by default when molecules are parsed or AssignStereochemistry() is called with the cleanIt argument set to True.
• The conformers generated for molecules with three-coordinate chiral centers will be somewhat different due to the fix for #5883.
• Molecules which come from Mol or SDF files will now always have the "_MolFileChiralFlag" property set to the value of the chiral flag in the CTAB. In previous versions the property was not set if the chiral flag was 0.

Bug Fixes:

• GetSubstructMatches uniquify and maxMatches don't work well together
  (github issue #888 from adalke)
• DrawRDKBits raised RDKit error when it applied to the compounds that contains imidazole.
  (github issue #2164 from yamasakih)
• MolFromMol2File: O.co2 atom type correctness check ignores phosphate groups
  (github issue #3246 from chmnk)
• Enhanced Stereo is lost when using GetMolFrags(m, asMols=True)
  (github issue #4845 from kienerj)
• Segfault with coordgen v3.0.0
  (github issue #4845 from lucasmorin222)
• Dative bond and alkali and alkaline earth metals
  (github issue #5120 from marcostenta)
• RGD Stereochemistry in decomposed structure is not copied to the matching core
  (github issue #5613 from jones-gareth)
• fp.ToList() fails for empty molecule
  (github issue #5677 from baoilleach)
• SMILES and SMARTS parse bonds in a different order
  (github issue #5683 from ricrogz)
• postgresql makefile needs to be updated to use c++17
  (github issue #5685 from mbanck)
• Exception raised when reading very large SMILES file
  (github issue #5692 from DavidACosgrove)
• Update warning message about aromaticity detection
  (github pull #5696 from d-b-w)
• stop building catch_main when tests are disabled
  (github pull #5697 from greglandrum)
• Make PandasTools.RGroupDecompositionToFrame re-entrant
  (github pull #5698 from greglandrum)
• PandasTools.RGroupDecompositionToFrame() should call ChangeMoleculeRendering()
  (github issue #5702 from greglandrum)
• MolDraw2D should automatically set bond highlight color when atom colors are changed
  (github issue #5704 from greglandrum)
• Use correct _WIN32 macro for checking Windows target
  (github pull #5710 from giordano)
• Environment not set properly in chirality tests for MinGW builds
  (github pull #5711 from ptosco)
• windows.h header should be lowercase
  (github pull #5712 from ptosco)
• Fixes bond index parsing for w/c/t/ctu labels in CXSMILES/CXSMARTS
  (github pull #5722 from ricrogz)
• Fix a deprecation warning in pythonTestDirRoot
  (github pull #5723 from ricrogz)
• allowNontetrahedralChiralty should be honored when reading/writing SMILES
  (github pull #5728 from greglandrum)
• CFFI/MinimalLib fixes
  (github pull #5729 from ptosco)
• Allow setting custom FREETYPE_LIBRARY/FREETYPE_INCLUDE_DIRS through CMake
  (github pull #5730 from ptosco)
• Missing update path for postgreSQL from 3.8 to 4.2
  (github issue #5734 from Deltaus)
• Avoid passing a NULL pointer to CanSmiles()
  (github pull #5750 from ptosco)
• CDXML reader incorrectly sets stereo on crossed double bonds
  (github issue #5752 from baoilleach)
• R atom label information lost in molfile if not backed by a M RGP entry
  (github issue #5763 from eloyfelix)
• Missing monomer labels when depicting MON SGroups
  (github issue #5767 from eloyfelix)
• Wrongly oriented SGroup bracket
  (github issue #5768 from eloyfelix)
• Adjust LocaleSwitcher on Windows when RDK_BUILD_THREADSAFE_SSS not set
  (github pull #5783 from roccomoretti)
• KekulizationException in tautomer canonicalization
  (github issue #5784 from d-b-w)
• ChemicalReactionToRxnBlock ignores separateAgents if forceV3000 is true
  (github issue #5785 from jacobbloom)
• extend the allowed valences of the alkali earths
  (github pull #5786 from greglandrum)
• Minimallib build (rdkit-js) not working for release 2022.09.2
  (github issue #5792 from MichelML)
• Remove dependency on MSVC runtime DLL in MinGW builds
  (github pull #5800 from ptosco)
• Update macOS target platform to 10.13
  (github pull #5802 from ptosco)
• R# atom label information lost in molfile if not handled by the RGP spec
  (github issue #5810 from eloyfelix)
• Stop using recommonmark in the documentation
  (github issue #5812 from greglandrum)
• Properties with new lines can create invalid SDFiles
  (github issue #5827 from bp-kelley)
• Allow building PgSQL RPM and DEB packages
  (github pull #5836 from ptosco)
• Additional output is incorrect when FP count simulation is active
  (github issue #5838 from ptosco)
• Explicit valence check SiPa13fails for certain SMILES
  (github issue #5849 from josh-collaborationspharma)
• Set emsdk path for freetype in emscripten builds
  (github pull #5857 from ptosco)
• DrawMorganBit fails by default
  (github issue #5863 from eguidotti)
• Fix #5810 in V2000 mol files.
  (github pull #5864 from eloyfelix)
• Chemical drawings should be automatically enabled on Colab
  (github pull #5868 from kuelumbus)
• use enhanced stereo when uniquifying in SimpleEnum
  (github pull #5874 from greglandrum)
• Conformer Generation Fails for three-coordinate Ns with specified stereo
  (github issue #5883 from gncs)
• Fix documentation example for KeyFromPropHolder
  (github pull #5886 from gedeck)
• Allow unrecognized atom types when strictParsing=False
  (github pull #5891 from greglandrum)
• DetermineBonds assigning methyl carbon as tetrahedral center
  (github issue #5894 from jasondbiggs)
• numpy.float is no longer supported and causes exceptions
  (github issue #5895 from PatWalters)
• moldraw2DTest1 failure when building on aarch64
  (github issue #5899 from vfscalfani)
• DetermineBondOrders running out of memory on medium-sized disconnected structure
  (github issue #5902 from jasondbiggs)
• clear MDL Rgroup labels from core atoms when we aren't using them
  (github pull #5904 from greglandrum)
• Conformer generator produces strange structure for substituted butadiene
  (github issue #5913 from gncs)
• MHFPEncoder::Distance doesn't compute a (Jaccard) distance
  (github issue #5919 from althonos)
• AvalonTools: Avoid that trailing garbage pollutes the fmemopen buffer
  (github pull #5928 from ptosco)
• "not" queries in molfiles get inverted
  (github issue #5930 from d-b-w)
• CalcTPSA() doesn't use options when caching
  (github issue #5941 from greglandrum)
• Bad drawing of end points for dative bonds
  (github issue #5943 from DavidACosgrove)
• Extremes of drawn ellipses not being calculated correctly.
  (github issue #5947 from DavidACosgrove)
• Arrow heads of dative bonds are different sizes
  (github issue #5949 from DavidACosgrove)
• stop caching ring-finding results
  (github pull #5955 from greglandrum)
• Wrong bond endpoint when connecting to wedge bond in 2D image
  (github issue #5963 from stgeo)
• Tiny change to get demo.html to load in legacy browsers
  (github pull #5964 from ptosco)
• detect bad double bond stereo in conformer generation
  (github pull #5967 from greglandrum)
• drawing code should not generate kekulization errors
  (github issue #5974 from greglandrum)
• Adjust expected test results for newer freetype versions
  (github pull #5979 from greglandrum)
• CanonicalRankAtomsInFragment example in the documentation is not reproducible
  ...

2022_09_5 (Q3 2022) Release

Release_2022.09.5

(Changes relative to Release_2022.09.4)

Important Note:

Due to a mistake Greg made while going through his release workflow, the
following bug fixes which were on the "fixed" list for the 2022.09.4 release
were not actually included in that release:

• Allow building PgSQL RPM and DEB packages
  (github #5836 from ptosco)
• Set emsdk path for freetype in emscripten builds
  (github #5857 from ptosco)
• Fix #5810 in V2000 mol files.
  (github #5864 from eloyfelix)
• use enhanced stereo when uniquifying in SimpleEnum
  (github #5874 from greglandrum)
• Fix documentation example for KeyFromPropHolder
  (github #5886 from gedeck)
• Allow unrecognized atom types when strictParsing=False
  (github #5891 from greglandrum)
• clear MDL Rgroup labels from core atoms when we aren't using them
  (github #5904 from greglandrum)
• AvalonTools: Avoid that trailing garbage pollutes the fmemopen buffer
  (github #5928 from ptosco)
• Tiny change to get demo.html to load in legacy browsers
  (github #5964 from ptosco)

These fixes are all included in this release.

Acknowledgements

Christopher Von Bargen, Jonathan Bisson, shang chien, David Cosgrove, Iren Azra
Azra Coskun, Maria Kadukova, Brian Kelley, Chris Kuenneth, Dan Nealschneider,
Ricardo Rodriguez-Schmidt, Paolo Tosco, Franz Waibl, 'Derek', 'dangthatsright'

Bug Fixes:

• Missing update path for postgreSQL from 3.8 to 4.2
  (github #5734 from Deltaus)
• Chemical drawings should be automatically enabled on Colab
  (github #5868 from kuelumbus)
• Adjust expected test results for newer freetype versions
  (github #5979 from greglandrum)
• CanonicalRankAtomsInFragment example in the documentation is not reproducible
  (github #5986 from chmnk)
• Exception in RegistrationHash for molecules with bad bond directions
  (github #5987 from d-b-w)
• Updated the GetMolHash docstring for accuracy
  (github #5988 from irenazra)
• Fix a problem with pickling molecules with more than 255 rings
  (github #5992 from greglandrum)
• Support Python 3.11
  (github #5994 from greglandrum)
• Incorrect disconnection of CC(=O)O[Mg]OC(=O)C
  (github #5997 from DavidACosgrove)
• Remove and from C++ headers
  (github #6003 from d-b-w)
• [PH3] incorrectly recognized as potential stereo center
  (github #6011 from greglandrum)
• Potential nontetrahedral stereo is recognized when nontetrahedral stereo is disabled.
  (github #6012 from greglandrum)
• MolEnumerator is not propagating query information to molecules
  (github #6014 from greglandrum)
• Reactions do not propagate query information to products
  (github #6015 from greglandrum)
• Error rendering to very small canvas
  (github #6025 from DavidACosgrove)
• Bad double bond drawn for collinear atoms
  (github #6027 from DavidACosgrove)
• Fix some minor leaks
  (github #6029 from ricrogz)
• Cannot draw molecule which includes an atom with a [!#X] query (for any X)
  (github #6033 from ShangChien)
• FragmentOnBonds may create unexpected radicals
  (github #6034 from ricrogz)
• Calling MurckoScaffold on molecule causes bug in pickling
  (github #6036 from dangthatsright)
• Bump maeparser and coordgen versions
  (github #6039 from ricrogz)
• Issues with ACS1996 drawing mode on a small canvas
  (github #6041 from DavidACosgrove)
• Cyclobutyl group in a macrocycle triggers a stereo center
  (github #6049 from cdvonbargen)
• stereogroups not combined when parsing CXSMILES
  (github #6050 from greglandrum)
• Regression in depicting molecules with MDL query atoms
  (github #6054 from ptosco)
• Remove check for ring information from Atom::Match
  (github #6063 from fwaibl)
• Correct docstring for minFontSize.
  (github #6066 from DavidACosgrove)
• Disable POPCNT on M1
  (github #6081 from bjonnh-work)
• Dummy atoms should not be considered to be metals for M and MH queries
  (github #6106 from greglandrum)
  Other pull requests:
• Enable optional visualization of complex query atoms in a more compact form
  (github pull #6056 from ptosco)
• Fixes #6049
  (github pull #6061 from greglandrum)
• Fixes #6050
  (github pull #6071 from greglandrum)
• Fixes #5986
  (github pull #6072 from greglandrum)
• Properly check for boost::any in rdvalue_is
  (github pull #6086 from bp-kelley)
• Fixes #6100
  (github pull #6105 from greglandrum)
• Fixes #6106
  (github pull #6107 from greglandrum)

2022_09_4 (Q3 2022) Release

Release_2022.09.4

(Changes relative to Release_2022.09.3)

Acknowledgements

Jason Biggs, Jacob Bloom, David Cosgrove, Eloy Félix, Peter Gedeck,
Emanuele Guidotti, Gareth Jones, Maria Kadukova, Brian Kelley, Chris Kuenneth,
Lucas Morin, Dan Nealschneider, Ricardo Rodriguez-Schmidt. Vincent F. Scalfani,
Georgi Stoychev, Paolo Tosco, Patrick Walters, josh-collaborationspharma

Bug Fixes:

• MolFromMol2File: O.co2 atom type correctness check ignores phosphate groups
  (github #3246 from chmnk)
• Segfault with coordgen v3.0.0
  (github #4845 from lucasmorin222)
• Update CoordGen version
  (github pull #5927 from jasondbiggs)
• ChemicalReactionToRxnBlock ignores separateAgents if forceV3000 is true
  (github #5785 from jacobbloom)
• Properties with new lines can create invalid SDFiles
  (github #5827 from bp-kelley)
• Allow building PgSQL RPM and DEB packages
  (github #5836 from ptosco)
• Explicit valence check fails for certain SMILES
  (github #5849 from josh-collaborationspharma)
• Set emsdk path for freetype in emscripten builds
  (github #5857 from ptosco)
• DrawMorganBit fails by default
  (github #5863 from eguidotti)
• Fix #5810 in V2000 mol files.
  (github #5864 from eloyfelix)
• Chemical drawings should be automatically enabled on Colab
  (github #5868 from kuelumbus)
• use enhanced stereo when uniquifying in SimpleEnum
  (github #5874 from greglandrum)
• Fix documentation example for KeyFromPropHolder
  (github #5886 from gedeck)
• Allow unrecognized atom types when strictParsing=False
  (github #5891 from greglandrum)
• DetermineBonds assigning methyl carbon as tetrahedral center
  (github #5894 from jasondbiggs)
• numpy.float is no longer supported and causes exceptions
  (github #5895 from PatWalters)
• moldraw2DTest1 failure when building on aarch64
  (github #5899 from vfscalfani)
• DetermineBondOrders running out of memory on medium-sized disconnected structure
  (github #5902 from jasondbiggs)
• clear MDL Rgroup labels from core atoms when we aren't using them
  (github #5904 from greglandrum)
• AvalonTools: Avoid that trailing garbage pollutes the fmemopen buffer
  (github #5928 from ptosco)
• "not" queries in molfiles get inverted
  (github #5930 from d-b-w)
• CalcTPSA() doesn't use options when caching
  (github #5941 from greglandrum)
• Bad drawing of end points for dative bonds
  (github #5943 from DavidACosgrove)
• Extremes of drawn ellipses not being calculated correctly.
  (github #5947 from DavidACosgrove)
• Arrow heads of dative bonds are different sizes
  (github #5949 from DavidACosgrove)
• Wrong bond endpoint when connecting to wedge bond in 2D image
  (github #5963 from stgeo)
• Tiny change to get demo.html to load in legacy browsers
  (github #5964 from ptosco)
• Drawing code should not generate kekulization errors
  (github #5974 from greglandrum)

2022_09_3 (Q3 2022) Release

Release_2022.09.3

(Changes relative to Release_2022.09.2)

Acknowledgements

David Cosgrove, Eloy Félix, Michel Moreau, Rocco Moretti, Dan Nealschneider, Paolo Tosco

Bug Fixes:

• Missing monomer labels when depicting MON SGroups
  (github #5767 from eloyfelix)
• Wrongly oriented SGroup bracket
  (github #5768 from eloyfelix)
• Adjust LocaleSwitcher on Windows when RDK_BUILD_THREADSAFE_SSS not set
  (github #5783 from roccomoretti)
• KekulizationException in tautomer canonicalization
  (github #5784 from d-b-w)
• extend the allowed valences of the alkali earths
  (github #5786 from greglandrum)
• Minimallib build (rdkit-js) not working for release 2022.09.2
  (github #5792 from MichelML)
• Remove dependency on MSVC runtime DLL in MinGW builds
  (github #5800 from ptosco)
• Update macOS target platform to 10.13
  (github #5802 from ptosco)
• R# atom label information lost in molfile if not handled by the RGP spec
  (github #5810 from eloyfelix)
• Stop using recommonmark in the documentation
  (github #5812 from greglandrum)

2022_09_2 (Q3 2022) Release

Release_2022.09.2

(Changes relative to Release_2022.09.1)

Acknowledgements

Michael Banck, David Cosgrove, Eloy Félix, Mosè Giordano, Brian Kelley, Dan
Nealschneider, Noel O'Boyle, Ricardo Rodriguez-Schmidt, Paolo Tosco,

Bug Fixes:

• fp.ToList() fails for empty molecule
  (github #5677 from baoilleach)
• SMILES and SMARTS parse bonds in a different order
  (github #5683 from ricrogz)
• postgresql makefile needs to be updated to use c++17
  (github #5685 from mbanck)
• Exception raised when reading very large SMILES file
  (github #5692 from DavidACosgrove)
• Update warning message about aromaticity detection
  (github #5696 from d-b-w)
• stop building catch_main when tests are disabled
  (github #5697 from greglandrum)
• Make PandasTools.RGroupDecompositionToFrame re-entrant
  (github #5698 from greglandrum)
• PandasTools.RGroupDecompositionToFrame() should call ChangeMoleculeRendering()
  (github #5702 from greglandrum)
• MolDraw2D should automatically set bond highlight color when atom colors are changed
  (github #5704 from greglandrum)
• Use correct _WIN32 macro for checking Windows target
  (github #5710 from giordano)
• Environment not set properly in chirality tests for MinGW builds
  (github #5711 from ptosco)
• windows.h header should be lowercase
  (github #5712 from ptosco)
• Fixes bond index parsing for w/c/t/ctu labels in CXSMILES/CXSMARTS
  (github #5722 from ricrogz)
• Fix a deprecation warning in pythonTestDirRoot
  (github #5723 from ricrogz)
• allowNontetrahedralChiralty should be honored when reading/writing SMILES
  (github #5728 from greglandrum)
• Allow setting custom FREETYPE_LIBRARY/FREETYPE_INCLUDE_DIRS through CMake
  (github #5730 from ptosco)
• Avoid passing a NULL pointer to CanSmiles()
  (github #5750 from ptosco)
• CDXML reader incorrectly sets stereo on crossed double bonds
  (github #5752 from baoilleach)
• Add wavy stereo bond support to cdxml
  (github pull #5755 from bp-kelley)
• R atom label information lost in molfile if not backed by a M RGP entry
  (github #5763 from eloyfelix)

2022_09_1 (Q3 2022) Release

Release_2022.09.1

(Changes relative to Release_2022.03.1)

Acknowledgements

Jonathan Bisson, Andy Cai, David Cosgrove, JP Ebejer, Aleš Erjavec, Peter
Gedeck, Mosè Giordano, Sreya Gogineni, Emanuele Guidotti, Hyeonki Hong, Gareth
Jones, Per Johnsson, Maria Kadukova, Eisuke Kawashima, Brian Kelley, Alan
Kerstjens, Michel Moreau, Dan Nealschneider, Santeri Puranen, Ricardo
Rodriguez-Schmidt, Guy Rosin Jeff van Santen, David Schaller, David W.H.
Swenson, Paolo Tosco, Antonio Trande, Ivan Tubert-Brohman, Alexandra Wahab,
Rachel Walker, balducci, GLPG-GT

Highlights

• The new RegistrationHash module provides one of the last pieces required to
  build a registration system with the RDKit.
• This release includes an initial version of a C++ implementation of the
  xyz2mol algorithm for assigning bonds and bond orders based on atomic
  positions. This work was done as part of the 2022 Google Summer of Code.
• A collection of new functionality has been added to minimallib and is now
  accessible from JavaScript and other programming languages.

Backwards incompatible changes

• Changes to the way atomic chirality is used in the canonicalization algorithm
  mean that canonical atom ranking and canonical SMILES generated with this
  RDKit version can be different from those generated with previous versions
• GetBestRMS() and CalcRMS() by default now treat terminal conjugated functional
  groups like carboxylate and nitro symmetrically. For example, the group
  C(=[O:1])[O-:2] can match in either orientation. The SMARTS pattern which is
  used to recognize affected groups is:
  [{atomP};$([{atomP}]-[*]=[{atomP}]),$([{atomP}]=[*]-[{atomP}])]~[*] where
  {atomP} is O,N;D1. The previous behavior can be restored using by setting
  the symmetrizeConjugatedTerminalGroups argument to false when calling
  GetBestRMS() and CalcRMS()
• The following #defines are no longer provided in/used by the C++ code or RDConfig.h:
  • BUILD_COORDGEN_SUPPORT: use RDK_BUILD_COORDGEN_SUPPORT instead
  • RDK_THREADSAFE_SSS: use RDK_BUILD_THREADSAFE_SSS instead
  • USE_BUILTIN_POPCOUNT: use RDK_OPTIMIZE_POPCNT instead
• The Python function Chem.GetSSSR() now returns the SSSR rings found instead
  of just returning the count of rings. This is consistent with
  Chem.GetSymmSSSR() and more useful.
• The SMILES parser will ignore the value of
  SmilesParserParams.useLegacyStereo unless it is set to false. See the
  deprecation note about useLegacyStereo below for more information.
• The CFFI function set_2d_coords_aligned() now takes an additional char **match_json
  parameter; if match_json is not not NULL, *match_json will point to a
  JSON string containing the atoms and bonds which are part of the match.
  It is up to the user to free this string.
• The aliphatic imine rule used in tautomer enumeration has been changed to more
  closely match the definition in the original paper.

Bug Fixes:

• H atoms in SGroups cause RDKit to clear SGroups after parsing
  (github issue #2716 from ricrogz)
• RDKit misplaces stereochemistry/chirality information for small ring
  (github issue #2984 from d-b-w)
• DrawMorganBit returns empty image for "isolated" fingerprints
  (github issue #4242 from eguidotti)
• Cores with query atoms may fail to R-group-decompose molecules
  (github issue #4505 from ptosco)
• Unable to serialize coordinates as floats in combination with *Props
  (github issue #4621 from santeripuranen)
• Image Generation: Highlighting looks off when bondLineWidth is increased for PNG generation
  (github issue #5122 from rachelnwalker)
• RDKit crashes on CIP label calculation
  (github issue #5142 from ricrogz)
• Modified the JS tests to comply with older nodejs versions
  (github pull #5148 from ptosco)
• Presence of exocyclic S/D, S/A or D/A query bonds prevents benzene from being recognized as aromatic
  (github issue #5152 from rachelnwalker)
• Fix for RGD dummy atom bug in RDKit::replaceCore
  (github pull #5154 from jones-gareth)
• KekulizeException of molecule from Smarts pattern with new RDKit release
  (github issue #5156 from schallerdavid)
• Very small fix to avoid an AttributeError
  (github pull #5163 from ptosco)
• issue with V3000 SD files containing enhanced stereochemistry information
  (github issue #5165 from GLPG-GT)
• Draw.MolToQPixmap raises a TypeError with Python 3.10
  (github issue #5166 from ales-erjavec)
• Standardization via RDKit breaks molecules
  (github issue #5169 from malteseunderdog)
• Multiple calls to BlockLogs() permanently disable logging
  (github issue #5172 from ricrogz)
• Check architecture of the target system to optimise popcnt
  (github pull #5182 from giordano)
• More consistently check for WIN32 instead of MSVC in CMake files
  (github pull #5183 from giordano)
• Atom indices inside double bond
  (github issue #5185 from DavidACosgrove)
• Bug in IPython display after setting a molecule property
  (github issue #5192 from dwhswenson)
• Zero & coordinate bonds are being taken into account for chirality
  (github issue #5196 from ricrogz)
• FindPotentialStereo does not clean stereoflags from atoms which cannot be stereocenters
  (github issue #5200 from greglandrum)
• Fixes array overflow in FMCS code
  (github pull #5205 from ricrogz)
• PeriodicTable initialization is not thread safe
  (github issue #5207 from ricrogz)
• Find and remove deprecated ifdefs
  (github issue #5210 from greglandrum)
• Fix use of not thread safe function localtime()
  (github pull #5211 from ricrogz)
• Fix duplicate non thread safe check in VarianceDataForLabel
  (github pull #5212 from ricrogz)
• RDKit::Utils::LocaleSwitcher is not thread safe
  (github issue #5214 from ricrogz)
• Core with query atoms and no user definded attachment points may create poor decompostions
  (github issue #5222 from jones-gareth)
• error: format not a string literal and no format arguments
  (github issue #5234 from sagitter)
• Fix qt build under VS2019
  (github pull #5238 from ricrogz)
• Precondition violation on chiral Atoms with zero order bonds
  (github issue #5239 from ricrogz)
• pyForceFieldConstraints test failed
  (github issue #5252 from sagitter)
• drawReaction() should not hit a PRECONDITION with prepareMolsBeforeDrawing=false
  (github issue #5259 from ptosco)
• Atom annotations poorly placed on highlighted atoms
  (github issue #5269 from DavidACosgrove)
• Make the aliphatic imine rule more closely match the definition in the paper
  (github pull #5270 from greglandrum)
• rdMolDraw2D.PrepareMolForDrawing(None) causes segmentation fault
  (github issue #5298 from perjo)
• MolStandardize: uncharger failing in molecules with zwitterionic sulfone
  (github issue #5317 from greglandrum)
• MolStandardize: some operations throwing on non-standardized molecules
  (github issue #5318 from greglandrum)
• MolStandardize: cleanup() function not correctly reassigning stereochemistry
  (github issue #5320 from greglandrum)
• Runtime error when writing reaction with substance group to V3000 rxnblock
  (github issue #5324 from rachelnwalker)
• MolFromMolBlock should correctly assign stereochemistry to 3D molecules
  (github issue #5327 from greglandrum)
• assignChiralTypesFrom3D() ignores wiggly bonds
  (github issue #5328 from greglandrum)
• Molzip segfaults instead of throwing an error when multiple bonds are formed to the same pairs of atoms
  (github issue #5334 from loluwot)
• leftover debugging code makes build of 2022_03_3 tarball fail
  (github issue #5351 from balducci)
• Prevent wedging ring bonds
  (github pull #5356 from greglandrum)
• Class info info missing for for wavy bonds in SVGs.
  (github pull #5358 from DavidACosgrove)
• MolToSmiles with doRandom=True raises errors with molecules containing fragments.
  (github issue #5372 from greglandrum)
• Restore #5103 that was accidentally reverted in #5132
  (github pull #5381 from ptosco)
• cairo error when using similarity maps
  (github issue #5383 from greglandrum)
• MolDraw2DQt and MolDraw2DJS don't draw wavy bonds
  (github issue #5386 from greglandrum)
• MolDraw2DQt draws brackets incorrectly
  (github issue #5389 from greglandrum)
• PandasTools should not always bring in IPythonConsole
  (github pull #5392 from greglandrum)
• Tautomer enumeration removes stereochemistry depending on how aromatic rings are defined in SMILES
  (github issue #5402 from greglandrum)
• Incorrect perception of pseudoasymmetric centers on non-canonical molecules
  (github issue #5403 from ptosco)
• Fix performance issue in RingUtils::checkFused
  (github pull #5410 from rachelnwalker)
• Multi-coloured highlights go wrong with small fonts
  (github issue #5420 from DavidACosgrove)
• Parsing a Mol block/file does not clear the "molTotValence" property from atoms
  (github issue #5423 from ricrogz)
• Pre-condition Violation - Failed Expression: dir == Bond::ENDUPRIGHT || dir == Bond::ENDDOWNRIGHT
  (github issue #5433 from bjonnh-work)
• MolZip doesn't preserve bond directions when zipping
  (github issue #5450 from bp-kelley)
• Draw option noAtomLabels and explicit hydrogen works badly
  (github issue #5453 from DavidACosgrove)
• Fix integer overflow in RGroupDecomposition strategy GA
  (github pull #5460 from bp-kelley)
• Invalid number of radical electrons calculated for [Pr+4]
  (github issue #5462 from bjonnh-work)
• CXSmiles isn't properly escaping floating point properties
  (github issue #5466 from bp-kelley)
• Crossed trans bonds in rings
  (github issue #5486 from DavidACosgrove)
• MolDraw2D::drawMolecules() should not crash on null molecules
  (github pull #5503 from ptosco)
• Running kekulization on mols with query bonds will either fail or return incorrect results.
  (github...

2022_09_1b1 (Q3 2022) Release

Release_2022.09.1b1

(Changes relative to Release_2022.03.1)

Acknowledgements

Jonathan Bisson, Andy Cai, David Cosgrove, JP Ebejer, Aleš Erjavec, Peter
Gedeck, Mosè Giordano, Sreya Gogineni, Emanuele Guidotti, Hyeonki Hong, Gareth
Jones, Per Johnsson, Maria Kadukova, Eisuke Kawashima, Brian Kelley, Alan
Kerstjens, Michel Moreau, Dan Nealschneider, Santeri Puranen, Ricardo
Rodriguez-Schmidt, Guy Rosin Jeff van Santen, David Schaller, David W.H.
Swenson, Paolo Tosco, Antonio Trande, Ivan Tubert-Brohman, Rachel Walker,
balducci, GLPG-GT

Highlights

Backwards incompatible changes

• GetBestRMS() and CalcRMS() by default now treat terminal conjugated functional
  groups like carboxylate and nitro symmetrically. For example, the group
  C(=[O:1])[O-:2] can match in either orientation. The SMARTS pattern which is
  used to recognize affected groups is:
  [{atomP};$([{atomP}]-[*]=[{atomP}]),$([{atomP}]=[*]-[{atomP}])]~[*] where
  {atomP} is O,N;D1. The previous behavior can be restored using by setting
  the symmetrizeConjugatedTerminalGroups argument to false when calling
  GetBestRMS() and CalcRMS()
• The following #defines are no longer provided in/used by the C++ code or RDConfig.h:
  • BUILD_COORDGEN_SUPPORT: use RDK_BUILD_COORDGEN_SUPPORT instead
  • RDK_THREADSAFE_SSS: use RDK_BUILD_THREADSAFE_SSS instead
  • USE_BUILTIN_POPCOUNT: use RDK_OPTIMIZE_POPCNT instead
• The Python function Chem.GetSSSR() now returns the SSSR rings found instead
  of just returning the count of rings. This is consistent with
  Chem.GetSymmSSSR() and more useful.
• The SMILES parser will ignore the value of
  SmilesParserParams.useLegacyStereo unless it is set to false. See the
  deprecation note about useLegacyStereo below for more information.
• The CFFI function set_2d_coords_aligned() now takes an additional char **match_json
  parameter; if match_json is not not NULL, *match_json will point to a
  JSON string containing the atoms and bonds which are part of the match.
  It is up to the user to free this string.

Bug Fixes:

• H atoms in SGroups cause RDKit to clear SGroups after parsing
  (github issue #2716 from ricrogz)
• RDKit misplaces stereochemistry/chirality information for small ring
  (github issue #2984 from d-b-w)
• DrawMorganBit returns empty image for "isolated" fingerprints
  (github issue #4242 from eguidotti)
• Unable to serialize coordinates as floats in combination with *Props
  (github issue #4621 from santeripuranen)
• Image Generation: Highlighting looks off when bondLineWidth is increased for PNG generation
  (github issue #5122 from rachelnwalker)
• RDKit crashes on CIP label calculation
  (github issue #5142 from ricrogz)
• Modified the JS tests to comply with older nodejs versions
  (github pull #5148 from ptosco)
• Presence of exocyclic S/D, S/A or D/A query bonds prevents benzene from being recognized as aromatic
  (github issue #5152 from rachelnwalker)
• Fix for RGD dummy atom bug in RDKit::replaceCore
  (github pull #5154 from jones-gareth)
• KekulizeException of molecule from Smarts pattern with new RDKit release
  (github issue #5156 from schallerdavid)
• Very small fix to avoid an AttributeError
  (github pull #5163 from ptosco)
• issue with V3000 SD files containing enhanced stereochemistry information
  (github issue #5165 from GLPG-GT)
• Draw.MolToQPixmap raises a TypeError with Python 3.10
  (github issue #5166 from ales-erjavec)
• Standardization via RDKit breaks molecules
  (github issue #5169 from malteseunderdog)
• Multiple calls to BlockLogs() permanently disable logging
  (github issue #5172 from ricrogz)
• Check architecture of the target system to optimise popcnt
  (github pull #5182 from giordano)
• More consistently check for WIN32 instead of MSVC in CMake files
  (github pull #5183 from giordano)
• Atom indices inside double bond
  (github issue #5185 from DavidACosgrove)
• Bug in IPython display after setting a molecule property
  (github issue #5192 from dwhswenson)
• Zero & coordinate bonds are being taken into account for chirality
  (github issue #5196 from ricrogz)
• FindPotentialStereo does not clean stereoflags from atoms which cannot be stereocenters
  (github issue #5200 from greglandrum)
• Fixes array overflow in FMCS code
  (github pull #5205 from ricrogz)
• PeriodicTable initialization is not thread safe
  (github issue #5207 from ricrogz)
• Find and remove deprecated ifdefs
  (github issue #5210 from greglandrum)
• Fix use of not thread safe function localtime()
  (github pull #5211 from ricrogz)
• Fix duplicate non thread safe check in VarianceDataForLabel
  (github pull #5212 from ricrogz)
• RDKit::Utils::LocaleSwitcher is not thread safe
  (github issue #5214 from ricrogz)
• Core with query atoms and no user definded attachment points may create poor decompostions
  (github issue #5222 from jones-gareth)
• error: format not a string literal and no format arguments
  (github issue #5234 from sagitter)
• Fix qt build under VS2019
  (github pull #5238 from ricrogz)
• Precondition violation on chiral Atoms with zero order bonds
  (github issue #5239 from ricrogz)
• pyForceFieldConstraints test failed
  (github issue #5252 from sagitter)
• drawReaction() should not hit a PRECONDITION with prepareMolsBeforeDrawing=false
  (github issue #5259 from ptosco)
• Atom annotations poorly placed on highlighted atoms
  (github issue #5269 from DavidACosgrove)
• Make the aliphatic imine rule more closely match the definition in the paper
  (github pull #5270 from greglandrum)
• rdMolDraw2D.PrepareMolForDrawing(None) causes segmentation fault
  (github issue #5298 from perjo)
• MolStandardize: uncharger failing in molecules with zwitterionic sulfone
  (github issue #5317 from greglandrum)
• MolStandardize: some operations throwing on non-standardized molecules
  (github issue #5318 from greglandrum)
• MolStandardize: cleanup() function not correctly reassigning stereochemistry
  (github issue #5320 from greglandrum)
• Runtime error when writing reaction with substance group to V3000 rxnblock
  (github issue #5324 from rachelnwalker)
• MolFromMolBlock should correctly assign stereochemistry to 3D molecules
  (github issue #5327 from greglandrum)
• assignChiralTypesFrom3D() ignores wiggly bonds
  (github issue #5328 from greglandrum)
• Molzip segfaults instead of throwing an error when multiple bonds are formed to the same pairs of atoms
  (github issue #5334 from loluwot)
• leftover debugging code makes build of 2022_03_3 tarball fail
  (github issue #5351 from balducci)
• Prevent wedging ring bonds
  (github pull #5356 from greglandrum)
• Class info info missing for for wavy bonds in SVGs.
  (github pull #5358 from DavidACosgrove)
• MolToSmiles with doRandom=True raises errors with molecules containing fragments.
  (github issue #5372 from greglandrum)
• Restore #5103 that was accidentally reverted in #5132
  (github pull #5381 from ptosco)
• cairo error when using similarity maps
  (github issue #5383 from greglandrum)
• MolDraw2DQt and MolDraw2DJS don't draw wavy bonds
  (github issue #5386 from greglandrum)
• MolDraw2DQt draws brackets incorrectly
  (github issue #5389 from greglandrum)
• PandasTools should not always bring in IPythonConsole
  (github pull #5392 from greglandrum)
• Tautomer enumeration removes stereochemistry depending on how aromatic rings are defined in SMILES
  (github issue #5402 from greglandrum)
• Incorrect perception of pseudoasymmetric centers on non-canonical molecules
  (github issue #5403 from ptosco)
• Fix performance issue in RingUtils::checkFused
  (github pull #5410 from rachelnwalker)
• Multi-coloured highlights go wrong with small fonts
  (github issue #5420 from DavidACosgrove)
• Parsing a Mol block/file does not clear the "molTotValence" property from atoms
  (github issue #5423 from ricrogz)
• Pre-condition Violation - Failed Expression: dir == Bond::ENDUPRIGHT || dir == Bond::ENDDOWNRIGHT
  (github issue #5433 from bjonnh-work)
• MolZip doesn't preserve bond directions when zipping
  (github issue #5450 from bp-kelley)
• Draw option noAtomLabels and explicit hydrogen works badly
  (github issue #5453 from DavidACosgrove)
• Fix integer overflow in RGroupDecomposition strategy GA
  (github pull #5460 from bp-kelley)
• Invalid number of radical electrons calculated for [Pr+4]
  (github issue #5462 from bjonnh-work)
• CXSmiles isn't properly escaping floating point properties
  (github issue #5466 from bp-kelley)
• Crossed trans bonds in rings
  (github issue #5486 from DavidACosgrove)
• MolDraw2D::drawMolecules() should not crash on null molecules
  (github pull #5503 from ptosco)
• Running kekulization on mols with query bonds will either fail or return incorrect results.
  (github issue #5505 from ricrogz)
• Regression in the way aldehydes are drawn in current master
  (github issue #5511 from ptosco)
• Drawing code gives segmentation fault.
  (github issue #5534 from DavidACosgrove)
• RGD may yield poor depictions
  (github issue #5569 from jones-gareth)
• Fix a problem when generating conformers for molecules with larger heteroatoms in conjugated 5-rings
  (github pull #5586 from greglandrum)
• Avoid incurring into division by zero in normalizeDepiction
  (github pull #5619 from ptosco)
• Allow properties to be displayed in jupyter when 3D rendering is enabled
  (github pull #5624 from greglandrum)

Cleanup work:

• update release notes, do deprecations
  (github pull #5161 from greglandrum)
• Fix typo: quarternary --> quaternary
  (github pull #5243 from guyrosin)
• fix doxygen comments
  (github pull #5254 from e-kwsm)
• make the catch tests build faster
  (github pull #5284 from greglandrum)
• mak...