2021_09_1 (Q3 2021) Release

Release_2021.09.1

(Changes relative to Release_2021.03.1)

Backwards incompatible changes

• RWMol.replaceAtom() no longer removes SubstanceGroups which reference that atom.
• The keepSGroups argument to RWMol.replaceBond() now defaults to true.
• The SMARTS parser now by default accepts CXSMILES extensions and molecule
  names. SMARTS which previously failed to parse like CCC fail will now return
  valid molecules.
• Molecule names in SMILES and SMARTS are now parsed by default. Previously they
  were ignored.
• The getParams() function for retrieving UFF parameters now returns a const
  pointer instead of a standard pointer. This shouldn't affect the functionality
  of any code since the only method of the class is also const.

Highlights

• Single reactant/single product reactions can now be applied in-place. This
  really helps with the performance of these kinds of transformations.
• The CFFI wrapper around MinimalLib greatly expands the number of possible
  places the RDKit can be used from.
• A number of general enhancements and quality-of-life improvements were made
  to the PostgreSQL cartridge.

Acknowledgements

Jason Biggs, Kit Choi, David Cosgrove, Eloy Félix, Harrison Green, Gareth Jones,
Eisuke Kawashima, Alan Kerstjens, Brian Kelley, John Konecny, Stephanie
Labouille, Rasmus Lundsgaard, Hadrien Mary, Michel Moreau, Dan Nealschneider,
Axel Pahl, Maximilian Peters, Alessio Ragno, Ricardo Rodriguez-Schmidt, Riccardo
Sabatini, Roger Sayle, Vincent F. Scalfani, Dan Skatov, David Slochower, Peter
St. John, Mihaly Szabo, Ichiru Take, Paolo Tosco, Ivan Tubert-Brohman, Kazuya
Ujihara, Alain Vaucher, Riccardo Vianello, Rachel Walker, Shuzhe Wang, Maciej
Wójcikowski, bzoracler, jungb-basf, charly828, yoer77,

Code removed in this release:

• The minimizeOnly option for coordgen has been removed.

Contrib updates:

• Contribute FreeWilson analysis
  (github pull #4026 from bp-kelley)

Bug Fixes:

• cannot pass drawOptions to MolsToGridImage when using notebook
  (github issue #3101 from slochower)
• Draw.MolToImage() cannot highlight with highlightMap (v > '2019.09.3' )
  (github issue #3616 from spideralessio)
• EnumerateStereoisomers fail with STEREOANY bonds from molblock
  (github issue #3759 from TermeHansen)
• Double bond stereo gets flipped by SMILES reader/writer
  (github issue #3967 from mwojcikowski)
• SparseIntVect copy constructor and assignment operators not clearing existing data
  (github issue #3994 from AlanKerstjens)
• MolFragmentToSmiles with kekuleSmiles=True raises AtomKekulizeException
  (github issue #3998 from kazuyaujihara)
• update clang version for linux CI fuzzer builds
  (github pull #4012 from greglandrum)
• Update coordgen to 2.0.3
  (github pull #4017 from d-b-w)
• Get SWIG wrappers working with C# again
  (github pull #4020 from kazuyaujihara)
• replaceSidechains creates aromatic dummy atoms
  (github pull #4022 from ptosco)
• A set of fixes for problems caused by bad input
  (github pull #4033 from greglandrum)
• Cleanup some problems found during an ASAN build
  (github pull #4054 from greglandrum)
• Avoid that lone atoms which are part of a ring in one of the molecules become part of the MCS
  (github pull #4065 from ptosco)
• StereoGroups not preserved by RenumberAtoms()
  (github issue #4071 from greglandrum)
• call to pyAvalonTools.Generate2DCoords results in an assert violation
  (github issue #4075 from rvianello)
• Update boost download location in Dockerfile
  (github pull #4094 from greglandrum)
• HCount field in v2000 Mol blocks ignored
  (github issue #4099 from riccardosabatini)
• Reactions don't propagate bond properties
  (github issue #4114 from d-b-w)
• RemoveStereochemistry should also remove stereogroups
  (github issue #4115 from greglandrum)
• Avoid that MolStandardizer segfaults on empty mols
  (github pull #4119 from ptosco)
• SEGV in RWMol::commitBatchEdit
  (github issue #4122 from hgarrereyn)
• SEGV in ROMol::getAtomDegree if atom is not in graph
  (github issue #4127 from hgarrereyn)
• SEGV from unsigned integer overflow in Conformer::setAtomPos
  (github issue #4128 from hgarrereyn)
• HCOUNT from v3000 CTABS incorrectly interpreted
  (github issue #4131 from greglandrum)
• Empty query produces empty match, but at the same time is considered non-matching
  (github issue #4138 from i-tub)
• fixed AddBond documentation
  (github pull #4142 from Ashafix)
• Possible bug with EnumerateStereoisomers
  (github issue #4144 from stephanielabouille)
• Odd drawing behavior with radicals and MolsToGridImage
  (github issue #4156 from pstjohn)
• pre-condition violation when sanitizing a de-pickled reaction
  (github issue #4162 from jasondbiggs)
• Many of the PMI descriptors are not being recalculated for different conformers
  (github issue #4167 from greglandrum)
• bug in MDLParser.cpp when reading a rxn file in v3000 format that contains agents
  (github issue #4183 from jungb-basf)
• Potentially chiral bridgehead atoms not being identified.
  (github pull #4192 from greglandrum)
• allow more recoverable V3000 parsing errors when strictParsing=false
  (github pull #4210 from greglandrum)
• RGD: Fix memory leak with deleting array
  (github pull #4211 from bp-kelley)
• UnfoldedRDKFingerprintCountBased returns a different fingerprint length for every molecule
  (github issue #4212 from greglandrum)
• rdMolHash.MolHash fails on non-standard valences
  (github issue #4222 from ricrogz)
• Fix a couple of problems with fingerprint count simulation
  (github pull #4228 from greglandrum)
• Chem.MolFromSmiles using SmilesParserParams throws exceptions
  (github issue #4232 from greglandrum)
• Parse failure for data groups in CXSMILES
  (github issue #4233 from greglandrum)
• double bonds now have EITHER stereo if no coordinates are present
  (github pull #4239 from greglandrum)
• Fix CMakeLists for FileParsers
  (github pull #4240 from kazuyaujihara)
• Multiple ATTCHPT entries for one atom handled incorrectly
  (github issue #4256 from greglandrum)
• Exception thrown by reionizer when dealing with Mg+2
  (github issue #4260 from greglandrum)
• Fallback ring finding failing on molecules with multiple fragments
  (github issue #4266 from avaucher)
• Make sure that ResonanceMolSupplier substructure matches are uniquified consistently
  (github pull #4274 from ptosco)
• FindPotentialStereo() doesn't find marked ring stereo when flagPossible=False
  (github issue #4279 from greglandrum)
• The normalization pattern for pyridine N-oxide is not specific enough
  (github issue #4281 from ptosco)
• computeCanonicalTransform may generate non-canonical coords
  (github issue #4302 from ptosco)
• Unreasonable calculation of implicit valence for atoms with query bonds
  (github issue #4311 from greglandrum)
• call to AvalonTools::set2DCoords results in an assert violation
  (github issue #4330 from jasondbiggs)
• MolBlock writer gives non-stereo double bonds "unspecified" parity
  (github issue #4345 from d-b-w)
• Specified trans stereo being ignored during conformation generation in macrocycles
  (github issue #4346 from greglandrum)
• Two MinGW build fixes and one MSVC build fix
  (github pull #4347 from ptosco)
• Fixes RDK_BUILD_THREADSAFE_SSS=OFF build
  (github pull #4349 from ptosco)
• clean up some leaks identified by an ASAN build
  (github pull #4354 from greglandrum)
• Three more Windows build fixes
  (github pull #4356 from ptosco)
• Specified grid spacing for ShapeTanimotoDistance is ignored.
  (github issue #4364 from greglandrum)
• Need implicit H cleanup after rdMolEnumerator.Enumerate()
  (github issue #4381 from greglandrum)
• rdMolEnumerator.Enumerate fails on variable attachment points with queries
  (github issue #4382 from greglandrum)
• RDKit reaction produces wrong double bond stereochemistry
  (github issue #4410 from mwojcikowski)
• "to-Python converter already registered; second conversion method ignored." warnings issued at import
  (github issue #4425 from ricrogz)
• v2000 SGroups do not generate an "index" property
  (github issue #4434 from ricrogz)
• pg_restore does not work with some mol type molecule
  (github issue #4442 from mihalyszabo88)
• Building with static dependencies breaks CMake exports
  (github issue #4449 from ricrogz)
• DataStruct vectors leak when iterating
  (github issue #4465 from bp-kelley)
• SGroups: Additional SDT properties not decoded if FIELDNAME is empty
  (github issue #4476 from greglandrum)
• Test failure in reaction.sql
  (github issue #4486 from yoer77)
• Small rings can have STEREOANY/EITHERDOUBLE bonds
  (github issue #4494 from ricrogz)
• OR queries involving aromatic atoms cannot be drawn
  (github issue #4496 from ptosco)
• MolFromSmiles and MolFromSmarts incorrectly accepting input with spaces
  (github issue #4503 from greglandrum)
• Native 2D layout engine may generate overlapping coordinates
  (github issue #4504 from ptosco)
• SubstanceGroup labels sometimes overlap with atoms in image generation
  (github issue #4508 from rachelnwalker)
• SGroups do not have a way of unsetting properties from Python
  (github issue #4514 from ricrogz)
• operator<< is declared for AtomPDBResidueInfo but not defined
  (github issue #4535 from greglandrum)
• Improve test coverage and some bug fixes
  (github pull #4536 from greglandrum)
• Seg fault in MolDraw2D::drawMolecules()
  (github issue #4538 from greglandrum)
• Salt removal forces sanitization
  (github issue #4550 from ricrogz)
• fix a thread-safety bug in the UFF parameter loading
  (github pull #4553 from greglandrum)
• GetSubstructMatches() loops at 43690 iterations.
  (github issue #4558 from ricrogz)
• failure to parse CTAB with LINKNODE and SGR...

2021_09_1b1 (Q3 2021) Release

Release_2021.09.1b1

(Changes relative to Release_2021.03.1)

Backwards incompatible changes

• RWMol.replaceAtom() no longer removes SubstanceGroups which reference that atom.
• The keepSGroups argument to RWMol.replaceBond() now defaults to true.
• The SMARTS parser now by default accepts CXSMILES extensions and molecule
  names. SMARTS which previously failed to parse like CCC fail will now return
  valid molecules.
• Molecule names in SMILES and SMARTS are now parsed by default. Previously they
  were ignored.
• The getParams() function for retrieving UFF parameters now returns a const
  pointer instead of a standard pointer. This shouldn't affect the functionality
  of any code since the only method of the class is also const.

Highlights

• t.b.d.

Acknowledgements

Jason Biggs, Kit Choi, David Cosgrove, Eloy Félix, Harrison Green, Gareth Jones,
Eisuke Kawashima, Alan Kerstjens, Brian Kelley, John Konecny, Stephanie
Labouille, Rasmus Lundsgaard, Hadrien Mary, Michel Moreau, Dan Nealschneider,
Axel Pahl, Maximilian Peters, Alessio Ragno, Ricardo Rodriguez-Schmidt, Riccardo
Sabatini, Roger Sayle, Vincent F. Scalfani, Dan Skatov, David Slochower, Peter
St. John, Mihaly Szabo, Ichiru Take, Paolo Tosco, Ivan Tubert-Brohman, Kazuya
Ujihara, Alain Vaucher, Riccardo Vianello Rachel Walker, Shuzhe Wang, Maciej
Wójcikowski, bzoracler, jungb-basf, charly828, yoer77,

Bug Fixes:

• cannot pass drawOptions to MolsToGridImage when using notebook
  (github issue #3101 from slochower)
• Draw.MolToImage() cannot highlight with highlightMap (v > '2019.09.3' )
  (github issue #3616 from spideralessio)
• EnumerateStereoisomers fail with STEREOANY bonds from molblock
  (github issue #3759 from TermeHansen)
• Double bond stereo gets flipped by SMILES reader/writer
  (github issue #3967 from mwojcikowski)
• SparseIntVect copy constructor and assignment operators not clearing existing data
  (github issue #3994 from AlanKerstjens)
• MolFragmentToSmiles with kekuleSmiles=True raises AtomKekulizeException
  (github issue #3998 from kazuyaujihara)
• update clang version for linux CI fuzzer builds
  (github pull #4012 from greglandrum)
• Update coordgen to 2.0.3
  (github pull #4017 from d-b-w)
• Get SWIG wrappers working with C# again
  (github pull #4020 from kazuyaujihara)
• replaceSidechains creates aromatic dummy atoms
  (github pull #4022 from ptosco)
• A set of fixes for problems caused by bad input
  (github pull #4033 from greglandrum)
• Cleanup some problems found during an ASAN build
  (github pull #4054 from greglandrum)
• Avoid that lone atoms which are part of a ring in one of the molecules become part of the MCS
  (github pull #4065 from ptosco)
• StereoGroups not preserved by RenumberAtoms()
  (github issue #4071 from greglandrum)
• call to pyAvalonTools.Generate2DCoords results in an assert violation
  (github issue #4075 from rvianello)
• Update boost download location in Dockerfile
  (github pull #4094 from greglandrum)
• HCount field in v2000 Mol blocks ignored
  (github issue #4099 from riccardosabatini)
• Reactions don't propagate bond properties
  (github issue #4114 from d-b-w)
• RemoveStereochemistry should also remove stereogroups
  (github issue #4115 from greglandrum)
• Avoid that MolStandardizer segfaults on empty mols
  (github pull #4119 from ptosco)
• SEGV in RWMol::commitBatchEdit
  (github issue #4122 from hgarrereyn)
• SEGV in ROMol::getAtomDegree if atom is not in graph
  (github issue #4127 from hgarrereyn)
• SEGV from unsigned integer overflow in Conformer::setAtomPos
  (github issue #4128 from hgarrereyn)
• HCOUNT from v3000 CTABS incorrectly interpreted
  (github issue #4131 from greglandrum)
• Empty query produces empty match, but at the same time is considered non-matching
  (github issue #4138 from i-tub)
• fixed AddBond documentation
  (github pull #4142 from Ashafix)
• Possible bug with EnumerateStereoisomers
  (github issue #4144 from stephanielabouille)
• Odd drawing behavior with radicals and MolsToGridImage
  (github issue #4156 from pstjohn)
• pre-condition violation when sanitizing a de-pickled reaction
  (github issue #4162 from jasondbiggs)
• Many of the PMI descriptors are not being recalculated for different conformers
  (github issue #4167 from greglandrum)
• bug in MDLParser.cpp when reading a rxn file in v3000 format that contains agents
  (github issue #4183 from jungb-basf)
• Potentially chiral bridgehead atoms not being identified.
  (github pull #4192 from greglandrum)
• allow more recoverable V3000 parsing errors when strictParsing=false
  (github pull #4210 from greglandrum)
• RGD: Fix memory leak with deleting array
  (github pull #4211 from bp-kelley)
• UnfoldedRDKFingerprintCountBased returns a different fingerprint length for every molecule
  (github issue #4212 from greglandrum)
• rdMolHash.MolHash fails on non-standard valences
  (github issue #4222 from ricrogz)
• Fix a couple of problems with fingerprint count simulation
  (github pull #4228 from greglandrum)
• Chem.MolFromSmiles using SmilesParserParams throws exceptions
  (github issue #4232 from greglandrum)
• Parse failure for data groups in CXSMILES
  (github issue #4233 from greglandrum)
• double bonds now have EITHER stereo if no coordinates are present
  (github pull #4239 from greglandrum)
• Fix CMakeLists for FileParsers
  (github pull #4240 from kazuyaujihara)
• Multiple ATTCHPT entries for one atom handled incorrectly
  (github issue #4256 from greglandrum)
• Exception thrown by reionizer when dealing with Mg+2
  (github issue #4260 from greglandrum)
• Fallback ring finding failing on molecules with multiple fragments
  (github issue #4266 from avaucher)
• Make sure that ResonanceMolSupplier substructure matches are uniquified consistently
  (github pull #4274 from ptosco)
• FindPotentialStereo() doesn't find marked ring stereo when flagPossible=False
  (github issue #4279 from greglandrum)
• The normalization pattern for pyridine N-oxide is not specific enough
  (github issue #4281 from ptosco)
• computeCanonicalTransform may generate non-canonical coords
  (github issue #4302 from ptosco)
• Unreasonable calculation of implicit valence for atoms with query bonds
  (github issue #4311 from greglandrum)
• call to AvalonTools::set2DCoords results in an assert violation
  (github issue #4330 from jasondbiggs)
• MolBlock writer gives non-stereo double bonds "unspecified" parity
  (github issue #4345 from d-b-w)
• Specified trans stereo being ignored during conformation generation in macrocycles
  (github issue #4346 from greglandrum)
• Two MinGW build fixes and one MSVC build fix
  (github pull #4347 from ptosco)
• Fixes RDK_BUILD_THREADSAFE_SSS=OFF build
  (github pull #4349 from ptosco)
• clean up some leaks identified by an ASAN build
  (github pull #4354 from greglandrum)
• Three more Windows build fixes
  (github pull #4356 from ptosco)
• Specified grid spacing for ShapeTanimotoDistance is ignored.
  (github issue #4364 from greglandrum)
• Need implicit H cleanup after rdMolEnumerator.Enumerate()
  (github issue #4381 from greglandrum)
• rdMolEnumerator.Enumerate fails on variable attachment points with queries
  (github issue #4382 from greglandrum)
• RDKit reaction produces wrong double bond stereochemistry
  (github issue #4410 from mwojcikowski)
• "to-Python converter already registered; second conversion method ignored." warnings issued at import
  (github issue #4425 from ricrogz)
• v2000 SGroups do not generate an "index" property
  (github issue #4434 from ricrogz)
• pg_restore does not work with some mol type molecule
  (github issue #4442 from mihalyszabo88)
• Building with static dependencies breaks CMake exports
  (github issue #4449 from ricrogz)
• DataStruct vectors leak when iterating
  (github issue #4465 from bp-kelley)
• SGroups: Additional SDT properties not decoded if FIELDNAME is empty
  (github issue #4476 from greglandrum)
• Test failure in reaction.sql
  (github issue #4486 from yoer77)
• Small rings can have STEREOANY/EITHERDOUBLE bonds
  (github issue #4494 from ricrogz)
• OR queries involving aromatic atoms cannot be drawn
  (github issue #4496 from ptosco)
• MolFromSmiles and MolFromSmarts incorrectly accepting input with spaces
  (github issue #4503 from greglandrum)
• Native 2D layout engine may generate overlapping coordinates
  (github issue #4504 from ptosco)
• SubstanceGroup labels sometimes overlap with atoms in image generation
  (github issue #4508 from rachelnwalker)
• SGroups do not have a way of unsetting properties from Python
  (github issue #4514 from ricrogz)
• operator<< is declared for AtomPDBResidueInfo but not defined
  (github issue #4535 from greglandrum)
• Improve test coverage and some bug fixes
  (github pull #4536 from greglandrum)
• Seg fault in MolDraw2D::drawMolecules()
  (github issue #4538 from greglandrum)
• Salt removal forces sanitization
  (github issue #4550 from ricrogz)
• fix a thread-safety bug in the UFF parameter loading
  (github pull #4553 from greglandrum)
• GetSubstructMatches() loops at 43690 iterations.
  (github issue #4558 from ricrogz)
• failure to parse CTAB with LINKNODE and SGROUP
  (github issue #4561 from greglandrum)
• Requesting "density" fingerprint Hydrogen molecule fails with exception
  (github issue #4567 from ricrogz)
• Incorrect double bond stereo in output SMILES around ring closures
  (github issue #4582 from greglandrum)

New Features and Enhancements:

• Support Chemical Markup Language, CML, for writing
  (github pull #3024 from e-kwsm)
• Add Eigen to ExternalProject and automatically download if RDK_BUILD_DESCRIPTORS3D
  (github pull #3075 from e-kwsm)
• updates to postgreSQL cartridge
  (g...

2021_03_5 (Q1 2021) Release

Release_2021.03.5

(Changes relative to Release_2021.03.4)

Acknowledgements

Jason Biggs, Brian Kelley, Lewis J. Martin, Dan Nealschneider, Ricardo
Rodriguez-Schmidt, David Slochower, Paolo Tosco, Maciej Wójcikowski

Bug Fixes:

• cannot pass drawOptions to MolsToGridImage when using notebook
  (github #3101 from slochower)
• call to AvalonTools::set2DCoords results in an assert violation
  (github #4330 from jasondbiggs)
• MolBlock writer gives non-stereo double bonds "unspecified" parity
  (github #4345 from d-b-w)
• Specified trans stereo being ignored during conformation generation in macrocycles
  (github #4346 from greglandrum)
• Two MinGW build fixes and one MSVC build fix
  (github #4347 from ptosco)
• Fixes RDK_BUILD_THREADSAFE_SSS=OFF build
  (github #4349 from ptosco)
• Three more Windows build fixes
  (github #4356 from ptosco)
• Specified grid spacing for ShapeTanimotoDistance is ignored.
  (github #4364 from greglandrum)
• Need implicit H cleanup after rdMolEnumerator.Enumerate()
  (github #4381 from greglandrum)
• rdMolEnumerator.Enumerate fails on variable attachment points with queries
  (github #4382 from greglandrum)
• RDKit reaction produces wrong double bond stereochemistry
  (github #4410 from mwojcikowski)
• v2000 SGroups do not generate an "index" property
  (github #4434 from ricrogz)

2021_03_4 (Q1 2021) Release

Release_2021.03.4

(Changes relative to Release_2021.03.3)

Acknowledgements

Brian Kelley, Rasmus Lundsgaard, Dan Nealschneider, Ricardo Rodriguez-Schmidt,
Matt Swain, Paolo Tosco, Kazuya Ujihara, Alain Vaucher, 'jungb-basf'

Bug Fixes:

• EnumerateStereoisomers fail with STEREOANY bonds from molblock
  (github #3759 from TermeHansen)
• MolFragmentToSmiles with kekuleSmiles=True raises AtomKekulizeException
  (github #3998 from kazuyaujihara)
• bug in MDLParser.cpp when reading a rxn file in v3000 format that contains agents
  (github #4183 from jungb-basf)
• allow more recoverable V3000 parsing errors when strictParsing=false
  (github #4210 from greglandrum)
• Fix a couple of problems with fingerprint count simulation
  (github #4228 from greglandrum)
• Chem.MolFromSmiles using SmilesParserParams throws exceptions
  (github #4232 from greglandrum)
• double bonds now have EITHER stereo if no coordinates are present
  (github #4239 from greglandrum)
• Fix CMakeLists for FileParsers
  (github #4240 from kazuyaujihara)
• Multiple ATTCHPT entries for one atom handled incorrectly
  (github #4256 from greglandrum)
• Exception thrown by reionizer when dealing with Mg+2
  (github #4260 from greglandrum)
• Fallback ring finding failing on molecules with multiple fragments
  (github #4266 from avaucher)
• FindPotentialStereo() doesn't find marked ring stereo when flagPossible=False
  (github #4279 from greglandrum)
• The normalization pattern for pyridine N-oxide is not specific enough
  (github #4281 from ptosco)
• Unreasonable calculation of implicit valence for atoms with query bonds
  (github #4311 from greglandrum)

2021_03_3 (Q1 2021) Release

Release_2021.03.2

(Changes relative to Release_2021.03.2)

Acknowledgements

Jason Biggs, James Davidson, Harrison Green, Brian Kelley, Stephanie Labouille,
Dan Nealschneider, Maximilian Peters, Ricardo Rodriguez-Schmidt Riccardo
Sabatini, Peter St. John, Paolo Tosco, Ivan Tubert-Brohman, Rachel Walker,
Maciej Wójcikowski,

Bug Fixes:

• Double bond stereo gets flipped by SMILES reader/writer
  (github #3967 from mwojcikowski)
• StereoGroups not preserved by RenumberAtoms()
  (github #4071 from greglandrum)
• HCount field in v2000 Mol blocks ignored
  (github #4099 from riccardosabatini)
• Reactions don't propagate bond properties
  (github #4114 from d-b-w)
• SEGV in ROMol::getAtomDegree if atom is not in graph
  (github #4127 from hgarrereyn)
• SEGV from unsigned integer overflow in Conformer::setAtomPos
  (github #4128 from hgarrereyn)
• HCOUNT from v3000 CTABS incorrectly interpreted
  (github #4131 from greglandrum)
• Empty query produces empty match, but at the same time is considered non-matching
  (github #4138 from i-tub)
• fixed AddBond documentation
  (github #4142 from Ashafix)
• Possible bug with EnumerateStereoisomers
  (github #4144 from stephanielabouille)
• Odd drawing behavior with radicals and MolsToGridImage
  (github #4156 from pstjohn)
• pre-condition violation when sanitizing a de-pickled reaction
  (github #4162 from jasondbiggs)
• Many of the PMI descriptors are not being recalculated for different conformers
  (github #4167 from greglandrum)
• Fix python to C++ pointer conversion issue in moldrawFromQPainter
  (github #4182 from rachelnwalker)
• Potentially chiral bridgehead atoms not being identified.
  (github #4192 from greglandrum)
• allow more recoverable V3000 parsing errors when strictParsing=false
  (github #4210 from greglandrum)
• RGD: Fix memory leak with deleting array
  (github #4211 from bp-kelley)
• UnfoldedRDKFingerprintCountBased returns a different fingerprint length for every molecule
  (github #4212 from greglandrum)
• rdMolHash.MolHash fails on non-standard valences
  (github #4222 from ricrogz)

2021_03_2 (Q1 2021) Release

Release_2021.03.2

(Changes relative to Release_2021.03.1)

Acknowledgements

Harrison Green, Brian Kelley, Alan Kerstjens, Dan Nealschneider, Alessio Ragno,
Paolo Tosco, Kazuya Ujihara, Riccardo Vianello

Bug Fixes:

• Draw.MolToImage() cannot highlight with highlightMap (v > '2019.09.3' )
  (github #3616 from spideralessio)
• SparseIntVect copy constructor and assignment operators not clearing existing data
  (github #3994 from AlanKerstjens)
• update clang version for linux CI fuzzer builds
  (github #4012 from greglandrum)
• Update coordgen to 2.0.3
  (github #4017 from d-b-w)
• Get SWIG wrappers working with C# again
  (github #4020 from kazuyaujihara)
• replaceSidechains creates aromatic dummy atoms
  (github #4022 from ptosco)
• A set of fixes for problems caused by bad input
  (github #4033 from greglandrum)
• Cleanup some problems found during an ASAN build
  (github #4054 from greglandrum)
• Avoid that lone atoms which are part of a ring in one of the molecules become part of the MCS
  (github #4065 from ptosco)
• call to pyAvalonTools.Generate2DCoords results in an assert violation
  (github #4075 from rvianello)
• Update boost download location in Dockerfile
  (github #4094 from greglandrum)
• RemoveStereochemistry should also remove stereogroups
  (github #4115 from greglandrum)
• Avoid that MolStandardizer segfaults on empty mols
  (github #4119 from ptosco)
• SEGV in RWMol::commitBatchEdit
  (github #4122 from hgarrereyn)

2021_03_1 (Q1 2021) Release

Release_2021.03.1

(Changes relative to Release_2020.09.1)

Backwards incompatible changes

• The distance-geometry based conformer generation now by defaults generates
  trans(oid) conformations for amides, esters, and related structures. This can
  be toggled off with the forceTransAmides flag in EmbedParameters. Note that
  this change does not impact conformers created using one of the ET versions.
  (#3794)
• The conformer generator now uses symmetry by default when doing RMS pruning.
  This can be disabled using the useSymmetryForPruning flag in
  EmbedParameters. (#3813)
• Double bonds with unspecified stereochemistry in the products of chemical
  reactions now have their stereo set to STEREONONE instead of STEREOANY (#3078)
• The MolToSVG() function has been moved from rdkit.Chem to rdkit.Chem.Draw
  (#3696)
• There have been numerous changes to the RGroup Decomposition code which change
  the results. (#3767)
• In RGroup Decomposition, when onlyMatchAtRGroups is set to false, each molecule
  is now decomposed based on the first matching scaffold which adds/uses the
  least number of non-user-provided R labels, rather than simply the first
  matching scaffold.
  Among other things, this allows the code to provide the same results for both
  onlyMatchAtRGroups=true and onlyMatchAtRGroups=false when suitable scaffolds
  are provided without requiring the user to get overly concerned about the
  input ordering of the scaffolds. (#3969)
• There have been numerous changes to GenerateDepictionMatching2DStructure() (#3811)
• Setting the kekuleSmiles argument (doKekule in C++) to MolToSmiles will now
  cause the molecule to be kekulized before SMILES generation. Note that this
  can lead to an exception being thrown. Previously this argument would only
  write kekulized SMILES if the molecule had already been kekulized (#2788)
• Using the kekulize argument in the MHFP code will now cause the molecule to be
  kekulized before the fingerprint is generated. Note that becaues kekulization
  is not canonical, using this argument currently causes the results to depend
  on the input atom numbering. Note that this can lead to an exception being
  thrown. (#3942)
• Gradients for angle and torsional restraints in both UFF and MMFF were computed
  incorrectly, which could give rise to potential instability during minimization.
  As part of fixing this problem, force constants have been switched to using
  kcal/degree^2 units instead of kcal/rad^2 units, consistently with the fact that
  angle and dihedral restraints are specified in degrees. (#3975)

Highlights

• MolDraw2D now does a much better job of handling query features like common
  query bond types, atom lists, variable attachment points, and link nodes. It
  also supports adding annotations at the molecule level, displaying brackets
  for Sgroups, rendering the ABS flag for stereochemistry, and a new "comic"
  mode.
• There are two new Contrib packages: NIBRStructureFilters and CalcLigRMSD
• There have been a number of improvements made to the R-Group Decomposition
  code which make it both more flexible and considerably faster

Acknowledgements

Michael Banck, Christopher Von Bargen, Jason Biggs, Patrick Buder, Ivan
Chernyshov, Andrew Dalke, Xiaorui Dong, Carmen Esposito, Nicholas Firth, Enrico
Gandini, James Gayvert, Gareth Jones, Eisuke Kawashima, Steven Kearnes, Brian
Kelley, Mark Mackey, Niels Kristian Kjærgård Madsen, Luca Naef, Dan
Nealschneider, Jin Pan, Daniel Paoliello, António JM Ribeiro, Sereina Riniker,
Braxton Robbason, Jaime Rodríguez-Guerra, Ricardo Rodriguez-Schmidt, Steve
Roughley, Vincent F. Scalfani, Nadine Schneider, Philippe Schwaller, Dan Skatov,
Pascal Soveaux, Paolo Tosco, Kazuya Ujihara, Riccardo Vianello, Shuzhe Wang,
Piotr Wawrzyniak, Maciej Wójcikowski, Zhijiang Yang, Yutong Zhao
'driesvr', 'GintasKam', 'SPKorhonen', 'pkubaj', 'AnPallo', 'darintay',
'slchan3', 'Robins', 'sirbiscuit', 'amateurcat', 'noncomputable', 'yurivict',
'magattaca'

Contrib updates:

• Added NIBRStructureFilters: a set of substructure filters for hit-list triaging together with python code for applying them. The filters are described in the publication https://dx.doi.org/10.1021/acs.jmedchem.0c01332
  (github pull #3516 from NadineSchneider)
• Added CalcLigRMSD: flexible python code for calculating RMSD between pre-aligned molecules
  (github pull #3812 from cespos)

Bug Fixes:

• Casting int to uint in MorganFingerprintHelper leads to unexpected behaviour.
  (github issue #1761 from SiPa13)
• MolChemicalFeature.GetPos() returns value for molecule's default conformer
  (github issue #2530 from greglandrum)
• Unable to catch RDKit exceptions in linked library when compiling with fvisibility=hidden
  (github issue #2753 from cdvonbargen)
• Reaction rendering always shows molecules in aromatic form
  (github issue #2976 from greglandrum)
• Reactions setting unspecified double-bond stereo to STEREOANY
  (github issue #3078 from ricrogz)
• PDB output flavor&2 documentation change
  (github issue #3089 from adalke)
• WedgeMolBonds() should prefer degree-1 atoms
  (github issue #3216 from greglandrum)
• Error in ChemAxon SMILES "parsing"
  (github issue #3320 from IvanChernyshov)
• Incorrect number of radical electrons calculated for metals
  (github issue #3330 from greglandrum)
• Problem with lifetime linkage of mols and conformers
  (github issue #3492 from amateurcat)
• Traceback when pickling ROMol after BCUT descriptors are calculated
  (github issue #3511 from d-b-w)
• Fix AUTOCORR2D descriptors
  (github pull #3512 from ricrogz)
• SDMolSupplier requires several attempts to load a SDF file in Python 3.6/3.7
  (github issue #3517 from jaimergp)
• Remove accidentally included boost header
  (github pull #3518 from ricrogz)
• legend_height_ should be preserved after drawing the molecule
  (github pull #3520 from greglandrum)
• remove the include directive for unused <access/tuptoaster.h> header
  (github pull #3525 from rvianello)
• C++ build fails when configured with RDKIT_USE_BOOST_SERIALIZATION=OFF
  (github issue #3529 from rvianello)
• Newest RDKIT version allowing chemically invalid smiles
  (github issue #3531 from GintasKam)
• Behaviour of generate_aligned_coords for erroneous inputs
  (github issue #3539 from dskatov)
• Drawing artifacts in draw_to_canvas_with_offset
  (github issue #3540 from dskatov)
• Error adding PNG metadata when kekulize=False
  (github issue #3543 from gayverjr)
• Add missing methods to remove SubstanceGroup attributes
  (github pull #3547 from greglandrum)
• Error writing SDF data containing UTF-8 to a StringIO object
  (github issue #3553 from greglandrum)
• correct handling of amide distances for macrocycles
  (github pull #3559 from hjuinj)
• rdMolDraw2D, problems during generation of pictures from SMARTS, differences between Cairo and SVG
  (github issue #3572 from wopozka)
• Fix example of SmilesToMol
  (github pull #3575 from kazuyaujihara)
• atom/bond notes handle capital letters incorrectly
  (github issue #3577 from greglandrum)
• Get MolDraw2DQt working again
  (github pull #3592 from greglandrum)
• Scientific notation in SDF V3000 files
  (github issue #3597 from mark-cresset)
• Fix: add missing python wrappers for MolDraw2DQt
  (github pull #3613 from greglandrum)
• V3K mol block parser not saving the chiral flag
  (github issue #3620 from greglandrum)
• Inconsistent metal disconnectors
  (github issue #3625 from pschwllr)
• Ring stereochemistry not properly removed from N atoms
  (github issue #3631 from greglandrum)
• moldraw2djs should not close all polygonal paths
  (github pull #3634 from greglandrum)
• Unidentifiable C++ Exception with FMCS
  (github issue #3635 from proteneer)
• Bump catch2 version to allow builds on Apple M1
  (github pull #3641 from naefl)
• Segmentation fault when parsing InChI
  (github issue #3645 from AnPallo)
• RDK_BUILD_THREADSAFE_SSS does not work as expected
  (github issue #3646 from pascal-soveaux)
• Disabling MaeParser and CoordGen Support Breaks the Build
  (github issue #3648 from proteneer)
• BondStereo info lost in FragmentOnBonds()
  (github pull #3649 from bp-kelley)
• memory leak when sanitization fails in InChIToMol()
  (github issue #3655 from greglandrum)
• Qt GUI libraries being linked into rdmolops.so when Qt support is enabled
  (github issue #3658 from ricrogz)
• Documentation of Chem.rdmolops.GetMolFrags's frag argument is wrong
  (github issue #3670 from noncomputable)
• fmcs() + bogus input causes engine crash
  (github issue #3687 from robins)
• qmol_from_ctab() with NULL crashes engine
  (github issue #3688 from robins)
• qmol_from_smiles() + bogus input causes engine crash
  (github issue #3689 from robins)
• Check PIL support for tostring and fromstring
  (github pull #3690 from sirbiscuit)
• Move MolToSVG() to rdkit.Chem.Draw (Addresses #3694)
  (github pull #3696 from ricrogz)
• Pandas AttributeError when rendering Molecule in DataFrame
  (github issue #3701 from enricogandini)
• Memory leak in EnumerateLibrary
  (github issue #3702 from jose-mr)
• Fix to add ZLIB_INCLUDE_DIRS for Windows build
  (github pull #3714 from kazuyaujihara)
• Docs/Book: Unexpected unicode character makes pdflatex build fail
  (github issue #3738 from mbanck)
• Test suite failures if eigen3 is not available
  (github issue #3740 from mbanck)
• Regression in depiction of double bonds in aromatic rings
  (github issue #3744 from ptosco)
• RGD with RGroupMatching.GA leaks memory and takes too long
  (github issue #3746 from ptosco)
• Fix comment to match the code in RemoveHsParameters
  (github pull #3747 from jasondbiggs)
• Inconsistent canonical tautomer on repeated application
  (github issue #3755 from darintay)
  ...

2021_03_1b1 (Q1 2021) Release

Release_2021.03.1b1

(Changes relative to Release_2020.09.1)

Backwards incompatible changes

• The distance-geometry based conformer generation now by defaults generates
  trans(oid) conformations for amides, esters, and related structures. This can
  be toggled off with the forceTransAmides flag in EmbedParameters. Note that
  this change does not impact conformers created using one of the ET versions.
  (#3794)
• The conformer generator now uses symmetry by default when doing RMS pruning.
  This can be disabled using the useSymmetryForPruning flag in
  EmbedParameters. (#3813)
• Double bonds with unspecified stereochemistry in the products of chemical
  reactions now have their stereo set to STEREONONE instead of STEREOANY (#3078)
• The MolToSVG() function has been moved from rdkit.Chem to rdkit.Chem.Draw
  (#3696)
• There have been numerous changes to the RGroup Decomposition code which change
  the results. (#3767)
• There have been numerous changes to GenerateDepictionMatching2DStructure() (#3811)
• Setting the kekuleSmiles argument (doKekule in C++) to MolToSmiles will now
  cause the molecule to be kekulized before SMILES generation. Note that this
  can lead to an exception being thrown. Previously this argument would only
  write kekulized SMILES if the molecule had already been kekulized (#2788)
• Using the kekulize argument in the MHFP code will now cause the molecule to be
  kekulized before the fingerprint is generated. Note that becaues kekulization
  is not canonical, using this argument currently causes the results to depend
  on the input atom numbering. Note that this can lead to an exception being
  thrown. (#3942)

Highlights

Acknowledgements

Michael Banck, Christopher Von Bargen, Jason Biggs, Patrick Buder, Ivan
Chernyshov, Andrew Dalke, Xiaorui Dong, Carmen Esposito, Nicholas Firth, Enrico
Gandini, James Gayvert, Gareth Jones, Eisuke Kawashima, Steven Kearnes, Brian
Kelley, Mark Mackey, Niels Kristian Kjærgård Madsen, Luca Naef, Dan
Nealschneider, Jin Pan, Daniel Paoliello, António JM Ribeiro, Sereina Riniker,
Braxton Robbason, Jaime Rodríguez-Guerra, Ricardo Rodriguez-Schmidt, Steve
Roughley, Vincent F. Scalfani, Nadine Schneider, Philippe Schwaller, Dan Skatov,
Pascal Soveaux, Paolo Tosco, Kazuya Ujihara, Riccardo Vianello, Shuzhe Wang,
Piotr Wawrzyniak, Maciej Wójcikowski, Yutong Zhao
'driesvr', 'GintasKam', 'SPKorhonen', 'pkubaj', 'AnPallo', 'darintay',
'slchan3', 'Robins', 'sirbiscuit', 'amateurcat', 'noncomputable', 'yurivict',
'magattaca'

Contrib updates:

• Added NIBRStructureFilters: a set of substructure filters for hit-list triaging together with python code for applying them. The filters are described in the publication https://dx.doi.org/10.1021/acs.jmedchem.0c01332
  (github pull #3516 from NadineSchneider)
• Added CalcLigRMSD: flexible python code for calculating RMSD between pre-aligned molecules
  (github pull #3812 from cespos)

Bug Fixes:

• Casting int to uint in MorganFingerprintHelper leads to unexpected behaviour.
  (github issue #1761 from SiPa13)
• MolChemicalFeature.GetPos() returns value for molecule's default conformer
  (github issue #2530 from greglandrum)
• Unable to catch RDKit exceptions in linked library when compiling with fvisibility=hidden
  (github issue #2753 from cdvonbargen)
• Reaction rendering always shows molecules in aromatic form
  (github issue #2976 from greglandrum)
• Reactions setting unspecified double-bond stereo to STEREOANY
  (github issue #3078 from ricrogz)
• PDB output flavor&2 documentation change
  (github issue #3089 from adalke)
• WedgeMolBonds() should prefer degree-1 atoms
  (github issue #3216 from greglandrum)
• Error in ChemAxon SMILES "parsing"
  (github issue #3320 from IvanChernyshov)
• Incorrect number of radical electrons calculated for metals
  (github issue #3330 from greglandrum)
• Problem with lifetime linkage of mols and conformers
  (github issue #3492 from amateurcat)
• Traceback when pickling ROMol after BCUT descriptors are calculated
  (github issue #3511 from d-b-w)
• Fix AUTOCORR2D descriptors
  (github pull #3512 from ricrogz)
• SDMolSupplier requires several attempts to load a SDF file in Python 3.6/3.7
  (github issue #3517 from jaimergp)
• Remove accidentally included boost header
  (github pull #3518 from ricrogz)
• legend_height_ should be preserved after drawing the molecule
  (github pull #3520 from greglandrum)
• remove the include directive for unused <access/tuptoaster.h> header
  (github pull #3525 from rvianello)
• C++ build fails when configured with RDKIT_USE_BOOST_SERIALIZATION=OFF
  (github issue #3529 from rvianello)
• Newest RDKIT version allowing chemically invalid smiles
  (github issue #3531 from GintasKam)
• Behaviour of generate_aligned_coords for erroneous inputs
  (github issue #3539 from dskatov)
• Drawing artifacts in draw_to_canvas_with_offset
  (github issue #3540 from dskatov)
• Error adding PNG metadata when kekulize=False
  (github issue #3543 from gayverjr)
• Add missing methods to remove SubstanceGroup attributes
  (github pull #3547 from greglandrum)
• Error writing SDF data containing UTF-8 to a StringIO object
  (github issue #3553 from greglandrum)
• correct handling of amide distances for macrocycles
  (github pull #3559 from hjuinj)
• rdMolDraw2D, problems during generation of pictures from SMARTS, differences between Cairo and SVG
  (github issue #3572 from wopozka)
• Fix example of SmilesToMol
  (github pull #3575 from kazuyaujihara)
• atom/bond notes handle capital letters incorrectly
  (github issue #3577 from greglandrum)
• Get MolDraw2DQt working again
  (github pull #3592 from greglandrum)
• Scientific notation in SDF V3000 files
  (github issue #3597 from mark-cresset)
• Fix: add missing python wrappers for MolDraw2DQt
  (github pull #3613 from greglandrum)
• V3K mol block parser not saving the chiral flag
  (github issue #3620 from greglandrum)
• Inconsistent metal disconnectors
  (github issue #3625 from pschwllr)
• Ring stereochemistry not properly removed from N atoms
  (github issue #3631 from greglandrum)
• moldraw2djs should not close all polygonal paths
  (github pull #3634 from greglandrum)
• Unidentifiable C++ Exception with FMCS
  (github issue #3635 from proteneer)
• Bump catch2 version to allow builds on Apple M1
  (github pull #3641 from naefl)
• Segmentation fault when parsing InChI
  (github issue #3645 from AnPallo)
• RDK_BUILD_THREADSAFE_SSS does not work as expected
  (github issue #3646 from pascal-soveaux)
• Disabling MaeParser and CoordGen Support Breaks the Build
  (github issue #3648 from proteneer)
• BondStereo info lost in FragmentOnBonds()
  (github pull #3649 from bp-kelley)
• memory leak when sanitization fails in InChIToMol()
  (github issue #3655 from greglandrum)
• Qt GUI libraries being linked into rdmolops.so when Qt support is enabled
  (github issue #3658 from ricrogz)
• Documentation of Chem.rdmolops.GetMolFrags's frag argument is wrong
  (github issue #3670 from noncomputable)
• fmcs() + bogus input causes engine crash
  (github issue #3687 from robins)
• qmol_from_ctab() with NULL crashes engine
  (github issue #3688 from robins)
• qmol_from_smiles() + bogus input causes engine crash
  (github issue #3689 from robins)
• Check PIL support for tostring and fromstring
  (github pull #3690 from sirbiscuit)
• Move MolToSVG() to rdkit.Chem.Draw (Addresses #3694)
  (github pull #3696 from ricrogz)
• Pandas AttributeError when rendering Molecule in DataFrame
  (github issue #3701 from enricogandini)
• Memory leak in EnumerateLibrary
  (github issue #3702 from jose-mr)
• Fix to add ZLIB_INCLUDE_DIRS for Windows build
  (github pull #3714 from kazuyaujihara)
• Docs/Book: Unexpected unicode character makes pdflatex build fail
  (github issue #3738 from mbanck)
• Test suite failures if eigen3 is not available
  (github issue #3740 from mbanck)
• Regression in depiction of double bonds in aromatic rings
  (github issue #3744 from ptosco)
• RGD with RGroupMatching.GA leaks memory and takes too long
  (github issue #3746 from ptosco)
• Fix comment to match the code in RemoveHsParameters
  (github pull #3747 from jasondbiggs)
• Inconsistent canonical tautomer on repeated application
  (github issue #3755 from darintay)
• bonds no longer highlighted in substruct matches in jupyter
  (github issue #3762 from greglandrum)
• SubstanceGroup output doesn't correctly quote " symbols
  (github issue #3768 from greglandrum)
• MolToSmarts inverts direction of dative bond
  (github issue #3774 from IvanChernyshov)
• Fix pillow error in IPythonConsole.py
  (github pull #3783 from skearnes)
• lock swig version in MacOS CI builds
  (github pull #3789 from greglandrum)
• DrawMorganBit errors when useSVG is False
  (github issue #3796 from ncfirth)
• SubstructLibrary Cached Smiles Holders have bad behavior with bad smiles
  (github issue #3797 from bp-kelley)
• MolFromSmiles('[He]') produces a diradical helium atom
  (github issue #3805 from jasondbiggs)
• NaNs from AUTOCORR2D descriptor
  (github issue #3806 from greglandrum)
• MaeMolSupplier throws an invariant exception on parsing an "undefined" chirality label
  (github issue #3815 from ricrogz)
• Sanitize molecules when SMILES needs to be produced in PandasTools
  (github pull #3818 from mwojcikowski)
• Tautomer Query copy constructor is shallow not deep causing segfaults in destructor
  (github issue #3821 from bp-kelley)
• OptimizeMolecule and OptimizeMoleculeConfs Argument Bug
  (github issue #3824 from xiaoruiDong)
• rdMolEnumerator.Enumerate() fragile w.r.t. atom ordering
  (github issue #3844 from greglandrum)
• MinimalLib: Bonds are parallel in SVG but not on an HTML5 Canvas
  (github issue #38...

2020_09_5 (Q3 2020) Release

Release_2020.09.5

(Changes relative to Release_2020.09.4)

Acknowledgements

Michael Banck, Jason Biggs, Ivan Chernyshov, Nicholas Firth, Eisuke Kawashima
Steven Kearnes, Brian Kelley, Ricardo Rodriguez Schmidt, Edward Williams

Bug Fixes:

• Docs/Book: Unexpected unicode character makes pdflatex build fail
  (github #3738 from mbanck)
• Test suite failures if eigen3 is not available
  (github #3740 from mbanck)
• bonds no longer highlighted in substruct matches in jupyter
  (github #3762 from greglandrum)
• SubstanceGroup output doesn't correctly quote " symbols
  (github #3768 from greglandrum)
• MolToSmarts inverts direction of dative bond
  (github #3774 from IvanChernyshov)
• Fix pillow error in IPythonConsole.py
  (github #3783 from skearnes)
• lock swig version in MacOS CI builds
  (github #3789 from greglandrum)
• DrawMorganBit errors when useSVG is False
  (github #3796 from ncfirth)
• SubstructLibrary Cached Smiles Holders have bad behavior with bad smiles
  (github #3797 from bp-kelley)
• MolFromSmiles('[He]') produces a diradical helium atom
  (github #3805 from jasondbiggs)
• NaNs from AUTOCORR2D descriptor
  (github #3806 from greglandrum)
• MaeMolSupplier throws an invariant exception on parsing an "undefined" chirality label
  (github #3815 from ricrogz)
• AddHs creates H atom with nan coordinates on edge case 2D structure
  (github #3854 from ricrogz)

2020_09_4 (Q3 2020) Release

Release_2020.09.4

(Changes relative to Release_2020.09.3)

Acknowledgements

Jason Biggs Patrick Buder, Andrew Dalke, Enrico Gandini, Maximilian Greil, Brian
Kelley, Luca Naef, António JM Ribeiro, Ricardo Rodriguez Schmidt, Pascal
Soveaux, Paolo Tosco, Yutong Zhao, 'Robins', 'sirbiscuit', 'AnPallo',
'noncomputable'

Bug Fixes:

• Casting int to uint in MorganFingerprintHelper leads to unexpected behaviour.
  (github #1761 from SiPa13)
• MolChemicalFeature.GetPos() returns value for molecule's default conformer
  (github #2530 from greglandrum)
• PDB output flavor&2 documentation change
  (github #3089 from adalke)
• Unidentifiable C++ Exception with FMCS
  (github #3635 from proteneer)
• Bump catch2 version to allow builds on Apple M1
  (github #3641 from naefl)
• Segmentation fault when parsing InChI
  (github #3645 from AnPallo)
• RDK_BUILD_THREADSAFE_SSS does not work as expected
  (github #3646 from pascal-soveaux)
• Disabling MaeParser and CoordGen Support Breaks the Build
  (github #3648 from proteneer)
• BondStereo info lost in FragmentOnBonds()
  (github #3649 from bp-kelley)
• memory leak when sanitization fails in InChIToMol()
  (github #3655 from greglandrum)
• Qt GUI libraries being linked into rdmolops.so when Qt support is enabled
  (github #3658 from ricrogz)
• Documentation of Chem.rdmolops.GetMolFrags's frag argument is wrong
  (github #3670 from noncomputable)
• fmcs() + bogus input causes engine crash
  (github #3687 from robins)
• qmol_from_ctab() with NULL crashes engine
  (github #3688 from robins)
• qmol_from_smiles() + bogus input causes engine crash
  (github #3689 from robins)
• Check PIL support for tostring and fromstring
  (github #3690 from sirbiscuit)
• Pandas AttributeError when rendering Molecule in DataFrame
  (github #3701 from enricogandini)
• Memory leak in EnumerateLibrary
  (github #3702 from jose-mr)
• Regression in depiction of double bonds in aromatic rings
  (github #3744 from ptosco)
• Fix comment to match the code in RemoveHsParameters
  (github #3747 from jasondbiggs)