2022_03_5 (Q1 2022) Release

Release_2022.03.5

(Changes relative to Release_2022.03.4)

Acknowledgements

Gabriele Balducci, Jonathan Bisson, David Cosgrove, Eisuke Kawashima, Brian
Kelley, Ricardo Rodriguez-Schmidt, David Schaller, Jeff van Santen Paolo Tosco,
Rachel Walker, 'sagitter'

Bug Fixes:

• KekulizeException of molecule from Smarts pattern with new RDKit release
  (github #5156 from schallerdavid)
• error: format not a string literal and no format arguments
  (github #5234 from sagitter)
• leftover debugging code makes build of 2022_03_3 tarball fail
  (github #5351 from balducci)
• Incorrect perception of pseudoasymmetric centers on non-canonical molecules
  (github #5403 from ptosco)
• fix: rdkit.Chem.rdDistGeom.EmbedMultipleConfs docstring indentation
  (github #5404 from jvansan)
• Fix performance issue in RingUtils::checkFused
  (github #5410 from rachelnwalker)
• Multi-coloured highlights go wrong with small fonts
  (github #5420 from DavidACosgrove)
• Parsing a Mol block/file does not clear the "molTotValence" property from atoms
  (github #5423 from ricrogz)
• Pre-condition Violation - Failed Expression: dir == Bond::ENDUPRIGHT || dir == Bond::ENDDOWNRIGHT
  (github #5433 from bjonnh-work)
• Draw option noAtomLabels and explicit hydrogen works badly
  (github #5453 from DavidACosgrove)
• Fix integer overflow in RGroupDecomposition strategy GA
  (github #5460 from bp-kelley)
• Invalid number of radical electrons calculated for [Pr+4]
  (github #5462 from bjonnh-work)
• CXSmiles isn't properly escaping floating point properties
  (github #5466 from bp-kelley)
• Fixes "DeprecationWarning: invalid escape sequence \C" when importing EnumerateStereoisomers
  (github #5478 from ricrogz)
• Fix double to float downcasting warning
  (github #5479 from ricrogz)

2022_03_4 (Q1 2022) Release

Release_2022.03.4

(Changes relative to Release_2022.03.3)

Acknowledgements

David Cosgrove, Peter Gedeck, Chris Kuenneth, Michel Moreau, Alex Rich, Ricardo
Rodriguez-Schmidt, Paolo Tosco, Ivan Tubert-Brohman, Rachel Walker,

Bug Fixes:

• Runtime error when writing reaction with substance group to V3000 rxnblock
  (github #5324 from rachelnwalker)
• Update docs for ReplaceSubstructs
  (github #5343 from i-tub)
• Minimallib NPM release fixes - wrong node bin command in Dockerfile and prepublish npm script command replacement
  (github #5349 from MichelML)
• Update code formatting in GettingStartedInPython.rst
  (github #5350 from gedeck)
• Prevent wedging ring bonds
  (github #5356 from greglandrum)
• Class info info missing for for wavy bonds in SVGs.
  (github #5358 from DavidACosgrove)
• MolToSmiles with doRandom=True raises errors with molecules containing fragments.
  (github #5372 from greglandrum)
• Fixes #1812
  (github #5373 from kuelumbus)
• Fix typos in docString.
  (github #5377 from DavidACosgrove)
• Restore #5103 that was accidentally reverted in #5132
  (github #5381 from ptosco)
• cairo error when using similarity maps
  (github #5383 from glandrum)
• MolDraw2DQt and MolDraw2DJS don't draw wavy bonds
  (github #5386 from greglandrum)
• Typos in Install.md
  (github #5388 from gedeck)
• MolDraw2DQt draws brackets incorrectly
  (github #5389 from greglandrum)
• PandasTools should not always bring in IPythonConsole
  (github #5392 from greglandrum)

2022_03_3 (Q1 2022) Release

Release_2022.03.3

(Changes relative to Release_2022.03.2)

Acknowledgements

Andy Cai, David Cosgrove, JP Ebejer, Emanuele Guidotti, Per Johnsson, Gareth
Jones, Brian Kelley, Ricardo Rodriguez-Schmidt, Paolo Tosco, Antonio Trande

Bug Fixes:

• DrawMorganBit returns empty image for "isolated" fingerprints
  (github #4242 from eguidotti)
• Fix for RGD dummy atom bug in RDKit::replaceCore
  (github #5154 from jones-gareth)
• Standardization via RDKit breaks molecules
  (github #5169 from malteseunderdog)
• Fix duplicate non thread safe check in VarianceDataForLabel
  (github #5212 from ricrogz)
• RDKit::Utils::LocaleSwitcher is not thread safe
  (github #5214 from ricrogz)
• Core with query atoms and no user definded attachment points may create poor decompostions
  (github #5222 from jones-gareth)
• Fix qt build under VS2019
  (github #5238 from ricrogz)
• Precondition violation on chiral Atoms with zero order bonds
  (github #5239 from ricrogz)
• pyForceFieldConstraints test failed
  (github #5252 from sagitter)
• drawReaction() should not hit a PRECONDITION with prepareMolsBeforeDrawing=false
  (github #5259 from ptosco)
• Atom annotations poorly placed on highlighted atoms
  (github #5269 from DavidACosgrove)
• make the catch tests build faster
  (github #5284 from greglandrum)
• rdMolDraw2D.PrepareMolForDrawing(None) causes segmentation fault
  (github #5298 from perjo)
• make the logging tests more robust
  (github #5312 from greglandrum)
• MolStandardize: uncharger failing in molecules with zwitterionic sulfone
  (github #5317 from greglandrum)
• MolStandardize: some operations throwing on non-standardized molecules
  (github #5318 from greglandrum)
• MolStandardize: cleanup() function not correctly reassigning stereochemistry
  (github #5320 from greglandrum)
• MolFromMolBlock should correctly assign stereochemistry to 3D molecules
  (github #5327 from greglandrum)
• assignChiralTypesFrom3D() ignores wiggly bonds
  (github #5328 from greglandrum)
• Molzip segfaults instead of throwing an error when multiple bonds are formed to the same pairs of atoms
  (github #5334 from loluwot)

2022_03_2 (Q1 2022) Release

Release_2022.03.2

(Changes relative to Release_2022.03.1)

Acknowledgements

David Cosgrove, Aleš Erjavec, Mosè Giordano, Sreya Gogineni, Ricardo
Rodriguez-Schmidt, David W.H. Swenson, Paolo Tosco, Rachel Walker, 'GLPG-GT'

Bug Fixes:

• Image Generation: Highlighting looks off when bondLineWidth is increased for PNG generation
  (github #5122 from rachelnwalker)
• RDKit crashes on CIP label calculation
  (github #5142 from ricrogz)
• Modified the JS tests to comply with older nodejs versions
  (github #5148 from ptosco)
• Presence of exocyclic S/D, S/A or D/A query bonds prevents benzene from being recognized as aromatic
  (github #5152 from rachelnwalker)
• Very small fix to avoid an AttributeError
  (github #5163 from ptosco)
• issue with V3000 SD files containing enhanced stereochemistry information
  (github #5165 from GLPG-GT)
• Draw.MolToQPixmap raises a TypeError with Python 3.10
  (github #5166 from ales-erjavec)
• Multiple calls to BlockLogs() permanently disable logging
  (github #5172 from ricrogz)
• Check architecture of the target system to optimise popcnt
  (github #5182 from giordano)
• More consistently check for WIN32 instead of MSVC in CMake files
  (github #5183 from giordano)
• Atom indices inside double bond
  (github #5185 from DavidACosgrove)
• Bug in IPython display after setting a molecule property
  (github #5192 from dwhswenson)
• Zero & coordinate bonds are being taken into account for chirality
  (github #5196 from ricrogz)
• FindPotentialStereo does not clean stereoflags from atoms which cannot be stereocenters
  (github #5200 from greglandrum)
• Fixes array overflow in FMCS code
  (github #5205 from ricrogz)
• PeriodicTable initialization is not thread safe
  (github #5207 from ricrogz)
• Fix use of not thread safe function localtime()
  (github #5211 from ricrogz)

2022_03_1 (Q1 2022) Release

Release_2022.03.1

(Changes relative to Release_2021.09.1)

Backwards incompatible changes

• When running in Jupyter Notebook, logs are now sent only to Python's
  standard error stream, and no longer include the RDKit LEVEL prefix.
• The Debug and Info logs are now disabled by default. If you would like to
  enable them within your code you can call rdBase.EnableLog("rdApp.info")
  and/or rdBase.EnableLog("rdApp.debug").
• The MolHash functions now reassign stereochemistry after modifying the
  molecule and before calculating the hash. Previous versions would still
  include information about atom/bond stereochemistry in the output hash even if
  that no longer applies in the modified molecule.
• The rules for aromaticity in rings containing dummy atoms have been changed.
  The general intention of the new handling is that aromaticity will not be
  perceived for rings containing dummy atoms unless it's clear that the dummies
  should be aromatic. As an example: the SMILES C1=C*2=CC=CC=*2C=C1 is
  perceived to be aromatic while the SMILES C1=C*2C=CC=C*2C=C1 (which does not
  have any double bonds to the dummy atoms) is not; in previous RDKit releases
  both of these structures were aromatic. There's more information about this in
  the discussion of PR #4722 (#4722) and
  Issue #4721 (#4721).
• In the PostgreSQL cartridge the mol_in() function no longer performs full
  sanitization of the molecule. One consequence of this is that directly casting
  from strings to molecules also no longer does sanitization, so select 'CN(=O)=O'::mol
  does not sanitize the molecule. If you want to convert a string to a molecule
  with full sanitization you can either cast to text first
  (i.e. select 'CN(=O)=O'::text::mol or use the mol_from_smiles() function.
• The code to calculate bit vector topological torsion fingerprints for
  reactions no longer ignore the fingerprint size argument.
• The rules for tautomer enumeration in MolStandardize have been updated to
  more closely match the rules in the original publication. These changes
  primarily consist of making the rules more specific; the consequence is that
  less tautomers will be generated with this version. The previous rules can
  still be accessed via the function GetV1TautomerEnumerator() (Python) or
  getV1TautomerEnumerator() (C++)

Highlights

• The RDKit can now integrate with the python logger: calling
  rdBase.LogToPythonLogger() enables this. All log messages are sent to a
  logger named "rdkit".
• The backend of the MolDraw2D code has been extensively refactored. This should
  be mostly invisible to RDKit users, but it makes supporting and extending that
  code much easier.
• Beilstein generics (i.e. things like "ARY", "ALK", or "CAL") are now supported
  when doing substructure queries. This is a first step towards enabling some
  really cool substructure search possibilities.

Acknowledgements

Marcel Baltruschat, Jason Biggs, Kevin Burk, Cédric Bouysset, David Cosgrove,
Joel Duerksen, Jacob Gora, Gareth Jones, Toshiki Kataoka, Eisuke Kawashima,
Brian Kelley, Sonia Liggi, Niels Kristian Kjærgård Madsen, Hector
Martinez-Seara, Dan Nealschneider, Alex Rebert, Ricardo Rodriguez-Schmidt, Steve
Roughley, Roger Sayle, Nikolai Schapin, Ansgar Schuffenhauer, Kaushalesh Shukla,
Jon Sorenson, Ichiru Take, Paolo Tosco, Kazuya Ujihara, Fabio Urbina, Riccardo
Vianello Rachel Walker, Maciej Wójcikowski, SPKorhonen, yuri@FreeBSD,

Code removed in this release:

• The useCountSimulation keyword argument for
  rdFingerprintGenerator.GetMorganGenerator and
  rdFingerprintGenerator.GetAtomPairGenerator has been removed. Please use the
  countSimulation keyword argument instead.
• The function mol_from_smarts() in the PostgreSQL cartridge has been removed.
  Please use the qmol_from_smarts() function instead.
• The computeBalabanJ() functions from the MolOps namespace were removed.
  These were not exposed to Python, so this will not affect any Python code.

Bug Fixes:

• Fix Flake8 erorrs
  (github pull #4252 from e-kwsm)
• handle sqlalchemy deprecation
  (github pull #4625 from greglandrum)
• Debug build of the postgres cartridge fails pg_regress tests for reaction.sql
  (github issue #4631 from rvianello)
• fix parsing beyond the end of the input string in findMCSsmiles
  (github pull #4636 from rvianello)
• Mem leak fixes
  (github pull #4637 from ricrogz)
• Subsequent call to rdChemReactions.ChemicalReaction.RunReactants will block indefinitely.
  (github issue #4651 from goraj)
• Fix docstring of ConstrainedEmbed
  (github pull #4666 from kazuyaujihara)
• Postgres cartridge build fails under Ubuntu
  (github issue #4681 from SPKorhonen)
• Molfile SDD records not properly displayed
  (github pull #4690 from jones-gareth)
• RGD: fix for cores with MOL block atom lists
  (github pull #4695 from jones-gareth)
• Wrong tautomers generated
  (github issue #4700 from sonial)
• RGD align output core to input structure
  (github pull #4709 from jones-gareth)
• TorsionFingerprints raises error with S(Cl)F4 group
  (github issue #4720 from kazuyaujihara)
• Dummy atoms next to aromatic are always kekulized even when they should not
  (github issue #4721 from ptosco)
• TautomerEnumerator will crash if copied with a callback set
  (github issue #4736 from ptosco)
• Minor PandasTools cleanup
  (github pull #4744 from ptosco)
• Reaction parser fails when CX extensions are present
  (github issue #4759 from greglandrum)
• GetSimilarityMapFromWeights changes behavior of parameter "colorMap" depending on whether the parameter "draw2d" is provided or not
  (github issue #4763 from FabioUrbina)
• Highlight bond width is different for different PNG image sizes
  (github issue #4764 from rachelnwalker)
• Fixes crashing bug with finalSubstructChecks
  (github pull #4782 from greglandrum)
• MDL query with aromatic bond sets aromatic flag on atoms even though they are not in an aromatic ring
  (github issue #4785 from ptosco)
• [Cartridge]: qmol_from_ctab and qmol_from_smiles are sanitizing molecules
  (github issue #4787 from greglandrum)
• AdjustQueryProperties() is inconsistent when adjustConjugatedFiveRings is set
  (github issue #4789 from greglandrum)
• Draw.MolToFile to SVG raises "Can't kekulize" error
  (github issue #4792 from toslunar)
• Ring double bonds written as crossed bonds after RGD
  (github issue #4809 from greglandrum)
• Fix a number of crashing bugs in the python wrappers
  (github pull #4810 from greglandrum)
• correctly tag unspecified branch-begin bonds in SMARTS
  (github pull #4811 from greglandrum)
• AttributeError in PandasTools
  (github issue #4821 from greglandrum)
• reloading PandasTools leads to infinite recursion
  (github issue #4823 from greglandrum)
• ReplaceCore should set stereo on ring bonds when it breaks rings
  (github issue #4825 from greglandrum)
• MolDraw2D::drawArc() starts at wrong angle
  (github issue #4836 from greglandrum)
• MolDraw2D::drawArc() not exposed to Python
  (github issue #4837 from greglandrum)
• align argument to MolDraw2D::DrawString() cannot be used from Python
  (github issue #4838 from greglandrum)
• Fix RunFilterCatalog() thread counts.
  (github pull #4856 from xavierholt)
• RGD: dummy atom in input structure is mishandled
  (github pull #4863 from jones-gareth)
• Fix bug with wedges being drawn backwards
  (github pull #4868 from greglandrum)
• Missing dependency on RDKit::RingDecomposerLib_static in RDKit::GraphMol_static
  (github issue #4875 from nielskm)
• cannot parse coordinate bonds from CXSMARTS
  (github issue #4878 from greglandrum)
• fix some leaks in the SWIG wrappers
  (github pull #4916 from greglandrum)
• Fix some problems turned up by ossfuzz
  (github pull #4927 from greglandrum)
• Fix i-files for RDK_USE_BOOST_IOSTREAMS=OFF
  (github pull #4933 from kazuyaujihara)
• Fails on i386: non-constant-expression cannot be narrowed from type 'unsigned int' to 'npy_intp' (aka 'int') in initializer list
  (github issue #4934 from yurivict)
• Fix SWIG wrappers for C#
  (github pull #4935 from kazuyaujihara)
• Definition of eccentricity in documentation is wrong
  (github issue #4952 from drkeoni)
• fix CMakeLists.txt extracting link line from python LDSHARED config var
  (github pull #4954 from rvianello)
• add JavaGzStreamTests
  (github pull #4973 from kazuyaujihara)
• Invalid SMARTS generated by MolToSmarts
  (github issue #4981 from nielskm)
• Fix memory safety issues found by OSS-Fuzz
  (github pull #4983 from alpire)
• AssignStereochemistry should remove nonchiral atoms from StereoGroups
  (github pull #4986 from greglandrum)
• Transform3D#SetRotation() around arbitrary axis scales coordinates
  (github issue #4995 from sroughley)
• Bad handling of dummy atoms in the CIP assignment code
  (github issue #4996 from greglandrum)
• Bad handling of fragments in CIP code
  (github issue #4998 from greglandrum)
• Drawing query atoms containing an AND query raises an exception
  (github issue #5006 from ptosco)
• Bad tautomers produced for phosphorous compounds
  (github issue #5008 from NikSchap2107)
• Fix warning when generating coordinates for ZOBs
  (github pull #5011 from d-b-w)
• Code in the docstring for FindMolChiralCenters() doesn't work
  (github pull #5014 from greglandrum)
• Mol images in DataFrames are drawn only once in Jupyter Lab
  (github issue #5017 from mrcblt)
• Drop gist_qmol_ops in upgrade scripts in case it exists
  (github pull #5021 from mwojcikowski)
• Remove extra newline from Kekulize error message.
  (github pull #5022 from xavierholt)
• Neighboring Hs not taken into account in connectivity invariants
  (gith...

2022_03_1b1 (Q1 2022) Release

Release_2022.03.1b1

(Changes relative to Release_2021.09.1)

Backwards incompatible changes

• When running in Jupyter Notebook, logs are now sent only to Python's
  standard error stream, and no longer include the RDKit LEVEL prefix.
• The Debug and Info logs are now disabled by default. If you would like to
  enable them within your code you can call rdBase.EnableLog("rdApp.info")
  and/or rdBase.EnableLog("rdApp.debug").
• The MolHash functions now reassign stereochemistry after modifying the
  molecule and before calculating the hash. Previous versions would still
  include information about atom/bond stereochemistry in the output hash even if
  that no longer applies in the modified molecule.
• The rules for aromaticity in rings containing dummy atoms have been changed.
  The general intention of the new handling is that aromaticity will not be
  perceived for rings containing dummy atoms unless it's clear that the dummies
  should be aromatic. As an example: the SMILES C1=C*2=CC=CC=*2C=C1 is
  perceived to be aromatic while the SMILES C1=C*2C=CC=C*2C=C1 (which does not
  have any double bonds to the dummy atoms) is not; in previous RDKit releases
  both of these structures were aromatic. There's more information about this in
  the discussion of PR #4722 (#4722) and
  Issue #4721 (#4721).
• In the PostgreSQL cartridge the mol_in() function no longer performs full
  sanitization of the molecule. One consequence of this is that directly casting
  from strings to molecules also no longer does sanitization, so select 'CN(=O)=O'::mol
  does not sanitize the molecule. If you want to convert a string to a molecule
  with full sanitization you can either cast to text first
  (i.e. select 'CN(=O)=O'::text::mol or use the mol_from_smiles() function.
• The code to calculate bit vector topological torsion fingerprints for
  reactions no longer ignore the fingerprint size argument.

Highlights

• The RDKit can now integrate with the python logger: calling
  rdBase.LogToPythonLogger() enables this. All log messages are sent to a
  logger named "rdkit".
• The backend of the MolDraw2D code has been extensively refactored. This should
  be mostly invisible to RDKit users, but it makes supporting and extending that
  code much easier.
• Beilstein generics (i.e. things like "ARY", "ALK", or "CAL") are now supported
  when doing substructure queries. This is a first step towards enabling some
  really cool substructure search possibilities.

Acknowledgements

Marcel Baltruschat, Jason Biggs, Kevin Burk, Cédric Bouysset, David Cosgrove,
Joel Duerksen, Jacob Gora, Gareth Jones, Toshiki Kataoka, Eisuke Kawashima,
Brian Kelley, Niels Kristian Kjærgård Madsen, Hector Martinez-Seara, Dan
Nealschneider, Alex Rebert, Ricardo Rodriguez-Schmidt, Steve Roughley, Roger
Sayle, Nikolai Schapin, Ansgar Schuffenhauer, Kaushalesh Shukla, Jon Sorenson,
Ichiru Take, Paolo Tosco, Kazuya Ujihara, Fabio Urbina, Riccardo Vianello Rachel
Walker, Maciej Wójcikowski, SPKorhonen, yuri@FreeBSD,

Code removed in this release:

• The useCountSimulation keyword argument for
  rdFingerprintGenerator.GetMorganGenerator and
  rdFingerprintGenerator.GetAtomPairGenerator has been removed. Please use the
  countSimulation keyword argument instead.
• The function mol_from_smarts() in the PostgreSQL cartridge has been removed.
  Please use the qmol_from_smarts() function instead.
• The computeBalabanJ() functions from the MolOps namespace were removed.
  These were not exposed to Python, so this will not affect any Python code.

Bug Fixes:

• Fix Flake8 erorrs
  (github pull #4252 from e-kwsm)
• handle sqlalchemy deprecation
  (github pull #4625 from greglandrum)
• Debug build of the postgres cartridge fails pg_regress tests for reaction.sql
  (github issue #4631 from rvianello)
• fix parsing beyond the end of the input string in findMCSsmiles
  (github pull #4636 from rvianello)
• Mem leak fixes
  (github pull #4637 from ricrogz)
• Subsequent call to rdChemReactions.ChemicalReaction.RunReactants will block indefinitely.
  (github issue #4651 from goraj)
• Fix docstring of ConstrainedEmbed
  (github pull #4666 from kazuyaujihara)
• Postgres cartridge build fails under Ubuntu
  (github issue #4681 from SPKorhonen)
• Molfile SDD records not properly displayed
  (github pull #4690 from jones-gareth)
• RGD: fix for cores with MOL block atom lists
  (github pull #4695 from jones-gareth)
• RGD align output core to input structure
  (github pull #4709 from jones-gareth)
• TorsionFingerprints raises error with S(Cl)F4 group
  (github issue #4720 from kazuyaujihara)
• Dummy atoms next to aromatic are always kekulized even when they should not
  (github issue #4721 from ptosco)
• TautomerEnumerator will crash if copied with a callback set
  (github issue #4736 from ptosco)
• Minor PandasTools cleanup
  (github pull #4744 from ptosco)
• Reaction parser fails when CX extensions are present
  (github issue #4759 from greglandrum)
• GetSimilarityMapFromWeights changes behavior of parameter "colorMap" depending on whether the parameter "draw2d" is provided or not
  (github issue #4763 from FabioUrbina)
• Highlight bond width is different for different PNG image sizes
  (github issue #4764 from rachelnwalker)
• Fixes crashing bug with finalSubstructChecks
  (github pull #4782 from greglandrum)
• MDL query with aromatic bond sets aromatic flag on atoms even though they are not in an aromatic ring
  (github issue #4785 from ptosco)
• [Cartridge]: qmol_from_ctab and qmol_from_smiles are sanitizing molecules
  (github issue #4787 from greglandrum)
• AdjustQueryProperties() is inconsistent when adjustConjugatedFiveRings is set
  (github issue #4789 from greglandrum)
• Draw.MolToFile to SVG raises "Can't kekulize" error
  (github issue #4792 from toslunar)
• Ring double bonds written as crossed bonds after RGD
  (github issue #4809 from greglandrum)
• Fix a number of crashing bugs in the python wrappers
  (github pull #4810 from greglandrum)
• correctly tag unspecified branch-begin bonds in SMARTS
  (github pull #4811 from greglandrum)
• AttributeError in PandasTools
  (github issue #4821 from greglandrum)
• reloading PandasTools leads to infinite recursion
  (github issue #4823 from greglandrum)
• ReplaceCore should set stereo on ring bonds when it breaks rings
  (github issue #4825 from greglandrum)
• MolDraw2D::drawArc() starts at wrong angle
  (github issue #4836 from greglandrum)
• MolDraw2D::drawArc() not exposed to Python
  (github issue #4837 from greglandrum)
• align argument to MolDraw2D::DrawString() cannot be used from Python
  (github issue #4838 from greglandrum)
• Fix RunFilterCatalog() thread counts.
  (github pull #4856 from xavierholt)
• RGD: dummy atom in input structure is mishandled
  (github pull #4863 from jones-gareth)
• Fix bug with wedges being drawn backwards
  (github pull #4868 from greglandrum)
• Missing dependency on RDKit::RingDecomposerLib_static in RDKit::GraphMol_static
  (github issue #4875 from nielskm)
• cannot parse coordinate bonds from CXSMARTS
  (github issue #4878 from greglandrum)
• fix some leaks in the SWIG wrappers
  (github pull #4916 from greglandrum)
• Fix some problems turned up by ossfuzz
  (github pull #4927 from greglandrum)
• Fix i-files for RDK_USE_BOOST_IOSTREAMS=OFF
  (github pull #4933 from kazuyaujihara)
• Fails on i386: non-constant-expression cannot be narrowed from type 'unsigned int' to 'npy_intp' (aka 'int') in initializer list
  (github issue #4934 from yurivict)
• Fix SWIG wrappers for C#
  (github pull #4935 from kazuyaujihara)
• Definition of eccentricity in documentation is wrong
  (github issue #4952 from drkeoni)
• fix CMakeLists.txt extracting link line from python LDSHARED config var
  (github pull #4954 from rvianello)
• add JavaGzStreamTests
  (github pull #4973 from kazuyaujihara)
• Invalid SMARTS generated by MolToSmarts
  (github issue #4981 from nielskm)
• Fix memory safety issues found by OSS-Fuzz
  (github pull #4983 from alpire)
• AssignStereochemistry should remove nonchiral atoms from StereoGroups
  (github pull #4986 from greglandrum)
• Transform3D#SetRotation() around arbitrary axis scales coordinates
  (github issue #4995 from sroughley)
• Bad handling of dummy atoms in the CIP assignment code
  (github issue #4996 from greglandrum)
• Bad handling of fragments in CIP code
  (github issue #4998 from greglandrum)
• Drawing query atoms containing an AND query raises an exception
  (github issue #5006 from ptosco)
• Bad tautomers produced for phosphorous compounds
  (github issue #5008 from NikSchap2107)
• Fix warning when generating coordinates for ZOBs
  (github pull #5011 from d-b-w)
• Code in the docstring for FindMolChiralCenters() doesn't work
  (github pull #5014 from greglandrum)
• Mol images in DataFrames are drawn only once in Jupyter Lab
  (github issue #5017 from mrcblt)
• Drop gist_qmol_ops in upgrade scripts in case it exists
  (github pull #5021 from mwojcikowski)
• Remove extra newline from Kekulize error message.
  (github pull #5022 from xavierholt)
• Neighboring Hs not taken into account in connectivity invariants
  (github issue #5036 from greglandrum)
• smiles parsing error due to erroneous ring perception
  (github issue #5055 from AnsgarSchuffenhauer)
• To INCHI conversion leaks on kekulization failure
  (github pull #5057 from ricrogz)
• Add a CXSMILES option to the MolHash
  (github pull #5058 from greglandrum)
• Make the RGD code work when rgroupLabelling is Isotope
  (github pull #5088 from greglandrum)
• Compilation issue with catch.hpp
  (github issue #5089 from hseara)
• pg_restore: ...

2021_09_5 (Q3 2021) Release

Release_2021.09.5

(Changes relative to Release_2021.09.4)

Acknowledgements

Kevin Burk, Niels Kristian Kjærgård Madsen, Dan Nealschneider, Steve Roughley,
Ricardo Rodriguez-Schmidt, Paolo Tosco, Kazuya Ujihara, Fabio Urbina, Riccardo
Vianello, Maciej Wójcikowski, yuri@FreeBSD

Bug Fixes:

• GetSimilarityMapFromWeights changes behavior of parameter "colorMap" depending on whether the parameter "draw2d" is provided or not
  (github #4763 from FabioUrbina)
• Missing dependency on RDKit::RingDecomposerLib_static in RDKit::GraphMol_static
  (github #4875 from nielskm)
• cannot parse coordinate bonds from CXSMARTS
  (github #4878 from greglandrum)
• update MD5 for the comicneue font
  (github #4885 from greglandrum)
• fix some leaks in the SWIG wrappers
  (github #4916 from greglandrum)
• Fix i-files for RDK_USE_BOOST_IOSTREAMS=OFF
  (github #4933 from kazuyaujihara)
• Fails on i386: non-constant-expression cannot be narrowed from type 'unsigned int' to 'npy_intp' (aka 'int') in initializer list
  (github #4934 from yurivict)
• Fix SWIG wrappers for C#
  (github #4935 from kazuyaujihara)
• fix CMakeLists.txt extracting link line from python LDSHARED config var
  (github #4954 from rvianello)
• add JavaGzStreamTests
  (github #4973 from kazuyaujihara)
• Invalid SMARTS generated by MolToSmarts
  (github #4981 from nielskm)
• Transform3D#SetRotation() around arbitrary axis scales coordinates
  (github #4995 from sroughley)
• Bad handling of dummy atoms in the CIP assignment code
  (github #4996 from greglandrum)
• Bad handling of fragments in CIP code
  (github #4998 from greglandrum)
• Drawing query atoms containing an AND query raises an exception
  (github #5006 from ptosco)
• Fix warning when generating coordinates for ZOBs
  (github #5011 from d-b-w)
• Code in the docstring for FindMolChiralCenters() doesn't work
  (github #5014 from greglandrum)
• Drop gist_qmol_ops in upgrade scripts in case it exists
  (github #5021 from mwojcikowski)
• Remove extra newline from Kekulize error message.
  (github #5022 from xavierholt)
• Neighboring Hs not taken into account in connectivity invariants
  (github #5036 from greglandrum)
• To INCHI conversion leaks on kekulization failure
  (github #5057 from ricrogz)

2021_09_4 (Q3 2021) Release

Release_2021.09.4

(Changes relative to Release_2021.09.3)

Acknowledgements

Kevin Burk, Gareth Jones, Toshiki Kataoka, Brian Kelley, Ricardo
Rodriguez-Schmidt, Paolo Tosco, Rachel Walker

Bug Fixes:

• Highlight bond width is different for different PNG image sizes
  (github #4764 from rachelnwalker)
• AdjustQueryProperties() is inconsistent when adjustConjugatedFiveRings is set
  (github #4789 from greglandrum)
• Draw.MolToFile to SVG raises "Can't kekulize" error
  (github #4792 from toslunar)
• Ring double bonds written as crossed bonds after RGD
  (github #4809 from greglandrum)
• Fix a number of crashing bugs in the python wrappers
  (github #4810 from greglandrum)
• correctly tag unspecified branch-begin bonds in SMARTS
  (github #4811 from greglandrum)
• AttributeError in PandasTools
  (github #4821 from greglandrum)
• reloading PandasTools leads to infinite recursion
  (github #4823 from greglandrum)
• ReplaceCore should set stereo on ring bonds when it breaks rings
  (github #4825 from greglandrum)
• MolDraw2D::drawArc() starts at wrong angle
  (github #4836 from greglandrum)
• MolDraw2D::drawArc() not exposed to Python
  (github #4837 from greglandrum)
• align argument to MolDraw2D::DrawString() cannot be used from Python
  (github #4838 from greglandrum)
• Fix RunFilterCatalog() thread counts.
  (github #4856 from xavierholt)
• RGD: dummy atom in input structure is mishandled
  (github #4863 from jones-gareth)
• Fix bug with wedges being drawn backwards
  (github #4868 from greglandrum)

2021_09_3 (Q3 2021) Release

Release_2021.09.3

(Changes relative to Release_2021.09.2)

Acknowledgements

Jacob Gora, Gareth Jones, Brian Kelley, Ricardo Rodriguez-Schmidt, Paolo Tosco,
Kazuya Ujihara, Riccardo Vianello

Bug Fixes:

• handle sqlalchemy deprecation
  (github #4625 from greglandrum)
• fix parsing beyond the end of the input string in findMCSsmiles
  (github #4636 from rvianello)
• Mem leak fixes
  (github #4637 from ricrogz)
• Subsequent call to rdChemReactions.ChemicalReaction.RunReactants will block indefinitely.
  (github #4651 from goraj)
• Fix docstring of ConstrainedEmbed
  (github #4666 from kazuyaujihara)
• [Operational] get windows CI builds working again
  (github #4672 from greglandrum)
• Molfile SDD records not properly displayed
  (github #4690 from jones-gareth)
• RGD: fix for cores with MOL block atom lists
  (github #4695 from jones-gareth)
• RGD align output core to input structure
  (github #4709 from jones-gareth)
• TorsionFingerprints raises error with S(Cl)F4 group
  (github #4720 from kazuyaujihara)
• TautomerEnumerator will crash if copied with a callback set
  (github #4736 from ptosco)
• Update mac CI builds
  (github #4738 from greglandrum)
• Minor PandasTools cleanup
  (github #4744 from ptosco)
• Reaction parser fails when CX extensions are present
  (github #4759 from greglandrum)
• Fixes crashing bug with finalSubstructChecks
  (github #4782 from greglandrum)
• [Cartridge]: qmol_from_ctab and qmol_from_smiles are sanitizing molecules
  (github #4787 from greglandrum)

2021_09_2 (Q3 2021) Release

This is a technical release to fix a version number problem in the 2021.09.1 release.
There are no substantive changes.