2022_09_1b1 (Q3 2022) Release

[greglandrum]

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 H atoms in SGroups cause RDKit to clear SGroups after parsing #2716 from ricrogz)
• RDKit misplaces stereochemistry/chirality information for small ring
  (github issue RDKit misplaces stereochemistry/chirality information for small ring #2984 from d-b-w)
• DrawMorganBit returns empty image for "isolated" fingerprints
  (github issue DrawMorganBit returns empty image for "isolated" fingerprints #4242 from eguidotti)
• Unable to serialize coordinates as floats in combination with *Props
  (github issue Unable to serialize coordinates as floats in combination with *Props #4621 from santeripuranen)
• Image Generation: Highlighting looks off when bondLineWidth is increased for PNG generation
  (github issue Image Generation: Highlighting looks off when bondLineWidth is increased for PNG generation #5122 from rachelnwalker)
• RDKit crashes on CIP label calculation
  (github issue RDKit crashes on CIP label calculation #5142 from ricrogz)
• Modified the JS tests to comply with older nodejs versions
  (github pull Modified the JS tests to comply with older nodejs versions #5148 from ptosco)
• Presence of exocyclic S/D, S/A or D/A query bonds prevents benzene from being recognized as aromatic
  (github issue Presence of exocyclic S/D, S/A or D/A query bonds prevents benzene from being recognized as aromatic #5152 from rachelnwalker)
• Fix for RGD dummy atom bug in RDKit::replaceCore
  (github pull Fix for RGD dummy atom bug in RDKit::replaceCore #5154 from jones-gareth)
• KekulizeException of molecule from Smarts pattern with new RDKit release
  (github issue KekulizeException of molecule from Smarts pattern with new RDKit release  #5156 from schallerdavid)
• Very small fix to avoid an AttributeError
  (github pull Very small fix to avoid an AttributeError #5163 from ptosco)
• issue with V3000 SD files containing enhanced stereochemistry information
  (github issue issue with V3000 SD files containing enhanced stereochemistry information #5165 from GLPG-GT)
• Draw.MolToQPixmap raises a TypeError with Python 3.10
  (github issue Draw.MolToQPixmap raises a TypeError with Python 3.10 #5166 from ales-erjavec)
• Standardization via RDKit breaks molecules
  (github issue Standardization via RDKit breaks molecules #5169 from malteseunderdog)
• Multiple calls to BlockLogs() permanently disable logging
  (github issue Multiple calls to BlockLogs() permanently disable logging #5172 from ricrogz)
• Check architecture of the target system to optimise popcnt
  (github pull Check architecture of the target system to optimise popcnt #5182 from giordano)
• More consistently check for WIN32 instead of MSVC in CMake files
  (github pull More consistently check for WIN32 instead of MSVC in CMake files #5183 from giordano)
• Atom indices inside double bond
  (github issue Atom indices inside double bond #5185 from DavidACosgrove)
• Bug in IPython display after setting a molecule property
  (github issue Bug in IPython display after setting a molecule property #5192 from dwhswenson)
• Zero & coordinate bonds are being taken into account for chirality
  (github issue Zero & coordinate bonds are being taken into account for chirality #5196 from ricrogz)
• FindPotentialStereo does not clean stereoflags from atoms which cannot be stereocenters
  (github issue FindPotentialStereo does not clean stereoflags from atoms which cannot be stereocenters #5200 from greglandrum)
• Fixes array overflow in FMCS code
  (github pull Fixes array overflow in FMCS code #5205 from ricrogz)
• PeriodicTable initialization is not thread safe
  (github issue PeriodicTable initialization is not thread safe #5207 from ricrogz)
• Find and remove deprecated ifdefs
  (github issue Find and remove deprecated ifdefs #5210 from greglandrum)
• Fix use of not thread safe function localtime()
  (github pull Fix use of not thread safe function localtime()  #5211 from ricrogz)
• Fix duplicate non thread safe check in VarianceDataForLabel
  (github pull Fix duplicate non thread safe check in VarianceDataForLabel #5212 from ricrogz)
• RDKit::Utils::LocaleSwitcher is not thread safe
  (github issue RDKit::Utils::LocaleSwitcher is not thread safe #5214 from ricrogz)
• Core with query atoms and no user definded attachment points may create poor decompostions
  (github issue Core with query atoms and no user definded attachment points may create poor decompostions #5222 from jones-gareth)
• error: format not a string literal and no format arguments
  (github issue error: format not a string literal and no format arguments #5234 from sagitter)
• Fix qt build under VS2019
  (github pull Fix qt build under VS2019 #5238 from ricrogz)
• Precondition violation on chiral Atoms with zero order bonds
  (github issue Precondition violation on chiral Atoms with zero order bonds #5239 from ricrogz)
• pyForceFieldConstraints test failed
  (github issue pyForceFieldConstraints test failed #5252 from sagitter)
• drawReaction() should not hit a PRECONDITION with prepareMolsBeforeDrawing=false
  (github issue drawReaction() should not hit a PRECONDITION with prepareMolsBeforeDrawing=false #5259 from ptosco)
• Atom annotations poorly placed on highlighted atoms
  (github issue Atom annotations poorly placed on highlighted atoms #5269 from DavidACosgrove)
• Make the aliphatic imine rule more closely match the definition in the paper
  (github pull Make the aliphatic imine rule more closely match the definition in the paper #5270 from greglandrum)
• rdMolDraw2D.PrepareMolForDrawing(None) causes segmentation fault
  (github issue rdMolDraw2D.PrepareMolForDrawing(None) causes segmentation fault #5298 from perjo)
• MolStandardize: uncharger failing in molecules with zwitterionic sulfone
  (github issue MolStandardize: uncharger failing in molecules with zwitterionic sulfone #5317 from greglandrum)
• MolStandardize: some operations throwing on non-standardized molecules
  (github issue MolStandardize: some operations throwing on non-standardized molecules #5318 from greglandrum)
• MolStandardize: cleanup() function not correctly reassigning stereochemistry
  (github issue MolStandardize: cleanup() function not correctly reassigning stereochemistry #5320 from greglandrum)
• Runtime error when writing reaction with substance group to V3000 rxnblock
  (github issue Runtime error when writing reaction with substance group to V3000 rxnblock #5324 from rachelnwalker)
• MolFromMolBlock should correctly assign stereochemistry to 3D molecules
  (github issue MolFromMolBlock should correctly assign stereochemistry to 3D molecules #5327 from greglandrum)
• assignChiralTypesFrom3D() ignores wiggly bonds
  (github issue assignChiralTypesFrom3D() ignores wiggly bonds #5328 from greglandrum)
• Molzip segfaults instead of throwing an error when multiple bonds are formed to the same pairs of atoms
  (github issue Molzip segfaults instead of throwing an error when multiple bonds are formed to the same pairs of atoms #5334 from loluwot)
• leftover debugging code makes build of 2022_03_3 tarball fail
  (github issue leftover debugging code makes build of 2022_03_3 tarball fail #5351 from balducci)
• Prevent wedging ring bonds
  (github pull Prevent wedging ring bonds #5356 from greglandrum)
• Class info info missing for for wavy bonds in SVGs.
  (github pull Class info info missing for for wavy bonds in SVGs. #5358 from DavidACosgrove)
• MolToSmiles with doRandom=True raises errors with molecules containing fragments.
  (github issue MolToSmiles with doRandom=True raises errors with molecules containing fragments. #5372 from greglandrum)
• Restore Fixes #5017 #5103 that was accidentally reverted in Enables rdkit-structure-renderer.js in Jupyter Lab and Notebook #5132
  (github pull Restore #5103 that was accidentally reverted in #5132 #5381 from ptosco)
• cairo error when using similarity maps
  (github issue cairo error when using similarity maps #5383 from greglandrum)
• MolDraw2DQt and MolDraw2DJS don't draw wavy bonds
  (github issue MolDraw2DQt and MolDraw2DJS don't draw wavy bonds #5386 from greglandrum)
• MolDraw2DQt draws brackets incorrectly
  (github issue MolDraw2DQt draws brackets incorrectly #5389 from greglandrum)
• PandasTools should not always bring in IPythonConsole
  (github pull PandasTools should not always bring in IPythonConsole #5392 from greglandrum)
• Tautomer enumeration removes stereochemistry depending on how aromatic rings are defined in SMILES
  (github issue Tautomer enumeration removes stereochemistry depending on how aromatic rings are defined in SMILES #5402 from greglandrum)
• Incorrect perception of pseudoasymmetric centers on non-canonical molecules
  (github issue Incorrect perception of pseudoasymmetric centers on non-canonical molecules #5403 from ptosco)
• Fix performance issue in RingUtils::checkFused
  (github pull Fix performance issue in RingUtils::checkFused #5410 from rachelnwalker)
• Multi-coloured highlights go wrong with small fonts
  (github issue Multi-coloured highlights go wrong with small fonts #5420 from DavidACosgrove)
• Parsing a Mol block/file does not clear the "molTotValence" property from atoms
  (github issue Parsing a Mol block/file does not clear the "molTotValence" property from atoms #5423 from ricrogz)
• Pre-condition Violation - Failed Expression: dir == Bond::ENDUPRIGHT || dir == Bond::ENDDOWNRIGHT
  (github issue Pre-condition Violation - Failed Expression: dir == Bond::ENDUPRIGHT || dir == Bond::ENDDOWNRIGHT #5433 from bjonnh-work)
• MolZip doesn't preserve bond directions when zipping
  (github issue MolZip doesn't preserve bond directions when zipping #5450 from bp-kelley)
• Draw option noAtomLabels and explicit hydrogen works badly
  (github issue Draw option noAtomLabels and explicit hydrogen works badly #5453 from DavidACosgrove)
• Fix integer overflow in RGroupDecomposition strategy GA
  (github pull Fix integer overflow in RGroupDecomposition strategy GA #5460 from bp-kelley)
• Invalid number of radical electrons calculated for [Pr+4]
  (github issue Invalid number of radical electrons calculated for [Pr+4] #5462 from bjonnh-work)
• CXSmiles isn't properly escaping floating point properties
  (github issue CXSmiles isn't properly escaping floating point properties #5466 from bp-kelley)
• Crossed trans bonds in rings
  (github issue Crossed trans bonds in rings #5486 from DavidACosgrove)
• MolDraw2D::drawMolecules() should not crash on null molecules
  (github pull MolDraw2D::drawMolecules() should not crash on null molecules #5503 from ptosco)
• Running kekulization on mols with query bonds will either fail or return incorrect results.
  (github issue Running kekulization on mols with query bonds will either fail or return incorrect results. #5505 from ricrogz)
• Regression in the way aldehydes are drawn in current master
  (github issue Regression in the way aldehydes are drawn in current master #5511 from ptosco)
• Drawing code gives segmentation fault.
  (github issue Drawing code gives segmentation fault. #5534 from DavidACosgrove)
• RGD may yield poor depictions
  (github issue RGD may yield poor depictions #5569 from jones-gareth)
• Fix a problem when generating conformers for molecules with larger heteroatoms in conjugated 5-rings
  (github pull Fix a problem when generating conformers for molecules with larger heteroatoms in conjugated 5-rings #5586 from greglandrum)
• Avoid incurring into division by zero in normalizeDepiction
  (github pull Avoid incurring into division by zero in normalizeDepiction #5619 from ptosco)
• Allow properties to be displayed in jupyter when 3D rendering is enabled
  (github pull Allow properties to be displayed in jupyter when 3D rendering is enabled #5624 from greglandrum)

Cleanup work:

• update release notes, do deprecations
  (github pull update release notes, do deprecations #5161 from greglandrum)
• Fix typo: quarternary --> quaternary
  (github pull Fix typo: quarternary --> quaternary #5243 from guyrosin)
• fix doxygen comments
  (github pull fix doxygen comments #5254 from e-kwsm)
• make the catch tests build faster
  (github pull make the catch tests build faster #5284 from greglandrum)
• make the logging tests more robust
  (github pull make the logging tests more robust #5312 from greglandrum)
• Update docs for ReplaceSubstructs
  (github pull Update docs for ReplaceSubstructs #5343 from i-tub)
• Minimallib NPM release fixes - wrong node bin command in Dockerfile and prepublish npm script command replacement
  (github pull Minimallib NPM release fixes - wrong node bin command in Dockerfile and prepublish npm script command replacement #5349 from MichelML)
• Update code formatting in GettingStartedInPython.rst
  (github pull Update code formatting in GettingStartedInPython.rst #5350 from gedeck)
• fix: rdkit.Chem.rdDistGeom.EmbedMultipleConfs docstring indentation
  (github pull fix: rdkit.Chem.rdDistGeom.EmbedMultipleConfs docstring indentation #5404 from jvansan)
• Remove obsolete files related to rdkit-js + write a rescoped README for MinimalLib
  (github pull Remove obsolete files related to rdkit-js + write a rescoped README for MinimalLib #5432 from MichelML)
• Fixes "DeprecationWarning: invalid escape sequence \C" when importing EnumerateStereoisomers
  (github pull Fixes "DeprecationWarning: invalid escape sequence \C" when importing EnumerateStereoisomers #5478 from ricrogz)
• Fix double to float downcasting warning
  (github pull Fix double to float downcasting warning #5479 from ricrogz)
• Remove spurious doxygen tag
  (github pull Remove spurious doxygen tag #5488 from ptosco)
• Add deprecation warning to docstring.
  (github pull Add deprecation warning to docstring. #5498 from DavidACosgrove)
• Remove unnecessary compiler flags that would be ignored anyway
  (github pull Remove unnecessary compiler flags that would be ignored anyway #5587 from ptosco)
• Update AvalonTools to version 2.0.1
  (github pull Update AvalonTools to version 2.0.1 #5591 from ptosco)

New Features and Enhancements:

• Initial support for non-tetrahedral stereochemistry
  (github pull Initial support for non-tetrahedral stereochemistry #5084 from greglandrum)
• Move to C++17
  (github pull Move to C++17 #5155 from greglandrum)
• Add multi-template isMoleculeXOfReaction overloads
  (github pull Add multi-template isMoleculeXOfReaction overloads #5171 from AlanKerstjens)
• Add support for Qt6
  (github pull Add support for Qt6 #5203 from ricrogz)
• Make atom, bond iterators usable in STL algorithms
  (github pull Make atom, bond iterators usable in STL algorithms #5204 from ricrogz)
• Make TautomerQuery serializable
  (github pull Make TautomerQuery serializable #5248 from greglandrum)
• add boost::serialization support to ROMol
  (github pull add boost::serialization support to ROMol #5249 from greglandrum)
• Add support for Pol and Mod pseudoatoms
  (github pull Add support for Pol and Mod pseudoatoms #5264 from greglandrum)
• Allow the compiler to generate default ChemicalReaction copy assignment operator
  (github pull Allow the compiler to generate default ChemicalReaction copy assignment operator #5265 from AlanKerstjens)
• cdxml parser
  (github pull cdxml parser #5273 from bp-kelley)
• Expose reaction drawing and additional FPs in MinimalLib
  (github pull Expose reaction drawing and additional FPs in MinimalLib #5277 from ptosco)
• Expose mappings of atom/bond indices abbreviated mol->original mol
  (github pull Expose mappings of atom/bond indices abbreviated mol->original mol #5300 from ptosco)
• Start using string_views in the file parsers
  (github pull Start using string_views in the file parsers #5301 from greglandrum)
• Add a global feature flag to enable the "new" stereo perception code
  (github pull Add a global feature flag to enable the "new" stereo perception code #5309 from greglandrum)
• Support conjugated terminal groups in GetBestRMS()
  (github pull Support conjugated terminal groups in GetBestRMS() #5322 from greglandrum)
• Open sources Schrodinger's implementation of "molhash"
  (github pull Open sources Schrodinger's implementation of "molhash" #5360 from d-b-w)
• Drop usage of CIP information from the canonicalization code
  (github pull Drop usage of CIP information from the canonicalization code #5385 from greglandrum)
• GetSSSR should have same return type as GetSymmSSSR
  (github issue GetSSSR should have same return type as GetSymmSSSR #5395 from chmnk)
• Add prop related method into JSMol
  (github pull Add prop related method into JSMol #5414 from hhk7734)
• Add draw option to force use of wedge information in MolBlock if pres…
  (github pull Add draw option to force use of wedge information in MolBlock if pres… #5417 from DavidACosgrove)
• Add ACS1996 drawing style
  (github pull Add ACS1996 drawing style #5425 from DavidACosgrove)
• Treat unspecified stereo as unknown
  (github issue Treat unspecified stereo as unknown #5436 from DavidACosgrove)
• New version of AssignStereochemistry
  (github pull New version of AssignStereochemistry #5442 from greglandrum)
• MolZip: add atom property labels for mol-zipping
  (github pull MolZip: add atom property labels for mol-zipping #5446 from bp-kelley)
• Add atom property (int/unsigned int) to indicate which atoms to MolZip
  (github issue Add atom property (int/unsigned int) to indicate which atoms to MolZip #5451 from bp-kelley)
• Improved bond highlights
  (github pull Improved bond highlights #5484 from DavidACosgrove)
• Include element name in atomic data
  (github pull Include element name in atomic data #5524 from rachelnwalker)
• Add Substance Groups and Stereo Groups to debugMol()
  (github pull Add Substance Groups and Stereo Groups to debugMol() #5526 from ricrogz)
• make it easy to create DAT SGroups from Python
  (github pull make it easy to create DAT SGroups from Python #5544 from greglandrum)
• Integrating xyz2mol Into The RDKit Core (GSoC 2022)
  (github pull Integrating xyz2mol Into The RDKit Core (GSoC 2022) #5557 from gosreya)
• Switch yaehmop wrapper to basic cmake
  (github pull Switch yaehmop wrapper to basic cmake #5558 from greglandrum)
• fix warnings ahead of 2022.09 release
  (github pull fix warnings ahead of 2022.09 release #5561 from ricrogz)
• add mergeIsotopes option to mergeQueryHs
  (github pull add mergeIsotopes option to mergeQueryHs #5563 from jones-gareth)
• Add CXSMILES support for bond wedging and wiggly bonds
  (github pull Add CXSMILES support for bond wedging and wiggly bonds #5575 from greglandrum)
• Add GetBestTFDBetweenMolecules()
  (github pull Add GetBestTFDBetweenMolecules() #5577 from greglandrum)
• Add ColorPalette_Vect to SWIG bindings
  (github pull Add ColorPalette_Vect to SWIG bindings #5580 from jones-gareth)
• small changes to get the RDKit to build with C++20
  (github pull small changes to get the RDKit to build with C++20 #5581 from greglandrum)
• Improvements to 2D depiction and alignment/RMSD calculation
  (github pull Improvements to 2D depiction and alignment/RMSD calculation #5598 from ptosco)
• Expose additional functionality to SWIG wrappers
  (github pull Expose additional functionality to SWIG wrappers #5614 from ptosco)
• Add an RGroupDecomp aware molzip to the FreeWilson Contribution
  (github pull Add an RGroupDecomp aware molzip to the FreeWilson Contribution #5615 from bp-kelley)
• PandasTools and InteractiveRenderer improvements
  (github pull PandasTools and InteractiveRenderer improvements #5628 from ptosco)
• Add updateMolDrawOptionsFromJSON()
  (github pull Add updateMolDrawOptionsFromJSON() #5630 from ptosco)

Code removed in this release:

• The C++ class RDLog::BlockLogs has been removed. Please use the class RDLog::LogStateSetter. The Python class rdBase.BlockLogs() is still available and supported.
• Python function rdkit.Chem.WrapLogs() has been removed. Please use
  rdkit.rdBase.LogToPythonStderr(). rdkit.rdBase.WrapLogs() also exists, but
  unless you need the old teeing behavior, prefer the former.
• Python function rdkit.Chem.LogWarningMsg() has been removed. Please use
  rdkit.rdBase.LogWarningMsg().
• Python function rdkit.Chem.LogErrorMsg() has been removed. Please use
  rdkit.rdBase.LogErrorMsg().

Deprecated code (to be removed in a future release):

• The SmilesParserParams option useLegacyStereo is deprecated and will be
  removed in the 2023.03 release. Please use SetUseLegacyStereoPerception()
  instead. In the meantime the SMILES parser will use only use the value of
  SmilesParserParams.useLegacyStereo if it is set to false, otherwise the
  value of the global useLegacyStereoPerception parameter will control the
  behavior of the SMILES parser.
• The following JS methods:
  • generate_aligned_coords()
  • get_morgan_fp()
  • get_morgan_fp_as_uint8array()
  • get_pattern_fp()
  • get_pattern_fp_as_uint8array()
    which used to take several individual parameters now take a single JSON string parameter.
    The overloads taking several individual parameters are now deprecated and will be
    removed in a future release.
• The PrintAsBase64PNGString function in PandasTools is deprecated and replaced
  by PrintAsImageString, which has a more appropriate name given it actually supports
  both PNG and SVG images.

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This discussion was created from the release 2022_09_1b1 (Q3 2022) Release.