2023_09_1 (Q3 2023) Release Beta

[greglandrum]

Release_2023.09.1b1

(Changes relative to Release_2023.03.1)

Acknowledgements

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

Jason Biggs, Jonathan Bisson, David Cosgrove, Andrew Dalke, Christian W.
Feldmann, Eloy Félix, Richard Gowers, Tadd Hurst, Gareth Jones, Eisuke
Kawashima, Brian Kelley, Joos Kiener, Juuso Lehtivarjo, John Mayfield, Vedran
Miletić, Jeremy Monat, Dan Nealschneider, Timothy Ngotiaoco, Axel Pahl, Ricardo
Rodriguez-Schmidt, Ernst-Georg Schmid, Paolo Tosco, Ivan Tubert-Brohman,
Riccardo Vianello, Rachel Walker, Maciej Wójcikowski, pierred5, lhyuen,
paconius, BartlomiejF, thomp-j, wangyingxie, teltim, Meteor-han, abefrandsen,

Highlights

to be completed

Backwards incompatible changes

• The CDXML parser now returns mols with reasonable coordinates and in
  the same coordinate axes as the other RDKit file parsers.
• All methods returning JSMol and JSReaction objects now return a
  nullptr (null in JS) when faling to generate a valid object, while
  previously they were returning objects whose is_valid() method would
  return false. The new implementation avoids the overhead of having to
  call delete() on invalid objects and was approved in a
  public discussion on the rdkit-js GitHub repository
• In JS MinimalLib, MolIterator was renamed to MolList: since now it
  includes at(), append(), insert() and pop() methods, MolIterator
  felt inappropriate. This change should have minimal impact on existing
  JS code since so far there was no constructor for this class.
  The only place where JS code needs to be updated is when parsing the return
  value of JSMol::get_frags(): the return value consists of an object with
  two keys, molIterator and mappings. The molIterator key has now
  been renamed to molList.
• The user-configurable MCSParameters::FinalMatchChecker function is now
  called after the built-in FinalMatchChecker function, rather as
  alternatively to the built-in FinalMatchChecker function. This was a
  design flaw which is worth correcting.
• Setting MCSParameters::Timeout to 0 means no timeout, rather than 0s
  timeout, which is rather pointless as it would cause MCS to be canceled
  immediately.
• Result SMARTS strings generated by FindMCS when
  MCSParameters::MatchRingFusionStrict is true now include ring membership
  queries where appropriate in order to ensure more specific substructure
  matches.
• In MCS Verbose statistics, SingleBondExcluded was renamed to
  IndividualBondExcluded to avoid confusion, since single bond has a
  different meaning in chemistry.
• The error messages from failed type conversions in calls to GetProp() now
  differ slightly between compilers. Instead of always including "boost::bad_any
  cast", they now need to be matched with the regex [B,b]ad any[\ ,_]cast
• The functions for determining connectivity in DetermineBonds now use a more
  efficient method by default. To go back to the old behavior, set the useVdw argument
  to True.
• The algorithm for perception of atomic stereochemistry from 2D structures has
  been rewritten. The new algorithm is more accurate, which results in some
  differences in perceived stereo between this release and the previous ones.

New Features and Enhancements:

• Mols matrix to grid image
  (github pull Mols matrix to grid image #6080 from bertiewooster)
• Reduce space overhead of enabling the inclusion of properties when serializing molecules
  (github issue Reduce space overhead of enabling the inclusion of properties when serializing molecules #6312 from rvianello)
• Add optional sortsupport methods to the PostgreSQL GiST indices
  (github pull Add optional sortsupport methods to the PostgreSQL GiST indices #6313 from rvianello)
• Add a new parameter to mol_adjust_query_properties for generic query parameters
  (github pull Add a new parameter to mol_adjust_query_properties for generic query parameters #6332 from bjonnh-work)
• add DebugDraw() function
  (github pull add DebugDraw() function #6340 from greglandrum)
• Optimize GetPropsFromDict: use tags for conversion
  (github pull Optimize GetPropsFromDict: use tags for conversion #6355 from bp-kelley)
• Fix cleanupOrganometallics and reinstate to sanitisation
  (github pull Fix cleanupOrganometallics and reinstate to sanitisation #6357 from DavidACosgrove)
• postgres cartridge: cleanup a few obsolete build options
  (github pull postgres cartridge: cleanup a few obsolete build options #6363 from rvianello)
• Fixes some issues in the SubstructLibrary JS implementation
  (github pull Fixes some issues in the SubstructLibrary JS implementation #6385 from ptosco)
• Support TautomerQuery and MolBundle queries in the cartridge
  (github pull Support TautomerQuery and MolBundle queries in the cartridge #6393 from greglandrum)
• JS: Implement in-place aromatisation/kekulisation and avoid undesired exception
  (github pull JS: Implement in-place aromatisation/kekulisation and avoid undesired exception #6407 from ptosco)
• Optionally expose MCS to JS and extend optional compilation to JSReaction and JSSubstructLibrary
  (github pull Optionally expose MCS to JS and extend optional compilation to JSReaction and JSSubstructLibrary #6409 from ptosco)
• Add a method "HasQuery()" to Mol class
  (github issue Add a method "HasQuery()" to Mol class #6411 from kienerj)
• Enable using JSSubstructLibrary without pattern fps
  (github pull Enable using JSSubstructLibrary without pattern fps #6431 from ptosco)
• Add support for generalized substructure searching
  (github pull Add support for generalized substructure searching #6443 from greglandrum)
• Add atom and bond property parameters to substruct matching
  (github pull Add atom and bond property parameters to substruct matching #6453 from rachelnwalker)
• Replace a try..catch block with an if clause
  (github pull Replace a try..catch block with an if clause #6488 from ptosco)
• Add an in place version of most of the MolStandardize functionality
  (github pull Add an in place version of most of the MolStandardize functionality #6491 from greglandrum)
• Exposed partial sanitization options to MinimalLib (both JS and CFFI)
  (github pull Exposed partial sanitization options to MinimalLib (both JS and CFFI) #6519 from ptosco)
• Optionally forward Enhanced Stereo Group ids
  (github pull Optionally forward Enhanced Stereo Group ids #6560 from ricrogz)
• Add support for dative bonds in MOL files
  (github pull Add support for dative bonds in MOL files #6566 from bjonnh-work)
• RASCAL MCES
  (github pull RASCAL MCES #6568 from DavidACosgrove)
• Support additional generic groups
  (github pull Support additional generic groups #6570 from bjonnh-work)
• Add support for Marvin files
  (github pull Add support for Marvin files #6575 from bjonnh-work)
• Add a "rootedAtAtom" to MolToSmarts
  (github pull Add a "rootedAtAtom" to MolToSmarts #6581 from ricrogz)
• RGD to support tautomers of core
  (github issue RGD to support tautomers of core #6609 from jones-gareth)
• Fix some build warnings
  (github pull Fix some build warnings #6618 from ricrogz)
• Exposed log capture functionality to MinimalLib
  (github pull Exposed log capture functionality to MinimalLib #6628 from ptosco)
• add option to use sequential random seeds in the conformer generator
  (github pull add option to use sequential random seeds in the conformer generator #6639 from greglandrum)
• Major MCS refactoring: new features and bug fixes
  (github pull Major MCS refactoring: new features and bug fixes #6646 from ptosco)
• Lasso highlights
  (github pull Lasso highlights #6653 from DavidACosgrove)
• extract continuous lines from the conrec code
  (github pull extract continuous lines from the conrec code #6676 from greglandrum)
• Allow some tolerance in flatness determination
  (github pull Allow some tolerance in flatness determination #6696 from ricrogz)
• Do not trust the 2D/3D tag in ctab mol files
  (github pull Do not trust the 2D/3D tag in ctab mol files #6697 from ricrogz)
• expose the CDXML reaction parsers to python
  (github pull expose the CDXML reaction parsers to python #6700 from greglandrum)
• Add hasQueryHs
  (github pull Add hasQueryHs #6702 from bp-kelley)
• Use the connect-the-dots algorithm by default in DetermineBonds
  (github pull Use the connect-the-dots algorithm by default in DetermineBonds #6740 from greglandrum)
• Add SpacialScore
  (github pull Add SpacialScore #6742 from apahl)
• Extract the core matching logic into a separate function
  (github pull Extract the core matching logic into a separate function #6754 from ptosco)

Bug Fixes:

• rdFMCS.FindMCS uses huge amounts of memory for this pair of molecules when CompleteRingsOnly is True
  (github issue rdFMCS.FindMCS uses huge amounts of memory for this pair of molecules when CompleteRingsOnly is True #3965 from i-tub)
• PF6- still can not get Bad Conformer Id after the Hexafluorophosphate cannot be handled #510 issue fix
  (github issue PF6- still can not get Bad Conformer Id after the #510 issue fix  #5145 from wangyingxie)
• Order dependence for rdFMCS.FindMCS with MatchFusedRingsStrict
  (github issue Order dependence for rdFMCS.FindMCS with MatchFusedRingsStrict #5411 from pierred5)
• Failed FMCS results with certain seed SMARTS and MatchFusedRings* parameters on
  (github issue Failed FMCS results with certain seed SMARTS and MatchFusedRings* parameters on #5440 from pierred5)
• Seed SMARTS to FindMCS() produces incorrect MCS
  (github issue Seed SMARTS to FindMCS() produces incorrect MCS #5457 from pierred5)
• FindMCS returns wrong result with monoatomic molecules
  (github issue FindMCS returns wrong result with monoatomic molecules #5510 from ptosco)
• queryMol from FindMCS doesn't match mols used to generate MCS
  (github issue queryMol from FindMCS doesn't match mols used to generate MCS #6082 from paconius)
• Crash when parsing InChI
  (github issue Crash when parsing InChI #6172 from eloyfelix)
• Iteration over Python GetAtoms is 10-20x slower than need be
  (github issue Iteration over Python GetAtoms is 10-20x slower than need be #6208 from d-b-w)
• refactor(python): replace deprecated unittest methods
  (github pull refactor(python): replace deprecated unittest methods #6304 from e-kwsm)
• generateDepictionMatching2DStructure: bonds to R groups should be generic when matching
  (github pull generateDepictionMatching2DStructure: bonds to R groups should be generic when matching #6306 from ptosco)
• MolToSmiles(canonical=False) creates the wrong _smilesBondOutputOrder property
  (github issue MolToSmiles(canonical=False) creates the wrong _smilesBondOutputOrder property #6315 from adalke)
• MolToMolBlock ignores unspecified information for double bonds in rings
  (github issue MolToMolBlock ignores unspecified information for double bonds in rings #6316 from mwojcikowski)
• bump yaehmop version
  (github pull bump yaehmop version #6330 from greglandrum)
• rdMolDraw2D.MolDraw2DCairo produces Pre-condition Violation: no draw context when SetColour, DrawRect or DrawLine was called.
  (github issue rdMolDraw2D.MolDraw2DCairo produces Pre-condition Violation: no draw context when SetColour, DrawRect or DrawLine was called. #6336 from lhyuen)
• Added cstdint include
  (github pull Added cstdint include #6338 from vedranmiletic)
• remove the dependency from python distutils in the top CMakeLists.txt file
  (github pull remove the dependency from python distutils in the top CMakeLists.txt file #6339 from rvianello)
• take drawOptions into account when exporting structure to xlsx format
  (github pull take drawOptions into account when exporting structure to xlsx format #6341 from ptosco)
• Fix swig memory leak
  (github pull Fix swig memory leak #6346 from jones-gareth)
• Add inlines to ForceFieldHelpers header functions
  (github pull Add inlines to ForceFieldHelpers header functions #6356 from JLVarjo)
• Bug relating to this PF6- still can not get Bad Conformer Id
  (github issue Bug relating to this PF6- still can not get Bad Conformer Id #6365 from teltim)
• straightenDepiction should not consider 0-degree rotations as multiples of 60
  (github pull straightenDepiction should not consider 0-degree rotations as multiples of 60 #6367 from ptosco)
• expose two missing EmbedFailureCauses tags to python
  (github pull expose two missing EmbedFailureCauses tags to python #6372 from greglandrum)
• Molfile Unsaturation Query Not Parsed Correctly
  (github issue Molfile Unsaturation Query Not Parsed Correctly #6395 from timothyngo)
• MolDraw2D: chiral tag overlapping atom label
  (github issue MolDraw2D: chiral tag overlapping atom label #6397 from greglandrum)
• MolDraw2D: increasing padding results in the legend not being displayed
  (github issue MolDraw2D: increasing padding results in the legend not being displayed #6400 from greglandrum)
• expose some missing CXSmiles flags to python
  (github pull expose some missing CXSmiles flags to python #6415 from greglandrum)
• V3000 structure segfaults when converting to SVG
  (github issue V3000 structure segfaults when converting to SVG #6416 from ergo70)
• WedgeMolBonds won't wedge/dash a 2nd bond when input already has a wedge/dash around the same chiral atom
  (github issue WedgeMolBonds won't wedge/dash a 2nd bond when input already has a wedge/dash around the same chiral atom #6423 from ricrogz)
• MolEnumerate should clear the reaction properties on its results
  (github issue MolEnumerate should clear the reaction properties on its results #6432 from greglandrum)
• RDKit hangs indefinitely when parsing not so big molblock
  (github issue RDKit hangs indefinitely when parsing not so big molblock #6434 from eloyfelix)
• Removing Hs on a pyrrol-like structure throws kekulization error
  (github issue Removing Hs on a pyrrol-like structure throws kekulization error #6437 from ricrogz)
• Molecules from CDXML Parser have inverted, unrealistic atomic coordinates
  (github issue Molecules from CDXML Parser have inverted, unrealistic atomic coordinates #6461 from greglandrum)
• CDXML Parser does not preserve information about bond wedging
  (github issue CDXML Parser does not preserve information about bond wedging #6462 from greglandrum)
• boost::bad_any_cast error when calling getProp on properties set by applyMolListPropsToAtoms<int64_t>
  (github issue boost::bad_any_cast error when calling getProp<string> on properties set by applyMolListPropsToAtoms<int64_t> #6465 from rachelnwalker)
• Allow systems like C/C=N/[H] to be stereogenic with the new chirality code
  (github pull Allow systems like C/C=N/[H] to be stereogenic with the new chirality code #6473 from greglandrum)
• Fix RWMol::addAtom docstring
  (github pull Fix RWMol::addAtom docstring #6477 from d-b-w)
• Fix a few broken docstrings
  (github pull Fix a few broken docstrings #6480 from ptosco)
• pin numpy to 1.24.3
  (github pull pin numpy to 1.24.3 #6483 from bp-kelley)
• CMAKE_INSTALL_PREFIX not honored for Python files installation on Windows
  (github pull CMAKE_INSTALL_PREFIX not honored for Python files installation on Windows #6485 from ricrogz)
• Fixed tests that weren't being run in testDepictor.py
  (github pull Fixed tests that weren't being run in testDepictor.py #6486 from rachelnwalker)
• Get tests to work when building without exception support (i.e., legacy pure JS library)
  (github pull Get tests to work when building without exception support (i.e., legacy pure JS library) #6487 from ptosco)
• Fixes rdkit-js/issues/347
  (github pull Fixes rdkit-js/issues/347 #6490 from ptosco)
• Make sure that molecules are shown as images by PandasTools also when DataFrames are truncated horizontally
  (github pull Make sure that molecules are shown as images by PandasTools also when DataFrames are truncated horizontally #6496 from ptosco)
• MolToMolBlock writes "either" stereo for double bonds which shouldn't be stereo
  (github issue MolToMolBlock writes "either" stereo for double bonds which shouldn't be stereo #6502 from ricrogz)
• Double bonds are not correctly drawn on sulfoximines
  (github issue Double bonds are not correctly drawn on sulfoximines #6504 from ptosco)
• RegistrationHash.GetMolLayers() with v2 tautomer hash does not filter CX extensions
  (github issue RegistrationHash.GetMolLayers() with v2 tautomer hash does not filter CX extensions #6505 from ricrogz)
• Drop the s_m_color_rgb property from MaeWriter
  (github pull Drop the s_m_color_rgb property from MaeWriter #6511 from ricrogz)
• update avalontools version to incorporate bug fixes
  (github pull update avalontools version to incorporate bug fixes #6513 from ptosco)
• update windows DLL CI build config
  (github pull update windows DLL CI build config #6535 from greglandrum)
• Add MolEnumerator to C#
  (github pull Add MolEnumerator to C# #6542 from jones-gareth)
• MolDraw2D: placement of bond or atom labels gets confused when atoms overlap
  (github issue MolDraw2D: placement of bond or atom labels gets confused when atoms overlap #6569 from greglandrum)
• partial MCS failure
  (github issue partial MCS failure #6578 from greglandrum)
• Fix vulnerabilities found by fuzzer.
  (github pull Fix vulnerabilities found by fuzzer. #6579 from thomp-j)
• allow building the cartridge against PostgreSQL 16
  (github pull allow building the cartridge against PostgreSQL 16 #6580 from ptosco)
• SIGSEGV while calculating molecular descriptors after using salt remover.
  (github issue SIGSEGV while calculating molecular descriptors after using salt remover. #6592 from BartlomiejF)
• Add newline to ConstrainedEmbed docstring.
  (github pull Add newline to ConstrainedEmbed docstring. #6596 from DavidACosgrove)
• Avoid leaking memory in case exceptions are thrown while generating FPs
  (github pull Avoid leaking memory in case exceptions are thrown while generating FPs #6630 from ptosco)
• Pre-condition violation in canonicalization of dative bond adjacent to double bond
  (github issue Pre-condition violation in canonicalization of dative bond adjacent to double bond #6633 from ricrogz)
• Incorrect most abundant isotope for Vanadium
  (github issue Incorrect most abundant isotope for Vanadium #6638 from abefrandsen)
• Simple imine-containing molecule causes an infinite loop in FindStereo.cpp
  (github issue Simple imine-containing molecule causes an infinite loop in FindStereo.cpp #6640 from ptosco)
• Mol file parser strips stereogenic H from imine bonds
  (github issue Mol file parser strips stereogenic H from imine bonds #6664 from ricrogz)
• ROMol move constructor and assignment do not update SubstanceGroup ownership
  (github issue ROMol move constructor and assignment do not update SubstanceGroup ownership #6681 from ricrogz)
• Flexicanvas cuts off bottom of reaction
  (github issue Flexicanvas cuts off bottom of reaction #6685 from DavidACosgrove)
• make sure bond attachpt info is pickled
  (github pull make sure bond attachpt info is pickled #6698 from greglandrum)
• Catch meanBondLen of 0.0
  (github pull Catch meanBondLen of 0.0 #6699 from DavidACosgrove)
• Add trans layout for double bonds in rings
  (github pull Add trans layout for double bonds in rings #6709 from d-b-w)
• Segmentation fault in MMFF
  (github issue Segmentation fault in MMFF #6728 from Meteor-han)
• Fix chirality handling when the chiral atom is the first one in a SMARTS
  (github pull Fix chirality handling when the chiral atom is the first one in a SMARTS #6730 from johnmay)
• ConnectTheDots can segfault if all atoms do not have residue info
  (github issue ConnectTheDots can segfault if all atoms do not have residue info #6756 from jasondbiggs)

Cleanup work:

• adjustQueryProperties cleanup
  (github pull adjustQueryProperties cleanup #6361 from ptosco)
• Fix identical for-loop variable names
  (github pull Fix identical for-loop variable names #6391 from JLVarjo)
• Deprecate JSMol::is_valid() and JSReaction::is_valid() and return nullptr instead
  (github pull Deprecate JSMol::is_valid() and JSReaction::is_valid() and return nullptr instead #6392 from ptosco)
• misc jswrapper.cpp cleanup
  (github pull misc jswrapper.cpp cleanup #6449 from ptosco)
• Deprecate the pure python MolStandardize implementations.
  (github pull Deprecate the pure python MolStandardize implementations. #6548 from greglandrum)
• clear up some compiler warnings
  (github pull clear up some compiler warnings #6627 from greglandrum)
• switch from boost::any to std::any
  (github pull switch from boost::any to std::any #6662 from greglandrum)
• Fail CI builds on compiler warnings + some fixes
  (github pull Fail CI builds on compiler warnings + some fixes #6675 from ricrogz)
• fix some more leaks
  (github pull fix some more leaks #6684 from ricrogz)
• Some small cleanups from the UGM Hackathon
  (github pull Some small cleanups from the UGM Hackathon #6744 from greglandrum)
• some modernization of the memory handing in the canonicalization code
  (github pull some modernization of the memory handing in the canonicalization code #6763 from greglandrum)

Code removed in this release:

• The compare and callback methods (deprecated since release 2021.01)
  were removed from the MCSProgress, MCSBondCompare and MCSAtomCompare
  Python classes of the rdFMCS module. Both compare and callback methods
  were replaced by __call__.
• The SetAtomTyper and SetBondTyper methods (deprecated since release 2021.01)
  were removed from the MCSParameters Python class of the rdFMCS module.
  The methods were replace by read-write properties AtomTyper and BondTyper,
  respectively.

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

• JSMol::is_valid() and JSReaction::is_valid() are now deprecated and always
  return true, as invalid JSMol and JSReaction cannot exist anymore.
• The python implementations of MolStandardize will be removed in the next release.
  Please use the implementation in rdkit.Chem.MolStandardize.rdMolStandardize instead.

---

This discussion was created from the release 2023_09_1 (Q3 2023) Release Beta.