2023_09_1 (Q3 2023) Release

Release_2023.09.1

(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, Rachael
Pirie, 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

• The new RascalMCES code adds a very fast maximum common substructure
  implementation for pairs of molecules.
• The RDKit core now supports "generalized substructure searching", making it
  easier to take link nodes, variable attachment points, and tautomer queries
  into account when doing substructure searches. This is now also supported in
  the PostgreSQL cartridge.
• The RDKit now has support for reading and writing MRV files.

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.
• Information about stereo groups is no longer used in the SMILES
  canonicalization process if CXSMILES are not being generated.

New Features and Enhancements:

• Mols matrix to grid image
  (github pull #6080 from bertiewooster)
• Reduce space overhead of enabling the inclusion of properties when serializing molecules
  (github issue #6312 from rvianello)
• Add optional sortsupport methods to the PostgreSQL GiST indices
  (github pull #6313 from rvianello)
• Add a new parameter to mol_adjust_query_properties for generic query parameters
  (github pull #6332 from bjonnh-work)
• add DebugDraw() function
  (github pull #6340 from greglandrum)
• Optimize GetPropsFromDict: use tags for conversion
  (github pull #6355 from bp-kelley)
• Fix cleanupOrganometallics and reinstate to sanitisation
  (github pull #6357 from DavidACosgrove)
• postgres cartridge: cleanup a few obsolete build options
  (github pull #6363 from rvianello)
• Fixes some issues in the SubstructLibrary JS implementation
  (github pull #6385 from ptosco)
• Support TautomerQuery and MolBundle queries in the cartridge
  (github pull #6393 from greglandrum)
• JS: Implement in-place aromatisation/kekulisation and avoid undesired exception
  (github pull #6407 from ptosco)
• Optionally expose MCS to JS and extend optional compilation to JSReaction and JSSubstructLibrary
  (github pull #6409 from ptosco)
• Add a method "HasQuery()" to Mol class
  (github issue #6411 from kienerj)
• Enable using JSSubstructLibrary without pattern fps
  (github pull #6431 from ptosco)
• Add support for generalized substructure searching
  (github pull #6443 from greglandrum)
• Add atom and bond property parameters to substruct matching
  (github pull #6453 from rachelnwalker)
• Replace a try..catch block with an if clause
  (github pull #6488 from ptosco)
• Add an in place version of most of the MolStandardize functionality
  (github pull #6491 from greglandrum)
• Exposed partial sanitization options to MinimalLib (both JS and CFFI)
  (github pull #6519 from ptosco)
• Optionally forward Enhanced Stereo Group ids
  (github pull #6560 from ricrogz)
• Add support for dative bonds in MOL files
  (github pull #6566 from bjonnh-work)
• RASCAL MCES
  (github pull #6568 from DavidACosgrove)
• Support additional generic groups
  (github pull #6570 from bjonnh-work)
• Add support for Marvin files
  (github pull #6575 from bjonnh-work)
• Add a "rootedAtAtom" to MolToSmarts
  (github pull #6581 from ricrogz)
• RGD to support tautomers of core
  (github issue #6609 from jones-gareth)
• Fix some build warnings
  (github pull #6618 from ricrogz)
• Exposed log capture functionality to MinimalLib
  (github pull #6628 from ptosco)
• add option to use sequential random seeds in the conformer generator
  (github pull #6639 from greglandrum)
• Major MCS refactoring: new features and bug fixes
  (github pull #6646 from ptosco)
• Lasso highlights
  (github pull #6653 from DavidACosgrove)
• extract continuous lines from the conrec code
  (github pull #6676 from greglandrum)
• Allow some tolerance in flatness determination
  (github pull #6696 from ricrogz)
• Do not trust the 2D/3D tag in ctab mol files
  (github pull #6697 from ricrogz)
• expose the CDXML reaction parsers to python
  (github pull #6700 from greglandrum)
• Add hasQueryHs
  (github pull #6702 from bp-kelley)
• Exporting to mol marks imine bonds EITHERDOUBLE when imine H is implicit
  (github issue #6703 from ricrogz)
• Use the connect-the-dots algorithm by default in DetermineBonds
  (github pull #6740 from greglandrum)
• Add function to calculate all 3D descriptors
  (github pull #6741 from RPirie96)
• Add SpacialScore
  (github pull #6742 from apahl)
• Extract the core matching logic into a separate function
  (github pull #6754 from ptosco)

Bug Fixes:

• rdFMCS.FindMCS uses huge amounts of memory for this pair of molecules when CompleteRingsOnly is True
  (github issue #3965 from i-tub)
• PF6- still can not get Bad Conformer Id after the #510 issue fix
  (github issue #5145 from wangyingxie)
• Order dependence for rdFMCS.FindMCS with MatchFusedRingsStrict
  (github issue #5411 from pierred5)
• Failed FMCS results with certain seed SMARTS and MatchFusedRings* parameters on
  (github issue #5440 from pierred5)
• Seed SMARTS to FindMCS() produces incorrect MCS
  (github issue #5457 from pierred5)
• FindMCS returns wrong result with monoatomic molecules
  (github issue #5510 from ptosco)
• queryMol from FindMCS doesn't match mols used to generate MCS
  (github issue #6082 from paconius)
• Crash when parsing InChI
  (github issue #6172 from eloyfelix)
• Iteration over Python GetAtoms is 10-20x slower than need be
  (github issue #6208 from d-b-w)
• refactor(python): replace deprecated unittest methods
  (github pull #6304 from e-kwsm)
• generateDepictionMatching2DStructure: bonds to R groups should be generic when matching
  (github pull #6306 from ptosco)
• MolToSmiles(canonical=False) creates the wrong _smilesBondOutputOrder property
  (github issue #6315 from adalke)
• MolToMolBlock ignores unspecified information for double bonds in rings
  (github issue #6316 from mwojcikowski)
• bump yaehmop version
  (github pull #6330 from greglandrum)
• rdMolDraw2D.MolDraw2DCairo produces Pre-condition Violation: no draw context when SetColour, DrawRect or DrawLine was called.
  (github issue #6336 from lhyuen)
• Added cstdint include
  (github pull #6338 from vedranmiletic)
• remove the dependency from python distutils in the top CMakeLists.txt file
  (github pull #6339 from rvianello)
• take drawOptions into account when exporting structure to xlsx format
  (github pull #6341 from ptosco)
• Fix swig memory leak
  (github pull #6346 from jones-gareth)
• Add inlines to ForceFieldHelpers header functions
  (github pull #6356 from JLVarjo)
• Bug relating to this PF6- still can not get Bad Conformer Id
  (github issue #6365 from teltim)
• straightenDepiction should not consider 0-degree rotations as multiples of 60
  (github pull #6367 from ptosco)
• expose two missing EmbedFailureCauses tags to python
  (github pull #6372 from greglandrum)
• Molfile Unsaturation Query Not Parsed Correctly
  (github issue #6395 from timothyngo)
• MolDraw2D: chiral tag overlapping atom label
  (github issue #6397 from greglandrum)
• MolDraw2D: increasing padding results in the legend not being displayed
  (github issue #6400 from greglandrum)
• expose some missing CXSmiles flags to python
  (github pull #6415 from greglandrum)
• V3000 structure segfaults when converting to SVG
  (github issue #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 #6423 from ricrogz)
• MolEnumerate should clear the reaction properties on its results
  (github issue #6432 from greglandrum)
• RDKit hangs indefinitely when parsing not so big molblock
  (github issue #6434 from eloyfelix)
• Removing Hs on a pyrrol-like structure throws kekulization error
  (github issue #6437 from ricrogz)
• Molecules from CDXML Parser have inverted, unrealistic atomic coordinates
  (github issue #6461 from greglandrum)
• CDXML Parser does not preserve information about bond wedging
  (github issue #6462 from greglandrum)
• boost::bad_any_cast error when calling getProp on properties set by applyMolListPropsToAtoms<int64_t>
  (github issue #6465 from rachelnwalker)
• Allow systems like C/C=N/[H] to be stereogenic with the new chirality code
  (github pull #6473 from greglandrum)
• Fix RWMol::addAtom docstring
  (github pull #6477 from d-b-w)
• StereoGroup information should not impact canonicalization when CXSMILES isn't being generated
  (github issue #6479 from greglandrum)
• Fix a few broken docstrings
  (github pull #6480 from ptosco)
• pin numpy to 1.24.3
  (github pull #6483 from bp-kelley)
• CMAKE_INSTALL_PREFIX not honored for Python files installation on Windows
  (github pull #6485 from ricrogz)
• Fixed tests that weren't being run in testDepictor.py
  (github pull #6486 from rachelnwalker)
• Get tests to work when building without exception support (i.e., legacy pure JS library)
  (github pull #6487 from ptosco)
• Fixes rdkit-js/issues/347
  (github pull #6490 from ptosco)
• Make sure that molecules are shown as images by PandasTools also when DataFrames are truncated horizontally
  (github pull #6496 from ptosco)
• MolToMolBlock writes "either" stereo for double bonds which shouldn't be stereo
  (github issue #6502 from ricrogz)
• Double bonds are not correctly drawn on sulfoximines
  (github issue #6504 from ptosco)
• RegistrationHash.GetMolLayers() with v2 tautomer hash does not filter CX extensions
  (github issue #6505 from ricrogz)
• Drop the s_m_color_rgb property from MaeWriter
  (github pull #6511 from ricrogz)
• update avalontools version to incorporate bug fixes
  (github pull #6513 from ptosco)
• update windows DLL CI build config
  (github pull #6535 from greglandrum)
• Add MolEnumerator to C#
  (github pull #6542 from jones-gareth)
• MolDraw2D: placement of bond or atom labels gets confused when atoms overlap
  (github issue #6569 from greglandrum)
• partial MCS failure
  (github issue #6578 from greglandrum)
• Fix vulnerabilities found by fuzzer.
  (github pull #6579 from thomp-j)
• allow building the cartridge against PostgreSQL 16
  (github pull #6580 from ptosco)
• SIGSEGV while calculating molecular descriptors after using salt remover.
  (github issue #6592 from BartlomiejF)
• Add newline to ConstrainedEmbed docstring.
  (github pull #6596 from DavidACosgrove)
• Avoid leaking memory in case exceptions are thrown while generating FPs
  (github pull #6630 from ptosco)
• Pre-condition violation in canonicalization of dative bond adjacent to double bond
  (github issue #6633 from ricrogz)
• Incorrect most abundant isotope for Vanadium
  (github issue #6638 from abefrandsen)
• Simple imine-containing molecule causes an infinite loop in FindStereo.cpp
  (github issue #6640 from ptosco)
• Mol file parser strips stereogenic H from imine bonds
  (github issue #6664 from ricrogz)
• ROMol move constructor and assignment do not update SubstanceGroup ownership
  (github issue #6681 from ricrogz)
• Flexicanvas cuts off bottom of reaction
  (github issue #6685 from DavidACosgrove)
• make sure bond attachpt info is pickled
  (github pull #6698 from greglandrum)
• Catch meanBondLen of 0.0
  (github pull #6699 from DavidACosgrove)
• Add trans layout for double bonds in rings
  (github pull #6709 from d-b-w)
• Segmentation fault in MMFF
  (github issue #6728 from Meteor-han)
• Fix chirality handling when the chiral atom is the first one in a SMARTS
  (github pull #6730 from johnmay)
• ConnectTheDots can segfault if all atoms do not have residue info
  (github issue #6756 from jasondbiggs)
• _moltoimg() should honor drawOptions.prepareMolsBeforeDrawing
  (github issue #6792 from ptosco)

Cleanup work:

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