rdkit/rdkit: 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 (https://github.com/rdkit/rdkit/pull/4722) and Issue #4721 (https://github.com/rdkit/rdkit/issues/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: error: COPY failed for table "mols": ERROR: could not create molecule from SMILES (github issue #5095 from joelduerksen) Removing H preserving only wedged ones strips all H (github issue #5099 from ricrogz) fix a mistake in the enhanced stereochemistry substructure table (github issue #5101 from greglandrum) Cleanup work: Do the deprecations for the 2022.03 release (github pull #4626 from greglandrum) clang-tidy: readability-simplify-boolean-expr (github pull #4639 from e-kwsm) Clean-up Python 4815 - P1.1: Chem\AtomPairs (github pull #4859 from IchiruTake) Clean-up Python #4815 - P1.2: Chem/ChemUtils (github pull #4860 from IchiruTake) Clean-up Python #4815 - P1.3: Chem\Draw (github pull #4891 from IchiruTake) Clean-up Python #4815 - P1.4: Chem\EState (github pull #4893 from IchiruTake) Clean-up Python #4815 - P1.5: Chem\FeatMaps (github pull #4894 from IchiruTake) Clean-up Python #4815 - P1.6: Chem\Features (github pull #4896 from IchiruTake) Clean-up Python #4815 - P1.8: Chem\fmcs (github pull #4898 from IchiruTake) Clean-up Python #4815 - P1.9: Chem\Fraggle (github pull #4906 from IchiruTake) Clean-up Python #4815 - P1.10: Chem\MolDb (github pull #4907 from IchiruTake) Clean-up Python #4815 - P1.11: Chem\MolKey (github pull #4910 from IchiruTake) Clean-up Python #4815 - P1.12: Chem\MolStandardize (github pull #4911 from IchiruTake) Clean-up Python #4815 - P1.13: Chem\Pharm2D & Chem\Pharm3D (github pull #4912 from IchiruTake) Clean-up Python #4815 - P1.14: Chem\Scaffolds & Chem\SimpleEnum (github pull #4913 from IchiruTake) Run clang-tidy (readability-braces-around-statements) (github pull #4977 from e-kwsm) silence warnings in MSVC compliatons (github pull #5044 from bp-kelley) Clean up the warning landscape (github pull #5048 from greglandrum) Cleanup of python API documentation stubs (github pull #5105 from greglandrum) New Features and Enhancements: Update coordgenlibs to v3.0.0 (github pull #4638 from ricrogz) Fix some compile-time warnings in the postgres cartridge code (github pull #4657 from rvianello) Add some new color palettes to MolDraw2D (github pull #4668 from greglandrum) Add support for Beilstein generics when doing substructure queries (github pull #4673 from greglandrum) Remove unnecessary mutex in InChI wrapper (github pull #4680 from greglandrum) Update mac CI builds (github pull #4738 from greglandrum) Remove dead code (github pull #4739 from ptosco) Refactor the memory management of the postgres cartridge cache module (github pull #4755 from rvianello) Improve CMake integration of PgSQL build (github pull #4767 from ptosco) Allow MolDraw2DCairo and MolDraw2DSVG to determine canvas size based on the molecule (github pull #4772 from greglandrum) generate the sql update files in the binary (build) directory (github pull #4777 from rvianello) Allow using heavy atoms only in the FragmentChooser (github pull #4791 from ptosco) silence warnings in MSVC compilations (github pull #4796 from bp-kelley) Support using the python logger (github issue #4840 from xavierholt) Add support for quadruple bonds in SMILES (github issue #4842 from jasondbiggs) Some refactoring of the depictor code (github pull #4865 from greglandrum) Build documentation for 3 missing modules (github pull #4879 from ptosco) Add access to query atom symbols from python or an option to render them in images (github issue #4880 from rachelnwalker) Start adding move constructors and move-assignment operators (github pull #4909 from greglandrum) Refactor mol draw2 d (github pull #4948 from DavidACosgrove) [ENH]: Support greater use of findAtomEnvironmentOfRadiusN() (github pull #4970 from IchiruTake) Move isEarlyAtom to a table to reduce lock contention in getPeriodicTable (github pull #4980 from bp-kelley) Support writing V3000 reactions (github pull #4982 from greglandrum) Make FMCS check bond stereo. (github pull #5009 from DavidACosgrove) Improving atom colors for dark mode. (github pull #5038 from kaushaleshshukla) enable the multithreaded LeaderPicker on linux (github pull #5043 from greglandrum) Expose MolzipParams::atomSymbols to python (github pull #5054 from bp-kelley) disable Info and Debug logs by default (github pull #5065 from greglandrum) Add sanitize option to molzip (github pull #5069 from bp-kelley) "Powered by RDKit" Badge (github pull #5085 from cbouy) Deprecated code (to be removed in a future release): Python function rdkit.Chem.WrapLogs() is deprecated in favor of rdkit.rdBase.LogToPythonStderr(). rdkit.rdBase.WrapLogs() also exists, but unless you need the old teeing behavior, prefer the former. Python function rdkit.Chem.LogWarning() is deprecated in favor of rdkit.rdBase.LogWarning(). Python function rdkit.Chem.LogError() is deprecated in favor of rdkit.rdBase.LogError(). The C++ class RDLog::BlockLogs is deprecated in favor of the the class RDLog::LogStateSetter