2024_03_1 (Q1 2024) Release #7313
greglandrum
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Release_2024.03.1
(Changes relative to Release_2023.09.1)
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)
Mark Archibald, Armin Ariamajd, Chris Von Bargen, Jason Biggs, Jonathan Bisson,
Jan C. Brammer, Jessica Braun, Benoît Claveau, David Cosgrove, James Davidson,
Hussein Faara, Théophile Gaudin, Gareth Jones, Christoph Hillisch, Tad Hurst,
Kevin Keating, Brian Kelley, Joos Kiener, David Lounsbrough, Jeremy Monat, Dan
Nealschneider, Yoshinobu Ogura, Marta Pasquini, Yakov Pechersky, Patrick Penner,
Rachael Pirie, Ricardo Rodriguez-Schmidt, Nate Russell, Ivan Tubert-Brohman,
Matthew Seddon, Leonid Stolbov, Paolo Tosco, Riccardo Vianello, Franz Waibl,
Rachel Walker, sitanshubhunia, skystreet8, dehaenw, dhibbit, vslashg, nbehrnd,
MarioAndWario, levineds-meta
Highlights
Backwards incompatible changes
[CH]
marked as aDOUBLET
will now have three radical electrons assigned. This is consistent with the value from SMILES.MolVSValidations
base class was removed and consolidated intoValidationMethod
. Consequently, thevalidate
method replacedrun
in the subclasses related to MolVS (namelyNoAtomValidation
,FragmentValidation
,NeutralValidation
, andIsotopeValidation
) and all subclasses ofValidationMethod
are now required to implement acopy
method. Moreover,MolStandardize::ValidationErrorInfo
was redefined as an alias forstd::string
. The changes related to the MolVS validation methods were similarly implemented in the Python API.New Features and Enhancements:
(github issue Support writing detailed SMARTS queries to CTABs using the SMARTSQ mechanism #5819 from greglandrum)
(github issue add more error checking to substance groups #5923 from greglandrum)
(github issue add maxRecursiveMatches to SubstructMatchParameters #6017 from greglandrum)
(github pull Removed some code duplication between Depictor.cpp and common.h #6799 from greglandrum)
(github pull Add support for writing chirality and stereo in MaeWriter #6810 from rachelnwalker)
(github pull Implement MinimalLib get_mcs() version that returns JSON #6812 from ptosco)
(github pull support generalized substructure search in the SubstructLibrary #6835 from greglandrum)
(github issue Support copying of GeneralizeQueryMolecules #6851 from greglandrum)
(github pull Enable chemist-friendly depiction of R-groups #6866 from ptosco)
(github pull Allow building DetermineBonds without YAeHMOP support #6885 from greglandrum)
(github pull Add multithreading to getBestRMS and new getAllConformerBestRMS #6896 from greglandrum)
(github pull switch to catch2 v3 #6898 from greglandrum)
(github pull minilib functions exposure: mmpa #6902 from StLeonidas)
(github pull atropisomer handling added #6903 from tadhurst-cdd)
(github pull Add multi-threaded versions of some MolStandardize operations #6909 from greglandrum)
(github pull Add (multithreaded) functions to the fingerprint generators for calculating multiple fingeprints in one call #6910 from greglandrum)
(github pull Add Python modules to generate stubs and automatically patch docstrings #6919 from ptosco)
(github pull Update molecular templates headers and drop bond-length tests #6960 from github-actions[bot])
(github pull Add in place and multithread support for more of the MolStandardize code #6970 from greglandrum)
(github pull Enable in-tree builds and improve overloaded constructor docstrings #6980 from ptosco)
(github pull Change the defaults for the conformer generation to be ETKDGv3 #6985 from greglandrum)
(github pull Added fingerprints to GeneralizedSubstruct search and extended SWIG wrappers #6991 from jones-gareth)
(github issue Allow sanitization to be disabled in PandasTools.LoadSDF #7019 from christophhillisch)
(github pull Add Atom::hasValenceViolation (Take 2) #7030 from cdvonbargen)
(github issue Please consider exposing maxBondMatchPairs param in rdRascalMCES.RascalOptions() #7054 from nate-russell)
(github issue Copy stereo and substance groups during insertMol #7064 from cdvonbargen)
(github issue [v2 API] FileParsers #7074 from greglandrum)
(github issue [v2 API] Reaction Parsers #7075 from greglandrum)
(github issue Rationalize attachment points #7078 from cdvonbargen)
(github pull refactoring of MolStandardize validation module #7085 from rvianello)
(github pull Add a 'force' option to MolStandardizer::Uncharger #7088 from rvianello)
(github pull support sanitization of reaction product templates #7095 from greglandrum)
(github pull Support atropisomers in the conformer generator #7098 from greglandrum)
(github pull Compatibility with pathlib.Path #7100 from PatrickPenner)
(github issue Add option to sanitize reaction components like molecules #7108 from MartaPasquini)
(github pull [v2 API] MRV parsers #7110 from greglandrum)
(github pull Add v2 API for the molecule CDXML parser #7113 from greglandrum)
(github issue Make addStereoAnnotation public #7140 from cdvonbargen)
(github pull optimize batch operations when editing molecules #7145 from bp-kelley)
(github pull V2 API for the MolSuppliers #7168 from greglandrum)
(github pull Improve output of debugMol #7172 from greglandrum)
(github pull update cookbook, draw molecule with atom indices #7173 from nbehrnd)
(github issue Colinear bonds in depiction cause stereo to be lost when converting to mol block #7177 from mps-hlx)
(github pull Update MinimalLib Dockerfiles #7182 from ptosco)
(github pull allow perception of stereo from T-shaped structures #7183 from greglandrum)
(github pull switch the TFD code to use a fingerprint generator #7187 from greglandrum)
(github pull Don't reset computed properties if already empty #7188 from rachelnwalker)
(github pull Enhance molzip to properly handle RGroupDecompositions #7202 from bp-kelley)
(github pull Add some ExplicitBitVect operations to Swig #7204 from jones-gareth)
(github pull Some modernization of core GraphMol classes #7228 from greglandrum)
(github pull Custom decimal precision #7229 from PatrickPenner)
(github pull Add Double Cubic Lattice Volume (DCLV). #7234 from RPirie96)
(github pull feat(minilib): expose the options parameter in get_inchi #7240 from BenoitClaveau)
(github pull Postpone clearing computed properties until after all Hs removed #7241 from rachelnwalker)
(github pull Speed up cleanMolStereo #7244 from ricrogz)
(github pull add HetAtomProtomerv2 #7253 from greglandrum)
(github pull Support zero order bonds in V3K CTABs #7269 from greglandrum)
(github pull add option to symmetrize conjugated terminal groups when RMS pruning conformers #7270 from greglandrum)
Bug Fixes:
(github issue STEREOANY bonds lead to non-stable SMILES/SMARTS strings #5499 from ricrogz)
(github issue Chemical reactions with radicals cannot be pickled and unpickled. #5890 from sitanshubhunia)
(github issue Postgresql: exact search showing false with radicals from CXSMILES #6276 from sitanshubhunia)
dummyLabel
property set(github issue CXSMILES: atom with labels should not also have
dummyLabel
property set #6309 from greglandrum)(github issue Query Features: Different input format leads to a different molecule #6349 from kienerj)
(github issue non-physical radical counts being preserved #6370 from greglandrum)
(github issue MolEnumerator: use repeat counts for SRUs when present #6429 from greglandrum)
(github issue Unexpected non-matching ElementGraph hashes #6472 from jepdavidson)
(github pull Fixes for canonicalization, and stereochemistry #6743 from tadhurst-cdd)
(github issue MCS query incorrect when ringCompare=RingCompare.StrictRingFusion #6773 from d-b-w)
(github pull Fixes bug in get_sss_json() #6806 from ptosco)
(github pull SWIG builds failing on Windows #6808 from jones-gareth)
(github issue Double bonds should not be depicted as crossed bonds in the presence of wavy bonds #6816 from ptosco)
(github issue We should be able to run the tests without boost::iostreams #6818 from greglandrum)
(github pull Fix stereo bond corruption on RGD. #6832 from jones-gareth)
(github issue MurckoScaffold.MakeScaffoldGeneric() has issues with isotopes #6836 from dehaenw)
(github pull Fix unclosed resource in BuildFuncGroupHierarchy #6846 from ricrogz)
(github pull RGD: Fix doEnumeration true for cores that are not bundles #6857 from jones-gareth)
(github pull Fix build error when serialization is off. #6867 from vslashg)
(github issue Wavy bonds in mol blocks can't be stereo enumerated #6876 from bp-kelley)
(github issue CDXML read of AND1 group (specifying racemic center) gets associated into an OR1 group #6887 from pechersky)
(github issue Segfault in JSONToMols when "commonchem" is an int #6890 from i-tub)
(github issue reapplyMolBlockWedging() should retain ENDDOWNRIGHT, ENDUPRIGHT dirs #6893 from ptosco)
(github issue MMPA FragmentMol segfaults when new stereo perception is turned on #6900 from jasondbiggs)
(github issue PositionVariationOp::getVariationCounts() does unnecessary copies of vectors #6906 from whosayn)
(github issue Obtaining descriptors via Descriptors.descList results in duplication of SPS. #6928 from wsuzume)
(github issue Some Clang-specific build instructions skip some clang compilers on mac #6941 from whosayn)
(github issue With new stereo, removing H from an Imine double bond does not remove bond stereo #6944 from ricrogz)
(github issue FindMolChiralCenters should honor RDK_USE_LEGACY_STEREO_PERCEPTION #6945 from ricrogz)
(github issue generateDepictionMatching2DStructure does not optimally align when refPatt!=None, allowRGroups=False, alignOnly=True #6952 from ptosco)
(github issue SpacialScore ignores undefined bond stereo #6957 from jasondbiggs)
(github issue GetAtomPairFingerprint yields different rooted FP from generator #6958 from ptosco)
(github issue DetermineBonds() for PH3 yields no bonding #6961 from dhibbit)
(github issue Highlights of triple bonds come out wrong #6968 from DavidACosgrove)
(github issue MaeMolSupplier cannot read dummy atoms from Maestro files #6973 from ricrogz)
(github issue Chem.FindMolChiralCenters function should not be sensitive to atom-map numbers #6975 from skystreet8)
(github issue Parsing a Mol leaks the "_needsDetectBondStereo" property #6981 from ricrogz)
(github issue SubstructMatch maxRecursiveMatches is not being honored #6983 from ricrogz)
(github issue HierarchicalClusterPicker::pick() randomly fails with Invariant Violation #7001 from ricrogz)
(github issue rdkit.Dbase doesn't work correctly with Python 3.12 #7009 from rvianello)
(github issue "Inconsistent state" when manually sanitizing and assigning stereo when using the new stereo algorithm #7023 from ricrogz)
(github issue Spacing bug in compute2DCoordsForReaction #7028 from KevKeating)
(github pull Update distance bounds calculation for conjugated double bonds in macrocycles #7032 from fwaibl)
(github issue Middle line in triple bond drawn to incorrect point when a wedged bond is present #7036 from greglandrum)
(github pull fragmentation of mol loses any sgroups #7056 from tadhurst-cdd)
(github issue CSharp Wrapper ExtendedQueryMol Read Access Violation #7069 from jones-gareth)
(github issue removing an atom should not remove all stereo groups involving that atom. #7071 from greglandrum)
(github issue Sanitizing and assigning stereo twice can change bond stereo with new stereo #7076 from ricrogz)
(github issue testConrec.cpp:130 fails on ARM64 #7083 from bjonnh-work)
(github issue Wrong stereochemistry in embedded rings from stereospecific SMILES #7109 from brje01)
(github issue Quaternary nitrogens with hydrogens are not a candidate for stereo #7115 from bp-kelley)
(github issue Some metal centers get radical electrons #7122 from cdvonbargen)
(github issue AddHs sets "no implicit Hs" on the atoms were Hs are added #7123 from ricrogz)
(github issue ReplaceBond may cause valence issues in specific edge cases #7128 from ricrogz)
(github issue Adding Wedge/Dash bond neighboring a stereo double bond causes a Precondition Violation #7131 from ricrogz)
(github issue Stereo Annotation Appears Incorrect #7157 from lounsbrough)
(github issue Unexpected exact mass values are returned for radium and radon #7162 from markarchibald)
(github pull Adding missing headers in ReactionParser.h #7163 from tgaudin)
(github pull fix: add PandasTools support for pandas 2.2 #7165 from AAriam)
(github pull Fix leaking Bonds on unmatched ring closures #7178 from ricrogz)
(github pull fix a problem with tautomeric systems being extended too far #7200 from greglandrum)
(github pull Fixes #7181 #7206 from greglandrum)
(github pull Fix Uncharger applying to already neutralized perhalic groups #7211 from rvianello)
Chem.Randomize.py
(github pull Fix
Chem.Randomize.py
#7232 from JanCBrammer)(github issue SGroup fields without values cause weird properties #7246 from ricrogz)
(github pull Remove duplicate entry in fragment descriptors #7249 from levineds-meta)
(github issue RDKit fails to parse "M RAD" lines were radical is 0 #7256 from ricrogz)
(github issue Writing StereoGroups to Mol files should break lines at 80 characters #7259 from ricrogz)
(github pull Update ring fusion cache when needed #7274 from ptosco)
(github issue Ring stereo in SMILES inverted after sanitization in molecule with fragments #7295 from greglandrum)
Cleanup work:
(github pull Switch over to using pytest to run the python tests #5916 from greglandrum)
hasCoreDummies
in R-group decomposition code(github issue Redundant variable
hasCoreDummies
in R-group decomposition code #6779 from MarioAndWario)(github pull cmake cleanup #6814 from greglandrum)
(github issue Remove boost::regex support #6817 from greglandrum)
(github pull remove the deprecated python implementation of MolStandardize #6819 from greglandrum)
(github pull Update CI, remove some warnings #6882 from greglandrum)
(github pull Deprecate some of the ancient python-based ML code #6891 from greglandrum)
(github pull Remove boost::regex support #6817 #6913 from whosayn)
(github pull Fix minimal build, allow building without boost::serialization #6932 from greglandrum)
(github pull Drop unrequired zlib include which may break the windows build #6966 from ricrogz)
(github pull Compile time and runtime deprecation warnings #7004 from greglandrum)
(github pull New tests for specical query atoms and atropisomers #7010 from tadhurst-cdd)
(github pull fix GCC 13.2 warnings about redundant move in return statement #7029 from rvianello)
(github pull fix check of python version when updating Filters.cpp #7035 from rvianello)
(github pull fix several warnings originating from the swig wrappers #7063 from rvianello)
(github pull lock the versions of a bunch of stuff used in the CI builds #7082 from greglandrum)
(github pull remove deprecated packages from rdkit.ML #7107 from greglandrum)
(github pull require SWIG 4.1+ at cmake config time #7139 from rvianello)
(github pull RGD code cleanup #7186 from ptosco)
(github pull remove the broken Dbase.DbReport module #7227 from greglandrum)
(github pull remove a bunch of std::endls #7233 from greglandrum)
(github pull Avoid rebuilding FreeSASA at every build for no good reason #7245 from ptosco)
Code removed in this release:
Please use the implementation in
rdkit.Chem.MolStandardize.rdMolStandardize
instead.and python 3, has been removed
removed. The affected packages include: rdkit.ML.Composite, rdkit.ML.DecTree,
rdkit.ML.KNN, rdkit.ML.ModelPackage, rdkit.ML.NaiveBayes, rdkit.ML.Neural
rdkit.ML.{Analyze,Screen,Grow,Build}Composite, rdkit.ML.CompositeRun,
rdkit.ML.EnrichPlot
Deprecated code (to be removed in a future release):
This discussion was created from the release 2024_03_1 (Q1 2024) Release.
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