From a8d4912f88ae2ea9ea7afa366ba5b9c0be09cb79 Mon Sep 17 00:00:00 2001 From: Greg Landrum Date: Tue, 19 Mar 2024 09:05:33 +0100 Subject: [PATCH] beta release prep (#7271) --- CMakeLists.txt | 2 +- ReleaseNotes.md | 305 +++++++++++++++++++++++++++++++++++++++++++++++- 2 files changed, 304 insertions(+), 3 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 30890c89c2..0587f60c0a 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -137,7 +137,7 @@ set(RDK_PYTHON_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/rdkit") set(RDKit_Year "2024") set(RDKit_Month "03") set(RDKit_Revision "1") -set(RDKit_RevisionModifier "pre") +set(RDKit_RevisionModifier "b1") set(RDKit_ABI "1") # we need an integer version of the month later, so remove the zero padding diff --git a/ReleaseNotes.md b/ReleaseNotes.md index b3a28909a2..21796feb78 100644 --- a/ReleaseNotes.md +++ b/ReleaseNotes.md @@ -1,4 +1,4 @@ -# Release_2024.03.1 +# Release_2024.03.1b1 (Changes relative to Release_2023.09.1) ## Acknowledgements @@ -6,6 +6,16 @@ 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, +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 @@ -18,11 +28,302 @@ GitHub) - RMS pruning during conformer generation now symmetrizes conjugated terminal groups by default. This can be disabled with the parameter "symmetrizeConjugatedTerminalGroupsForPruning" ## New Features and Enhancements: + - Support writing detailed SMARTS queries to CTABs using the SMARTSQ mechanism + (github issue #5819 from greglandrum) + - add more error checking to substance groups + (github issue #5923 from greglandrum) + - add maxRecursiveMatches to SubstructMatchParameters + (github issue #6017 from greglandrum) + - Removed some code duplication between Depictor.cpp and common.h + (github pull #6799 from greglandrum) + - Add support for writing chirality and stereo in MaeWriter + (github pull #6810 from rachelnwalker) + - Implement MinimalLib get_mcs() version that returns JSON + (github pull #6812 from ptosco) + - support generalized substructure search in the SubstructLibrary + (github pull #6835 from greglandrum) + - Support copying of GeneralizeQueryMolecules + (github issue #6851 from greglandrum) + - Enable chemist-friendly depiction of R-groups + (github pull #6866 from ptosco) + - Allow building DetermineBonds without YAeHMOP support + (github pull #6885 from greglandrum) + - Add multithreading to getBestRMS and new getAllConformerBestRMS + (github pull #6896 from greglandrum) + - switch to catch2 v3 + (github pull #6898 from greglandrum) + - minilib functions exposure: mmpa + (github pull #6902 from StLeonidas) + - atropisomer handling added + (github pull #6903 from tadhurst-cdd) + - Add multi-threaded versions of some MolStandardize operations + (github pull #6909 from greglandrum) + - Add (multithreaded) functions to the fingerprint generators for calculating multiple fingeprints in one call + (github pull #6910 from greglandrum) + - Add Python modules to generate stubs and automatically patch docstrings + (github pull #6919 from ptosco) + - Update molecular templates headers and drop bond-length tests + (github pull #6960 from github-actions[bot]) + - Add in place and multithread support for more of the MolStandardize code + (github pull #6970 from greglandrum) + - Enable in-tree builds and improve overloaded constructor docstrings + (github pull #6980 from ptosco) + - Change the defaults for the conformer generation to be ETKDGv3 + (github pull #6985 from greglandrum) + - Added fingerprints to GeneralizedSubstruct search and extended SWIG wrappers + (github pull #6991 from jones-gareth) + - Allow sanitization to be disabled in PandasTools.LoadSDF + (github issue #7019 from christophhillisch) + - Add Atom::hasValenceViolation (Take 2) + (github pull #7030 from cdvonbargen) + - Please consider exposing maxBondMatchPairs param in rdRascalMCES.RascalOptions() + (github issue #7054 from nate-russell) + - Copy stereo and substance groups during insertMol + (github issue #7064 from cdvonbargen) + - [v2 API] FileParsers + (github issue #7074 from greglandrum) + - [v2 API] Reaction Parsers + (github issue #7075 from greglandrum) + - Rationalize attachment points + (github issue #7078 from cdvonbargen) + - refactoring of MolStandardize validation module + (github pull #7085 from rvianello) + - Add a 'force' option to MolStandardizer::Uncharger + (github pull #7088 from rvianello) + - support sanitization of reaction product templates + (github pull #7095 from greglandrum) + - Support atropisomers in the conformer generator + (github pull #7098 from greglandrum) + - Compatibility with pathlib.Path + (github pull #7100 from PatrickPenner) + - Add option to sanitize reaction components like molecules + (github issue #7108 from MartaPasquini) + - [v2 API] MRV parsers + (github pull #7110 from greglandrum) + - Add v2 API for the molecule CDXML parser + (github pull #7113 from greglandrum) + - Make addStereoAnnotation public + (github issue #7140 from cdvonbargen) + - optimize batch operations when editing molecules + (github pull #7145 from bp-kelley) + - V2 API for the MolSuppliers + (github pull #7168 from greglandrum) + - Improve output of debugMol + (github pull #7172 from greglandrum) + - update cookbook, draw molecule with atom indices + (github pull #7173 from nbehrnd) + - Colinear bonds in depiction cause stereo to be lost when converting to mol block + (github issue #7177 from mps-hlx) + - Update MinimalLib Dockerfiles + (github pull #7182 from ptosco) + - allow perception of stereo from T-shaped structures + (github pull #7183 from greglandrum) + - switch the TFD code to use a fingerprint generator + (github pull #7187 from greglandrum) + - Don't reset computed properties if already empty + (github pull #7188 from rachelnwalker) + - Add some ExplicitBitVect operations to Swig + (github pull #7204 from jones-gareth) + - Some modernization of core GraphMol classes + (github pull #7228 from greglandrum) + - Custom decimal precision + (github pull #7229 from PatrickPenner) + - feat(minilib): expose the options parameter in get_inchi + (github pull #7240 from BenoitClaveau) + - Postpone clearing computed properties until after all Hs removed + (github pull #7241 from rachelnwalker) + - Speed up cleanMolStereo + (github pull #7244 from ricrogz) + - add HetAtomProtomerv2 + (github pull #7253 from greglandrum) + - Support zero order bonds in V3K CTABs + (github pull #7269 from greglandrum) + - add option to symmetrize conjugated terminal groups when RMS pruning conformers + (github pull #7270 from greglandrum) ## Bug Fixes: + - STEREOANY bonds lead to non-stable SMILES/SMARTS strings + (github issue #5499 from ricrogz) + - Chemical reactions with radicals cannot be pickled and unpickled. + (github issue #5890 from sitanshubhunia) + - Postgresql: exact search showing false with radicals from CXSMILES + (github issue #6276 from sitanshubhunia) + - CXSMILES: atom with labels should not also have `dummyLabel` property set + (github issue #6309 from greglandrum) + - Query Features: Different input format leads to a different molecule + (github issue #6349 from kienerj) + - non-physical radical counts being preserved + (github issue #6370 from greglandrum) + - MolEnumerator: use repeat counts for SRUs when present + (github issue #6429 from greglandrum) + - Unexpected non-matching ElementGraph hashes + (github issue #6472 from jepdavidson) + - Fixes for canonicalization, and stereochemistry + (github pull #6743 from tadhurst-cdd) + - MCS query incorrect when ringCompare=RingCompare.StrictRingFusion + (github issue #6773 from d-b-w) + - Fixes bug in get_sss_json() + (github pull #6806 from ptosco) + - SWIG builds failing on Windows + (github pull #6808 from jones-gareth) + - Double bonds should not be depicted as crossed bonds in the presence of wavy bonds + (github issue #6816 from ptosco) + - We should be able to run the tests without boost::iostreams + (github issue #6818 from greglandrum) + - Fix stereo bond corruption on RGD. + (github pull #6832 from jones-gareth) + - MurckoScaffold.MakeScaffoldGeneric() has issues with isotopes + (github issue #6836 from dehaenw) + - Fix unclosed resource in BuildFuncGroupHierarchy + (github pull #6846 from ricrogz) + - RGD: Fix doEnumeration true for cores that are not bundles + (github pull #6857 from jones-gareth) + - Fix build error when serialization is off. + (github pull #6867 from vslashg) + - Wavy bonds in mol blocks can't be stereo enumerated + (github issue #6876 from bp-kelley) + - CDXML read of AND1 group (specifying racemic center) gets associated into an OR1 group + (github issue #6887 from pechersky) + - Segfault in JSONToMols when "commonchem" is an int + (github issue #6890 from i-tub) + - reapplyMolBlockWedging() should retain ENDDOWNRIGHT, ENDUPRIGHT dirs + (github issue #6893 from ptosco) + - MMPA FragmentMol segfaults when new stereo perception is turned on + (github issue #6900 from jasondbiggs) + - PositionVariationOp::getVariationCounts() does unnecessary copies of vectors + (github issue #6906 from whosayn) + - Obtaining descriptors via Descriptors.descList results in duplication of SPS. + (github issue #6928 from wsuzume) + - Some Clang-specific build instructions skip some clang compilers on mac + (github issue #6941 from whosayn) + - With new stereo, removing H from an Imine double bond does not remove bond stereo + (github issue #6944 from ricrogz) + - FindMolChiralCenters should honor RDK_USE_LEGACY_STEREO_PERCEPTION + (github issue #6945 from ricrogz) + - generateDepictionMatching2DStructure does not optimally align when refPatt!=None, allowRGroups=False, alignOnly=True + (github issue #6952 from ptosco) + - SpacialScore ignores undefined bond stereo + (github issue #6957 from jasondbiggs) + - GetAtomPairFingerprint yields different rooted FP from generator + (github issue #6958 from ptosco) + - DetermineBonds() for PH3 yields no bonding + (github issue #6961 from dhibbit) + - Highlights of triple bonds come out wrong + (github issue #6968 from DavidACosgrove) + - MaeMolSupplier cannot read dummy atoms from Maestro files + (github issue #6973 from ricrogz) + - Chem.FindMolChiralCenters function should not be sensitive to atom-map numbers + (github issue #6975 from skystreet8) + - Parsing a Mol leaks the "_needsDetectBondStereo" property + (github issue #6981 from ricrogz) + - SubstructMatch maxRecursiveMatches is not being honored + (github issue #6983 from ricrogz) + - HierarchicalClusterPicker::pick() randomly fails with Invariant Violation + (github issue #7001 from ricrogz) + - rdkit.Dbase doesn't work correctly with Python 3.12 + (github issue #7009 from rvianello) + - "Inconsistent state" when manually sanitizing and assigning stereo when using the new stereo algorithm + (github issue #7023 from ricrogz) + - Spacing bug in compute2DCoordsForReaction + (github issue #7028 from KevKeating) + - Update distance bounds calculation for conjugated double bonds in macrocycles + (github pull #7032 from fwaibl) + - Middle line in triple bond drawn to incorrect point when a wedged bond is present + (github issue #7036 from greglandrum) + - fragmentation of mol loses any sgroups + (github pull #7056 from tadhurst-cdd) + - CSharp Wrapper ExtendedQueryMol Read Access Violation + (github issue #7069 from jones-gareth) + - removing an atom should not remove all stereo groups involving that atom. + (github issue #7071 from greglandrum) + - Sanitizing and assigning stereo twice can change bond stereo with new stereo + (github issue #7076 from ricrogz) + - testConrec.cpp:130 fails on ARM64 + (github issue #7083 from bjonnh-work) + - Wrong stereochemistry in embedded rings from stereospecific SMILES + (github issue #7109 from brje01) + - Quaternary nitrogens with hydrogens are not a candidate for stereo + (github issue #7115 from bp-kelley) + - Some metal centers get radical electrons + (github issue #7122 from cdvonbargen) + - AddHs sets "no implicit Hs" on the atoms were Hs are added + (github issue #7123 from ricrogz) + - ReplaceBond may cause valence issues in specific edge cases + (github issue #7128 from ricrogz) + - Adding Wedge/Dash bond neighboring a stereo double bond causes a Precondition Violation + (github issue #7131 from ricrogz) + - Stereo Annotation Appears Incorrect + (github issue #7157 from lounsbrough) + - Unexpected exact mass values are returned for radium and radon + (github issue #7162 from markarchibald) + - Adding missing headers in ReactionParser.h + (github pull #7163 from tgaudin) + - fix: add PandasTools support for pandas 2.2 + (github pull #7165 from AAriam) + - Fix leaking Bonds on unmatched ring closures + (github pull #7178 from ricrogz) + - fix a problem with tautomeric systems being extended too far + (github pull #7200 from greglandrum) + - Fixes #7181 + (github pull #7206 from greglandrum) + - Fix Uncharger applying to already neutralized perhalic groups + (github pull #7211 from rvianello) + - Fix `Chem.Randomize.py` + (github pull #7232 from JanCBrammer) + - SGroup fields without values cause weird properties + (github issue #7246 from ricrogz) + - Remove duplicate entry in fragment descriptors + (github pull #7249 from levineds-meta) + - RDKit fails to parse "M RAD" lines were radical is 0 + (github issue #7256 from ricrogz) + - Writing StereoGroups to Mol files should break lines at 80 characters + (github issue #7259 from ricrogz) ## Cleanup work: - + - Switch over to using pytest to run the python tests + (github pull #5916 from greglandrum) + - Redundant variable`hasCoreDummies` in R-group decomposition code + (github issue #6779 from MarioAndWario) + - cmake cleanup + (github pull #6814 from greglandrum) + - Remove boost::regex support + (github issue #6817 from greglandrum) + - remove the deprecated python implementation of MolStandardize + (github pull #6819 from greglandrum) + - Update CI, remove some warnings + (github pull #6882 from greglandrum) + - Deprecate some of the ancient python-based ML code + (github pull #6891 from greglandrum) + - Remove boost::regex support #6817 + (github pull #6913 from whosayn) + - Fix minimal build, allow building without boost::serialization + (github pull #6932 from greglandrum) + - Drop unrequired zlib include which may break the windows build + (github pull #6966 from ricrogz) + - Compile time and runtime deprecation warnings + (github pull #7004 from greglandrum) + - New tests for specical query atoms and atropisomers + (github pull #7010 from tadhurst-cdd) + - fix GCC 13.2 warnings about redundant move in return statement + (github pull #7029 from rvianello) + - fix check of python version when updating Filters.cpp + (github pull #7035 from rvianello) + - fix several warnings originating from the swig wrappers + (github pull #7063 from rvianello) + - lock the versions of a bunch of stuff used in the CI builds + (github pull #7082 from greglandrum) + - remove deprecated packages from rdkit.ML + (github pull #7107 from greglandrum) + - require SWIG 4.1+ at cmake config time + (github pull #7139 from rvianello) + - RGD code cleanup + (github pull #7186 from ptosco) + - remove the broken Dbase.DbReport module + (github pull #7227 from greglandrum) + - remove a bunch of std::endls + (github pull #7233 from greglandrum) + - Avoid rebuilding FreeSASA at every build for no good reason + (github pull #7245 from ptosco) ## Code removed in this release: - The python implementations of MolStandardize has been removed. Please use the implementation in `rdkit.Chem.MolStandardize.rdMolStandardize` instead.