rdkit/rdkit: 2020_09_1 (Q3 2020) Release

Release_2020.09.1

(Changes relative to Release_2020.03.1)

Backwards incompatible changes

• We've added additional allowed valences for Cl (now 1, 3, 5), Br (now 1, 3, 5), I (now 1, 3, 5), At (now 1, 3, 5), Xe (now 0, 2, 4, 6), and Po (now 2, 4, 6). Molecules with atoms in the new valence states will no longer generate sanitization errors. Note that this has an impact on the chemistry of molecules containing 3-valent I and at least one implict H (present 24 times in ChEMBL 27): previously this was incorrectly assigned two implicit Hs, now it has no implicit Hs.
• Aromaticity perception of molecules like Cc1nnc2n1c1ccccc1n1c(C)nnc12 now correctly recognizes the full outer envelope, i.e. the bonds joining the rings are now also aromatic.
• FindMCS() may return single atom MCSs, whereas previously it returned an empty MCS unless there was at least one commond bond across the input structures. So the MCS between molecules CC and CO is now [#6] rather than being null.
• The fontSize()/setFontSize() (FontSize()/SetFontSize()) methods in MolDraw2D now work in units of pixels (more or less) instead of the molecule units.
• The Open3DAlign functionality is now in its own separate library - O3AAlign in cmake. If you are working in C++ and using O3A functionality, you'll need to link against this library as well now.
• Due to improvements in the tautomer enumeration code, the method TautomerEnumerator::enumerate now returns a TautomerEnumeratorResult object instead of a vector of molecules. Note that if you are iterating over the results of a call to enumerate() you shouldn't need to change your code. If you want to invoke the old (and deprecated, see below) form from C++, call TautomerNumerator::enumerate(mol, nullptr) or explicitly pass a boost::dynamic_bitset* to capture the modified atoms.
• The default precision setting for coordgen has been changed. The new default was selected to greatly reduce the number of molecules for which it takes a very long time to generate coordinates while still producing nice looking structures. We may continue to tweak this default value if/when problems with it are reported. If you would like to go back to the previous setting, set CoordgenParams.minimizerPrecision to CoordgenParams.sketcherStandardPrecision when you invoke rdCoordGen.AddCoords()
• Uncharger::uncharge() will now neutralize [Cl,Br,I][O-], [Cl,Br,I](=O)[O-], [Cl,Br,I](=O)(=O)[O-], [Cl,Br,I](=O)(=O)(=O)[O-], [O-]N=N[O-], [N,P](=O)[O-], [N+](=O)([O-])[O-], P(=O)([O-])[O-], P(=O)([O-])([O-])[O-], S([O-])[O-], S(=O)([O-])[O-], S(=O)(=O)([O-])[O-], S(=O)(=O)([O-])OOS(=O)(=O)[O-]. Previously not all of these inorganic acid counterions were consistently neutralized.
• The None value in the RGroupCoreAlignment enum was renamed to NoAlignment in both C++ and Python, in order to avoid issues when attempting to access it from Python.

Highlights

• There's been another big improvement in the quality of molecule drawings: character and font handling is greatly improved thanks to the use of the FreeType library
• A new feature has been added to efficiently allow tautomer-insensitive substructure search.
• A new, much more accurate, algorithm is available for calculating CIP labels on atoms and bonds.
• There's a new rdDeprotect module to allow automatically deprotecting molecules before putting them into reactions
• Molecule and reaction metadata can now be added to PNG files generated by MolDraw2DCairo

Acknowledgements

Shrey Aryan, Jinserk Baik, Francois Berenger, Cédric Bouysset, David Cosgrove, Ivan Chernyshov, Guillaume Godin, Manan Goel, Jan H. Jensen, Gareth Jones, Maria Kadukova, Eisuke Kawashima, Steven Kearnes, Brian Kelley, Joos Kiener, Kenneth Lum, Joshua Meyers, Rocco Moretti, Paul R Moses, Dan Nealschneider, Jin Pan, Joann Prescott-Roy, Matthew Robinson, Jaime Rodríguez-Guerra, Ricardo Rodriguez-Schmidt, Jeff van Santen, Roger Sayle Vincent F. Scalfani Eric Taw, Ansgar Schuffenhauer, Paolo Tosco, Ivan Tubert-Brohman, Riccardo Vianello, Rachel Walker, Maciej Wójcikowski, Christopher Zou, daverona, hjuinj, intrigus-lgtm, autodataming, paconius, sailfish009

Bug Fixes:

• Python tests fail when RDK_BUILD_COMPRESSED_SUPPLIERS is enabled (github issue #1888 from greglandrum)
• ResonanceMolSupplier potentially stuck in infinite loop (github issue #2597 from tawe141)
• ctest pythonTestDirChem failed (github issue #2757 from jinserk)
• Issue with inversion/retention of stereochemistry (github issue #2891 from mc-robinson)
• cannot parse reaction SMILES/SMARTS with dative bonds (github issue #2954 from greglandrum)
• ResonanceMolSupplier can fail with small maxStructs values (github issue #3041 from greglandrum)
• seg fault in ResonanceMolSupplier() (github issue #3048 from greglandrum)
• Bug in image rendering of dative bonds (github issue #3056 from IvanChernyshov)
• Coordinates from coordgen are not centered around the origin (github pull #3058 from DavidACosgrove)
• fix a typo in ScaffoldNetwork/CMakeLists.txt (github pull #3060 from greglandrum)
• Bad double bond placement in polycyclic aromatics (github issue #3061 from DavidACosgrove)
• SGroups with more than one attachment point are now properly parsed (github pull #3072 from greglandrum)
• Reactions should not use strict implicit valence calculations (github issue #3097 from mwojcikowski)
• partial reacting atom detection (github issue #3119 from thegodone)
• DrawMolecules does not center molecules (github issue #3126 from JoshuaMeyers)
• results from coordgen are sometimes not centered (github issue #3131 from greglandrum)
• GCC 10.0.1 compile error (github issue #3135 from rvianello)
• Memory leak when parsing bad SMILES (github issue #3139 from intrigus-lgtm)
• Error breaking StereoBonds in reactions (github issue #3147 from mc-robinson)
• MolOps::removeHs() removes hydrides (github issue #3150 from jhjensen2)
• Kekulization error from CreateScaffoldNetwork (github issue #3153 from greglandrum)
• Fix drawing of N plus (github pull #3165 from DavidACosgrove)
• RWMol::clear() does not explicitly clean up SubstanceGroups or StereoGroups (github issue #3167 from greglandrum)
• Modifying a molecule should not automatically clear SubstanceGroups (github issue #3168 from greglandrum)
• removeHs() should not remove atoms in SubstanceGroups (github issue #3169 from greglandrum)
• fix a memory problem detected in malformed SMILES (github pull #3171 from greglandrum)
• Python wrapper: SetQuery and ExpandQuery for bonds (github pull #3172 from i-tub)
• S-groups: PARENT field should reference index (github issue #3175 from greglandrum)
• rdScaffoldNetwork causes segmenation fault upon None molecule (github issue #3177 from AnsgarSchuffenhauer)
• fix a small inconsistency in the name of the inchi package (github pull #3182 from rvianello)
• Molecule constructed from CXSMILES cannot be translated to SMARTS (github issue #3197 from greglandrum)
• Formatting fix of CalcRMS (github pull #3203 from chmnk)
• fix the CompressedSDMolSupplier python iterator interface (github pull #3204 from rvianello)
• Queries generated from PreprocessReaction cannot be translated to SMARTS (github issue #3206 from greglandrum)
• Attachment point info not being read from V2000 mol blocks (github issue #3207 from greglandrum)
• Memory Sanitizer fails on molFromPickle on empty file (github issue #3211 from intrigus-lgtm)
• Throw exception when reading from stream fails. (github pull #3212 from intrigus-lgtm)
• fix molstogridimage on certain fragments/smarts patterns (github pull #3217 from bp-kelley)
• Lines in wedge bonds being drawn too closely together (github issue #3226 from paconius)
• EnumerateStereochemistry should clear CIP labels (github issue #3231 from greglandrum)
• lock CI cairo version to force an install from the rdkit repo (github pull #3240 from greglandrum)
• XBCORR and XBHEAD in Sgroups no longer cause parse failures (github pull #3242 from greglandrum)
• LINKNODEs are ignored by the CTAB parsers (github pull #3247 from greglandrum)
• add GetStringVectProp() to SubstanceGroup class (github pull #3251 from greglandrum)
• Envelope aromaticity not detected in complex fused system (github issue #3256 from greglandrum)
• Draw.MolsToGridImage repeating atom indices (github issue #3258 from greglandrum)
• Atom indices clash with atom symbols in small pictures. (github issue #3262 from DavidACosgrove)
• MinimalLib Dockerfile is broken at HEAD (github issue #3267 from skearnes)
• Fixes #2757 (github pull #3268 from greglandrum)
• RGroupDecomposition restructuring (github pull #3270 from bp-kelley)
• Get PPC builds working (github pull #3285 from greglandrum)
• ScaffoldNetwork not in C# wrappers (github pull #3289 from jones-gareth)
• bonds with "either' stereo cannot be read from JSON (github pull #3290 from greglandrum)
• Small bug fixes and cleanups from fuzz testing (github pull #3299 from greglandrum)
• DrawOptions: bondLineWidth behaving differently since 2020 versions (github issue #3305 from kienerj)
• Not possible to copy SubstanceGroups in Python (github issue #3312 from greglandrum)
• Stereochemistry perception getting confused by a bad drawing. (github issue #3314 from greglandrum)
• SubstanceGroups should not be written with quotes around missing fields (github issue #3315 from greglandrum)
• SetDoubleBondNeighborDirections() not overwriting existing bond directions (github issue #3322 from greglandrum)
• AdjustQueryParameters.adjustSingleBondsBetweenAromaticAtoms does not modify ring bonds (github issue #3325 from greglandrum)
• Fixes for aromatic bond fuzzy queries (github pull #3328 from jones-gareth)
• lock sphinx version in CI due to problem with v3.2.0 (github pull #3332 from greglandrum)
• Remove deprecated Sphinx options (github pull #3335 from greglandrum)
• more bug fixes and cleanups from fuzz testing (github pull #3339 from greglandrum)
• unspecified branch bonds in SMARTS don't have aromaticity set (github issue #3342 from greglandrum)
• Incorrect resonance structures in presence of dative bonds (github issue #3349 from IvanChernyshov)
• Converting atoms with high radical counts to InChI generates incorrect results (github issue #3365 from greglandrum)
• Replace fill-opacity= with fill-opacity: in MolDraw2DSVG and tests (github pull #3368 from lummyk)
• Fixes a bug in AddHs() involving sp2 centers with degree 1 (github pull #3383 from ptosco)
• Information about charges and isotopes lost when calling AdjustQueryProperties (github issue #3388 from greglandrum)
• prepareMolForDrawing() incorrectly adds chiral Hs if no ring info is present (github issue #3392 from greglandrum)
• CXSMILES parser should not set atom maps for attachment points (github issue #3393 from greglandrum)
• Fixes a couple of query-related bugs (github pull #3398 from ptosco)
• Doing a match of a recursive smarts leaves traces of the previous match (github issue #3403 from bp-kelley)
• Recursive smarts cannot be used in the core for rgroup decomposition (github pull #3404 from bp-kelley)
• Improvements to reaction chirality handling (github pull #3412 from greglandrum)
• V3K mol blocks with no atoms fail to parse (github issue #3413 from greglandrum)
• Problem parsing SGroup data comtaining "" (github issue #3415 from greglandrum)
• MolEnumerator::enumerate() should call updatePropertyCache() (github pull #3420 from greglandrum)
  • Fixed bad draw scale in drawMolecules. Github3391. Take 2. (github pull #3424 from DavidACosgrove)
• Replace fill-opacity= to fill-opacity: in reaction.out (github pull #3426 from daverona)
• set the ChiralityPossible tag when using the new code with FindMolChiralCenters (github pull #3434 from greglandrum)
• Silence deprecation warning (github pull #3439 from ptosco)
• update minimallib python requirements to python3 (github pull #3449 from greglandrum)
• Fix dead links to inchi-trust (github pull #3451 from jvansan)
• ringMatchesRingOnly=True produces a SMARTS query that return no substructure matches (github issue #3458 from jaimergp)
• Normalization rule incorrectly matches sulfones (github issue #3460 from greglandrum)
• BlockLogs was reenabling all logs, not just the ones that were disabled (github pull #3466 from bp-kelley)
• Hydrogen is incorrectly identified as an "early" atom (github issue #3470 from greglandrum)
• Fixes typo that causes the build to fail (github pull #3477 from ptosco)
• Fix a crashing bug with None in rdMolStandardize (github pull #3481 from greglandrum)
• zlib.h not found if not in system directories (github issue #3493 from ricrogz)
• fix paths in ConformerParser tests (github pull #3504 from ricrogz)

New Features and Enhancements:

• Add GetBestRMS function (github issue #1820 from chmnk)
• Add reorder tautomers function and accompanying tests (github pull #3043 from chriswzou)
• Set RDK_BOOST_VERSION to pass minimum required version to FindBoost (github pull #3074 from e-kwsm)
• bug: the MCS of the molecules CH4 and CH3OH is empty. how to return C? (github issue #3095 from autodataming)
• start using boost:stacktrace (github pull #3124 from greglandrum)
• Add Fuzzing, fixes #2857 (github pull #3128 from intrigus-lgtm)
• Cookbook entry for ETKDG with rings (github pull #3129 from hjuinj)
• Fixes #2795 (github pull #3134 from manangoel99)
• Bump Catch2 to v2.12.1 (github pull #3136 from e-kwsm)
• Modernize how legacy C headers are included (github pull #3137 from e-kwsm)
• Avoid C preprocessor macros (github pull #3138 from e-kwsm)
• Modernization: use nullptr (github pull #3143 from e-kwsm)
• Update fuzzer dict (github pull #3162 from intrigus-lgtm)
• Add BCUT2D and AUTOCORR2D to desclist (github pull #3178 from bp-kelley)
• Remove usage of the deprecated random_shuffle() function (github pull #3187 from greglandrum)
• clang-tidy modernize-use-default-member-init and modernize-use-emplace (github pull #3190 from greglandrum)
• Tautomer search (github pull #3205 from jones-gareth)
• Add optional timeout to RGroupDecomposition (github pull #3223 from greglandrum)
• Allow symmetrization to be completely disabled in RGD code (github issue #3224 from greglandrum)
• gitignore source and build files from the RingFamilies external lib (github pull #3228 from d-b-w)
• Add new CIP labelling algorithm (github pull #3234 from ricrogz)
• Adds more options to adjustQueryProperties (github pull #3235 from greglandrum)
• Improve SSSR performance for large molecules (github pull #3236 from d-b-w)
• Support using FreeType for text rendering (github pull #3237 from DavidACosgrove)
• Cleanup warnings from clang-10 (github pull #3238 from greglandrum)
• DEB packaging: cairo support is needed to generate PNGs (github pull #3250 from UnixJunkie)
• Added call to test legends. (github pull #3252 from DavidACosgrove)
• Improve performance of aromaticity detection for large molecules (github pull #3253 from d-b-w)
• Speed up ring finding by skipping nodes not in rings (github pull #3254 from d-b-w)
• Support enumerating some mol file features into MolBundles (github pull #3257 from greglandrum)
• Add cxsmiles query atoms to CTAB parsers and writers (github pull #3261 from greglandrum)
• Update to Coordgen v1.4.1 (github pull #3265 from ricrogz)
• ScaffoldNetwork: add feature to count the number of molecules a scaffold originates from (github pull #3275 from greglandrum)
• rgroup speedup (github pull #3279 from bp-kelley)
• Stop trying to assign hybridization to actinides (github pull #3281 from greglandrum)
• Decouple coordgen and maeparser integrations (github pull #3286 from greglandrum)
• Avoid really slow Windows conda builds (github pull #3287 from ptosco)
• Embed default truetype font (github pull #3288 from greglandrum)
• Expanded support for CXSMILES features (github pull #3292 from greglandrum)
• Deprotection Library (github pull #3294 from bp-kelley)
• Use operator() and call() consistently across RDKit (github pull #3295 from ptosco)
• Molecule metadata in PNGs (github pull #3316 from greglandrum)
• Cleanup alignment dependencies (github pull #3317 from greglandrum)
• Add the option to minimize structures with coordgen (github pull #3319 from greglandrum)
• Updated code for chirality perception (github pull #3324 from greglandrum)
• Some work on TautomerEnumerator (github pull #3327 from ptosco)
• Add fragmentOnBonds to SWIG wrappers (github issue #3329 from greglandrum)
• Sped up SSSR by not storing every path back to root (github pull #3333 from rachelnwalker)
• Fix Cookbook formatting and added 4 new examples (github pull #3345 from vfscalfani)
• switch to using target_compile_definitions instead of add_definitions (github pull #3350 from greglandrum)
• [GSoC-2020] Generalized and Multithreaded File Reader (github pull #3363 from shrey183)
• support new CIP code and StereoGroups in MolDraw2D_detail::addStereoAnnotation() (github issue #3369 from greglandrum)
• expose additional SubstanceGroup data members to Python (github pull #3375 from greglandrum)
• Add MolDraw2DJS (github pull #3376 from greglandrum)
• Add APK package link for Alpine Linux distribution (github pull #3379 from daverona)
• Add SubstanceGroups to the SWIG Wrappers (github pull #3390 from jones-gareth)
• Add better support for isotopic Hs to removeHs() and addHs() (github pull #3396 from ptosco)
• Add support for abbreviations (github pull #3406 from greglandrum)
• Allow passing explicit removeHs, sanitize and strict flags to the MDL rxn parser (github pull #3411 from ptosco)
• Improvements to reaction chirality handling (github pull #3412 from greglandrum)
• RGD cleanup, optimization and a better fix for #1705 (github pull #3428 from ptosco)
• Tautomers with endocyclic double bonds should be preferred over exocyclic ones (github issue #3430 from ptosco)
• RGD: Code modernization and an optimization (github pull #3437 from ptosco)
• expose PNG metadata functions to python (github pull #3440 from greglandrum)
• Replace basestring (github pull #3441 from iammosespaulr)
• Get the Uncharger to deal with a larger set of acids correctly (github pull #3448 from ptosco)
• expose templated coordinate generation to the JS Wrapper (github pull #3450 from greglandrum)
• change default precision for coordgen (github pull #3452 from greglandrum)
• add coordgen support to demo.html (github pull #3453 from greglandrum)
• Two simple MolStandardizer code cleanups (github pull #3454 from ptosco)
• A few improvements to MolStandardize::Normalizer (github pull #3455 from ptosco)
• Add Cookbook entries 30-32 (github pull #3459 from vfscalfani)
• A few small tweaks to the drawing code (github pull #3464 from greglandrum)
• Make MetalDisconnector more robust against metallorganics (github pull #3465 from greglandrum)
• Add nocharge algorithm example to cookbook (github pull #3467 from vfscalfani)
• ROMol: add inline impl for common getNumAtoms call (github pull #3469 from jinpan)
• Improve sphinx formatting in rdSubstructLibrary (github issue #3471 from cbouy)
• Cmake config improvements (github pull #3478 from rvianello)
• allow fillColour to be changed from python (github pull #3480 from greglandrum)
• Fix undefined behavior in testCoordGen test (github pull #3495 from roccomoretti)
• Add a version for the pattern fingerprint (github pull #3496 from greglandrum)
• Fixes a number of issues flagged by clang (github pull #3498 from ptosco)
• Update to maeparser v1.2.4 (github pull #3506 from sailfish009)
• Fix python invalid escape sequences (github pull #3508 from ricrogz)

Code removed in this release:

• To improve API consistency of the exceptions in RDKit with the default ones in the STL, the several message() methods and Invariant::getMessage() in RDKit's exceptions have been removed in favor of what().
• The old MolHash code has been removed from the C++ code, all wrappers, and the PostgreSQL cartridge.

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

• The function FileParserUtils::replaceAtomWithQueryAtom() has been moved to the namespace QueryOps. Please use QueryOps::replaceAtomWithQueryAtom() instead. The version in the FileParserUtils namespace will be removed in the next release.
• The method std::vector<ROMOL_SPTR> TautomerEnumerator::enumerate(const ROMol &mol, boost::dynamic_bitset<> *modifiedAtoms, boost::dynamic_bitset<> *modifiedBonds = nullptr) is deprecated and will be removed in a future release. Please use TautomerEnumeratorResult TautomerEnumerator::enumerate(const ROMol &mol,bool reassignStereo = true) instead.
• The MolDraw2DQt class is no longer supported since we don't think anyone is using it. It will be removed in the 2021.03 release unless we learn otherwise.