rdkit/rdkit: 2021_09_1 (Q3 2021) Release

Release_2021.09.1

(Changes relative to Release_2021.03.1)

Backwards incompatible changes

• RWMol.replaceAtom() no longer removes SubstanceGroups which reference that atom.
• The keepSGroups argument to RWMol.replaceBond() now defaults to true.
• The SMARTS parser now by default accepts CXSMILES extensions and molecule names. SMARTS which previously failed to parse like CCC fail will now return valid molecules.
• Molecule names in SMILES and SMARTS are now parsed by default. Previously they were ignored.
• The getParams() function for retrieving UFF parameters now returns a const pointer instead of a standard pointer. This shouldn't affect the functionality of any code since the only method of the class is also const.

Highlights

• Single reactant/single product reactions can now be applied in-place. This really helps with the performance of these kinds of transformations.
• The CFFI wrapper around MinimalLib greatly expands the number of possible places the RDKit can be used from.
• A number of general enhancements and quality-of-life improvements were made to the PostgreSQL cartridge.

Acknowledgements

Jason Biggs, Kit Choi, David Cosgrove, Eloy Félix, Harrison Green, Gareth Jones, Eisuke Kawashima, Alan Kerstjens, Brian Kelley, John Konecny, Stephanie Labouille, Rasmus Lundsgaard, Hadrien Mary, Michel Moreau, Dan Nealschneider, Axel Pahl, Maximilian Peters, Alessio Ragno, Ricardo Rodriguez-Schmidt, Riccardo Sabatini, Roger Sayle, Vincent F. Scalfani, Dan Skatov, David Slochower, Peter St. John, Mihaly Szabo, Ichiru Take, Paolo Tosco, Ivan Tubert-Brohman, Kazuya Ujihara, Alain Vaucher, Riccardo Vianello, Rachel Walker, Shuzhe Wang, Maciej Wójcikowski, bzoracler, jungb-basf, charly828, yoer77,

Code removed in this release:

• The minimizeOnly option for coordgen has been removed.

Contrib updates:

• Contribute FreeWilson analysis (github pull #4026 from bp-kelley)

Bug Fixes:

• cannot pass drawOptions to MolsToGridImage when using notebook (github issue #3101 from slochower)
• Draw.MolToImage() cannot highlight with highlightMap (v > '2019.09.3' ) (github issue #3616 from spideralessio)
• EnumerateStereoisomers fail with STEREOANY bonds from molblock (github issue #3759 from TermeHansen)
• Double bond stereo gets flipped by SMILES reader/writer (github issue #3967 from mwojcikowski)
• SparseIntVect copy constructor and assignment operators not clearing existing data (github issue #3994 from AlanKerstjens)
• MolFragmentToSmiles with kekuleSmiles=True raises AtomKekulizeException (github issue #3998 from kazuyaujihara)
• update clang version for linux CI fuzzer builds (github pull #4012 from greglandrum)
• Update coordgen to 2.0.3 (github pull #4017 from d-b-w)
• Get SWIG wrappers working with C# again (github pull #4020 from kazuyaujihara)
• replaceSidechains creates aromatic dummy atoms (github pull #4022 from ptosco)
• A set of fixes for problems caused by bad input (github pull #4033 from greglandrum)
• Cleanup some problems found during an ASAN build (github pull #4054 from greglandrum)
• Avoid that lone atoms which are part of a ring in one of the molecules become part of the MCS (github pull #4065 from ptosco)
• StereoGroups not preserved by RenumberAtoms() (github issue #4071 from greglandrum)
• call to pyAvalonTools.Generate2DCoords results in an assert violation (github issue #4075 from rvianello)
• Update boost download location in Dockerfile (github pull #4094 from greglandrum)
• HCount field in v2000 Mol blocks ignored (github issue #4099 from riccardosabatini)
• Reactions don't propagate bond properties (github issue #4114 from d-b-w)
• RemoveStereochemistry should also remove stereogroups (github issue #4115 from greglandrum)
• Avoid that MolStandardizer segfaults on empty mols (github pull #4119 from ptosco)
• SEGV in RWMol::commitBatchEdit (github issue #4122 from hgarrereyn)
• SEGV in ROMol::getAtomDegree if atom is not in graph (github issue #4127 from hgarrereyn)
• SEGV from unsigned integer overflow in Conformer::setAtomPos (github issue #4128 from hgarrereyn)
• HCOUNT from v3000 CTABS incorrectly interpreted (github issue #4131 from greglandrum)
• Empty query produces empty match, but at the same time is considered non-matching (github issue #4138 from i-tub)
• fixed AddBond documentation (github pull #4142 from Ashafix)
• Possible bug with EnumerateStereoisomers (github issue #4144 from stephanielabouille)
• Odd drawing behavior with radicals and MolsToGridImage (github issue #4156 from pstjohn)
• pre-condition violation when sanitizing a de-pickled reaction (github issue #4162 from jasondbiggs)
• Many of the PMI descriptors are not being recalculated for different conformers (github issue #4167 from greglandrum)
• bug in MDLParser.cpp when reading a rxn file in v3000 format that contains agents (github issue #4183 from jungb-basf)
• Potentially chiral bridgehead atoms not being identified. (github pull #4192 from greglandrum)
• allow more recoverable V3000 parsing errors when strictParsing=false (github pull #4210 from greglandrum)
• RGD: Fix memory leak with deleting array (github pull #4211 from bp-kelley)
• UnfoldedRDKFingerprintCountBased returns a different fingerprint length for every molecule (github issue #4212 from greglandrum)
• rdMolHash.MolHash fails on non-standard valences (github issue #4222 from ricrogz)
• Fix a couple of problems with fingerprint count simulation (github pull #4228 from greglandrum)
• Chem.MolFromSmiles using SmilesParserParams throws exceptions (github issue #4232 from greglandrum)
• Parse failure for data groups in CXSMILES (github issue #4233 from greglandrum)
• double bonds now have EITHER stereo if no coordinates are present (github pull #4239 from greglandrum)
• Fix CMakeLists for FileParsers (github pull #4240 from kazuyaujihara)
• Multiple ATTCHPT entries for one atom handled incorrectly (github issue #4256 from greglandrum)
• Exception thrown by reionizer when dealing with Mg+2 (github issue #4260 from greglandrum)
• Fallback ring finding failing on molecules with multiple fragments (github issue #4266 from avaucher)
• Make sure that ResonanceMolSupplier substructure matches are uniquified consistently (github pull #4274 from ptosco)
• FindPotentialStereo() doesn't find marked ring stereo when flagPossible=False (github issue #4279 from greglandrum)
• The normalization pattern for pyridine N-oxide is not specific enough (github issue #4281 from ptosco)
• computeCanonicalTransform may generate non-canonical coords (github issue #4302 from ptosco)
• Unreasonable calculation of implicit valence for atoms with query bonds (github issue #4311 from greglandrum)
• call to AvalonTools::set2DCoords results in an assert violation (github issue #4330 from jasondbiggs)
• MolBlock writer gives non-stereo double bonds "unspecified" parity (github issue #4345 from d-b-w)
• Specified trans stereo being ignored during conformation generation in macrocycles (github issue #4346 from greglandrum)
• Two MinGW build fixes and one MSVC build fix (github pull #4347 from ptosco)
• Fixes RDK_BUILD_THREADSAFE_SSS=OFF build (github pull #4349 from ptosco)
• clean up some leaks identified by an ASAN build (github pull #4354 from greglandrum)
• Three more Windows build fixes (github pull #4356 from ptosco)
• Specified grid spacing for ShapeTanimotoDistance is ignored. (github issue #4364 from greglandrum)
• Need implicit H cleanup after rdMolEnumerator.Enumerate() (github issue #4381 from greglandrum)
• rdMolEnumerator.Enumerate fails on variable attachment points with queries (github issue #4382 from greglandrum)
• RDKit reaction produces wrong double bond stereochemistry (github issue #4410 from mwojcikowski)
• "to-Python converter already registered; second conversion method ignored." warnings issued at import (github issue #4425 from ricrogz)
• v2000 SGroups do not generate an "index" property (github issue #4434 from ricrogz)
• pg_restore does not work with some mol type molecule (github issue #4442 from mihalyszabo88)
• Building with static dependencies breaks CMake exports (github issue #4449 from ricrogz)
• DataStruct vectors leak when iterating (github issue #4465 from bp-kelley)
• SGroups: Additional SDT properties not decoded if FIELDNAME is empty (github issue #4476 from greglandrum)
• Test failure in reaction.sql (github issue #4486 from yoer77)
• Small rings can have STEREOANY/EITHERDOUBLE bonds (github issue #4494 from ricrogz)
• OR queries involving aromatic atoms cannot be drawn (github issue #4496 from ptosco)
• MolFromSmiles and MolFromSmarts incorrectly accepting input with spaces (github issue #4503 from greglandrum)
• Native 2D layout engine may generate overlapping coordinates (github issue #4504 from ptosco)
• SubstanceGroup labels sometimes overlap with atoms in image generation (github issue #4508 from rachelnwalker)
• SGroups do not have a way of unsetting properties from Python (github issue #4514 from ricrogz)
• operator<< is declared for AtomPDBResidueInfo but not defined (github issue #4535 from greglandrum)
• Improve test coverage and some bug fixes (github pull #4536 from greglandrum)
• Seg fault in MolDraw2D::drawMolecules() (github issue #4538 from greglandrum)
• Salt removal forces sanitization (github issue #4550 from ricrogz)
• fix a thread-safety bug in the UFF parameter loading (github pull #4553 from greglandrum)
• GetSubstructMatches() loops at 43690 iterations. (github issue #4558 from ricrogz)
• failure to parse CTAB with LINKNODE and SGROUP (github issue #4561 from greglandrum)
• Requesting "density" fingerprint Hydrogen molecule fails with exception (github issue #4567 from ricrogz)
• Incorrect double bond stereo in output SMILES around ring closures (github issue #4582 from greglandrum)
• migrate the MHFP implementation to use boost::random (github pull #4603 from rvianello)
• Fix EnumerateStereoisomers with tryEmbedding (github pull #4615 from kazuyaujihara)

New Features and Enhancements:

• Support Chemical Markup Language, CML, for writing (github pull #3024 from e-kwsm)
• Add Eigen to ExternalProject and automatically download if RDK_BUILD_DESCRIPTORS3D (github pull #3075 from e-kwsm)
• updates to postgreSQL cartridge (github pull #3976 from greglandrum)
• Update Overview.md (github pull #3992 from charly828)
• MinimalLib: add CFFI interface (github pull #4018 from greglandrum)
• Contribute FreeWilson analysis (github pull #4026 from bp-kelley)
• Allow partial deserialization of molecules (github pull #4040 from greglandrum)
• Add datamol project (github pull #4046 from hadim)
• Build BCUT when RDK_BUILD_DESCRIPTORS3D=OFF (github pull #4085 from kazuyaujihara)
• Making RDKit minimallib (JS lib) available through the npm package manager (github pull #4086 from MichelML)
• Normalize line endings in source code files (github pull #4104 from ptosco)
• Allow MolToQPixmap to support PySide2 (github pull #4110 from kitchoi)
• update ChEMBL projects in Projects using RDKit (github pull #4116 from eloyfelix)
• A collection of MolStandardize improvements (github pull #4118 from greglandrum)
• Run clang-format against header files (github pull #4143 from e-kwsm)
• Some miscellaneous MinimalLib enhancements (github pull #4169 from ptosco)
• [MinimalLib] Add number of heavy atoms to descriptors (github issue #4184 from apahl)
• Comments added to RGD core matching (github pull #4189 from jones-gareth)
• Fix/rdprop integer conversions (github pull #4194 from bp-kelley)
• RWMol cleanup (github pull #4198 from greglandrum)
• Test comparing SVGs via hash code - ready for review (github pull #4199 from DavidACosgrove)
• support getNumAtoms and getNumHeavyAtoms as Descriptors (github pull #4200 from greglandrum)
• Canon.cpp canonicalizeDoubleBond function refactor (github pull #4204 from jfkonecn)
• Add low level functions to bulk-update Substance Group atoms & bonds (github pull #4206 from ricrogz)
• Run clang-tidy (modernize-pass-by-value) (github pull #4224 from e-kwsm)
• Shift Trajectory and Snapshot constructors to methods on classes (github pull #4225 from bzoracler)
• Allow depiction of "either" double bonds as "wiggly neighbors" (github issue #4238 from d-b-w)
• Some cartridge enhancements (github pull #4271 from greglandrum)
• [Enhancement]: Allow every bit-vect fixed-size fingerprints can be directly embedded || attached into the (Numpy) Array or return the Numpy Array (github issue #4273 from IchiruTake)
• Turn MRV_COORDINATE_BOND_TYPE data Substance Groups into coordinate bonds (github pull #4299 from ricrogz)
• Support using SubstructMatchParameters in RGD (github pull #4318 from greglandrum)
• Add partial CXSMARTS support (github issue #4319 from greglandrum)
• Support toggling components of CXSMILES output (github issue #4320 from greglandrum)
• Switch to using InChI v1.06 (github issue #4322 from greglandrum)
• support using RGBA colors (github issue #4323 from greglandrum)
• MinimalLib: return fingerprints as BitSets (github issue #4329 from dskatov)
• Expose atomColourPalette as JSON drawOption (github pull #4337 from ptosco)
• Improved sgroup output (github pull #4343 from greglandrum)
• support get_json in the rdkitjs wrapper (github pull #4348 from greglandrum)
• Enable using the URF library in Windows static builds (github pull #4357 from ptosco)
• a few doxygen comment fixes (github pull #4368 from jasondbiggs)
• Enable building Java wrappers with MinGW compilers (github pull #4384 from ptosco)
• add exactmw to cartridge (github issue #4386 from greglandrum)
• Some cartridge additions and fixes (github pull #4387 from greglandrum)
• Remove SWIG kludge on Windows (github pull #4388 from ptosco)
• CXSMILES improvements (github pull #4396 from greglandrum)
• SubstructLibrary improvements (github pull #4403 from greglandrum)
• Add 3 new examples to Cookbook. (github pull #4404 from vfscalfani)
• cleanup the use of lambdas in the code (github pull #4432 from greglandrum)
• Swap from RDUNUSED_PARAM to unnamed parameters (github pull #4433 from greglandrum)
• Fix #4442 and other cartridge improvements (github pull #4448 from greglandrum)
• RDKit Cartridge: qmol GiST support (github issue #4463 from mwojcikowski)
• Add ToList method to Sparse/ExplicitBitVector (github pull #4467 from bp-kelley)
• GiST support to qmol type (github pull #4470 from mwojcikowski)
• be more tolerant when kekulizing (github pull #4492 from greglandrum)
• Allow applying single-reactant/single-product reactions in place (github pull #4511 from greglandrum)
• Add custom distance bounds parameter for ETKDG conformer generation (github pull #4516 from hjuinj)
• cleanup some compiler warnings (github pull #4521 from greglandrum)
• Improve test coverage and some bug fixes (github pull #4536 from greglandrum)
• Additions to the jupyter integration (github pull #4541 from greglandrum)
• another round of cartridge improvements (github pull #4543 from greglandrum)
• Major speed-up of RGD scoring (github pull #4544 from ptosco)
• Expose get_smarts to JS (github pull #4547 from ptosco)
• Improve performance of removing substruct/tautomer duplicates (github pull #4560 from ricrogz)
• Add support for SRUs to MolEnumerator (github pull #4563 from greglandrum)
• Adds KeyFromPropHolder to hold user defined indices (github pull #4571 from bp-kelley)
• add ROMol::atomNeighbors() and ROMol::atomBonds() (github pull #4573 from greglandrum)
• Improvements to some constructors in python wrappers (github pull #4581 from greglandrum)
• Add FreeSASA support to Windows builds (github pull #4584 from ptosco)
• use V3K mol blocks in PNG metadata (github pull #4588 from greglandrum)
• Prevent some loop variables from creating unnecessary copies (github pull #4610 from rvianello)
• Rename the molLinkNode property to _molLinkNode (github pull #4614 from greglandrum)
• Fix clang warning -Wabsolute-value (github pull #4616 from e-kwsm)

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

• The useCountSimulation keyword argument for rdFingerprintGenerator.GetMorganGenerator and rdFingerprintGenerator.GetAtomPairGenerator has been deprecated and will be removed in the next release. Please use the countSimulation keyword argument instead.
• The function mol_from_smarts() in the PostgreSQL cartridge has been deprecated and will be removed in the next release. Please use the qmol_from_smarts() function instead.
• The computeBalabanJ() functions from the MolOps namespace have been deprecated and will be removed in the next release. These have not been exposed to Python, so this will not affect any Python code.