Release_2024.03.6

(Changes relative to Release_2024.03.5)

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)

Christoph Berg, David Cosgrove, Andrew Kane, Eisuke Kawashima, Brian Kelley, Joos Kiener, Phong Lam, Niels Kristian Kjærgård Madsen, Amanda P, Julianus Pfeuffer, Ricardo Rodriguez, Ernst-Georg Schmid, Junior Sen, Paolo Tosco, Chad Townsend, Riccardo Vianello, nmaeder, spparel, buerbaumer

New Features and Enhancements:

• GIST index improvements for @= (github pull #7547 from ergo70)
• Rascal atom and bond equivalences (github pull #7612 from DavidACosgrove)
• Add support for building the CFFI lib without InChI (github pull #7698 from ankane)
• Move calculation of molecular weight, exact molecular weight, and moleuclar formula to MolOps (github issue #7701 from greglandrum)
• Add more "contribs" classes for use in conformer generation (github pull #7711 from nmaeder)
• Allow atom map numbers to be ignored when generating canonical SMILES (github pull #7732 from DavidACosgrove)
• Expose two additional boolean flags for mol creation to MinimalLib (github pull #7743 from ptosco)
• Complement JSMol with JSMolShared (github pull #7744 from ptosco)
• Fix vectToString such that it outputs valid JSON (github pull #7749 from ptosco)
• SaltRemover loses E/Z configuration (github issue #7750 from JuniorSen)

Bug Fixes:

• rdMolDescriptors.CalcNumAtomStereoCenters fails on Sanitized Molecule (github issue #6757 from C-Townsend)
• Pre-condition violations for BCUT descriptor calculations (github issue #7364 from paulsonak)
• PostgreSQL 17: ERROR: commutator operator = is already the commutator of operator = (github issue #7459 from df7cb)
• Index anomaly with mol @= mol operator on PostgreSQL. Exact match is extremely slow! (github issue #7493 from ergo70)
• CDXML Parser doesn't recognize dative bonds (github issue #7501 from kienerj)
• Handling of chiral sulfur in aromatic rings (github issue #7556 from spparel)
• Stub files contain duplicate argument names (github issue #7583 from nielskm)
• Update commutator/negator settings for operator @= (github pull #7596 from rvianello)
• EnumerateStereoisomers Runtime error when enumerate guanidine derivatives on rdkit 2024.03.4 (github issue #7608 from phonglam3103)
• Bad solid wedge to alkyne group (github issue #7620 from DavidACosgrove)
• Deprecation warning from Descriptors.CalcMolDescriptors (github issue #7625 from kienerj)
• Fix parsing RBCNT from mol files, and add exporting it (github pull #7638 from ricrogz)
• Multithreaded InPlace standardization functions seg fault if there's a duplicate molecule (github issue #7642 from greglandrum)
• MinimalLib: fix misformatted molblock and make sure unit test is actually executed (github pull #7647 from ptosco)
• Reaction pickling does not honor PicklePropertiesOptions (github issue #7674 from jpfeuffer)
• Make sure angleconstraints only take angles between 0 and 180 degrees. (github pull #7688 from nmaeder)
• Determine bonds calls debugMol in certain cases (github issue #7691 from bp-kelley)
• Double-bond geometry lost from CXSMILES? (github issue #7725 from greglandrum)
• Ensure 13 bounds constraints are added to angles that are part of an improper torsion (github pull #7729 from nmaeder)
• Bad 2-colour wedge (github issue #7739 from DavidACosgrove)

Cleanup work:

• fix(rdmolfiles): fix parameters and docstrings (github pull #7648 from e-kwsm)
• Refactor distgeom minimizations (github pull #7652 from nmaeder)
• Fix some missing headers when doing "make install" (github pull #7667 from greglandrum)
• Remove Descriptors as a dependency of many other RDKit libraries (github pull #7700 from greglandrum)
• Reduce code duplication in ff (github pull #7715 from nmaeder)
• Some cmake cleanup work (github pull #7720 from greglandrum)
• doc: fix -Wdocumentation-html (github pull #7721 from e-kwsm)
• Code cleanup, minor refactoring and typos (github pull #7742 from ptosco)