tag release (#6801)

CMakeLists.txt

@@ -137,7 +137,7 @@ set(RDK_PYTHON_OUTPUT_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/rdkit")
 set(RDKit_Year "2023")
 set(RDKit_Month "09")
 set(RDKit_Revision "1")
-set(RDKit_RevisionModifier "b1")
+set(RDKit_RevisionModifier "")
 set(RDKit_ABI "1")
 
 # we need an integer version of the month later, so remove the zero padding

Docs/Book/BackwardsIncompatibleChanges.md

@@ -8,6 +8,51 @@ generally include changes in results that arise due to bug fixes; we try to call
 those out in the release notes. The release notes, in general, contain a more
 comprehensive version of this list.
 
+## Release 2023.09
+
+### Changes in atomic stereochemistry perception
+
+The algorithm for perception of atomic stereochemistry from 2D structures has
+been rewritten. The new algorithm is more accurate, which results in some
+differences in perceived stereo between this release and the previous ones.
+
+### Changes in the MCS code
+
+- The user-configurable `MCSParameters::FinalMatchChecker` function is now
+called after the built-in `FinalMatchChecker` function, rather as
+alternatively to the built-in `FinalMatchChecker` function. This was a
+design flaw which is worth correcting.
+- Setting `MCSParameters::Timeout` to 0 means no timeout, rather than 0s
+timeout, which is rather pointless as it would cause MCS to be canceled
+immediately.
+- Result SMARTS strings generated by `FindMCS` when
+`MCSParameters::MatchRingFusionStrict` is `true` now include ring membership
+queries where appropriate in order to ensure more specific substructure
+matches.
+- In MCS Verbose statistics, `SingleBondExcluded` was renamed to
+`IndividualBondExcluded` to avoid confusion, since single bond has a
+different meaning in chemistry.
+
+### Changes to canonicalization
+
+Information about stereo groups is no longer used in the SMILES canonicalization
+process if CXSMILES are not being generated.
+
+
+## Release 2023.03
+
+### Changes to ring finding
+
+- The ring-finding functions will now run even if the molecule already has ring information. Older versions of the RDKit would return whatever ring information was present, even if it had been generated using a different algorithm.
+- The ring-finding functions now no longer consider dative bonds as possible ring bonds by default. All of the ring-finding functions have a new optional argument `includeDativeBonds` which can be used to change this behavior
+
+### Changes to canonicalization
+
+The canonical SMILES and CXSMILES generated for molecules with enhanced stereochemistry (stereo groups) is different than in previous releases. The enhanced stereochemistry information and the stereo groups themselves are now canonical. This does *not* affect molecules which do not have enhanced stereo and will not have any effect if you generate non-isomeric SMILES. This change also affects the output of the MolHash and RegistrationHash code when applied to molecules with enhanced stereo.
+
+
+
+
 ## Release 2022.09
 
 ### Changes in canonicalization

ReleaseNotes.md

@@ -1,4 +1,4 @@
-# Release_2023.09.1b1
+# Release_2023.09.1
 (Changes relative to Release_2023.03.1)
 
 ## Acknowledgements
@@ -9,13 +9,20 @@ GitHub)
 Jason Biggs, Jonathan Bisson, David Cosgrove, Andrew Dalke, Christian W.
 Feldmann, Eloy Félix, Richard Gowers, Tadd Hurst, Gareth Jones, Eisuke
 Kawashima, Brian Kelley, Joos Kiener, Juuso Lehtivarjo, John Mayfield, Vedran
-Miletić, Jeremy Monat, Dan Nealschneider, Timothy Ngotiaoco, Axel Pahl, Ricardo
-Rodriguez-Schmidt, Ernst-Georg Schmid, Paolo Tosco, Ivan Tubert-Brohman,
-Riccardo Vianello, Rachel Walker, Maciej Wójcikowski, pierred5, lhyuen,
-paconius, BartlomiejF, thomp-j, wangyingxie, teltim, Meteor-han, abefrandsen, 
+Miletić, Jeremy Monat, Dan Nealschneider, Timothy Ngotiaoco, Axel Pahl, Rachael
+Pirie, Ricardo Rodriguez-Schmidt, Ernst-Georg Schmid, Paolo Tosco, Ivan
+Tubert-Brohman, Riccardo Vianello, Rachel Walker, Maciej Wójcikowski, pierred5,
+lhyuen, paconius, BartlomiejF, thomp-j, wangyingxie, teltim, Meteor-han,
+abefrandsen, 
 
 ## Highlights
-to be completed
+- The new RascalMCES code adds a very fast maximum common substructure
+  implementation for pairs of molecules.
+- The RDKit core now supports "generalized substructure searching", making it
+  easier to take link nodes, variable attachment points, and tautomer queries
+  into account when doing substructure searches. This is now also supported in
+  the PostgreSQL cartridge.
+- The RDKit now has support for reading and writing MRV files.
 
 ## Backwards incompatible changes
 - The CDXML parser now returns mols with reasonable coordinates and in
@@ -58,6 +65,8 @@ to True.
 - The algorithm for perception of atomic stereochemistry from 2D structures has
 been rewritten. The new algorithm is more accurate, which results in some
 differences in perceived stereo between this release and the previous ones.
+- Information about stereo groups is no longer used in the SMILES
+canonicalization process if CXSMILES are not being generated.
 
 ## New Features and Enhancements:
   - Mols matrix to grid image
@@ -132,8 +141,12 @@ differences in perceived stereo between this release and the previous ones.
  (github pull #6700 from greglandrum)
   - Add hasQueryHs
  (github pull #6702 from bp-kelley)
+  - Exporting to mol marks imine bonds EITHERDOUBLE when imine H is implicit
+ (github issue #6703 from ricrogz) 
   - Use the connect-the-dots algorithm by default in DetermineBonds
  (github pull #6740 from greglandrum)
+  - Add function to calculate all 3D descriptors
+ (github pull #6741 from RPirie96)
   - Add SpacialScore
  (github pull #6742 from apahl)
   - Extract the core matching logic into a separate function
@@ -215,6 +228,8 @@ differences in perceived stereo between this release and the previous ones.
  (github pull #6473 from greglandrum)
   - Fix RWMol::addAtom docstring
  (github pull #6477 from d-b-w)
+  - StereoGroup information should not impact canonicalization when CXSMILES isn't being generated
+ (github issue #6479 from greglandrum)
   - Fix a few broken docstrings
  (github pull #6480 from ptosco)
   - pin numpy to 1.24.3
@@ -281,6 +296,8 @@ differences in perceived stereo between this release and the previous ones.
  (github pull #6730 from johnmay)
   - ConnectTheDots can segfault if all atoms do not have residue info
  (github issue #6756 from jasondbiggs)
+  - _moltoimg() should honor drawOptions.prepareMolsBeforeDrawing
+ (github issue #6792 from ptosco)
 
 ## Cleanup work:
  - adjustQueryProperties cleanup