From a9d6642f7dd732ee05814937f0279a05a7485754 Mon Sep 17 00:00:00 2001 From: Greg Landrum Date: Fri, 6 Oct 2023 13:07:26 +0200 Subject: [PATCH] update release notes and cmakelists for beta (#6788) --- CMakeLists.txt | 2 +- ReleaseNotes.md | 260 +++++++++++++++++++++++++++++++++++++++++++++++- 2 files changed, 259 insertions(+), 3 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index b7a63699b1..356acb8914 100644 --- a/CMakeLists.txt +++ b/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 "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 bd95bafbd5..b36f5cdac5 100644 --- a/ReleaseNotes.md +++ b/ReleaseNotes.md @@ -1,9 +1,21 @@ -# Release_2023.09.1 +# Release_2023.09.1b1 (Changes relative to Release_2023.03.1) ## 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) + +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, ## Highlights +to be completed ## Backwards incompatible changes - The CDXML parser now returns mols with reasonable coordinates and in @@ -43,13 +55,257 @@ cast", they now need to be matched with the regex `[B,b]ad any[\ ,_]cast` - The functions for determining connectivity in DetermineBonds now use a more efficient method by default. To go back to the old behavior, set the useVdw argument 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. + +## New Features and Enhancements: + - Mols matrix to grid image + (github pull #6080 from bertiewooster) + - Reduce space overhead of enabling the inclusion of properties when serializing molecules + (github issue #6312 from rvianello) + - Add optional sortsupport methods to the PostgreSQL GiST indices + (github pull #6313 from rvianello) + - Add a new parameter to mol_adjust_query_properties for generic query parameters + (github pull #6332 from bjonnh-work) + - add DebugDraw() function + (github pull #6340 from greglandrum) + - Optimize GetPropsFromDict: use tags for conversion + (github pull #6355 from bp-kelley) + - Fix cleanupOrganometallics and reinstate to sanitisation + (github pull #6357 from DavidACosgrove) + - postgres cartridge: cleanup a few obsolete build options + (github pull #6363 from rvianello) + - Fixes some issues in the SubstructLibrary JS implementation + (github pull #6385 from ptosco) + - Support TautomerQuery and MolBundle queries in the cartridge + (github pull #6393 from greglandrum) + - JS: Implement in-place aromatisation/kekulisation and avoid undesired exception + (github pull #6407 from ptosco) + - Optionally expose MCS to JS and extend optional compilation to JSReaction and JSSubstructLibrary + (github pull #6409 from ptosco) + - Add a method "HasQuery()" to Mol class + (github issue #6411 from kienerj) + - Enable using JSSubstructLibrary without pattern fps + (github pull #6431 from ptosco) + - Add support for generalized substructure searching + (github pull #6443 from greglandrum) + - Add atom and bond property parameters to substruct matching + (github pull #6453 from rachelnwalker) + - Replace a try..catch block with an if clause + (github pull #6488 from ptosco) + - Add an in place version of most of the MolStandardize functionality + (github pull #6491 from greglandrum) + - Exposed partial sanitization options to MinimalLib (both JS and CFFI) + (github pull #6519 from ptosco) + - Optionally forward Enhanced Stereo Group ids + (github pull #6560 from ricrogz) + - Add support for dative bonds in MOL files + (github pull #6566 from bjonnh-work) + - RASCAL MCES + (github pull #6568 from DavidACosgrove) + - Support additional generic groups + (github pull #6570 from bjonnh-work) + - Add support for Marvin files + (github pull #6575 from bjonnh-work) + - Add a "rootedAtAtom" to MolToSmarts + (github pull #6581 from ricrogz) + - RGD to support tautomers of core + (github issue #6609 from jones-gareth) + - Fix some build warnings + (github pull #6618 from ricrogz) + - Exposed log capture functionality to MinimalLib + (github pull #6628 from ptosco) + - add option to use sequential random seeds in the conformer generator + (github pull #6639 from greglandrum) + - Major MCS refactoring: new features and bug fixes + (github pull #6646 from ptosco) + - Lasso highlights + (github pull #6653 from DavidACosgrove) + - extract continuous lines from the conrec code + (github pull #6676 from greglandrum) + - Allow some tolerance in flatness determination + (github pull #6696 from ricrogz) + - Do not trust the 2D/3D tag in ctab mol files + (github pull #6697 from ricrogz) + - expose the CDXML reaction parsers to python + (github pull #6700 from greglandrum) + - Add hasQueryHs + (github pull #6702 from bp-kelley) + - Use the connect-the-dots algorithm by default in DetermineBonds + (github pull #6740 from greglandrum) + - Add SpacialScore + (github pull #6742 from apahl) + - Extract the core matching logic into a separate function + (github pull #6754 from ptosco) ## Bug Fixes: + - rdFMCS.FindMCS uses huge amounts of memory for this pair of molecules when CompleteRingsOnly is True + (github issue #3965 from i-tub) + - PF6- still can not get Bad Conformer Id after the #510 issue fix + (github issue #5145 from wangyingxie) + - Order dependence for rdFMCS.FindMCS with MatchFusedRingsStrict + (github issue #5411 from pierred5) + - Failed FMCS results with certain seed SMARTS and MatchFusedRings* parameters on + (github issue #5440 from pierred5) + - Seed SMARTS to FindMCS() produces incorrect MCS + (github issue #5457 from pierred5) + - FindMCS returns wrong result with monoatomic molecules + (github issue #5510 from ptosco) + - queryMol from FindMCS doesn't match mols used to generate MCS + (github issue #6082 from paconius) + - Crash when parsing InChI + (github issue #6172 from eloyfelix) + - Iteration over Python GetAtoms is 10-20x slower than need be + (github issue #6208 from d-b-w) + - refactor(python): replace deprecated unittest methods + (github pull #6304 from e-kwsm) + - generateDepictionMatching2DStructure: bonds to R groups should be generic when matching + (github pull #6306 from ptosco) + - MolToSmiles(canonical=False) creates the wrong _smilesBondOutputOrder property + (github issue #6315 from adalke) + - MolToMolBlock ignores unspecified information for double bonds in rings + (github issue #6316 from mwojcikowski) + - bump yaehmop version + (github pull #6330 from greglandrum) + - rdMolDraw2D.MolDraw2DCairo produces Pre-condition Violation: no draw context when SetColour, DrawRect or DrawLine was called. + (github issue #6336 from lhyuen) + - Added cstdint include + (github pull #6338 from vedranmiletic) + - remove the dependency from python distutils in the top CMakeLists.txt file + (github pull #6339 from rvianello) + - take drawOptions into account when exporting structure to xlsx format + (github pull #6341 from ptosco) + - Fix swig memory leak + (github pull #6346 from jones-gareth) + - Add inlines to ForceFieldHelpers header functions + (github pull #6356 from JLVarjo) + - Bug relating to this PF6- still can not get Bad Conformer Id + (github issue #6365 from teltim) + - straightenDepiction should not consider 0-degree rotations as multiples of 60 + (github pull #6367 from ptosco) + - expose two missing EmbedFailureCauses tags to python + (github pull #6372 from greglandrum) + - Molfile Unsaturation Query Not Parsed Correctly + (github issue #6395 from timothyngo) + - MolDraw2D: chiral tag overlapping atom label + (github issue #6397 from greglandrum) + - MolDraw2D: increasing padding results in the legend not being displayed + (github issue #6400 from greglandrum) + - expose some missing CXSmiles flags to python + (github pull #6415 from greglandrum) + - V3000 structure segfaults when converting to SVG + (github issue #6416 from ergo70) + - WedgeMolBonds won't wedge/dash a 2nd bond when input already has a wedge/dash around the same chiral atom + (github issue #6423 from ricrogz) + - MolEnumerate should clear the reaction properties on its results + (github issue #6432 from greglandrum) + - RDKit hangs indefinitely when parsing not so big molblock + (github issue #6434 from eloyfelix) + - Removing Hs on a pyrrol-like structure throws kekulization error + (github issue #6437 from ricrogz) + - Molecules from CDXML Parser have inverted, unrealistic atomic coordinates + (github issue #6461 from greglandrum) + - CDXML Parser does not preserve information about bond wedging + (github issue #6462 from greglandrum) + - boost::bad_any_cast error when calling getProp on properties set by applyMolListPropsToAtoms + (github issue #6465 from rachelnwalker) + - Allow systems like C/C=N/[H] to be stereogenic with the new chirality code + (github pull #6473 from greglandrum) + - Fix RWMol::addAtom docstring + (github pull #6477 from d-b-w) + - Fix a few broken docstrings + (github pull #6480 from ptosco) + - pin numpy to 1.24.3 + (github pull #6483 from bp-kelley) + - CMAKE_INSTALL_PREFIX not honored for Python files installation on Windows + (github pull #6485 from ricrogz) + - Fixed tests that weren't being run in testDepictor.py + (github pull #6486 from rachelnwalker) + - Get tests to work when building without exception support (i.e., legacy pure JS library) + (github pull #6487 from ptosco) + - Fixes rdkit-js/issues/347 + (github pull #6490 from ptosco) + - Make sure that molecules are shown as images by PandasTools also when DataFrames are truncated horizontally + (github pull #6496 from ptosco) + - MolToMolBlock writes "either" stereo for double bonds which shouldn't be stereo + (github issue #6502 from ricrogz) + - Double bonds are not correctly drawn on sulfoximines + (github issue #6504 from ptosco) + - RegistrationHash.GetMolLayers() with v2 tautomer hash does not filter CX extensions + (github issue #6505 from ricrogz) + - Drop the s_m_color_rgb property from MaeWriter + (github pull #6511 from ricrogz) + - update avalontools version to incorporate bug fixes + (github pull #6513 from ptosco) + - update windows DLL CI build config + (github pull #6535 from greglandrum) + - Add MolEnumerator to C# + (github pull #6542 from jones-gareth) + - MolDraw2D: placement of bond or atom labels gets confused when atoms overlap + (github issue #6569 from greglandrum) + - partial MCS failure + (github issue #6578 from greglandrum) + - Fix vulnerabilities found by fuzzer. + (github pull #6579 from thomp-j) + - allow building the cartridge against PostgreSQL 16 + (github pull #6580 from ptosco) + - SIGSEGV while calculating molecular descriptors after using salt remover. + (github issue #6592 from BartlomiejF) + - Add newline to ConstrainedEmbed docstring. + (github pull #6596 from DavidACosgrove) + - Avoid leaking memory in case exceptions are thrown while generating FPs + (github pull #6630 from ptosco) + - Pre-condition violation in canonicalization of dative bond adjacent to double bond + (github issue #6633 from ricrogz) + - Incorrect most abundant isotope for Vanadium + (github issue #6638 from abefrandsen) + - Simple imine-containing molecule causes an infinite loop in FindStereo.cpp + (github issue #6640 from ptosco) + - Mol file parser strips stereogenic H from imine bonds + (github issue #6664 from ricrogz) + - ROMol move constructor and assignment do not update SubstanceGroup ownership + (github issue #6681 from ricrogz) + - Flexicanvas cuts off bottom of reaction + (github issue #6685 from DavidACosgrove) + - make sure bond attachpt info is pickled + (github pull #6698 from greglandrum) + - Catch meanBondLen of 0.0 + (github pull #6699 from DavidACosgrove) + - Add trans layout for double bonds in rings + (github pull #6709 from d-b-w) + - Segmentation fault in MMFF + (github issue #6728 from Meteor-han) + - Fix chirality handling when the chiral atom is the first one in a SMARTS + (github pull #6730 from johnmay) + - ConnectTheDots can segfault if all atoms do not have residue info + (github issue #6756 from jasondbiggs) ## Cleanup work: + - adjustQueryProperties cleanup + (github pull #6361 from ptosco) + - Fix identical for-loop variable names + (github pull #6391 from JLVarjo) + - Deprecate JSMol::is_valid() and JSReaction::is_valid() and return nullptr instead + (github pull #6392 from ptosco) + - misc jswrapper.cpp cleanup + (github pull #6449 from ptosco) + - Deprecate the pure python MolStandardize implementations. + (github pull #6548 from greglandrum) + - clear up some compiler warnings + (github pull #6627 from greglandrum) + - switch from boost::any to std::any + (github pull #6662 from greglandrum) + - Fail CI builds on compiler warnings + some fixes + (github pull #6675 from ricrogz) + - fix some more leaks + (github pull #6684 from ricrogz) + - Some small cleanups from the UGM Hackathon + (github pull #6744 from greglandrum) + - some modernization of the memory handing in the canonicalization code + (github pull #6763 from greglandrum) -## New Features and Enhancements: ## Code removed in this release: - The `compare` and `callback` methods (deprecated since release 2021.01)