Re: [Rdkit-announce] 2021.03.1 RDKit Release

[Greg L. <gre...@gm...>]

Apologies, I forgot to remove the beta tag in a file in the release, so
I've deleted that tag and done a new one.
The new DOI is:
https://zenodo.org/record/4639764

Everything else remains the same.

sorry for the noise,
-greg
p.s. hopefully there are no other silly mistakes/oversights...

On Fri, Mar 26, 2021 at 4:13 PM Greg Landrum <gre...@gm...> wrote:

> Dear all,
>
> I'm pleased to announce that the 2021.03 version of the RDKit is released.
> We actually managed to get the .03 release done during March. Shocking! ;-)
> The release notes are below.[1]
>
> The release files are on the github release page:
> https://github.com/rdkit/rdkit/releases/tag/Release_2021_03_1
> The DOI for this release is:
> https://doi.org/10.5281/zenodo.4639022
>
> I do not plan to do conda builds for the Python wrappers in the rdkit
> channel for this release. The builds done as part of the conda-forge
> project are automated and cover more Python versions and operating systems
> than I could ever hope to do manually.
> Please install the rdkit using conda-forge:
> conda install -c conda-forge rdkit
> I believe that the conda-forge builds of the new version should appear
> over the next couple of days.
>
> I hope to finish the conda builds of the PostgreSQL cartridge for linux
> and the mac and have them available in the rdkit channel by later today
> or tomorrow.
>
> The online version of the documentation at rdkit.org (
> http://rdkit.org/docs/index.html) has been updated.
>
> Thanks to everyone who submitted code, bug reports, and suggestions for
> this release!
>
> Please let me know if you find any problems with the release or have
> suggestions for the next one, which is scheduled for September/October 2021.
>
> Best Regards,
> -greg
> [1] We probably should figure out some way to make the release notes a bit
> less verbose. ;-)
>
>
> # Release_2021.03.1
> (Changes relative to Release_2020.09.1)
>
> ## Backwards incompatible changes
> - The distance-geometry based conformer generation now by defaults
> generates
>   trans(oid) conformations for amides, esters, and related structures.
> This can
>   be toggled off with the `forceTransAmides` flag in EmbedParameters. Note
> that
>   this change does not impact conformers created using one of the ET
> versions.
>   (#3794)
> - The conformer generator now uses symmetry by default when doing RMS
> pruning.
>   This can be disabled using the `useSymmetryForPruning` flag in
>   EmbedParameters. (#3813)
> - Double bonds with unspecified stereochemistry in the products of chemical
>   reactions now have their stereo set to STEREONONE instead of STEREOANY
> (#3078)
> - The MolToSVG() function has been moved from rdkit.Chem to rdkit.Chem.Draw
>   (#3696)
> - There have been numerous changes to the RGroup Decomposition code which
> change
>   the results. (#3767)
> - In RGroup Decomposition, when onlyMatchAtRGroups is set to false, each
> molecule
>   is now decomposed based on the first matching scaffold which adds/uses
> the
>   least number of non-user-provided R labels, rather than simply the first
>   matching scaffold.
>   Among other things, this allows the code to provide the same results for
> both
>   onlyMatchAtRGroups=true and onlyMatchAtRGroups=false when suitable
> scaffolds
>   are provided without requiring the user to get overly concerned about the
>   input ordering of the scaffolds. (#3969)
> - There have been numerous changes to
> `GenerateDepictionMatching2DStructure()` (#3811)
> - Setting the kekuleSmiles argument (doKekule in C++) to MolToSmiles will
> now
>   cause the molecule to be kekulized before SMILES generation. Note that
> this
>   can lead to an exception being thrown. Previously this argument would
> only
>   write kekulized SMILES if the molecule had already been kekulized (#2788)
> - Using the kekulize argument in the MHFP code will now cause the molecule
> to be
>   kekulized before the fingerprint is generated. Note that becaues
> kekulization
>   is not canonical, using this argument currently causes the results to
> depend
>   on the input atom numbering. Note that this can lead to an exception
> being
>   thrown. (#3942)
> - Gradients for angle and torsional restraints in both UFF and MMFF were
> computed
>   incorrectly, which could give rise to potential instability during
> minimization.
>   As part of fixing this problem, force constants have been switched to
> using
>   kcal/degree^2 units instead of kcal/rad^2 units, consistently with the
> fact that
>   angle and dihedral restraints are specified in degrees. (#3975)
>
> ## Highlights
> - MolDraw2D now does a much better job of handling query features like
> common
>   query bond types, atom lists, variable attachment points, and link
> nodes. It
>   also supports adding annotations at the molecule level, displaying
> brackets
>   for Sgroups, rendering the ABS flag for stereochemistry, and a new
> "comic"
>   mode.
> - There are two new Contrib packages: NIBRStructureFilters and CalcLigRMSD
> - There have been a number of improvements made to the R-Group
> Decomposition
>   code which make it both more flexible and considerably faster
>
> ## Acknowledgements
> Michael Banck, Christopher Von Bargen, Jason Biggs, Patrick Buder, Ivan
> Chernyshov, Andrew Dalke, Xiaorui Dong, Carmen Esposito, Nicholas Firth,
> Enrico
> Gandini, James Gayvert, Gareth Jones, Eisuke Kawashima, Steven Kearnes,
> Brian
> Kelley, Mark Mackey, Niels Kristian Kjærgård Madsen, Luca Naef, Dan
> Nealschneider, Jin Pan, Daniel Paoliello, António JM Ribeiro, Sereina
> Riniker,
> Braxton Robbason, Jaime Rodríguez-Guerra, Ricardo Rodriguez-Schmidt, Steve
> Roughley, Vincent F. Scalfani, Nadine Schneider, Philippe Schwaller, Dan
> Skatov,
> Pascal Soveaux, Paolo Tosco, Kazuya Ujihara, Riccardo Vianello, Shuzhe
> Wang,
> Piotr Wawrzyniak, Maciej Wójcikowski, Zhijiang Yang, Yutong Zhao
> 'driesvr', 'GintasKam', 'SPKorhonen', 'pkubaj', 'AnPallo', 'darintay',
> 'slchan3', 'Robins', 'sirbiscuit', 'amateurcat', 'noncomputable',
> 'yurivict',
> 'magattaca'
>
> ## Contrib updates:
>   - Added NIBRStructureFilters: a set of substructure filters for hit-list
> triaging together with python code for applying them. The filters are
> described in the publication
> https://dx.doi.org/10.1021/acs.jmedchem.0c01332
>    (github pull #3516 from NadineSchneider)
>   - Added CalcLigRMSD: flexible python code for calculating RMSD between
> pre-aligned molecules
>    (github pull #3812 from cespos)
>
> ## Bug Fixes:
>   - Casting int to uint in MorganFingerprintHelper leads to unexpected
> behaviour.
>  (github issue #1761 from SiPa13)
>   - MolChemicalFeature.GetPos() returns value for molecule's default
> conformer
>  (github issue #2530 from greglandrum)
>   - Unable to catch RDKit exceptions in linked library when compiling with
> fvisibility=hidden
>  (github issue #2753 from cdvonbargen)
>   - Reaction rendering always shows molecules in aromatic form
>  (github issue #2976 from greglandrum)
>   - Reactions setting unspecified double-bond stereo to STEREOANY
>  (github issue #3078 from ricrogz)
>   - PDB output flavor&2 documentation change
>  (github issue #3089 from adalke)
>   - WedgeMolBonds() should prefer degree-1 atoms
>  (github issue #3216 from greglandrum)
>   - Error in ChemAxon SMILES "parsing"
>  (github issue #3320 from IvanChernyshov)
>   - Incorrect number of radical electrons calculated for metals
>  (github issue #3330 from greglandrum)
>   - Problem with lifetime linkage of mols and conformers
>  (github issue #3492 from amateurcat)
>   - Traceback when pickling ROMol after BCUT descriptors are calculated
>  (github issue #3511 from d-b-w)
>   - Fix AUTOCORR2D descriptors
>  (github pull #3512 from ricrogz)
>   - SDMolSupplier requires several attempts to load a SDF file in Python
> 3.6/3.7
>  (github issue #3517 from jaimergp)
>   - Remove accidentally included boost header
>  (github pull #3518 from ricrogz)
>   - legend_height_ should be preserved after drawing the molecule
>  (github pull #3520 from greglandrum)
>   - remove the include directive for unused <access/tuptoaster.h> header
>  (github pull #3525 from rvianello)
>   - C++ build fails when configured with RDKIT_USE_BOOST_SERIALIZATION=OFF
>  (github issue #3529 from rvianello)
>   - Newest RDKIT version allowing chemically invalid smiles
>  (github issue #3531 from GintasKam)
>   - Behaviour of generate_aligned_coords for erroneous inputs
>  (github issue #3539 from dskatov)
>   - Drawing artifacts in draw_to_canvas_with_offset
>  (github issue #3540 from dskatov)
>   - Error adding PNG metadata when kekulize=False
>  (github issue #3543 from gayverjr)
>   - Add missing methods to remove SubstanceGroup attributes
>  (github pull #3547 from greglandrum)
>   - Error writing SDF data containing UTF-8 to a StringIO object
>  (github issue #3553 from greglandrum)
>   - correct handling of amide distances for macrocycles
>  (github pull #3559 from hjuinj)
>   - rdMolDraw2D, problems during generation of pictures from SMARTS,
> differences between Cairo and SVG
>  (github issue #3572 from wopozka)
>   - Fix example of SmilesToMol
>  (github pull #3575 from kazuyaujihara)
>   - atom/bond notes handle capital letters incorrectly
>  (github issue #3577 from greglandrum)
>   - Get MolDraw2DQt working again
>  (github pull #3592 from greglandrum)
>   - Scientific notation in SDF V3000 files
>  (github issue #3597 from mark-cresset)
>   - Fix: add missing python wrappers for MolDraw2DQt
>  (github pull #3613 from greglandrum)
>   - V3K mol block parser not saving the chiral flag
>  (github issue #3620 from greglandrum)
>   - Inconsistent metal disconnectors
>  (github issue #3625 from pschwllr)
>   - Ring stereochemistry not properly removed from N atoms
>  (github issue #3631 from greglandrum)
>   - moldraw2djs should not close all polygonal paths
>  (github pull #3634 from greglandrum)
>   - Unidentifiable C++ Exception with FMCS
>  (github issue #3635 from proteneer)
>   - Bump catch2 version to allow builds on Apple M1
>  (github pull #3641 from naefl)
>   - Segmentation fault when parsing InChI
>  (github issue #3645 from AnPallo)
>   - RDK_BUILD_THREADSAFE_SSS does not work as expected
>  (github issue #3646 from pascal-soveaux)
>   - Disabling MaeParser and CoordGen Support Breaks the Build
>  (github issue #3648 from proteneer)
>   - BondStereo info lost in FragmentOnBonds()
>  (github pull #3649 from bp-kelley)
>   - memory leak when sanitization fails in InChIToMol()
>  (github issue #3655 from greglandrum)
>   - Qt GUI libraries being linked into rdmolops.so when Qt support is
> enabled
>  (github issue #3658 from ricrogz)
>   - Documentation of Chem.rdmolops.GetMolFrags's frag argument is wrong
>  (github issue #3670 from noncomputable)
>   - fmcs() + bogus input causes engine crash
>  (github issue #3687 from robins)
>   - qmol_from_ctab() with NULL crashes engine
>  (github issue #3688 from robins)
>   - qmol_from_smiles() + bogus input causes engine crash
>  (github issue #3689 from robins)
>   - Check PIL support for tostring and fromstring
>  (github pull #3690 from sirbiscuit)
>   - Move MolToSVG() to rdkit.Chem.Draw (Addresses #3694)
>  (github pull #3696 from ricrogz)
>   - Pandas AttributeError when rendering Molecule in DataFrame
>  (github issue #3701 from enricogandini)
>   - Memory leak in EnumerateLibrary
>  (github issue #3702 from jose-mr)
>   - Fix to add ZLIB_INCLUDE_DIRS for Windows build
>  (github pull #3714 from kazuyaujihara)
>   - Docs/Book: Unexpected unicode character makes pdflatex build fail
>  (github issue #3738 from mbanck)
>   - Test suite failures if eigen3 is not available
>  (github issue #3740 from mbanck)
>   - Regression in depiction of double bonds in aromatic rings
>  (github issue #3744 from ptosco)
>   - RGD with RGroupMatching.GA leaks memory and takes too long
>  (github issue #3746 from ptosco)
>   - Fix comment to match the code in RemoveHsParameters
>  (github pull #3747 from jasondbiggs)
>   - Inconsistent canonical tautomer on repeated application
>  (github issue #3755 from darintay)
>   - bonds no longer highlighted in substruct matches in jupyter
>  (github issue #3762 from greglandrum)
>   - SubstanceGroup output doesn't correctly quote " symbols
>  (github issue #3768 from greglandrum)
>   - MolToSmarts inverts direction of dative bond
>  (github issue #3774 from IvanChernyshov)
>   - Regression in dihedral constraints
>  (github issue #3781 from ptosco)
>   - Fix pillow error in IPythonConsole.py
>  (github pull #3783 from skearnes)
>   - lock swig version in MacOS CI builds
>  (github pull #3789 from greglandrum)
>   - DrawMorganBit errors when useSVG is False
>  (github issue #3796 from ncfirth)
>   - SubstructLibrary Cached Smiles Holders have bad behavior with bad
> smiles
>  (github issue #3797 from bp-kelley)
>   - MolFromSmiles('[He]') produces a diradical helium atom
>  (github issue #3805 from jasondbiggs)
>   - NaNs from AUTOCORR2D descriptor
>  (github issue #3806 from greglandrum)
>   - MaeMolSupplier throws an invariant exception on parsing an "undefined"
> chirality label
>  (github issue #3815 from ricrogz)
>   - Sanitize molecules when SMILES needs to be produced in PandasTools
>  (github pull #3818 from mwojcikowski)
>   - Tautomer Query copy constructor is shallow not deep causing segfaults
> in destructor
>  (github issue #3821 from bp-kelley)
>   - OptimizeMolecule and OptimizeMoleculeConfs Argument Bug
>  (github issue #3824 from xiaoruiDong)
>   - rdMolEnumerator.Enumerate() fragile w.r.t. atom ordering
>  (github issue #3844 from greglandrum)
>   - MinimalLib: Bonds are parallel in SVG but not on an HTML5 Canvas
>  (github issue #3852 from dskatov)
>   - AddHs creates H atom with nan coordinates on edge case 2D structure
>  (github issue #3854 from ricrogz)
>   - Build error with static boost libraries (v1.73)
>  (github issue #3865 from nielskm)
>   - Make sure that added R-groups have non-zero coordinates
>  (github pull #3877 from ptosco)
>   - Bad H coordinates on fused ring
>  (github issue #3879 from greglandrum)
>   - SubstructLibrary needs to check bond ring queries as well
>  (github issue #3881 from bp-kelley)
>   - Fixes Amine.Tertiary.Aromatic definition
>  (github pull #3883 from bp-kelley)
>   - inconsistency in seedSmarts in FMCS between and GetSubstructureMatches
>  (github issue #3886 from proteneer)
>   - PandasTools.RGroupDecomposition throws an error when redraw_sidechains
> is set to True.
>  (github pull #3888 from greglandrum)
>   - Dev/update glare to py3
>  (github pull #3892 from bp-kelley)
>   - ConfGen: Macrocycle torsion terms not being used with fused macrocycles
>  (github pull #3894 from greglandrum)
>   - Broken KNIME link in README
>  (github issue #3897 from yurivict)
>   - Change class to struct for forward declaration
>  (github pull #3906 from bp-kelley)
>   - Fixes issues with unlabelled groups on aromatic nitrogens
>  (github pull #3908 from ptosco)
>   - Fix #3659 regression introduced in #3832
>  (github pull #3909 from ricrogz)
>   - Error rendering SMARTS queries with atom OR lists
>  (github issue #3912 from greglandrum)
>   - MoDraw2D: Get tests working without freetype
>  (github pull #3923 from greglandrum)
>   - RGD default scoring function does not always work as expected
>  (github issue #3924 from jones-gareth)
>   - MolDraw2D: relative font size changes with bond lengths in molecule
>  (github issue #3929 from greglandrum)
>   - MolDraw2D: coordinates for reactions not being used
>  (github issue #3931 from greglandrum)
>   - Follow-on patch for changes in #3899
>  (github issue #3932 from greglandrum)
>   - Fix MolDraw2DQt exports
>  (github pull #3935 from ricrogz)
>   - Fix building JavaWrappers on Windows, dynamic linking
>  (github pull #3936 from ricrogz)
>   - Boost header warnings when compiling
>  (github issue #3956 from jasondbiggs)
>   - Adds removeAllHydrogenRGroupsAndLabels and fixes kekulization issues
>  (github pull #3944 from ptosco)
>   - MolToJSONData fails when mol has a property that can't be stringified
>  (github issue #3956 from jasondbiggs)
>   - RWMol should reset(), not release(), dp_delAtoms and dp_delBonds
>  (github pull #3970 from greglandrum)
>
>
> ## New Features and Enhancements:
>   - add context managers for writers
>  (github issue #2217 from greglandrum)
>   - MolToSmiles(kekuleSmiles=True) gives SMILES with aromatic bonds
>  (github issue #2788 from adalke)
>   - allow specification of color map when drawing similarity maps
>  (github issue #2904 from greglandrum)
>   - Clean up CMake files
>  (github pull #3417 from e-kwsm)
>   - Speed up GraphMol/Chirality.cpp/iterateCIPRanks
>  (github pull #3482 from jinpan)
>   - Removes function which is an exact duplicate of another function
>  (github pull #3524 from ptosco)
>   - A couple of minor improvements to FindCairo
>  (github pull #3535 from ptosco)
>   - Give a bit more time to RGD test in debug builds
>  (github pull #3536 from ptosco)
>   - A couple of fixes to the build system
>  (github pull #3538 from ptosco)
>   - Modularized WASM module
>  (github issue #3561 from dskatov)
>   - A couple changes to speedup bulk similarity calculations from Python
>  (github pull #3574 from greglandrum)
>   - add documentation for the JS wrappers
>  (github pull #3583 from greglandrum)
>   - add a "comic mode" to MolDraw2D
>  (github pull #3584 from greglandrum)
>   - Add rendering of SGroup brackets to MolDraw2D
>  (github pull #3586 from greglandrum)
>   - Update Install.md
>  (github pull #3589 from slchan3)
>   - Add explicit support for remaining CTAB query bond types
>  (github issue #3599 from greglandrum)
>   - update Cookbook stereochemistry examples
>  (github pull #3604 from vfscalfani)
>   - Add support for rendering SGroup data fields to MolDraw2D
>  (github pull #3619 from greglandrum)
>   - Support rendering the "ABS" flag in MolDraw2D
>  (github issue #3623 from greglandrum)
>   - Support drawing some query bonds
>  (github pull #3624 from greglandrum)
>   - Support rendering variable attachment points
>  (github pull #3626 from greglandrum)
>   - add configuration option to disable atom symbols in the rendering
>  (github pull #3630 from greglandrum)
>   - Render link nodes in MolDraw2D
>  (github issue #3637 from greglandrum)
>   - First pass at MolZip (now with bond stereo!)
>  (github pull #3644 from bp-kelley)
>   - Add molecule annotations/notes to MolDraw2D
>  (github pull #3651 from greglandrum)
>   - support setting MolDraw2DOptions using JSON from Python
>  (github pull #3660 from greglandrum)
>   - Make the scope control for Qt more idiomatic
>  (github pull #3663 from d-b-w)
>   - Expanded MolEnumerator functionality
>  (github pull #3664 from greglandrum)
>   - add support for generating pattern fps for MolBundles
>  (github pull #3665 from greglandrum)
>   - Add a callback function to EmbedParameters struct
>  (github issue #3667 from jasondbiggs)
>   - update SequenceParsers.cpp
>  (github pull #3683 from magattaca)
>   - MCS: extend completeRingsOnly to cover atoms as well
>  (github issue #3693 from driesvr)
>   - Add Molbundle search to SWIG
>  (github pull #3698 from jones-gareth)
>   - Added getMessage method to exceptions
>  (github pull #3700 from sroughley)
>   - add context manager for MolSuppliers
>  (github issue #3703 from greglandrum)
>   - Make better use of strictParsing for SGroups
>  (github pull #3705 from ptosco)
>   - Allow using  POPCNT on big-endian ppc64
>  (github pull #3727 from pkubaj)
>   - Cleanup: remove fromstring and tostring from functions working with
> pillow
>  (github issue #3730 from greglandrum)
>   - Set strictParsing to false in MinimalLib
>  (github pull #3737 from ptosco)
>   - 3D MCS - Minimal version, no refactoring
>  (github pull #3749 from robbason)
>   - Include Winsock2.h instead of Windows.h in DebugTrace.h
>  (github pull #3756 from dpaoliello)
>   - R group match any issue
>  (github pull #3767 from jones-gareth)
>   - Support new coordgen option to not always make bonds to metals
> zero-order
>  (github pull #3769 from greglandrum)
>   - DistanceGeometry: add flag to enforce trans amides
>  (github pull #3794 from greglandrum)
>   - MolDraw2D: first pass at rendering atom lists
>  (github pull #3804 from greglandrum)
>   - Issue a warning when embedding a molecule with no Hs
>  (github pull #3807 from greglandrum)
>   - Add tautomer query to the substructlibrary
>  (github pull #3808 from bp-kelley)
>   - Enhanced generateDepictionMatching2DStructure functionality
>  (github pull #3811 from ptosco)
>   - Confgen: add option to use symmetry when doing RMS pruning
>  (github pull #3813 from greglandrum)
>   - Remove boost::foreach from public headers
>  (github pull #3820 from ricrogz)
>   - Adds isotopeLabels and dummyIsotopeLabels MolDrawOptions
>  (github pull #3825 from ptosco)
>   - Added 2 Cookbook examples
>  (github pull #3831 from vfscalfani)
>   - Separate MolDraw2DQt into its own library
>  (github pull #3832 from d-b-w)
>   - Facilities for interactive modification of molecule drawing
>  (github pull #3833 from SPKorhonen)
>   - cleanup a bunch of compiler warnings
>  (github pull #3849 from greglandrum)
>   - add a new mol draw option to draw wedge bonds with a single color
>  (github pull #3860 from jasondbiggs)
>   - Add Kier Phi descriptor
>  (github pull #3864 from greglandrum)
>   - Add basic support for hydrogen bonds
>  (github pull #3871 from greglandrum)
>   - Allow batch editing of molecules: removal only
>  (github pull #3875 from greglandrum)
>   - Allow retrieving the _ErGAtomTypes property from Python
>  (github pull #3878 from ptosco)
>   - Exposes InsertMol to python RWMol
>  (github pull #3907 from bp-kelley)
>   - Use https for Avalon and Inchi downloads
>  (github pull #3915 from ptosco)
>   - support empty/missing SDT lines for SGroup data
>  (github pull #3916 from greglandrum)
>   - Cookbook entries should be updated
>  (github issue #3917 from greglandrum)
>   - MolDraw2D: support changing annotation colours
>  (github pull #3919 from greglandrum)
>   - include context managers for the multithreaded suppliers too
>  (github pull #3920 from greglandrum)
>   - Documentation cleanup and update
>  (github pull #3922 from greglandrum)
>   - remove an MSVC++ warning caused by #3849
>  (github pull #3927 from greglandrum)
>   - Adds removeAllHydrogenRGroupsAndLabels and fixes kekulization issues
>  (github pull #3944 from ptosco)
>   - Remove temporary labels from RGD results
>  (github pull #3947 from ptosco)
>   - appended a new project depend on RDKit
>  (github pull #3955 from kotori-y)
>   - Do not add unnecessary R-labels (and an optimization)
>  (github pull #3969 from ptosco)
>   - Add return codes and make RGroupDecomp less verbose
>  (github pull #3971 from bp-kelley)
>   - update to coordgen 2.0.0
>  (github pull #3974 from greglandrum)
>
>
> ## Deprecated code (to be removed in a future release):
> - The "minimizeOnly" option for coordgen will be removed in the next RDKit
> release
>
>