[Rdkit-devel] 2021.03.1 RDKit Release

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

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