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 <greg.land...@gmail.com> 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 > >
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