Hi Drew, Thanks for pointing out the problem. I had inadvertently done the conda builds using freetype, but I forgot to add a freetype dependency. It should be fixed now. Note: removed the old builds and uploaded new ones, so you'll probably need to do a conda uninstall and then conda install again.
-greg On Sat, Mar 27, 2021 at 8:09 PM Drew Gibson <drew.gibso...@googlemail.com> wrote: > Hi, > > just a heads-up that I'm seeing the following error on MacOS on trying to > create the rdkit extension in a chembl_28 db. > > chembl_28=# create extension if not exists rdkit; > ERROR: could not load library > "/Users/drew/anaconda3/envs/rdkit-psql-2021/lib/rdkit.so": > dlopen(/Users/drew/anaconda3/envs/rdkit-psql-2021/lib/rdkit.so, 10): > Library not loaded: /usr/local/opt/freetype/lib/libfreetype.6.dylib > Referenced from: /Users/drew/anaconda3/envs/rdkit-psql-2021/lib/rdkit.so > Reason: image not found > chembl_28=# > > I'm using a Mac Mini 2018 with Big Sur version 11.2.3. I created my conda > environment using the postgresql=12.2 option - haven't tried the others but > then the issue doesn't seem related to postgresql. > > I subsequently installed the 2020.03.3 version with postgresql=12.2 and > have had no problems. > > Thanks ! > > Drew > > > On Fri, 26 Mar 2021 at 15:14, 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 >> >> _______________________________________________ >> Rdkit-announce mailing list >> rdkit-annou...@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-announce >> >
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