rdkit-devel — Developers information and discussion.

Re: [Rdkit-devel] RDKit 2021.x build for Windows with Mingw is broken

[Paolo T. <pao...@gm...>]

Hi Thomas,

I have managed to identify a few relatively recent changes that have caused
the MinGW build to break and I have submitted a PR to get the MinGW build
to work again and all unit tests to pass:
https://github.com/rdkit/rdkit/pull/4347

Please find attached a small patch that should fix the MinGW build for you
too.

Cheers,
Paolo

On Sat, Jul 17, 2021 at 12:29 AM Paolo Tosco <pao...@gm...>
wrote:

> Hi Thomas,
>
> Thanks for reporting this. I’ll provide a fix ASAP.
>
> Cheers,
> p.
>
> > On 16 Jul 2021, at 16:22, Veith, Thomas <tho...@no...>
> wrote:
> >
> > Hi *,
> >
> > When trying to build RDKit for Windows with the MINGW toolchain, the
> build dies during linking:
> >
> > [ 49%] Building CXX object
> Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.obj
> > [ 49%] Building CXX object
> Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.obj
> > [ 49%] Linking CXX shared library ../../../bin/libRDKitFileParsers.dll
> > /usr/bin/x86_64-w64-mingw32-ld:
> CMakeFiles/FileParsers.dir/objects.a(MolFileWriter.cpp.obj):MolFileWriter.cpp:(.text+0xe3ba):
> undefined reference to `RDDepict::compute2DCoords(RDKit::ROMol&,
> std::map<int, RDGeom::Point2D, std::less<int>, std::allocator<std::pair<int
> const, RDGeom::Point2D> > > const*, bool, bool, unsigned int, unsigned int,
> int, bool, bool)'
> > collect2: error: ld returned 1 exit status
> > make[2]: ***
> [Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make:557:
> bin/libRDKitFileParsers.dll] Error 1
> > make[1]: *** [CMakeFiles/Makefile2:3249:
> Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all] Error 2
> > make: *** [Makefile:171: all] Error 2
> >
> > I’m using the following cmake options:
> >
> >    cmake -DRDK_BUILD_THREADSAFE_SSS=OFF \
> >      -DCMAKE_BUILD_TYPE=Release -DRDK_BUILD_AVALON_SUPPORT=ON
> -DRDK_BUILD_INCHI_SUPPORT=ON \
> >      -DRDK_BUILD_PYTHON_WRAPPERS=OFF  -DRDK_BUILD_SWIG_WRAPPERS=ON
> -DRDK_BUILD_SWIG_CSHARP_WRAPPER=ON -DRDK_BUILD_SWIG_JAVA_WRAPPER=OFF \
> >      -DRDK_USE_BOOST_IOSTREAMS=ON -DRDK_USE_BOOST_SERIALIZATION=ON
> -DRDK_USE_BOOST_STACKTRACE=OFF \
> >      -DBUILD_TESTING=OFF -DRDK_BUILD_CPP_TESTS=OFF \
> >      -DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=/image/rdk/win ..
>
> >
> > When looking a bit into it, the symbol is in the obj file:
> > /src/rdkit-Release_2021_03_3/buildw# nm
> Code/GraphMol/Depictor/CMakeFiles/Depictor_static.dir/RDDepictor.cpp.obj |
> grep compute2DCo
> > 00000000000030d0 T
> _ZN8RDDepict15compute2DCoordsERN5RDKit5ROMolEPKSt3mapIiN6RDGeom7Point2DESt4lessIiESaISt4pairIKiS5_EEEbbjjibb
> >
> > The symbol is in the DLL
> > bin/libRDKitDepictor.dll
> > 000000006f204470 T
> _ZN8RDDepict15compute2DCoordsERN5RDKit5ROMolEPKSt3mapIiN6RDGeom7Point2DESt4lessIiESaISt4pairIKiS5_EEEbbjjibb
> >
> > The symbol in in the tree in libRDKitDepictor_static.a
> > nm libRDKitDepictor_static.a | grep compute2DC
> > 00000000000030d0 T
> _ZN8RDDepict15compute2DCoordsERN5RDKit5ROMolEPKSt3mapIiN6RDGeom7Point2DESt4lessIiESaISt4pairIKiS5_EEEbbjjibb
> >
> > But the symbol is missing in lib/libRDKitDepictor.dll.a
> >
> > The build works for linux and osx, so it seems to be specific to windows.
> >
> > I tried to compile all releases from 2021 and the bug is there since
> 2021_03_1.
> >
> > I also tried crosscompile which has the same behavior as the native
> windows build (with two different versions of the toolchain for two
> different Ubuntu release) so it seems its not related to a specific gcc
> version/mingw version.
> > (cross compile cmake was  cmake -DCMAKE_CROSSCOMPILING=ON
> -DCMAKE_TOOLCHAIN_FILE=../win-x64.cmake
> -DMSVC_RUNTIME_DLL=/work/mingw/msvcr110.dll –
> > DRDK_BUILD_THREADSAFE_SSS=OFF \
> >      -DCMAKE_BUILD_TYPE=Release -DRDK_BUILD_AVALON_SUPPORT=ON
> -DRDK_BUILD_INCHI_SUPPORT=ON \
> >      -DRDK_BUILD_PYTHON_WRAPPERS=OFF  -DRDK_BUILD_SWIG_WRAPPERS=ON
> -DRDK_BUILD_SWIG_CSHARP_WRAPPER=ON -DRDK_BUILD_SWIG_JAVA_WRAPPER=OFF \
> >      -DRDK_USE_BOOST_IOSTREAMS=ON -DRDK_USE_BOOST_SERIALIZATION=ON
> -DRDK_USE_BOOST_STACKTRACE=OFF \
> >      -DBUILD_TESTING=OFF -DRDK_BUILD_CPP_TESTS=OFF \
> >      -DBOOST_ROOT=/work/mingw/mingw64 -DRDK_INSTALL_INTREE=OFF
> -DCMAKE_INSTALL_PREFIX=/image/rdk/win ..
> > )
> >
> > I attach a Dockerfile where you can easily reproduce the issue.
> >
> > Best,
> > Thomas
> >
> > p.s.: Also there was a minimal patch required to allow compiling of some
> explicit template instantiations, pls find attached
> >
> >
> > <fix_template.patch>
> > <win-x64.cmake>
> > <Dockerfile>
> > _______________________________________________
> > Rdkit-devel mailing list
> > Rdk...@li...
> > https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>

Re: [Rdkit-devel] RDKit 2021.x build for Windows with Mingw is broken

[Paolo T. <pao...@gm...>]

Hi Thomas,

Thanks for reporting this. I’ll provide a fix ASAP.

Cheers,
p.

> On 16 Jul 2021, at 16:22, Veith, Thomas <tho...@no...> wrote:
> 
> Hi *,
> 
> When trying to build RDKit for Windows with the MINGW toolchain, the build dies during linking:
> 
> [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.obj
> [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.obj
> [ 49%] Linking CXX shared library ../../../bin/libRDKitFileParsers.dll
> /usr/bin/x86_64-w64-mingw32-ld: CMakeFiles/FileParsers.dir/objects.a(MolFileWriter.cpp.obj):MolFileWriter.cpp:(.text+0xe3ba): undefined reference to `RDDepict::compute2DCoords(RDKit::ROMol&, std::map<int, RDGeom::Point2D, std::less<int>, std::allocator<std::pair<int const, RDGeom::Point2D> > > const*, bool, bool, unsigned int, unsigned int, int, bool, bool)'
> collect2: error: ld returned 1 exit status
> make[2]: *** [Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make:557: bin/libRDKitFileParsers.dll] Error 1
> make[1]: *** [CMakeFiles/Makefile2:3249: Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all] Error 2
> make: *** [Makefile:171: all] Error 2
> 
> I’m using the following cmake options:
> 
>    cmake -DRDK_BUILD_THREADSAFE_SSS=OFF \
>      -DCMAKE_BUILD_TYPE=Release -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_INCHI_SUPPORT=ON \
>      -DRDK_BUILD_PYTHON_WRAPPERS=OFF  -DRDK_BUILD_SWIG_WRAPPERS=ON -DRDK_BUILD_SWIG_CSHARP_WRAPPER=ON -DRDK_BUILD_SWIG_JAVA_WRAPPER=OFF \
>      -DRDK_USE_BOOST_IOSTREAMS=ON -DRDK_USE_BOOST_SERIALIZATION=ON -DRDK_USE_BOOST_STACKTRACE=OFF \
>      -DBUILD_TESTING=OFF -DRDK_BUILD_CPP_TESTS=OFF \
>      -DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=/image/rdk/win ..     
> 
> When looking a bit into it, the symbol is in the obj file:
> /src/rdkit-Release_2021_03_3/buildw# nm Code/GraphMol/Depictor/CMakeFiles/Depictor_static.dir/RDDepictor.cpp.obj | grep compute2DCo
> 00000000000030d0 T _ZN8RDDepict15compute2DCoordsERN5RDKit5ROMolEPKSt3mapIiN6RDGeom7Point2DESt4lessIiESaISt4pairIKiS5_EEEbbjjibb
> 
> The symbol is in the DLL
> bin/libRDKitDepictor.dll 
> 000000006f204470 T _ZN8RDDepict15compute2DCoordsERN5RDKit5ROMolEPKSt3mapIiN6RDGeom7Point2DESt4lessIiESaISt4pairIKiS5_EEEbbjjibb
> 
> The symbol in in the tree in libRDKitDepictor_static.a
> nm libRDKitDepictor_static.a | grep compute2DC 
> 00000000000030d0 T _ZN8RDDepict15compute2DCoordsERN5RDKit5ROMolEPKSt3mapIiN6RDGeom7Point2DESt4lessIiESaISt4pairIKiS5_EEEbbjjibb
> 
> But the symbol is missing in lib/libRDKitDepictor.dll.a
> 
> The build works for linux and osx, so it seems to be specific to windows.
> 
> I tried to compile all releases from 2021 and the bug is there since 2021_03_1.
> 
> I also tried crosscompile which has the same behavior as the native windows build (with two different versions of the toolchain for two different Ubuntu release) so it seems its not related to a specific gcc version/mingw version.
> (cross compile cmake was  cmake -DCMAKE_CROSSCOMPILING=ON -DCMAKE_TOOLCHAIN_FILE=../win-x64.cmake -DMSVC_RUNTIME_DLL=/work/mingw/msvcr110.dll –
> DRDK_BUILD_THREADSAFE_SSS=OFF \
>      -DCMAKE_BUILD_TYPE=Release -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_INCHI_SUPPORT=ON \
>      -DRDK_BUILD_PYTHON_WRAPPERS=OFF  -DRDK_BUILD_SWIG_WRAPPERS=ON -DRDK_BUILD_SWIG_CSHARP_WRAPPER=ON -DRDK_BUILD_SWIG_JAVA_WRAPPER=OFF \
>      -DRDK_USE_BOOST_IOSTREAMS=ON -DRDK_USE_BOOST_SERIALIZATION=ON -DRDK_USE_BOOST_STACKTRACE=OFF \
>      -DBUILD_TESTING=OFF -DRDK_BUILD_CPP_TESTS=OFF \
>      -DBOOST_ROOT=/work/mingw/mingw64 -DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=/image/rdk/win ..
> )
> 
> I attach a Dockerfile where you can easily reproduce the issue.
> 
> Best,
> Thomas
> 
> p.s.: Also there was a minimal patch required to allow compiling of some explicit template instantiations, pls find attached
> 
> 
> <fix_template.patch>
> <win-x64.cmake>
> <Dockerfile>
> _______________________________________________
> Rdkit-devel mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel

[Rdkit-devel] RDKit 2021.x build for Windows with Mingw is broken

[Veith, T. <tho...@no...>]

Hi *,

When trying to build RDKit for Windows with the MINGW toolchain, the build dies during linking:

 [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.obj
 [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.obj
 [ 49%] Linking CXX shared library ../../../bin/libRDKitFileParsers.dll
/usr/bin/x86_64-w64-mingw32-ld: CMakeFiles/FileParsers.dir/objects.a(MolFileWriter.cpp.obj):MolFileWriter.cpp:(.text+0xe3ba): undefined reference to `RDDepict::compute2DCoords(RDKit::ROMol&, std::map<int, RDGeom::Point2D, std::less<int>, std::allocator<std::pair<int const, RDGeom::Point2D> > > const*, bool, bool, unsigned int, unsigned int, int, bool, bool)'
collect2: error: ld returned 1 exit status
make[2]: *** [Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make:557: bin/libRDKitFileParsers.dll] Error 1
make[1]: *** [CMakeFiles/Makefile2:3249: Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/all] Error 2
make: *** [Makefile:171: all] Error 2

I’m using the following cmake options:

    cmake -DRDK_BUILD_THREADSAFE_SSS=OFF \
      -DCMAKE_BUILD_TYPE=Release -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_INCHI_SUPPORT=ON \
      -DRDK_BUILD_PYTHON_WRAPPERS=OFF  -DRDK_BUILD_SWIG_WRAPPERS=ON -DRDK_BUILD_SWIG_CSHARP_WRAPPER=ON -DRDK_BUILD_SWIG_JAVA_WRAPPER=OFF \
      -DRDK_USE_BOOST_IOSTREAMS=ON -DRDK_USE_BOOST_SERIALIZATION=ON -DRDK_USE_BOOST_STACKTRACE=OFF \
      -DBUILD_TESTING=OFF -DRDK_BUILD_CPP_TESTS=OFF \
      -DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=/image/rdk/win ..     

When looking a bit into it, the symbol is in the obj file:
/src/rdkit-Release_2021_03_3/buildw# nm Code/GraphMol/Depictor/CMakeFiles/Depictor_static.dir/RDDepictor.cpp.obj | grep compute2DCo
00000000000030d0 T _ZN8RDDepict15compute2DCoordsERN5RDKit5ROMolEPKSt3mapIiN6RDGeom7Point2DESt4lessIiESaISt4pairIKiS5_EEEbbjjibb

The symbol is in the DLL
bin/libRDKitDepictor.dll 
000000006f204470 T _ZN8RDDepict15compute2DCoordsERN5RDKit5ROMolEPKSt3mapIiN6RDGeom7Point2DESt4lessIiESaISt4pairIKiS5_EEEbbjjibb

The symbol in in the tree in libRDKitDepictor_static.a
nm libRDKitDepictor_static.a | grep compute2DC 
00000000000030d0 T _ZN8RDDepict15compute2DCoordsERN5RDKit5ROMolEPKSt3mapIiN6RDGeom7Point2DESt4lessIiESaISt4pairIKiS5_EEEbbjjibb

But the symbol is missing in lib/libRDKitDepictor.dll.a

The build works for linux and osx, so it seems to be specific to windows.

I tried to compile all releases from 2021 and the bug is there since 2021_03_1.

I also tried crosscompile which has the same behavior as the native windows build (with two different versions of the toolchain for two different Ubuntu release) so it seems its not related to a specific gcc version/mingw version.
(cross compile cmake was  cmake -DCMAKE_CROSSCOMPILING=ON -DCMAKE_TOOLCHAIN_FILE=../win-x64.cmake -DMSVC_RUNTIME_DLL=/work/mingw/msvcr110.dll –
DRDK_BUILD_THREADSAFE_SSS=OFF \
      -DCMAKE_BUILD_TYPE=Release -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_INCHI_SUPPORT=ON \
      -DRDK_BUILD_PYTHON_WRAPPERS=OFF  -DRDK_BUILD_SWIG_WRAPPERS=ON -DRDK_BUILD_SWIG_CSHARP_WRAPPER=ON -DRDK_BUILD_SWIG_JAVA_WRAPPER=OFF \
      -DRDK_USE_BOOST_IOSTREAMS=ON -DRDK_USE_BOOST_SERIALIZATION=ON -DRDK_USE_BOOST_STACKTRACE=OFF \
      -DBUILD_TESTING=OFF -DRDK_BUILD_CPP_TESTS=OFF \
      -DBOOST_ROOT=/work/mingw/mingw64 -DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=/image/rdk/win ..
)

I attach a Dockerfile where you can easily reproduce the issue.

Best,
Thomas

p.s.: Also there was a minimal patch required to allow compiling of some explicit template instantiations, pls find attached

Re: [Rdkit-devel] 2021.03.1 RDKit Release

[Rex D. <RD...@me...>]

HI, We are having problems with this release on Windows, and we need to fall back to the last version.  We have a tight deadline and don't have resources to investigate the error at this moment.  However, none of these seem to work:

C:\NewCompoundElucidation\elucidation>conda install -c conda-forge --revision 2020.09.1

CondaValueError: expected revision number, not: '2020.09.1'


C:\NewCompoundElucidation\elucidation>conda install -c conda-forge --revision Release_2020.09.1

CondaValueError: expected revision number, not: 'Release_2020.09.1'


C:\NewCompoundElucidation\elucidation>conda install -c conda-forge --revision v2020.09.1

CondaValueError: expected revision number, not: 'v2020.09.1'

(I also tried .01 instead of .1)

Can anyone advise me how to do this?

BTW I think the error is related to recent changes in pillow.  We draw literally thousands of molecules in a run, so it's hard to pin down without a good bit of effort. This is the error:

Fail to allocate bitmap
ORA-24550: signal received: Unhandled exception: Code=80000003 Flags=0

kpedbg_dmp_stack()+428<-kpeDbgCrash()+102<-kpeDbgSignalHandler()+123<-skgesig_Win_UnhandledExceptionFilter()+173<-00007FFAE49B719C<-00007FFAE87C8340<-00007FFAE87AFDD6<-00007FFAE87C492F<-00007FFAE8724CEF<-00007FFAE87C369E<-00007FFA6149735D<-00007FFA61497392<-00007FFA6124E953<-00007FFA612BED98<-00007FFA612BC9F8<-00007FFA612BD079<-00007FFA612ACB5B<-00007FFA61270B10<-00007FFA6126FFED<-00007FFA6126FC01<-00007FFA613C9CAC<-00007FFA71C72C21<-00007FFA6F8FD08C<-00007FFA6F8FD73C<-00007FFA6F8FDF33

Thanks very much,
Rex

From: Greg Landrum <gre...@gm...>
Sent: Friday, March 26, 2021 11:14 AM
To: RDKit Discuss <rdk...@li...>; RDKit Developers List <rdk...@li...>; rdk...@li...
Subject: [Rdkit-devel] 2021.03.1 RDKit Release

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<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Frdkit%2Frdkit%2Freleases%2Ftag%2FRelease_2021_03_1&data=04%7C01%7Crdwyer%40metabolon.com%7C25962483677c4f9373fa08d8f069e864%7C7fb8e81b6c5d4bfea0e2bab63ea5e1c5%7C0%7C0%7C637523684980670653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=7qJHhYMlVm7N35WYYuPso4CkshXLNqRI05OBAU%2F7J3A%3D&reserved=0>
The DOI for this release is:
https://doi.org/10.5281/zenodo.4639022
<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.5281%2Fzenodo.4639022&data=04%7C01%7Crdwyer%40metabolon.com%7C25962483677c4f9373fa08d8f069e864%7C7fb8e81b6c5d4bfea0e2bab63ea5e1c5%7C0%7C0%7C637523684980680647%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=BfQopOcFwdK%2B0NSw1W34Xbgecsp0IbXeUy123WjuCQs%3D&reserved=0>

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<https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Frdkit.org%2F&data=04%7C01%7Crdwyer%40metabolon.com%7C25962483677c4f9373fa08d8f069e864%7C7fb8e81b6c5d4bfea0e2bab63ea5e1c5%7C0%7C0%7C637523684980680647%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=WNxBbW914%2BECix%2FuHwusXr%2FmrTAmNDuUKAeXR4a1y3M%3D&reserved=0> (http://rdkit.org/docs/index.html<https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Frdkit.org%2Fdocs%2Findex.html&data=04%7C01%7Crdwyer%40metabolon.com%7C25962483677c4f9373fa08d8f069e864%7C7fb8e81b6c5d4bfea0e2bab63ea5e1c5%7C0%7C0%7C637523684980690647%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=YURjsg9YTrNkrUVUURLZyhKlEbzS2bKRqxqayPgc2NQ%3D&reserved=0>) 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<https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdx.doi.org%2F10.1021%2Facs.jmedchem.0c01332&data=04%7C01%7Crdwyer%40metabolon.com%7C25962483677c4f9373fa08d8f069e864%7C7fb8e81b6c5d4bfea0e2bab63ea5e1c5%7C0%7C0%7C637523684980690647%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=jPSdvNWs8Z7lrd1iGQ37axHn3SOB4gbPkicK9739nxI%3D&reserved=0>
   (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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Re: [Rdkit-devel] 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
>
>

[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

[Rdkit-devel] pandastool molecules -> excel

[Rex D. <RD...@me...>]

Hi,
I tried to use the rdkit.Chem.PandasTools.SaveXlsxFromFrame function, and found that it didn't work for me:

  *   It was only possible to have one column with molecules.
  *   It moved the molecule column to the left side of the spreadsheet.
  *   It did not preserve hyperlinks.
I'm sending along this alternative.  If someone wants to take it and run with it, that's great, and no need to give me any credit.
If not, I'm sorry, but my workload doesn't permit me to spend time to go through all the usual procedures for contributing.
The technical insight here is to rely on DataFrame.to_excel to fill the spreadsheet.  It preserves all the data (such as links) as stored in the dataframe.  Then the columns that need graphics can be modified after that.
I hope this is useful.
Cheers,
Rex


def to_excel_with_molecules(df, xlsx_name, mol_cols, sheet_name="Sheet1", size=(300, 300)):
    """
    Writes a dataframe into an excel spreadsheet, adding graphic of molecule to specified columns.
    @param df: dataframe to write
    @type df: dataframe
    @param xlsx_name: name of output excel file.  Must end ".xlsx"
    @type xlsx_name: str
    @param mol_cols: a column or list of columns with smiles strings to be expanded.
    If any element of the columns can't be parsed as as SMILES string, it will be left alone.
    @type mol_cols: str or list of str (actually, any iterable of str)
    @param sheet_name: The name of the sheet in the workbook.
    @type sheet_name: str
    @param size: (width,height) of images
    @type size: tuple (could be list)
    @return: None
    @rtype: NoneType
    """
    df = df.copy()

    if type(mol_cols) is str:
        mol_cols = [mol_cols]
    mol_cols = list(mol_cols)

    writer = pd.ExcelWriter(xlsx_name, engine="xlsxwriter")
    df.to_excel(writer, sheet_name=sheet_name, index=False)
    workbook = writer.book
    worksheet = writer.sheets[sheet_name]

    mol_cols = [i for i, col in enumerate(df.columns) if col in mol_cols]
    df.columns = list(range(len(df.columns)))

    for c in mol_cols:
        worksheet.set_column(c, c, width=size[0] / 6)
        for rr, smiles in enumerate(df[c]):
            try:
                r = rr + 1  # row 0 of df will be in row 1 of spreadsheet.
                image_data = BytesIO()
                img = MolToImage(MolFromSmiles(smiles), size=size)
                img.save(image_data, format="PNG")
                worksheet.set_row(r, height=size[1])
                worksheet.insert_image(r, c, "f", {"image_data": image_data})
            except:  # Some are expected to fail, e.g., None when there is no matching molecule.
                pass

    workbook.close()
    return

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[Rdkit-devel] Beta of the 2021.03 release available

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

Dear all,

The beta of the 2020.09 RDKit release has been tagged in github:
https://github.com/rdkit/rdkit/releases/tag/Release_2021_03_1b1

I'm doing a conda build for Python 3.7 on Linux now. If you would like to
test the new version and need a conda build for that, please let me know
and I can try to do builds for other python versions or platforms. The
conda builds use the beta label so that they do not install by default;
you'll need to run "conda install" as follows:

conda install -c rdkit/label/beta rdkit

Be sure to confirm that it's installing the right version when you are
prompted (if there's no build available, it will pick the current
production release instead).

The relevant section of the release notes is below (I still need to finish
the Highlights section), or you can see a nicely formatted version here:
https://github.com/rdkit/rdkit/releases/tag/Release_2021_03_1b1

As usual, if you have time to try out the new release I would love
feedback. If nothing major comes up, I plan to do the actual release
towards the end of next week.

Best,
-greg

# 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)
- 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)

## Highlights

## 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, 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)
  - 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)
  - Adds removeAllHydrogenRGroupsAndLabels and fixes kekulization issues
 (github pull #3944 from ptosco)

## 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)

[Rdkit-devel] 2020.09.1 RDKit Release

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

Dear all,

I'm pleased to announce that the 2020.09 version of the RDKit is released.
The release notes are below.

The release files are on the github release page:
https://github.com/rdkit/rdkit/releases/tag/Release_2020_09_1

Binaries have been uploaded to anaconda.org (https://anaconda.org/rdkit).
The available conda binaries for this release are:
Linux 64bit: python 3.6, 3.7
Mac OS 64bit: python 3.6, 3.7
Windows 64bit: python 3.6, 3.7

I hope to finish the conda builds of the PostgreSQL cartridge and do the PR
to update conda-forge this weekend.

The online version of the documentation at rdkit.org (
http://rdkit.org/docs/index.html) has been updated.

Some things that will be finished over the next couple of days:
- The conda build scripts will be updated to reflect the new version
- The homebrew script

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 March/April 2021.

Best Regards,
-greg

# Release_2020.09.1
(Changes relative to Release_2020.03.1)


## Backwards incompatible changes
- We've added additional allowed valences for Cl (now 1, 3, 5), Br (now 1,
3,
  5), I (now 1, 3, 5), At (now 1, 3, 5), Xe (now 0, 2, 4, 6), and Po (now
2, 4,
  6). Molecules with atoms in the new valence states will no longer generate
  sanitization errors. Note that this has an impact on the chemistry of
  molecules containing 3-valent I and at least one implict H (present 24
times
  in ChEMBL 27): previously this was incorrectly assigned two implicit Hs,
now
  it has no implicit Hs.
- Aromaticity perception of molecules like `Cc1nnc2n1c1ccccc1n1c(C)nnc12`
now
  correctly recognizes the full outer envelope, i.e. the bonds joining the
rings
  are now also aromatic.
- FindMCS() may return single atom MCSs, whereas previously it returned an
empty
  MCS unless there was at least one commond bond across the input
structures.
  So the MCS between molecules `CC` and `CO` is now `[#6]` rather than
being null.
- The fontSize()/setFontSize() (FontSize()/SetFontSize()) methods in
MolDraw2D
  now work in units of pixels (more or less) instead of the molecule units.
- The Open3DAlign functionality is now in its own separate library -
`O3AAlign`
  in cmake. If you are working in C++ and using O3A functionality, you'll
need
  to link against this library as well now.
- Due to improvements in the tautomer enumeration code, the method
  `TautomerEnumerator::enumerate` now returns a `TautomerEnumeratorResult`
  object instead of a vector of molecules. Note that if you are iterating
over
  the results of a call to `enumerate()` you shouldn't need to change your
code.
  If you want to invoke the old (and deprecated, see below) form from C++,
call
  `TautomerNumerator::enumerate(mol, nullptr)` or explicitly pass a
  `boost::dynamic_bitset*` to capture the modified atoms.
- The default precision setting for coordgen has been changed. The new
default
  was selected to greatly reduce the number of molecules for which it takes
a
  very long time to generate coordinates while still producing nice looking
  structures. We may continue to tweak this default value if/when problems
  with it are reported. If you would like to go back to the previous
setting, set
  CoordgenParams.minimizerPrecision to
CoordgenParams.sketcherStandardPrecision
  when you invoke rdCoordGen.AddCoords()
- Uncharger::uncharge() will now neutralize `[Cl,Br,I][O-],
[Cl,Br,I](=O)[O-],
  [Cl,Br,I](=O)(=O)[O-], [Cl,Br,I](=O)(=O)(=O)[O-], [O-]N=N[O-],
[N,P](=O)[O-],
  [N+](=O)([O-])[O-], P(=O)([O-])[O-], P(=O)([O-])([O-])[O-], S([O-])[O-],
  S(=O)([O-])[O-], S(=O)(=O)([O-])[O-], S(=O)(=O)([O-])OOS(=O)(=O)[O-]`.
  Previously not all of these inorganic acid counterions were consistently
  neutralized.
- The `None` value in the `RGroupCoreAlignment` enum was renamed to
`NoAlignment`
  in both C++ and Python, in order to avoid issues when attempting to
access it
  from Python.

## Highlights
- There's been another big improvement in the quality of molecule drawings:
  character and font handling is greatly improved thanks to the use of the
  FreeType library
- A new feature has been added to efficiently allow tautomer-insensitive
  substructure search.
- A new, much more accurate, algorithm is available for calculating CIP
labels
  on atoms and bonds.
- There's a new rdDeprotect module to allow automatically deprotecting
molecules
  before putting them into reactions
- Molecule and reaction metadata can now be added to PNG files generated by
  MolDraw2DCairo

## Acknowledgements
Shrey Aryan, Jinserk Baik, Francois Berenger, Cédric Bouysset, David
Cosgrove,
Ivan Chernyshov, Guillaume Godin, Manan Goel, Jan H. Jensen, Gareth Jones,
Maria
Kadukova, Eisuke Kawashima, Steven Kearnes, Brian Kelley, Joos Kiener,
Kenneth
Lum, Joshua Meyers, Rocco Moretti, Paul R Moses, Dan Nealschneider, Jin Pan,
Joann Prescott-Roy, Matthew Robinson, Jaime Rodríguez-Guerra, Ricardo
Rodriguez-Schmidt, Jeff van Santen, Roger Sayle Vincent F. Scalfani Eric
Taw,
Ansgar Schuffenhauer, Paolo Tosco, Ivan Tubert-Brohman, Riccardo Vianello,
Rachel Walker, Maciej Wójcikowski, Christopher Zou, daverona, hjuinj,
intrigus-lgtm, autodataming, paconius, sailfish009

## Bug Fixes:
  - Python tests fail when RDK_BUILD_COMPRESSED_SUPPLIERS is enabled
 (github issue #1888 from greglandrum)
  - ResonanceMolSupplier potentially stuck in infinite loop
 (github issue #2597 from tawe141)
  - ctest pythonTestDirChem failed
 (github issue #2757 from jinserk)
  - Issue with inversion/retention of stereochemistry
 (github issue #2891 from mc-robinson)
  - cannot parse reaction SMILES/SMARTS with dative bonds
 (github issue #2954 from greglandrum)
  - ResonanceMolSupplier can fail with small maxStructs values
 (github issue #3041 from greglandrum)
  - seg fault in ResonanceMolSupplier()
 (github issue #3048 from greglandrum)
  - Bug in image rendering of dative bonds
 (github issue #3056 from IvanChernyshov)
  - Coordinates from coordgen are not centered around the origin
 (github pull #3058 from DavidACosgrove)
  - fix a typo in ScaffoldNetwork/CMakeLists.txt
 (github pull #3060 from greglandrum)
  - Bad double bond placement in polycyclic aromatics
 (github issue #3061 from DavidACosgrove)
  - SGroups with more than one attachment point are now properly parsed
 (github pull #3072 from greglandrum)
  - Reactions should not use strict implicit valence calculations
 (github issue #3097 from mwojcikowski)
  - partial reacting atom detection
 (github issue #3119 from thegodone)
  - DrawMolecules does not center molecules
 (github issue #3126 from JoshuaMeyers)
  - results from coordgen are sometimes not centered
 (github issue #3131 from greglandrum)
  - GCC 10.0.1 compile error
 (github issue #3135 from rvianello)
  - Memory leak when parsing bad SMILES
 (github issue #3139 from intrigus-lgtm)
  - Error breaking StereoBonds in reactions
 (github issue #3147 from mc-robinson)
  - MolOps::removeHs() removes hydrides
 (github issue #3150 from jhjensen2)
  - Kekulization error from CreateScaffoldNetwork
 (github issue #3153 from greglandrum)
  - Fix drawing of N plus
 (github pull #3165 from DavidACosgrove)
  - RWMol::clear() does not explicitly clean up SubstanceGroups or
StereoGroups
 (github issue #3167 from greglandrum)
  - Modifying a molecule should not automatically clear SubstanceGroups
 (github issue #3168 from greglandrum)
  - removeHs() should not remove atoms in SubstanceGroups
 (github issue #3169 from greglandrum)
  - fix a memory problem detected in malformed SMILES
 (github pull #3171 from greglandrum)
  - Python wrapper: SetQuery and ExpandQuery for bonds
 (github pull #3172 from i-tub)
  - S-groups: PARENT field should reference index
 (github issue #3175 from greglandrum)
  - rdScaffoldNetwork causes segmenation fault upon None molecule
 (github issue #3177 from AnsgarSchuffenhauer)
  - fix a small inconsistency in the name of the inchi package
 (github pull #3182 from rvianello)
  - Molecule constructed from CXSMILES cannot be translated to SMARTS
 (github issue #3197 from greglandrum)
  - Formatting fix of CalcRMS
 (github pull #3203 from chmnk)
  - fix the CompressedSDMolSupplier python iterator interface
 (github pull #3204 from rvianello)
  - Queries generated from PreprocessReaction cannot be translated to SMARTS
 (github issue #3206 from greglandrum)
  - Attachment point info not being read from V2000 mol blocks
 (github issue #3207 from greglandrum)
  - Memory Sanitizer fails on molFromPickle on empty file
 (github issue #3211 from intrigus-lgtm)
  - Throw exception when reading from stream fails.
 (github pull #3212 from intrigus-lgtm)
  - fix molstogridimage on certain fragments/smarts patterns
 (github pull #3217 from bp-kelley)
  - Lines in wedge bonds being drawn too closely together
 (github issue #3226 from paconius)
  - EnumerateStereochemistry should clear CIP labels
 (github issue #3231 from greglandrum)
  - lock CI cairo version to force an install from the rdkit repo
 (github pull #3240 from greglandrum)
  - XBCORR and XBHEAD in Sgroups no longer cause parse failures
 (github pull #3242 from greglandrum)
  - LINKNODEs are ignored by the CTAB parsers
 (github pull #3247 from greglandrum)
  - add GetStringVectProp() to SubstanceGroup class
 (github pull #3251 from greglandrum)
  - Envelope aromaticity not detected in complex fused system
 (github issue #3256 from greglandrum)
  - Draw.MolsToGridImage repeating atom indices
 (github issue #3258 from greglandrum)
  - Atom indices clash with atom symbols in small pictures.
 (github issue #3262 from DavidACosgrove)
  - MinimalLib Dockerfile is broken at HEAD
 (github issue #3267 from skearnes)
  - Fixes #2757
 (github pull #3268 from greglandrum)
  - RGroupDecomposition restructuring
 (github pull #3270 from bp-kelley)
  - Get PPC builds working
 (github pull #3285 from greglandrum)
  - ScaffoldNetwork not in C# wrappers
 (github pull #3289 from jones-gareth)
  - bonds with "either' stereo cannot be read from JSON
 (github pull #3290 from greglandrum)
  - Small bug fixes and cleanups from fuzz testing
 (github pull #3299 from greglandrum)
  - DrawOptions: bondLineWidth behaving differently since 2020 versions
 (github issue #3305 from kienerj)
  - Not possible to copy SubstanceGroups in Python
 (github issue #3312 from greglandrum)
  - Stereochemistry perception getting confused by a bad drawing.
 (github issue #3314 from greglandrum)
  - SubstanceGroups should not be written with quotes around missing fields
 (github issue #3315 from greglandrum)
  - SetDoubleBondNeighborDirections() not overwriting existing bond
directions
 (github issue #3322 from greglandrum)
  - AdjustQueryParameters.adjustSingleBondsBetweenAromaticAtoms does not
modify ring bonds
 (github issue #3325 from greglandrum)
  - Fixes for aromatic bond fuzzy queries
 (github pull #3328 from jones-gareth)
  - lock sphinx version in CI due to problem with v3.2.0
 (github pull #3332 from greglandrum)
  - Remove deprecated Sphinx options
 (github pull #3335 from greglandrum)
  - more bug fixes and cleanups from fuzz testing
 (github pull #3339 from greglandrum)
  - unspecified branch bonds in SMARTS don't have aromaticity set
 (github issue #3342 from greglandrum)
  - Incorrect resonance structures in presence of dative bonds
 (github issue #3349 from IvanChernyshov)
  - Converting atoms with high radical counts to InChI generates incorrect
results
 (github issue #3365 from greglandrum)
  - Replace fill-opacity= with fill-opacity: in MolDraw2DSVG and tests
 (github pull #3368 from lummyk)
  - Fixes a bug in AddHs() involving sp2 centers with degree 1
 (github pull #3383 from ptosco)
  - Information about charges and isotopes lost when calling
AdjustQueryProperties
 (github issue #3388 from greglandrum)
  - prepareMolForDrawing() incorrectly adds chiral Hs if no ring info is
present
 (github issue #3392 from greglandrum)
  - CXSMILES parser should not set atom maps for attachment points
 (github issue #3393 from greglandrum)
  - Fixes a couple of query-related bugs
 (github pull #3398 from ptosco)
  - Doing a match of a recursive smarts leaves traces of the previous match
 (github issue #3403 from bp-kelley)
  - Recursive smarts cannot be used in the core for rgroup decomposition
 (github pull #3404 from bp-kelley)
  - Improvements to reaction chirality handling
 (github pull #3412 from greglandrum)
  - V3K mol blocks with no atoms fail to parse
 (github issue #3413 from greglandrum)
  - Problem parsing SGroup data comtaining `""`
 (github issue #3415 from greglandrum)
  - MolEnumerator::enumerate() should call updatePropertyCache()
 (github pull #3420 from greglandrum)
 - Fixed bad draw scale in drawMolecules. Github3391.  Take 2.
 (github pull #3424 from DavidACosgrove)
  - Replace fill-opacity= to fill-opacity: in reaction.out
 (github pull #3426 from daverona)
  - set the ChiralityPossible tag when using the new code with
FindMolChiralCenters
 (github pull #3434 from greglandrum)
  - Silence deprecation warning
 (github pull #3439 from ptosco)
  - update minimallib python requirements to python3
 (github pull #3449 from greglandrum)
  - Fix dead links to inchi-trust
 (github pull #3451 from jvansan)
  - ringMatchesRingOnly=True produces a SMARTS query that return no
substructure matches
 (github issue #3458 from jaimergp)
  - Normalization rule incorrectly matches sulfones
 (github issue #3460 from greglandrum)
  - BlockLogs was reenabling all logs, not just the ones that were disabled
 (github pull #3466 from bp-kelley)
  - Hydrogen is incorrectly identified as an "early" atom
 (github issue #3470 from greglandrum)
  - Fixes typo that causes the build to fail
 (github pull #3477 from ptosco)
  - Fix a crashing bug with None in rdMolStandardize
 (github pull #3481 from greglandrum)
  - zlib.h not found if not in system directories
 (github issue #3493 from ricrogz)
  - fix paths in ConformerParser tests
 (github pull #3504 from ricrogz)

## New Features and Enhancements:
  - Add GetBestRMS function
 (github issue #1820 from chmnk)
  - Add reorder tautomers function and accompanying tests
 (github pull #3043 from chriswzou)
  - Set RDK_BOOST_VERSION to pass minimum required version to FindBoost
 (github pull #3074 from e-kwsm)
  - bug: the MCS of the molecules CH4 and CH3OH is empty. how to return C?
 (github issue #3095 from autodataming)
  - start using boost:stacktrace
 (github pull #3124 from greglandrum)
  - Add Fuzzing, fixes #2857
 (github pull #3128 from intrigus-lgtm)
  - Cookbook entry for ETKDG with rings
 (github pull #3129 from hjuinj)
  - Fixes #2795
 (github pull #3134 from manangoel99)
  - Bump Catch2 to v2.12.1
 (github pull #3136 from e-kwsm)
  - Modernize how legacy C headers are included
 (github pull #3137 from e-kwsm)
  - Avoid C preprocessor macros
 (github pull #3138 from e-kwsm)
  - Modernization: use nullptr
 (github pull #3143 from e-kwsm)
  - Update fuzzer dict
 (github pull #3162 from intrigus-lgtm)
  - Add BCUT2D and AUTOCORR2D to desclist
 (github pull #3178 from bp-kelley)
  - Remove usage of the deprecated random_shuffle() function
 (github pull #3187 from greglandrum)
  - clang-tidy modernize-use-default-member-init and modernize-use-emplace
 (github pull #3190 from greglandrum)
  - Tautomer search
 (github pull #3205 from jones-gareth)
  - Add optional timeout to RGroupDecomposition
 (github pull #3223 from greglandrum)
  - Allow symmetrization to be completely disabled in RGD code
 (github issue #3224 from greglandrum)
  - gitignore source and build files from the RingFamilies external lib
 (github pull #3228 from d-b-w)
  - Add new CIP labelling algorithm
 (github pull #3234 from ricrogz)
  - Adds more options to adjustQueryProperties
 (github pull #3235 from greglandrum)
  - Improve SSSR performance for large molecules
 (github pull #3236 from d-b-w)
  - Support using FreeType for text rendering
 (github pull #3237 from DavidACosgrove)
  - Cleanup warnings from clang-10
 (github pull #3238 from greglandrum)
  - DEB packaging: cairo support is needed to generate PNGs
 (github pull #3250 from UnixJunkie)
  - Added call to test legends.
 (github pull #3252 from DavidACosgrove)
  - Improve performance of aromaticity detection for large molecules
 (github pull #3253 from d-b-w)
  - Speed up ring finding by skipping nodes not in rings
 (github pull #3254 from d-b-w)
  - Support enumerating some mol file features into `MolBundles`
 (github pull #3257 from greglandrum)
  - Add cxsmiles query atoms to CTAB parsers and writers
 (github pull #3261 from greglandrum)
  - Update to Coordgen v1.4.1
 (github pull #3265 from ricrogz)
  - ScaffoldNetwork: add feature to count the number of molecules a
scaffold originates from
 (github pull #3275 from greglandrum)
  - rgroup speedup
 (github pull #3279 from bp-kelley)
  - Stop trying to assign hybridization to actinides
 (github pull #3281 from greglandrum)
  - Decouple coordgen and maeparser integrations
 (github pull #3286 from greglandrum)
  - Avoid really slow Windows conda builds
 (github pull #3287 from ptosco)
  - Embed default truetype font
 (github pull #3288 from greglandrum)
  - Expanded support for CXSMILES features
 (github pull #3292 from greglandrum)
  - Deprotection Library
 (github pull #3294 from bp-kelley)
  - Use operator() and __call__() consistently across RDKit
 (github pull #3295 from ptosco)
  - Molecule metadata in PNGs
 (github pull #3316 from greglandrum)
  - Cleanup alignment dependencies
 (github pull #3317 from greglandrum)
  - Add the option to minimize structures with coordgen
 (github pull #3319 from greglandrum)
  - Updated code for chirality perception
 (github pull #3324 from greglandrum)
  - Some work on TautomerEnumerator
 (github pull #3327 from ptosco)
  - Add fragmentOnBonds to SWIG wrappers
 (github issue #3329 from greglandrum)
  - Sped up SSSR by not storing every path back to root
 (github pull #3333 from rachelnwalker)
  - Fix Cookbook formatting and added 4 new examples
 (github pull #3345 from vfscalfani)
  - switch to using target_compile_definitions instead of add_definitions
 (github pull #3350 from greglandrum)
  - [GSoC-2020] Generalized and Multithreaded File Reader
 (github pull #3363 from shrey183)
  - support new CIP code and StereoGroups in
MolDraw2D_detail::addStereoAnnotation()
 (github issue #3369 from greglandrum)
  - expose additional SubstanceGroup data members to Python
 (github pull #3375 from greglandrum)
  - Add MolDraw2DJS
 (github pull #3376 from greglandrum)
  - Add APK package link for Alpine Linux distribution
 (github pull #3379 from daverona)
  - Add SubstanceGroups to the SWIG Wrappers
 (github pull #3390 from jones-gareth)
  - Add better support for isotopic Hs to removeHs() and addHs()
 (github pull #3396 from ptosco)
  - Add support for abbreviations
 (github pull #3406 from greglandrum)
  - Allow passing explicit removeHs, sanitize and strict flags to the MDL
rxn parser
 (github pull #3411 from ptosco)
  - Improvements to reaction chirality handling
 (github pull #3412 from greglandrum)
  - RGD cleanup, optimization and a better fix for #1705
 (github pull #3428 from ptosco)
  - Tautomers with endocyclic double bonds should be preferred over
exocyclic ones
 (github issue #3430 from ptosco)
  - RGD: Code modernization and an optimization
 (github pull #3437 from ptosco)
  - expose PNG metadata functions to python
 (github pull #3440 from greglandrum)
  - Replace basestring
 (github pull #3441 from iammosespaulr)
  - Get the Uncharger to deal with a larger set of acids correctly
 (github pull #3448 from ptosco)
  - expose templated coordinate generation to the JS Wrapper
 (github pull #3450 from greglandrum)
  - change default precision for coordgen
 (github pull #3452 from greglandrum)
  - add coordgen support to demo.html
 (github pull #3453 from greglandrum)
  - Two simple MolStandardizer code cleanups
 (github pull #3454 from ptosco)
  - A few improvements to MolStandardize::Normalizer
 (github pull #3455 from ptosco)
  - Add Cookbook entries 30-32
 (github pull #3459 from vfscalfani)
  - A few small tweaks to the drawing code
 (github pull #3464 from greglandrum)
  - Make MetalDisconnector more robust against metallorganics
 (github pull #3465 from greglandrum)
  - Add nocharge algorithm example to cookbook
 (github pull #3467 from vfscalfani)
  - ROMol: add inline impl for common getNumAtoms call
 (github pull #3469 from jinpan)
  - Improve sphinx formatting in rdSubstructLibrary
 (github issue #3471 from cbouy)
  - Cmake config improvements
 (github pull #3478 from rvianello)
  - allow fillColour to be changed from python
 (github pull #3480 from greglandrum)
  - Fix undefined behavior in testCoordGen test
 (github pull #3495 from roccomoretti)
  - Add a version for the pattern fingerprint
 (github pull #3496 from greglandrum)
  - Fixes a number of issues flagged by clang
 (github pull #3498 from ptosco)
  - Update to maeparser v1.2.4
 (github pull #3506 from sailfish009)
  - Fix python invalid escape sequences
 (github pull #3508 from ricrogz)

## Code removed in this release:
- To improve API consistency of the exceptions in RDKit with the default
ones in
  the STL, the several `message()` methods and `Invariant::getMessage()` in
RDKit's
  exceptions have been removed in favor of `what()`.
- The old MolHash code has been removed from the C++ code, all wrappers,
and the
  PostgreSQL cartridge.

## Deprecated code (to be removed in a future release):
- The function `FileParserUtils::replaceAtomWithQueryAtom()` has been moved
to
  the namespace QueryOps. Please use `QueryOps::replaceAtomWithQueryAtom()`
  instead. The version in the `FileParserUtils` namespace will be removed
in the
  next release.
- The method `std::vector<ROMOL_SPTR> TautomerEnumerator::enumerate(const
ROMol &mol, boost::dynamic_bitset<> *modifiedAtoms, boost::dynamic_bitset<>
*modifiedBonds = nullptr)`
  is deprecated and will be removed in a future release.
  Please use `TautomerEnumeratorResult TautomerEnumerator::enumerate(const
ROMol &mol,bool reassignStereo = true)`
  instead.
- The `MolDraw2DQt` class is no longer supported since we don't think
anyone is
  using it. It will be removed in the 2021.03 release unless we learn
otherwise.

[Rdkit-devel] Beta of the 2020.09 release available

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

Dear all,

The beta of the 2020.09 RDKit release has been tagged in github:
https://github.com/rdkit/rdkit/releases/tag/Release_2020_09_1b1

There are a couple more bug fixes and maybe one more feature expected
before the actual release, but I wanted to go ahead and get the beta out
there.

I've done conda builds for Python 3.7 on Mac, and Linux and will hopefully
have one done for Windows later this morning. These all use the beta label
so that they do not install by default; you'll need to run "conda install"
as follows:

conda install -c rdkit/label/beta rdkit

Be sure to confirm that it's installing the right version when you are
prompted (if there's no build available, it will pick the current
production release instead).

The relevant section of the release notes is below (I still need to finish
the Highlights section), or you can see a nicely formatted version here:
https://github.com/rdkit/rdkit/releases/tag/Release_2020_09_1b1

As usual, if you have time to try out the new release I would love
feedback. If nothing major comes up, I plan to do the actual release either
later this week or early next week.

Best,
-greg

# Release_2020.09.1
(Changes relative to Release_2020.03.1)


## Backwards incompatible changes
- FindMCS() may return single atom MCSs, whereas previously it returned an
empty
  MCS unless there was at least one commond bond across the input
structures.
  So the MCS between molecules `CC` and `CO` is now `[#6]` rather than
being null.
- The fontSize()/setFontSize() (FontSize()/SetFontSize()) methods in
MolDraw2D
  now work in units of pixels (more or less) instead of the molecule units.
- The Open3DAlign functionality is now in its own separate library -
`O3AAlign`
  in cmake. If you are working in C++ and using O3A functionality, you'll
need
  to link against this library as well now.
- Due to improvements in the tautomer enumeration code, the method
  `TautomerEnumerator::enumerate` now returns a `TautomerEnumeratorResult`
  object instead of a vector of molecules. Note that if you are iterating
over
  the results of a call to `enumerate()` you shouldn't need to change your
code.
  If you want to invoke the old (and deprecated, see below) form from C++,
call
  `TautomerNumerator::enumerate(mol, nullptr)` or explicitly pass a
  `boost::dynamic_bitset*` to capture the modified atoms.
- The default precision setting for coordgen has been changed. The new
default
  was selected to greatly reduce the number of molecules for which it takes
a
  very long time to generate coordinates while still producing nice looking
  structures. We may continue to tweak this default value if/when problems
  with it are reported. If you would like to go back to the previous
setting, set
  CoordgenParams.minimizerPrecision to
CoordgenParams.sketcherStandardPrecision
  when you invoke rdCoordGen.AddCoords()
- Uncharger::uncharge() will now neutralize `[Cl,Br,I][O-],
[Cl,Br,I](=O)[O-],
  [Cl,Br,I](=O)(=O)[O-], [Cl,Br,I](=O)(=O)(=O)[O-], [O-]N=N[O-],
[N,P](=O)[O-],
  [N+](=O)([O-])[O-], P(=O)([O-])[O-], P(=O)([O-])([O-])[O-], S([O-])[O-],
  S(=O)([O-])[O-], S(=O)(=O)([O-])[O-], S(=O)(=O)([O-])OOS(=O)(=O)[O-]`.
  Previously not all of these inorganic acid counterions were consistently
  neutralized.
- We've added additional allowed valences for Cl (now 1, 3, 5), Br (now 1,
3,
  5), I (now 1, 3, 5), At (now 1, 3, 5), Xe (now 0, 2, 4, 6), and Po (now
2, 4,
  6). Molecules with atoms in the new valence states will no longer generate
  sanitization errors

## Highlights
- There's been another big improvement in the quality of molecule drawings:
character
  and font handling is greatly improved thanks to the use of the FreeType
library
- A new feature has been added to efficiently allow tautomer-insensitive
  substructure search.
- A new, much more accurate, algorithm is available for calculating CIP
labels on
  atoms and bonds.
- There's a new rdDeprotect module to allow automatically deprotecting
molecules
  before putting them into reactions

## Acknowledgements
Shrey Aryan, Jinserk Baik, Francois Berenger, Cédric Bouysset, David
Cosgrove,
Ivan Chernyshov, Guillaume Godin, Manan Goel, Jan H. Jensen, Gareth Jones,
Maria
Kadukova, Eisuke Kawashima, Steven Kearnes, Brian Kelley, Joos Kiener,
Kenneth
Lum, Joshua Meyers, Paul R Moses, Dan Nealschneider, Jin Pan, Joann
Prescott-Roy, Matthew Robinson, Jaime Rodríguez-Guerra, Ricardo
Rodriguez-Schmidt, Jeff van Santen, Roger Sayle Vincent F. Scalfani Eric
Taw,
Ansgar Schuffenhauer, Paolo Tosco, Ivan Tubert-Brohman, Riccardo Vianello,
Rachel Walker, Maciej Wójcikowski, Christopher Zou, daverona, hjuinj,
intrigus-lgtm, autodataming, paconius

## Bug Fixes:
  - Python tests fail when RDK_BUILD_COMPRESSED_SUPPLIERS is enabled
 (github issue #1888 from greglandrum)
  - ResonanceMolSupplier potentially stuck in infinite loop
 (github issue #2597 from tawe141)
  - ctest pythonTestDirChem failed
 (github issue #2757 from jinserk)
  - Issue with inversion/retention of stereochemistry
 (github issue #2891 from mc-robinson)
  - cannot parse reaction SMILES/SMARTS with dative bonds
 (github issue #2954 from greglandrum)
  - ResonanceMolSupplier can fail with small maxStructs values
 (github issue #3041 from greglandrum)
  - seg fault in ResonanceMolSupplier()
 (github issue #3048 from greglandrum)
  - Bug in image rendering of dative bonds
 (github issue #3056 from IvanChernyshov)
  - Coordinates from coordgen are not centered around the origin
 (github pull #3058 from DavidACosgrove)
  - fix a typo in ScaffoldNetwork/CMakeLists.txt
 (github pull #3060 from greglandrum)
  - Bad double bond placement in polycyclic aromatics
 (github issue #3061 from DavidACosgrove)
  - SGroups with more than one attachment point are now properly parsed
 (github pull #3072 from greglandrum)
  - Reactions should not use strict implicit valence calculations
 (github issue #3097 from mwojcikowski)
  - partial reacting atom detection
 (github issue #3119 from thegodone)
  - DrawMolecules does not center molecules
 (github issue #3126 from JoshuaMeyers)
  - results from coordgen are sometimes not centered
 (github issue #3131 from greglandrum)
  - GCC 10.0.1 compile error
 (github issue #3135 from rvianello)
  - Memory leak when parsing bad SMILES
 (github issue #3139 from intrigus-lgtm)
  - Error breaking StereoBonds in reactions
 (github issue #3147 from mc-robinson)
  - MolOps::removeHs() removes hydrides
 (github issue #3150 from jhjensen2)
  - Kekulization error from CreateScaffoldNetwork
 (github issue #3153 from greglandrum)
  - Fix drawing of N plus
 (github pull #3165 from DavidACosgrove)
  - RWMol::clear() does not explicitly clean up SubstanceGroups or
StereoGroups
 (github issue #3167 from greglandrum)
  - Modifying a molecule should not automatically clear SubstanceGroups
 (github issue #3168 from greglandrum)
  - removeHs() should not remove atoms in SubstanceGroups
 (github issue #3169 from greglandrum)
  - fix a memory problem detected in malformed SMILES
 (github pull #3171 from greglandrum)
  - Python wrapper: SetQuery and ExpandQuery for bonds
 (github pull #3172 from i-tub)
  - S-groups: PARENT field should reference index
 (github issue #3175 from greglandrum)
  - rdScaffoldNetwork causes segmenation fault upon None molecule
 (github issue #3177 from AnsgarSchuffenhauer)
  - fix a small inconsistency in the name of the inchi package
 (github pull #3182 from rvianello)
  - Molecule constructed from CXSMILES cannot be translated to SMARTS
 (github issue #3197 from greglandrum)
  - Formatting fix of CalcRMS
 (github pull #3203 from chmnk)
  - fix the CompressedSDMolSupplier python iterator interface
 (github pull #3204 from rvianello)
  - Queries generated from PreprocessReaction cannot be translated to SMARTS
 (github issue #3206 from greglandrum)
  - Attachment point info not being read from V2000 mol blocks
 (github issue #3207 from greglandrum)
  - Memory Sanitizer fails on molFromPickle on empty file
 (github issue #3211 from intrigus-lgtm)
  - Throw exception when reading from stream fails.
 (github pull #3212 from intrigus-lgtm)
  - fix molstogridimage on certain fragments/smarts patterns
 (github pull #3217 from bp-kelley)
  - Lines in wedge bonds being drawn too closely together
 (github issue #3226 from paconius)
  - EnumerateStereochemistry should clear CIP labels
 (github issue #3231 from greglandrum)
  - lock CI cairo version to force an install from the rdkit repo
 (github pull #3240 from greglandrum)
  - XBCORR and XBHEAD in Sgroups no longer cause parse failures
 (github pull #3242 from greglandrum)
  - LINKNODEs are ignored by the CTAB parsers
 (github pull #3247 from greglandrum)
  - add GetStringVectProp() to SubstanceGroup class
 (github pull #3251 from greglandrum)
  - Envelope aromaticity not detected in complex fused system
 (github issue #3256 from greglandrum)
  - Draw.MolsToGridImage repeating atom indices
 (github issue #3258 from greglandrum)
  - Atom indices clash with atom symbols in small pictures.
 (github issue #3262 from DavidACosgrove)
  - MinimalLib Dockerfile is broken at HEAD
 (github issue #3267 from skearnes)
  - Fixes #2757
 (github pull #3268 from greglandrum)
  - RGroupDecomposition restructuring
 (github pull #3270 from bp-kelley)
  - Get PPC builds working
 (github pull #3285 from greglandrum)
  - ScaffoldNetwork not in C# wrappers
 (github pull #3289 from jones-gareth)
  - bonds with "either' stereo cannot be read from JSON
 (github pull #3290 from greglandrum)
  - Small bug fixes and cleanups from fuzz testing
 (github pull #3299 from greglandrum)
  - DrawOptions: bondLineWidth behaving differently since 2020 versions
 (github issue #3305 from kienerj)
  - Not possible to copy SubstanceGroups in Python
 (github issue #3312 from greglandrum)
  - Stereochemistry perception getting confused by a bad drawing.
 (github issue #3314 from greglandrum)
  - SubstanceGroups should not be written with quotes around missing fields
 (github issue #3315 from greglandrum)
  - SetDoubleBondNeighborDirections() not overwriting existing bond
directions
 (github issue #3322 from greglandrum)
  - AdjustQueryParameters.adjustSingleBondsBetweenAromaticAtoms does not
modify ring bonds
 (github issue #3325 from greglandrum)
  - Fixes for aromatic bond fuzzy queries
 (github pull #3328 from jones-gareth)
  - lock sphinx version in CI due to problem with v3.2.0
 (github pull #3332 from greglandrum)
  - Remove deprecated Sphinx options
 (github pull #3335 from greglandrum)
  - more bug fixes and cleanups from fuzz testing
 (github pull #3339 from greglandrum)
  - unspecified branch bonds in SMARTS don't have aromaticity set
 (github issue #3342 from greglandrum)
  - Incorrect resonance structures in presence of dative bonds
 (github issue #3349 from IvanChernyshov)
  - Converting atoms with high radical counts to InChI generates incorrect
results
 (github issue #3365 from greglandrum)
  - Replace fill-opacity= with fill-opacity: in MolDraw2DSVG and tests
 (github pull #3368 from lummyk)
  - Fixes a bug in AddHs() involving sp2 centers with degree 1
 (github pull #3383 from ptosco)
  - Information about charges and isotopes lost when calling
AdjustQueryProperties
 (github issue #3388 from greglandrum)
  - prepareMolForDrawing() incorrectly adds chiral Hs if no ring info is
present
 (github issue #3392 from greglandrum)
  - CXSMILES parser should not set atom maps for attachment points
 (github issue #3393 from greglandrum)
  - Fixes a couple of query-related bugs
 (github pull #3398 from ptosco)
  - Doing a match of a recursive smarts leaves traces of the previous match
 (github issue #3403 from bp-kelley)
  - Recursive smarts cannot be used in the core for rgroup decomposition
 (github pull #3404 from bp-kelley)
  - Improvements to reaction chirality handling
 (github pull #3412 from greglandrum)
  - V3K mol blocks with no atoms fail to parse
 (github issue #3413 from greglandrum)
  - Problem parsing SGroup data comtaining `""`
 (github issue #3415 from greglandrum)
  - MolEnumerator::enumerate() should call updatePropertyCache()
 (github pull #3420 from greglandrum)
 - Fixed bad draw scale in drawMolecules. Github3391.  Take 2.
 (github pull #3424 from DavidACosgrove)
  - Replace fill-opacity= to fill-opacity: in reaction.out
 (github pull #3426 from daverona)
  - set the ChiralityPossible tag when using the new code with
FindMolChiralCenters
 (github pull #3434 from greglandrum)
  - Silence deprecation warning
 (github pull #3439 from ptosco)
  - update minimallib python requirements to python3
 (github pull #3449 from greglandrum)
  - Fix dead links to inchi-trust
 (github pull #3451 from jvansan)
  - ringMatchesRingOnly=True produces a SMARTS query that return no
substructure matches
 (github issue #3458 from jaimergp)
  - Normalization rule incorrectly matches sulfones
 (github issue #3460 from greglandrum)
  - BlockLogs was reenabling all logs, not just the ones that were disabled
 (github pull #3466 from bp-kelley)
  - Hydrogen is incorrectly identified as an "early" atom
 (github issue #3470 from greglandrum)
  - Fixes typo that causes the build to fail
 (github pull #3477 from ptosco)
  - Fix a crashing bug with None in rdMolStandardize
 (github pull #3481 from greglandrum)

## New Features and Enhancements:
  - Add GetBestRMS function
 (github issue #1820 from chmnk)
  - Add reorder tautomers function and accompanying tests
 (github pull #3043 from chriswzou)
  - Set RDK_BOOST_VERSION to pass minimum required version to FindBoost
 (github pull #3074 from e-kwsm)
  - bug: the MCS of the molecules CH4 and CH3OH is empty. how to return C?
 (github issue #3095 from autodataming)
  - start using boost:stacktrace
 (github pull #3124 from greglandrum)
  - Add Fuzzing, fixes #2857
 (github pull #3128 from intrigus-lgtm)
  - Cookbook entry for ETKDG with rings
 (github pull #3129 from hjuinj)
  - Fixes #2795
 (github pull #3134 from manangoel99)
  - Bump Catch2 to v2.12.1
 (github pull #3136 from e-kwsm)
  - Modernize how legacy C headers are included
 (github pull #3137 from e-kwsm)
  - Avoid C preprocessor macros
 (github pull #3138 from e-kwsm)
  - Modernization: use nullptr
 (github pull #3143 from e-kwsm)
  - Update fuzzer dict
 (github pull #3162 from intrigus-lgtm)
  - Add BCUT2D and AUTOCORR2D to desclist
 (github pull #3178 from bp-kelley)
  - Remove usage of the deprecated random_shuffle() function
 (github pull #3187 from greglandrum)
  - clang-tidy modernize-use-default-member-init and modernize-use-emplace
 (github pull #3190 from greglandrum)
  - Tautomer search
 (github pull #3205 from jones-gareth)
  - Add optional timeout to RGroupDecomposition
 (github pull #3223 from greglandrum)
  - Allow symmetrization to be completely disabled in RGD code
 (github issue #3224 from greglandrum)
  - gitignore source and build files from the RingFamilies external lib
 (github pull #3228 from d-b-w)
  - Add new CIP labelling algorithm
 (github pull #3234 from ricrogz)
  - Adds more options to adjustQueryProperties
 (github pull #3235 from greglandrum)
  - Improve SSSR performance for large molecules
 (github pull #3236 from d-b-w)
  - Support using FreeType for text rendering
 (github pull #3237 from DavidACosgrove)
  - Cleanup warnings from clang-10
 (github pull #3238 from greglandrum)
  - DEB packaging: cairo support is needed to generate PNGs
 (github pull #3250 from UnixJunkie)
  - Added call to test legends.
 (github pull #3252 from DavidACosgrove)
  - Improve performance of aromaticity detection for large molecules
 (github pull #3253 from d-b-w)
  - Speed up ring finding by skipping nodes not in rings
 (github pull #3254 from d-b-w)
  - Support enumerating some mol file features into `MolBundles`
 (github pull #3257 from greglandrum)
  - Add cxsmiles query atoms to CTAB parsers and writers
 (github pull #3261 from greglandrum)
  - Update to Coordgen v1.4.1
 (github pull #3265 from ricrogz)
  - ScaffoldNetwork: add feature to count the number of molecules a
scaffold originates from
 (github pull #3275 from greglandrum)
  - rgroup speedup
 (github pull #3279 from bp-kelley)
  - Stop trying to assign hybridization to actinides
 (github pull #3281 from greglandrum)
  - Decouple coordgen and maeparser integrations
 (github pull #3286 from greglandrum)
  - Avoid really slow Windows conda builds
 (github pull #3287 from ptosco)
  - Embed default truetype font
 (github pull #3288 from greglandrum)
  - Expanded support for CXSMILES features
 (github pull #3292 from greglandrum)
  - Deprotection Library
 (github pull #3294 from bp-kelley)
  - Use operator() and __call__() consistently across RDKit
 (github pull #3295 from ptosco)
  - Molecule metadata in PNGs
 (github pull #3316 from greglandrum)
  - Cleanup alignment dependencies
 (github pull #3317 from greglandrum)
  - Add the option to minimize structures with coordgen
 (github pull #3319 from greglandrum)
  - Updated code for chirality perception
 (github pull #3324 from greglandrum)
  - Some work on TautomerEnumerator
 (github pull #3327 from ptosco)
  - Add fragmentOnBonds to SWIG wrappers
 (github issue #3329 from greglandrum)
  - Sped up SSSR by not storing every path back to root
 (github pull #3333 from rachelnwalker)
  - Fix Cookbook formatting and added 4 new examples
 (github pull #3345 from vfscalfani)
  - switch to using target_compile_definitions instead of add_definitions
 (github pull #3350 from greglandrum)
  - [GSoC-2020] Generalized and Multithreaded File Reader
 (github pull #3363 from shrey183)
  - support new CIP code and StereoGroups in
MolDraw2D_detail::addStereoAnnotation()
 (github issue #3369 from greglandrum)
  - expose additional SubstanceGroup data members to Python
 (github pull #3375 from greglandrum)
  - Add MolDraw2DJS
 (github pull #3376 from greglandrum)
  - Add APK package link for Alpine Linux distribution
 (github pull #3379 from daverona)
  - Add SubstanceGroups to the SWIG Wrappers
 (github pull #3390 from jones-gareth)
  - Add better support for isotopic Hs to removeHs() and addHs()
 (github pull #3396 from ptosco)
  - Add support for abbreviations
 (github pull #3406 from greglandrum)
  - Allow passing explicit removeHs, sanitize and strict flags to the MDL
rxn parser
 (github pull #3411 from ptosco)
  - Improvements to reaction chirality handling
 (github pull #3412 from greglandrum)
  - RGD cleanup, optimization and a better fix for #1705
 (github pull #3428 from ptosco)
  - Tautomers with endocyclic double bonds should be preferred over
exocyclic ones
 (github issue #3430 from ptosco)
  - RGD: Code modernization and an optimization
 (github pull #3437 from ptosco)
  - expose PNG metadata functions to python
 (github pull #3440 from greglandrum)
  - Replace basestring
 (github pull #3441 from iammosespaulr)
  - Get the Uncharger to deal with a larger set of acids correctly
 (github pull #3448 from ptosco)
  - expose templated coordinate generation to the JS Wrapper
 (github pull #3450 from greglandrum)
  - change default precision for coordgen
 (github pull #3452 from greglandrum)
  - add coordgen support to demo.html
 (github pull #3453 from greglandrum)
  - Two simple MolStandardizer code cleanups
 (github pull #3454 from ptosco)
  - A few improvements to MolStandardize::Normalizer
 (github pull #3455 from ptosco)
  - Add Cookbook entries 30-32
 (github pull #3459 from vfscalfani)
  - A few small tweaks to the drawing code
 (github pull #3464 from greglandrum)
  - Make MetalDisconnector more robust against metallorganics
 (github pull #3465 from greglandrum)
  - Add nocharge algorithm example to cookbook
 (github pull #3467 from vfscalfani)
  - ROMol: add inline impl for common getNumAtoms call
 (github pull #3469 from jinpan)
  - Improve sphinx formatting in rdSubstructLibrary
 (github issue #3471 from cbouy)
  - Cmake config improvements
 (github pull #3478 from rvianello)
  - allow fillColour to be changed from python
 (github pull #3480 from greglandrum)

## Code removed in this release:
- To improve API consistency of the exceptions in RDKit with the default
ones in
  the STL, the several `message()` methods and `Invariant::getMessage()` in
RDKit's
  exceptions have been removed in favor of `what()`.
- The old MolHash code has been removed from the C++ code, all wrappers,
and the
  PostgreSQL cartridge.

## Deprecated code (to be removed in a future release):
- The function `FileParserUtils::replaceAtomWithQueryAtom()` has been moved
to
  the namespace QueryOps. Please use `QueryOps::replaceAtomWithQueryAtom()`
  instead. The version in the `FileParserUtils` namespace will be removed
in the
  next release.
- The method `std::vector<ROMOL_SPTR> TautomerEnumerator::enumerate(const
ROMol &mol, boost::dynamic_bitset<> *modifiedAtoms, boost::dynamic_bitset<>
*modifiedBonds = nullptr)`
  is deprecated and will be removed in a future release.
  Please use `TautomerEnumeratorResult TautomerEnumerator::enumerate(const
ROMol &mol,bool reassignStereo = true)`
  instead.
- The `MolDraw2DQt` class is no longer supported since we don't think
anyone is
  using it. It will be removed in the 2021.03 release unless we learn
otherwise.

Re: [Rdkit-devel] SDF String Generation Include Stereo information

[Emanuel E. <ema...@gm...>]

Hi Greg, Hi Paolo,

Thank you for that amazingly fast response! Seems like the bug in NAOMI is
the most likely scenario here.
Thank you for the thorough explanation and your time. I'll post new
information on this if anything unexpected comes up.

Kind regards,
Emanuel

Am Mi., 29. Juli 2020 um 13:56 Uhr schrieb Greg Landrum <
gre...@gm...>:

> Hi Emanuel,
>
> The chirality bit doesn't have anything to do with double bond
> stereochemistry.[1] So that's not what's going on here
>
> The RDKit has the ability to pass the mol block provided directly to the
> InChI code without interpreting it. I believe that the ChEMBL team is using
> that to generate InChIs. In any case, where I use that to pass the molblock
> downloaded from ChEMBL (
> https://www.ebi.ac.uk/chembl/api/data/molecule/CHEMBL6223.sdf) to the
> InChI code I get the same InChI that is found in ChEMBL.
>
> In this particular case I believe the bug may be in the NAOMI code.
>
> -greg
> [1] According to the documentation it tells you about whether or not a
> molfile with specified atomic stereochemistry represents a single
> stereoisomer  (the one drawn) or that only the relative configurations of
> the specified stereocenters is known and that the structure is either a
> single diastereomer or a mixture of the two stereoisomers.
>
> On Wed, Jul 29, 2020 at 11:17 AM Emanuel Ehmki <ema...@gm...>
> wrote:
>
>> Dear All,
>>
>> I am currently working with the RDKit generated SDF String that is stored
>> in the ChEMBL COMPOUND_STRUCTURES table in the ChEMBL database release 26.
>> My workflow is:
>>
>>    - pull SDF (V2000) from SQL table
>>    - generate internal molecule representation (NAOMI ChemBio tool-kit
>>    if that means anything to you)
>>    - generate InChI string and key from molecule
>>    - compare with InChI string and key that are stored in the ChEMBL
>>    database
>>
>> When comparing the InChI string for the molecule with the id CHEMBL6223,
>> I get two differing strings due to different stereochemistry (last
>> characters)
>>
>> ChEMBL
>> InChI: InChI=1S/C16H13IO2/c17-10-12-8-9-15(16(18)19-12)14-7-3-5-11-4-1-2-6-13(11)14/h1-7,10,15H,8-9H2/
>>    *b12-10+*
>> NAOMI InChI
>> : InChI=1S/C16H13IO2/c17-10-12-8-9-15(16(18)19-12)14-7-3-5-11-4-1-2-6-13(11)14/h1-7,10,15H,8-9H2/
>>     *b12-10-*
>>
>> While researching why that happens I realized that the SDF string doesn't
>> make use of the chirality bit that can be set in the counts line.
>> When digging deeper I found the disabled block in the MolFileWriter.cpp
>> -> MolToMolBlock function
>>
>> https://github.com/rdkit/rdkit/blob/f14f8a60de0ecf4bf5294d73b177d19055e0096d/Code/GraphMol/FileParsers/MolFileWriter.cpp#L1395
>>
>> Do I understand correctly that RDKit does not store any information about
>> chirality in V2000 and includes chiral information only in V3000 SDF format?
>>
>> Does anyone know when ChEMBL might switch to that version?
>>
>> Kind regards,
>> Emanuel
>> _______________________________________________
>> Rdkit-devel mailing list
>> Rdk...@li...
>> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>>
>

Re: [Rdkit-devel] SDF String Generation Include Stereo information

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

Hi Emanuel,

The chirality bit doesn't have anything to do with double bond
stereochemistry.[1] So that's not what's going on here

The RDKit has the ability to pass the mol block provided directly to the
InChI code without interpreting it. I believe that the ChEMBL team is using
that to generate InChIs. In any case, where I use that to pass the molblock
downloaded from ChEMBL (
https://www.ebi.ac.uk/chembl/api/data/molecule/CHEMBL6223.sdf) to the InChI
code I get the same InChI that is found in ChEMBL.

In this particular case I believe the bug may be in the NAOMI code.

-greg
[1] According to the documentation it tells you about whether or not a
molfile with specified atomic stereochemistry represents a single
stereoisomer  (the one drawn) or that only the relative configurations of
the specified stereocenters is known and that the structure is either a
single diastereomer or a mixture of the two stereoisomers.

On Wed, Jul 29, 2020 at 11:17 AM Emanuel Ehmki <ema...@gm...>
wrote:

> Dear All,
>
> I am currently working with the RDKit generated SDF String that is stored
> in the ChEMBL COMPOUND_STRUCTURES table in the ChEMBL database release 26.
> My workflow is:
>
>    - pull SDF (V2000) from SQL table
>    - generate internal molecule representation (NAOMI ChemBio tool-kit if
>    that means anything to you)
>    - generate InChI string and key from molecule
>    - compare with InChI string and key that are stored in the ChEMBL
>    database
>
> When comparing the InChI string for the molecule with the id CHEMBL6223, I
> get two differing strings due to different stereochemistry (last characters)
>
> ChEMBL
> InChI: InChI=1S/C16H13IO2/c17-10-12-8-9-15(16(18)19-12)14-7-3-5-11-4-1-2-6-13(11)14/h1-7,10,15H,8-9H2/
>    *b12-10+*
> NAOMI InChI
> : InChI=1S/C16H13IO2/c17-10-12-8-9-15(16(18)19-12)14-7-3-5-11-4-1-2-6-13(11)14/h1-7,10,15H,8-9H2/
>     *b12-10-*
>
> While researching why that happens I realized that the SDF string doesn't
> make use of the chirality bit that can be set in the counts line.
> When digging deeper I found the disabled block in the MolFileWriter.cpp ->
> MolToMolBlock function
>
> https://github.com/rdkit/rdkit/blob/f14f8a60de0ecf4bf5294d73b177d19055e0096d/Code/GraphMol/FileParsers/MolFileWriter.cpp#L1395
>
> Do I understand correctly that RDKit does not store any information about
> chirality in V2000 and includes chiral information only in V3000 SDF format?
>
> Does anyone know when ChEMBL might switch to that version?
>
> Kind regards,
> Emanuel
> _______________________________________________
> Rdkit-devel mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>

Re: [Rdkit-devel] SDF String Generation Include Stereo information

[Paolo T. <pao...@gm...>]

Hi Emanuel,

the RDKit perceives double bond stereochemistry on read, and encodes on
write, based on 2D coordinates in the molblock,

I put together an example gist here:

https://gist.github.com/ptosco/9ffae8814e84bcf189da7663775748e5

I hope that addresses your question , if not feel free to get back to me.

Cheers,
p.

On Wed, Jul 29, 2020 at 11:17 AM Emanuel Ehmki <ema...@gm...>
wrote:

> Dear All,
>
> I am currently working with the RDKit generated SDF String that is stored
> in the ChEMBL COMPOUND_STRUCTURES table in the ChEMBL database release 26.
> My workflow is:
>
>    - pull SDF (V2000) from SQL table
>    - generate internal molecule representation (NAOMI ChemBio tool-kit if
>    that means anything to you)
>    - generate InChI string and key from molecule
>    - compare with InChI string and key that are stored in the ChEMBL
>    database
>
> When comparing the InChI string for the molecule with the id CHEMBL6223, I
> get two differing strings due to different stereochemistry (last characters)
>
> ChEMBL
> InChI: InChI=1S/C16H13IO2/c17-10-12-8-9-15(16(18)19-12)14-7-3-5-11-4-1-2-6-13(11)14/h1-7,10,15H,8-9H2/
>    *b12-10+*
> NAOMI InChI
> : InChI=1S/C16H13IO2/c17-10-12-8-9-15(16(18)19-12)14-7-3-5-11-4-1-2-6-13(11)14/h1-7,10,15H,8-9H2/
>     *b12-10-*
>
> While researching why that happens I realized that the SDF string doesn't
> make use of the chirality bit that can be set in the counts line.
> When digging deeper I found the disabled block in the MolFileWriter.cpp ->
> MolToMolBlock function
>
> https://github.com/rdkit/rdkit/blob/f14f8a60de0ecf4bf5294d73b177d19055e0096d/Code/GraphMol/FileParsers/MolFileWriter.cpp#L1395
>
> Do I understand correctly that RDKit does not store any information about
> chirality in V2000 and includes chiral information only in V3000 SDF format?
>
> Does anyone know when ChEMBL might switch to that version?
>
> Kind regards,
> Emanuel
> _______________________________________________
> Rdkit-devel mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>

[Rdkit-devel] SDF String Generation Include Stereo information

[Emanuel E. <ema...@gm...>]

Dear All,

I am currently working with the RDKit generated SDF String that is stored
in the ChEMBL COMPOUND_STRUCTURES table in the ChEMBL database release 26.
My workflow is:

   - pull SDF (V2000) from SQL table
   - generate internal molecule representation (NAOMI ChemBio tool-kit if
   that means anything to you)
   - generate InChI string and key from molecule
   - compare with InChI string and key that are stored in the ChEMBL
   database

When comparing the InChI string for the molecule with the id CHEMBL6223, I
get two differing strings due to different stereochemistry (last characters)

ChEMBL
InChI: InChI=1S/C16H13IO2/c17-10-12-8-9-15(16(18)19-12)14-7-3-5-11-4-1-2-6-13(11)14/h1-7,10,15H,8-9H2/
   *b12-10+*
NAOMI InChI
: InChI=1S/C16H13IO2/c17-10-12-8-9-15(16(18)19-12)14-7-3-5-11-4-1-2-6-13(11)14/h1-7,10,15H,8-9H2/
    *b12-10-*

While researching why that happens I realized that the SDF string doesn't
make use of the chirality bit that can be set in the counts line.
When digging deeper I found the disabled block in the MolFileWriter.cpp ->
MolToMolBlock function
https://github.com/rdkit/rdkit/blob/f14f8a60de0ecf4bf5294d73b177d19055e0096d/Code/GraphMol/FileParsers/MolFileWriter.cpp#L1395

Do I understand correctly that RDKit does not store any information about
chirality in V2000 and includes chiral information only in V3000 SDF format?

Does anyone know when ChEMBL might switch to that version?

Kind regards,
Emanuel

Re: [Rdkit-devel] PostgreSQL PGXS-style Makefile, and RDGeneral/export.h: No such file or directory

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

[Deleted the previous contents of the thread because it was causing
formatting problems for me in gmail, sorry]

One thing you might consider trying here is to build and install the RDKit
(without the cartridge or Python wrappers)
like a normal library using the standard RDKit build process.
This should install all the header files (include export.h) and libraries
you need. You can then put the cartridge source wherever is most convenient
for you and then make sure your Makefile for the cartridge has the relevant
-I and -L directives to point to where that install is.

I *think* this would end up making things a lot easier in the end.
-greg

Re: [Rdkit-devel] PostgreSQL PGXS-style Makefile, and RDGeneral/export.h: No such file or directory

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

On Tue, Mar 31, 2020 at 12:24 AM Finnerty, Jim via Rdkit-devel <
rdk...@li...> wrote:

> Thank you, Paolo.  I found a generated export.h in Oxygen, used that, and
> got past that issue.
>
>
>
> The CMake script enforces a minimum Boost version of Boost-1.56.0, whereas
> we’re on Boost-1.55.0.  Since I’m using a PGXS-style make now, I tried
> building on Boost-1.55.0, and make doesn’t fail.  What is it that depends
> on Boost-1.56.0 that would probably fail if we’re running on Boost-1.55.0?
>
>
That's an interesting question. I'm really not sure what the answer is at
this point. It may be that whatever new features are being used or
whichever boost bug fixes happened are in parts of the code that you won't
end up using. So I think the best thing to probably do is just try things
out and see what happens.
If the build works and the tests pass, you're probably ok.
As an aside: boost 1.55 is pretty ancient (Nov 2013). I realize that this
likely isn't in your control, but it might be worth seeing if you can
update that.
(I notice below that it looks like you're actually using RHEL5, which is
even more ancient and out of support, so I'm going to guess you can't
change anything there)



>
>
> The CMake process also replaces some strings in the rdkit--3.8.sql file.
> One looks odd, though.  In OPERATOR CLASS gin_bfp_ops, the replacement
> skips over “5”.  Is this expected?
>
>
>
>     FUNCTION    4   gin_bfp_consistent(internal, int2, bfp, int4,
> internal, internal, internal, internal),
>
>
>     FUNCTION    6   gin_bfp_triconsistent(internal, int2, bfp, int4,
> internal, internal, internal), -- jlf    @RDKIT_GIN_BFP_TRICONSISTENT@
>
>
>

Yes, we don't define support function 5 for that operator. I don't have an
explanation for why not.


> Running with Boost-1.55.0 and using the definition above, without running
> CMake (and with a PGXS-style Makefile), rdkit.so does in fact build;
> however, when the extension is loaded it fails because symbol rdErrorLog is
> not defined.  How should I define it with my PGXS-style build process?
>
>
>
> postgres=# create extension rdkit;
>
> ERROR:  could not load library
> "/local/home/jfinnert/workspace/AuroraML/build/RDSManfredDev/RDSManfredDev-Development/RHEL5_64/DEV.STD.PTHREAD/build/RDSManfred/lib/postgresql/rdkit.so":
> /local/home/jfinnert/workspace/AuroraML/build/RDSManfredDev/RDSManfredDev-Development/RHEL5_64/DEV.STD.PTHREAD/build/RDSManfred/lib/postgresql/rdkit.so:
> undefined symbol: rdErrorLog
>
>
>

The symbol rdErrorLog should be defined in the library RDGeneral. Are you
linking against that?

-greg

>
>

Re: [Rdkit-devel] PostgreSQL PGXS-style Makefile, and RDGeneral/export.h: No such file or directory

[Finnerty, J. <jfi...@am...>]

Thank you, Paolo.  I found a generated export.h in Oxygen, used that, and got past that issue.

The CMake script enforces a minimum Boost version of Boost-1.56.0, whereas we’re on Boost-1.55.0.  Since I’m using a PGXS-style make now, I tried building on Boost-1.55.0, and make doesn’t fail.  What is it that depends on Boost-1.56.0 that would probably fail if we’re running on Boost-1.55.0?

The CMake process also replaces some strings in the rdkit--3.8.sql file.  One looks odd, though.  In OPERATOR CLASS gin_bfp_ops, the replacement skips over “5”.  Is this expected?

    FUNCTION    4   gin_bfp_consistent(internal, int2, bfp, int4, internal, internal, internal, internal),
    FUNCTION    6   gin_bfp_triconsistent(internal, int2, bfp, int4, internal, internal, internal), -- jlf    @RDKIT_GIN_BFP_TRICONSISTENT@

Running with Boost-1.55.0 and using the definition above, without running CMake (and with a PGXS-style Makefile), rdkit.so does in fact build; however, when the extension is loaded it fails because symbol rdErrorLog is not defined.  How should I define it with my PGXS-style build process?

postgres=# create extension rdkit;
ERROR:  could not load library "/local/home/jfinnert/workspace/AuroraML/build/RDSManfredDev/RDSManfredDev-Development/RHEL5_64/DEV.STD.PTHREAD/build/RDSManfred/lib/postgresql/rdkit.so": /local/home/jfinnert/workspace/AuroraML/build/RDSManfredDev/RDSManfredDev-Development/RHEL5_64/DEV.STD.PTHREAD/build/RDSManfred/lib/postgresql/rdkit.so: undefined symbol: rdErrorLog

Thank you,

    /Jim

From: Paolo Tosco <pao...@gm...>
Date: Sunday, March 29, 2020 at 12:58 PM
To: "Finnerty, Jim" <jfi...@am...>, "rdk...@li..." <rdk...@li...>
Subject: RE: [EXTERNAL] [Rdkit-devel] PostgreSQL PGXS-style Makefile, and RDGeneral/export.h: No such file or directory


CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you can confirm the sender and know the content is safe.



Hi Jim,

RDGeneral/export.h is generated when you run cmake; it is not part of the distribution.

If you do a

mkdir build && cd build && cmake ..

in the RDKit root directory the file will be generated, then you may copy it in your RDGeneral directory.

It is worth mentioning that the PGXS-style Makefile is currently deprecated; you can build the PostgreSQL cartridge as part of a standard CMake build by setting the relevant cmake variables, e.g.

  -DRDK_BUILD_PGSQL=ON \
  -DRDK_PGSQL_STATIC=ON \
  -DPostgreSQL_ROOT=/usr/pgsql-12 \
  -DPostgreSQL_INCLUDE_DIR=/usr/pgsql-12/include \
  -DPostgreSQL_TYPE_INCLUDE_DIR=/usr/pgsql-12/include/server \
  -DPostgreSQL_LIBRARY_DIR=/usr/pgsql-12/lib \

However, if you prefer to use the PGXS-style Makefile, it should work provided you generate RDGeneral/export.h by running cmake once and then copy it to your own RDGeneral directory.

I hope the above helps, cheers
p.
On 29/03/2020 17:18, Finnerty, Jim via Rdkit-devel wrote:
Hello RDKit developers.  I’m trying to make the RDKit extension available for use in AWS Aurora PostgreSQL.  Usually the way we integrate new extensions is with a PGXS-style Makefile, and with all of the C or C++ sourcefiles, .config, PGXS-style Makefile, .sql, and /sql files in one directory.

I copied the following files into a separate build directory (on Linux):


adapter.cpp  bfp_gist.c  bitstring.c  cache.c  CMakeLists.txt  DataStructs  Geometry  guc.c  low_gist.c  mol_op.c   rdkit--3.8.sql  rdkit_gist.c  rdkit_io.c    README    sfp_op.c

bfp_gin.c    bfp_op.c    bitstring.h  cache.h  data            expected     GraphMol  guc.h  Makefile    RDGeneral  rdkit.control   rdkit.h       rdkit.sql.in  rxn_op.c  sql

where /Geometry, /GraphMol, /RDGeneral, and /DataStructs are rsync’d from the source directories under /Code, rdkit—3.8.sql is generated, and Makefile replaces what CMake would have generated with a simpler PGXS-style Makefile:

MODULE_big = rdkit
OBJS = adapter.o bfp_gin.o bfp_gist.o bfp_op.o bitstring.o cache.o guc.o low_gist.o mol_op.o rdkit_gist.o rdkit_io.o rxn_op.o sfp_op.o
EXTENSION = rdkit
DATA = rdkit--3.8.sql
REGRESS = bfpgin bfpgist-91 btree fpgist fps molgist props rdkit-91 reaction sfpgist slfpgist
PG_CONFIG = pg_config
PGXS := $(shell $(PG_CONFIG) --pgxs)
include $(PGXS)

When I attempt to ‘make’ with this definition and with these files, I get:

In file included from adapter.cpp:32:0:
./GraphMol/RDKitBase.h:17:30: fatal error: RDGeneral/export.h: No such file or directory
 #include <RDGeneral/export.h>

and this is true:  export.h isn’t in /RDGeneral, but it is included from <GraphMol/RDKitBase.h>, at adapter.cpp line 32.

Where can I find export.h, and why isn’t it in RDGeneral/export.h?

Once I get past this issue, is there some reason why building RDKit in this way won’t work?

Are the list of source files above complete for building the RDKit extension, if you don’t need Python wrapper support?

Thank you,

    /Jim







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[Rdkit-devel] 2020.03.1 RDKit Release

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

Dear all,

I'm pleased to announce that the next version of the RDKit - 2020.03 - is
released. This time we even managed to get it out during the correct month!
:-) The release notes are below.

The release files are on the github release page:
https://github.com/rdkit/rdkit/releases/tag/Release_2020_03_1

Binaries have been uploaded to anaconda.org (https://anaconda.org/rdkit).
The available conda binaries for this release are:
Linux 64bit: python 3.6, 3.7
Mac OS 64bit: python 3.6, 3.7
Windows 64bit: python 3.6, 3.7

Conda builds of the PostgreSQL cartridge are also available:
Linux 64bit: postgresql 9.6, 10, 11
Mac OS 64bit: postgresql 9.6, 10, 11

The PR is in to switch conda-forge to the new version as well. There are
currently some non-RDKit-related build problems with conda-forge, but
hopefully that will be updated soon as well.

The online version of the documentation at rdkit.org (
http://rdkit.org/docs/index.html) has been updated.

Some things that will be finished over the next couple of days:
- The conda build scripts will be updated to reflect the new version
- The homebrew script

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 2020.

Best Regards,
-greg

# Release_2020.03.1
(Changes relative to Release_2019.09.1)

## Backwards incompatible changes
- Searches for equal molecules (i.e. `mol1 @= mol2`) in the PostgreSQL
cartridge
  now use the `do_chiral_sss` option. So if `do_chiral_sss` is false (the
  default), the molecules `CC(F)Cl` and `C[C@H](F)Cl` will be considered to
be equal.
  Previously these molecules were always considered to be different.
- Attempting to create a MolSupplier from a filename pointing to an empty
file,
  a file that does not exist or sometihing that is not a standard file (i.e.
  something like a directory) now generates an exception.
- The cmake option `RDK_OPTIMIZE_NATIVE` has been renamed to
`RDK_OPTIMIZE_POPCNT`

# Highlights:
- The drawings generated by the MolDraw2D objects are now significantly
improved
  and can include simple atom and bond annotations (#2931 and #3010)
- An initial implementation of a modified scaffold network algorithm is now
  available (#2911)
- A few new descriptor/fingerprint types are available - BCUTs (#2957),
Morse
  atom fingerprints (#1773), Coulomb matrices (#2993), and MHFP and SECFP
  fingerprints (#2643)
- There is a new, and greatly improved, version of the RDKit Cookbook
(#2884)
- There is a new version (v3) of the ETKDG conformer generator along with
  optional new terms for handling small rings and macrocyles (
http://doi.org/dqnh) (#2999)


## Acknowledgements:
Marcel Baltruschat, Jason Biggs, Eliane Briand, Ben Cornett, David Cosgrove,
Andrew Dalke, Tim Dudgeon, Zhenting Gao, Guillaume Godin, Manan Goel, Gareth
Jones, Zachary Kaplan, Eisuke Kawashima, Steven Kearnes, Brian Kelley, Maxim
Koltsov, Franziska Kruger, Mieszko Manijak, Dan Nealschneider, Daniil
Polykovskiy, Daniel Probst, Sereina Riniker, Matthew Robinson, Steve
Roughley,
Kevin Ryan, Vincent F. Scalfani, Ricardo Rodriguez Schmidt, Rim
Shayakhmetov,
Aryan Shrey, Nik Stiefl, Matt Swain, Paolo Tosco, Wiep van der Toorn,
Riccardo
Vianello, Shuzhe Wang, Piotr Wawrzyniak, Hsiao Yi, 'jasad1',
'luancarvalhomartins'


## Bug Fixes:
  - Mol rendering within DataFrames in a Jupyter Notebook is broken with
Pandas 0.25.1
 (github issue #2673 from mrcblt)
  - Removed RDKIT_SIMDIVPICKERS_EXPORT
 (github pull #2740 from ptosco)
  - - enable building RDKitRingDecomposerLib.dll under Windows
 (github pull #2742 from ptosco)
  - Do a windows DLL build as part of the Azure DevOps setup
 (github pull #2743 from greglandrum)
  - Fix data race in sascorer.py
 (github pull #2744 from skearnes)
  - Uncharger not properly setting explicit/implicit H count
 (github issue #2749 from greglandrum)
  - MSVC compile error: MolHash scoped enum cannot be redeclared as unscoped
 (github issue #2752 from mcs07)
  - Molecules whose Y size is very small won't display as SVG
 (github issue #2762 from ptosco)
  - Make the cartridge tests work with PostgreSQL 12
 (github pull #2767 from greglandrum)
  - Salt stripper should consider bond matches as well as atom matches
 (github pull #2768 from greglandrum)
  - Bismuth should count as an early element
 (github issue #2775 from greglandrum)
  - addHs() fails on atoms with "bad" valences
 (github issue #2782 from greglandrum)
  - Element symbol lookup for some transuranics returns incorrect results
 (github issue #2784 from LeanAndMean)
  - [cartridge] molecular equality should use do_chiral_sss setting
 (github issue #2790 from greglandrum)
  - uncharger removes Hs from carbocations instead of adding them
 (github issue #2792 from greglandrum)
  - Fix build without boost serialization library
 (github pull #2796 from maksbotan)
  - Using `SetBoundsMat` significantly slows down conformer generation
process.
 (github issue #2800 from hjuinj)
  - rdkit.Ched.rdFMCS.FindMCS generates invalid smarts
 (github issue #2801 from luancarvalhomartins)
  - Remove confId from *FFOptimizeMoleculeConfs Python docs
 (github issue #2805 from ptosco)
  - Hybridization queries on dummy atoms not written properly to SMARTS
 (github issue #2814 from greglandrum)
  - Charge range queries not properly written to SMARTS
 (github issue #2815 from greglandrum)
  - RDKit segfaults in MMFFOptimizeMoleculeConfs()
 (github issue #2820 from ptosco)
  - Trusted Smiles holder doesn't handle ring queries
 (github issue #2830 from bp-kelley)
  - Fix windows substructure crash
 (github pull #2836 from greglandrum)
  - Fix YAeHMOP build
 (github pull #2838 from ptosco)
  - testGithub2245 in testPickers.cpp occasionally fails
 (github issue #2839 from ptosco)
  - add define for RDK_USE_BOOST_SERIALIZATION
 (github pull #2859 from greglandrum)
  - fix start/end atoms when wedging bonds
 (github pull #2861 from greglandrum)
  - Fixes the size of the reduced charge matrix from eHT calculations
 (github pull #2864 from greglandrum)
  - Dev/pvs studio cleanups2
 (github pull #2877 from greglandrum)
  - segfault in MaeMolSupplier
 (github issue #2881 from greglandrum)
  - update maven url in build system
 (github pull #2889 from greglandrum)
  - EnumerateStereoisomers cannot handle STEREOANY bonds
 (github issue #2890 from ricrogz)
  - Update one of the cartridge tests that got missed
 (github pull #2894 from greglandrum)
  - acepentalene aromaticity perception
 (github issue #2895 from adalke)
  - New Similarity Maps drawing code Java Wrappers non-functional
 (github issue #2896 from sroughley)
  - Fix to allow multistructure images in Java/C# and use MCS for c# wrapper
 (github pull #2898 from jones-gareth)
  - Remove bogus URFLib library
 (github pull #2900 from greglandrum)
  - java wrapper build cleanups
 (github pull #2901 from greglandrum)
  - SMARTS parser fails on high-numbered ring closures in branches
 (github issue #2909 from greglandrum)
  - patch to make PandasTools tests pass with pandas v0.22
 (github pull #2913 from greglandrum)
  - fix doctest problem with Pandas v1.0
 (github pull #2918 from greglandrum)
  - Build with -D RDK_BUILD_COORDGEN_SUPPORT=OFF includes a test case that
depends on MaeMolSupplier
 (github issue #2929 from rvianello)
  - MinimalLib: get_stereo_tags() should also return unspecified centers
 (github issue #2936 from greglandrum)
  - Fix regression introduced by e245349c
 (github pull #2945 from cornett)
  - Avoid data race warning in SmilesParse.cpp
 (github pull #2946 from skearnes)
  - Empty molecule has non-zero LabuteASA
 (github issue #2948 from jasondbiggs)
  - Fix a problem with aromatic heteroatom tautomer enumeration
 (github pull #2952 from greglandrum)
  - Molecule properties not retained with
MolStandardize.rdMolStandardize.Cleanup()
 (github issue #2965 from ZacharyKaplan)
  - Fix build without boost serialization.
 (github pull #2972 from ricrogz)
  - RDKFuncs.chargeParent() core dumps when standardization is skipped
 (bithub issue #2970 from tdudgeon)
  - fix a typo in the scaffold network wrappers and add some tests
 (github pull #2982 from greglandrum)
  - Tautomer enumeration should remove stereo in all tautomers
 (github issue #2990 from greglandrum)
  - Segmentation fault on EmbedMolecule
 (github issue #3019 from shayakhmetov)
  - Removed dllexport from a function that lives in the anonymous namespace
 (github pull #3027 from ptosco)


## New Features and Enhancements:
  - Morse atom fingerprint
 (github pull #1773 from thegodone)
  - Allow serializing coordinates as doubles
 (github issue #2510 from danpol)
  - Rework MaeMolSupplier, fix #2617
 (github pull #2620 from ricrogz)
  - Implementation of MHFP and SECFP Fingerprints
 (github pull #2643 from daenuprobst)
  - MatchFusedRings does not imply CompleteRingsOnly anymore
 (github pull #2748 from ptosco)
  - Improvements to JS wrappers
 (github pull #2751 from greglandrum)
  - Fix installed header directory structure
 (github pull #2754 from ricrogz)
  - Add doRandom to the header docs
 (github pull #2756 from bp-kelley)
  - Add queryMol data member to MCSResult
 (github pull #2759 from ptosco)
  - Add functions to enable/disable the substructure matching monkey
patching in IPythonConsole.py
 (github issue #2786 from greglandrum)
  - Add a function to assign chiral tags from sss atom parity
 (github issue #2823 from ptosco)
  - Support MRV_IMPLICIT_H S groups when reading Mol blocks
 (github issue #2829 from greglandrum)
  - Unset executable flag
 (github pull #2833 from e-kwsm)
  - Remove O(N) behavior of getNumBonds
 (github pull #2847 from bp-kelley)
  - Feature proposal: add remove_stereochemistry=False flag for RemoveHs()
 (github issue #2848 from shayakhmetov)
  - Expose SubstructLibrary serialization stream
 (github pull #2853 from bp-kelley)
  - Fix typo
 (github pull #2862 from e-kwsm)
  - Rename RDK_OPTIMIZE_NATIVE to RDK_OPTIMIZE_POPCNT
 (github pull #2865 from ElianeBriand)
  - Update Draw.MolToImage() and Draw.MolToFile() to use the new drawing
code
 (github pull #2866 from greglandrum)
  - Improve PostgreSQL cartridge install documentation
 (github pull #2870 from yellowBirdy)
  - Fixes #2858
 (github pull #2871 from greglandrum)
  - Add a cartridge test to the azure devops config
 (github pull #2873 from greglandrum)
  - Add a new Cookbook v2 to the RDKit docs
 (github pull #2884 from vfscalfani)
  - Add MolVS tautomer canonicalization
 (github pull #2886 from greglandrum)
  - add a convenience function for RGD--Pandas integration
 (github pull #2887 from greglandrum)
  - run clang-tidy with readability-braces-around-statements
 (github pull #2899 from greglandrum)
  - Allow RDProps::clearProp to succeed even if the prop doesn't exist
 (github issue #2910 from greglandrum)
  - Add a scaffold network implementation
 (github pull #2911 from greglandrum)
  - cleanup of the SMILES/SMARTS parsing and writing code
 (github pull #2912 from greglandrum)
  - Add _ctab, _mol2, _pdb to allow direct mol construction from strings
 (github issue #2916 from greglandrum)
  - Parse and handle the stereoCare or STBOX flags in CTABs
 (github pull #2917 from greglandrum)
  - RDKit exceptions do not override the default `what()` method
 (github issue #2920 from ricrogz)
  - Allow custom post-match filters for substructure matching
 (github pull #2927 from greglandrum)
  - Proposed improvements to 2D Drawing Code
 (github issue #2931 from DavidACosgrove)
  - Include running the documentation tests as part of the CI runs
 (github pull #2932 from greglandrum)
  - Add support for phosphine and arsine chirality
 (github issue #2949 from wopozka)
  - A couple additions to the extended Hueckel integration
 (github pull #2955 from greglandrum)
  - Add BCUT 2D descriptors
 (github pull #2957 from bp-kelley)
  - Add multithreaded pattern/fp generator
 (github pull #2973 from bp-kelley)
  - Description for the data files.
 (github pull #2975 from zhentg)
  - Enable larger ring matches in SMARTS expressions
 (github pull #2981 from d-b-w)
  - ScaffoldNetwork rearrangements
 (github pull #2985 from greglandrum)
  - add add_hs() and remove_hs() to JS wrappers
 (github pull #2986 from greglandrum)
  - Add Atom Feature Vectors
 (github pull #2988 from thegodone)
  - Add CoulombMat calculator
 (github pull #2993 from thegodone)
  - Update azure-pipelines.yml
 (github pull #2997 from greglandrum)
  - Improve Conformational Sampling of Small and Large Ring Molecules
 (github pull #2999 from hjuinj)
  - Fix atom highlighting in notebook PNGs
 (github pull #3000 from greglandrum)
  - adds a one-liner for getting a vector of random smiles for a molecule
 (github pull #3002 from greglandrum)
  - Allow enhanced stereo to be used in substructure search
 (github pull #3003 from d-b-w)
  - Add support for the rest of the v3000 atom properties
 (github pull #3007 from greglandrum)
  - Move jupyter extension logging to the python logger
 (github pull #3008 from bp-kelley)
  - Commit of 2D draw annotation.
 (github pull #3010 from DavidACosgrove)
  - Update Maeparser & Coordgen Dependencies
 (github pull #3011 from ricrogz)
  - Remove unnecessary files
 (github pull #3012 from e-kwsm)
  - allow retrieval of the atoms/bonds modified by the tautomerization
 (github pull #3013 from greglandrum)
  - Add 5 new recipes to Cookbook
 (github pull #3014 from vfscalfani)
  - Turns on cairo support (and testing) in the Azure DevOps CI builds
 (github pull #3022 from greglandrum)
  - Added support for Python FMCS functors
 (github pull #3023 from ptosco)
  - add random seed to docs to get reproducible conformations
 (github pull #3026 from greglandrum)
  - update docs for 2020.03
 (github pull #3028 from greglandrum)
  - update Getting Started in C++ document
 (github pull #3039 from DavidACosgrove)



## Deprecated code (to be removed in a future release):
- To improve API consistency of the exceptions in RDKit with the default
ones in
  the STL, the several `message()` methods and `Invariant::getMessage()` in
RDKit's
  exceptions are from now on deprecated in favor of `what()`. Both
`message()` and
  `Invariant::getMessage()` will be removed in the next release.
- The old MolHash code should be considered deprecated. This release
introduces
  a more flexible alternative. Specifically the following pieces will be
removed in the next release:
  - The python functionality
`rdkit.Chem.rdMolHash.GenerateMoleculeHashString()`
  - The C++ functionality directly present in the header file
`GraphMol/MolHash/MolHash.h`

Re: [Rdkit-devel] PostgreSQL PGXS-style Makefile, and RDGeneral/export.h: No such file or directory

[Paolo T. <pao...@gm...>]

Hi Jim,

RDGeneral/export.h is generated when you run cmake; it is not part of 
the distribution.

If you do a

mkdir build && cd build && cmake ..

in the RDKit root directory the file will be generated, then you may 
copy it in your RDGeneral directory.

It is worth mentioning that the PGXS-style Makefile is currently 
deprecated; you can build the PostgreSQL cartridge as part of a standard 
CMake build by setting the relevant cmake variables, e.g.

   -DRDK_BUILD_PGSQL=ON \
   -DRDK_PGSQL_STATIC=ON \
   -DPostgreSQL_ROOT=/usr/pgsql-12 \
   -DPostgreSQL_INCLUDE_DIR=/usr/pgsql-12/include \
   -DPostgreSQL_TYPE_INCLUDE_DIR=/usr/pgsql-12/include/server \
   -DPostgreSQL_LIBRARY_DIR=/usr/pgsql-12/lib \

However, if you prefer to use the PGXS-style Makefile, it should work 
provided you generate RDGeneral/export.h by running cmake once and then 
copy it to your own RDGeneral directory.

I hope the above helps, cheers
p.

On 29/03/2020 17:18, Finnerty, Jim via Rdkit-devel wrote:
>
> Hello RDKit developers.  I’m trying to make the RDKit extension 
> available for use in AWS Aurora PostgreSQL.  Usually the way we 
> integrate new extensions is with a PGXS-style Makefile, and with all 
> of the C or C++ sourcefiles, .config, PGXS-style Makefile, .sql, and 
> /sql files in one directory.
>
> I copied the following files into a separate build directory (on Linux):
>
> adapter.cppbfp_gist.cbitstring.ccache.cCMakeLists.txt*DataStructs**Geometry*guc.clow_gist.cmol_op.crdkit--3.8.sqlrdkit_gist.crdkit_io.cREADMEsfp_op.c
>
> bfp_gin.cbfp_op.cbitstring.hcache.h*data**expected**GraphMol*guc.hMakefile*RDGeneral*rdkit.control 
> rdkit.hrdkit.sql.inrxn_op.c*sql*
>
> where /Geometry, /GraphMol, /RDGeneral, and /DataStructs are rsync’d 
> from the source directories under /Code, rdkit—3.8.sql is generated, 
> and Makefile replaces what CMake would have generated with a simpler 
> PGXS-style Makefile:
>
> MODULE_big = rdkit
>
> OBJS = adapter.o bfp_gin.o bfp_gist.o bfp_op.o bitstring.o cache.o 
> guc.o low_gist.o mol_op.o rdkit_gist.o rdkit_io.o rxn_op.o sfp_op.o
>
> EXTENSION = rdkit
>
> DATA = rdkit--3.8.sql
>
> REGRESS = bfpgin bfpgist-91 btree fpgist fps molgist props rdkit-91 
> reaction sfpgist slfpgist
>
> PG_CONFIG = pg_config
>
> PGXS := $(shell $(PG_CONFIG) --pgxs)
>
> include $(PGXS)
>
> When I attempt to ‘make’ with this definition and with these files, I get:
>
> In file included from adapter.cpp:32:0:
>
> ./GraphMol/RDKitBase.h:17:30: fatal error: RDGeneral/export.h: No such 
> file or directory
>
>  #include <RDGeneral/export.h>
>
> and this is true:  export.h isn’t in /RDGeneral, but it is included 
> from <GraphMol/RDKitBase.h>, at adapter.cpp line 32.
>
> Where can I find export.h, and why isn’t it in RDGeneral/export.h?
>
> Once I get past this issue, is there some reason why building RDKit in 
> this way won’t work?
>
> Are the list of source files above complete for building the RDKit 
> extension, if you don’t need Python wrapper support?
>
> Thank you,
>
>     /Jim
>
>
>
> _______________________________________________
> Rdkit-devel mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel

[Rdkit-devel] PostgreSQL PGXS-style Makefile, and RDGeneral/export.h: No such file or directory

[Finnerty, J. <jfi...@am...>]

Hello RDKit developers.  I’m trying to make the RDKit extension available for use in AWS Aurora PostgreSQL.  Usually the way we integrate new extensions is with a PGXS-style Makefile, and with all of the C or C++ sourcefiles, .config, PGXS-style Makefile, .sql, and /sql files in one directory.

I copied the following files into a separate build directory (on Linux):


adapter.cpp  bfp_gist.c  bitstring.c  cache.c  CMakeLists.txt  DataStructs  Geometry  guc.c  low_gist.c  mol_op.c   rdkit--3.8.sql  rdkit_gist.c  rdkit_io.c    README    sfp_op.c

bfp_gin.c    bfp_op.c    bitstring.h  cache.h  data            expected     GraphMol  guc.h  Makefile    RDGeneral  rdkit.control   rdkit.h       rdkit.sql.in  rxn_op.c  sql

where /Geometry, /GraphMol, /RDGeneral, and /DataStructs are rsync’d from the source directories under /Code, rdkit—3.8.sql is generated, and Makefile replaces what CMake would have generated with a simpler PGXS-style Makefile:

MODULE_big = rdkit
OBJS = adapter.o bfp_gin.o bfp_gist.o bfp_op.o bitstring.o cache.o guc.o low_gist.o mol_op.o rdkit_gist.o rdkit_io.o rxn_op.o sfp_op.o
EXTENSION = rdkit
DATA = rdkit--3.8.sql
REGRESS = bfpgin bfpgist-91 btree fpgist fps molgist props rdkit-91 reaction sfpgist slfpgist
PG_CONFIG = pg_config
PGXS := $(shell $(PG_CONFIG) --pgxs)
include $(PGXS)

When I attempt to ‘make’ with this definition and with these files, I get:

In file included from adapter.cpp:32:0:
./GraphMol/RDKitBase.h:17:30: fatal error: RDGeneral/export.h: No such file or directory
 #include <RDGeneral/export.h>

and this is true:  export.h isn’t in /RDGeneral, but it is included from <GraphMol/RDKitBase.h>, at adapter.cpp line 32.

Where can I find export.h, and why isn’t it in RDGeneral/export.h?

Once I get past this issue, is there some reason why building RDKit in this way won’t work?

Are the list of source files above complete for building the RDKit extension, if you don’t need Python wrapper support?

Thank you,

    /Jim

[Rdkit-devel] (no subject)

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

Dear all,

The beta of the 2020.03 RDKit release has been tagged in github:
https://github.com/rdkit/rdkit/releases/tag/Release_2020_03_1b1

I've done conda builds for Python 3.6 and 3.7 for Mac, and Linux and I'm
working on the Windows builds now. These all use the beta label so that
they do not install by default; you'll need to run "conda install" as
follows:

conda install -c rdkit/label/beta rdkit

Be sure to confirm that it's installing the right version when you are
prompted (if there's no build available, it will pick the current
production release instead).

The relevant section of the release notes (which still may need a highlight
or two added) is below, or you can see a nicely formatted version here:
https://github.com/rdkit/rdkit/releases/tag/Release_2020_03_1b1

As usual, if you have time to try out the new release I would love
feedback. If nothing major comes up, I plan to do the actual release next
Monday.

Best,
-greg

# Release_2020.03.1
(Changes relative to Release_2019.09.1)

## Backwards incompatible changes
- Searches for equal molecules (i.e. `mol1 @= mol2`) in the PostgreSQL
cartridge
  now use the `do_chiral_sss` option. So if `do_chiral_sss` is false (the
  default), the molecules `CC(F)Cl` and `C[C@H](F)Cl` will be considered to
be equal.
  Previously these molecules were always considered to be different.
- Attempting to create a MolSupplier from a filename pointing to an empty
file,
  a file that does not exist or sometihing that is not a standard file (i.e.
  something like a directory) now generates an exception.
- The cmake option `RDK_OPTIMIZE_NATIVE` has been renamed to
`RDK_OPTIMIZE_POPCNT`

# Highlights:
- The drawings generated by the MolDraw2D objects are now significantly
improved
  and can include simple atom and bond annotations (#2931 and #3010)
- An initial implementation of a modified scaffold network algorithm is now
  available (#2911)
- A few new descriptor/fingerprint types are available - BCUTs (#2957),
Morse
  atom fingerprints (#1773), Coulomb matrices (#2993), and MHFP and SECFP
  fingerprints (#2643)


## Acknowledgements:
Marcel Baltruschat, Jason Biggs, Eliane Briand, Ben Cornett, David Cosgrove,
Zhenting Gao, Guillaume Godin, Gareth Jones, Zachary Kaplan, Eisuke
Kawashima,
Steven Kearnes, Brian Kelley, Maxim Koltsov, Mieszko Manijak, Dan
Nealschneider,
Daniil Polykovskiy, Daniel Probst, Steve Roughley, Kevin Ryan, Vincent F.
Scalfani, Ricardo Rodriguez Schmidt, Rim Shayakhmetov, Aryan Shrey, Matt
Swain,
Paolo Tosco, Wiep van der Toorn, Riccardo Vianello, Shuzhe Wang, Piotr
Wawrzyniak, Hsiao Yi, 'luancarvalhomartins'


## Bug Fixes:
  - Mol rendering within DataFrames in a Jupyter Notebook is broken with
Pandas 0.25.1
 (github issue #2673 from mrcblt)
  - Removed RDKIT_SIMDIVPICKERS_EXPORT
 (github pull #2740 from ptosco)
  - - enable building RDKitRingDecomposerLib.dll under Windows
 (github pull #2742 from ptosco)
  - Do a windows DLL build as part of the Azure DevOps setup
 (github pull #2743 from greglandrum)
  - Fix data race in sascorer.py
 (github pull #2744 from skearnes)
  - Uncharger not properly setting explicit/implicit H count
 (github issue #2749 from greglandrum)
  - MSVC compile error: MolHash scoped enum cannot be redeclared as unscoped
 (github issue #2752 from mcs07)
  - Molecules whose Y size is very small won't display as SVG
 (github issue #2762 from ptosco)
  - Make the cartridge tests work with PostgreSQL 12
 (github pull #2767 from greglandrum)
  - Salt stripper should consider bond matches as well as atom matches
 (github pull #2768 from greglandrum)
  - Bismuth should count as an early element
 (github issue #2775 from greglandrum)
  - addHs() fails on atoms with "bad" valences
 (github issue #2782 from greglandrum)
  - Element symbol lookup for some transuranics returns incorrect results
 (github issue #2784 from LeanAndMean)
  - [cartridge] molecular equality should use do_chiral_sss setting
 (github issue #2790 from greglandrum)
  - uncharger removes Hs from carbocations instead of adding them
 (github issue #2792 from greglandrum)
  - Fix build without boost serialization library
 (github pull #2796 from maksbotan)
  - Using `SetBoundsMat` significantly slows down conformer generation
process.
 (github issue #2800 from hjuinj)
  - rdkit.Ched.rdFMCS.FindMCS generates invalid smarts
 (github issue #2801 from luancarvalhomartins)
  - Remove confId from *FFOptimizeMoleculeConfs Python docs
 (github issue #2805 from ptosco)
  - Hybridization queries on dummy atoms not written properly to SMARTS
 (github issue #2814 from greglandrum)
  - Charge range queries not properly written to SMARTS
 (github issue #2815 from greglandrum)
  - RDKit segfaults in MMFFOptimizeMoleculeConfs()
 (github issue #2820 from ptosco)
  - Trusted Smiles holder doesn't handle ring queries
 (github issue #2830 from bp-kelley)
  - Fix windows substructure crash
 (github pull #2836 from greglandrum)
  - Fix YAeHMOP build
 (github pull #2838 from ptosco)
  - testGithub2245 in testPickers.cpp occasionally fails
 (github issue #2839 from ptosco)
  - add define for RDK_USE_BOOST_SERIALIZATION
 (github pull #2859 from greglandrum)
  - fix start/end atoms when wedging bonds
 (github pull #2861 from greglandrum)
  - Fixes the size of the reduced charge matrix from eHT calculations
 (github pull #2864 from greglandrum)
  - Dev/pvs studio cleanups2
 (github pull #2877 from greglandrum)
  - segfault in MaeMolSupplier
 (github issue #2881 from greglandrum)
  - update maven url in build system
 (github pull #2889 from greglandrum)
  - EnumerateStereoisomers cannot handle STEREOANY bonds
 (github issue #2890 from ricrogz)
  - Update one of the cartridge tests that got missed
 (github pull #2894 from greglandrum)
  - New Similarity Maps drawing code Java Wrappers non-functional
 (github issue #2896 from sroughley)
  - Fix to allow multistructure images in Java/C# and use MCS for c# wrapper
 (github pull #2898 from jones-gareth)
  - Remove bogus URFLib library
 (github pull #2900 from greglandrum)
  - java wrapper build cleanups
 (github pull #2901 from greglandrum)
  - SMARTS parser fails on high-numbered ring closures in branches
 (github issue #2909 from greglandrum)
  - patch to make PandasTools tests pass with pandas v0.22
 (github pull #2913 from greglandrum)
  - fix doctest problem with Pandas v1.0
 (github pull #2918 from greglandrum)
  - Build with -D RDK_BUILD_COORDGEN_SUPPORT=OFF includes a test case that
depends on MaeMolSupplier
 (github issue #2929 from rvianello)
  - MinimalLib: get_stereo_tags() should also return unspecified centers
 (github issue #2936 from greglandrum)
  - Fix regression introduced by e245349c
 (github pull #2945 from cornett)
  - Avoid data race warning in SmilesParse.cpp
 (github pull #2946 from skearnes)
  - Empty molecule has non-zero LabuteASA
 (github issue #2948 from jasondbiggs)
  - Fix a problem with aromatic heteroatom tautomer enumeration
 (github pull #2952 from greglandrum)
  - Molecule properties not retained with
MolStandardize.rdMolStandardize.Cleanup()
 (github issue #2965 from ZacharyKaplan)
  - Fix build without boost serialization.
 (github pull #2972 from ricrogz)
  - fix a typo in the scaffold network wrappers and add some tests
 (github pull #2982 from greglandrum)
  - Tautomer enumeration should remove stereo in all tautomers
 (github issue #2990 from greglandrum)
  - Removed dllexport from a function that lives in the anonymous namespace
 (github pull #3027 from ptosco)


## New Features and Enhancements:
  - Morse atom fingerprint
 (github pull #1773 from thegodone)
  - Allow serializing coordinates as doubles
 (github issue #2510 from danpol)
  - Rework MaeMolSupplier, fix #2617
 (github pull #2620 from ricrogz)
  - Implementation of MHFP and SECFP Fingerprints
 (github pull #2643 from daenuprobst)
  - MatchFusedRings does not imply CompleteRingsOnly anymore
 (github pull #2748 from ptosco)
  - Improvements to JS wrappers
 (github pull #2751 from greglandrum)
  - Fix installed header directory structure
 (github pull #2754 from ricrogz)
  - Add doRandom to the header docs
 (github pull #2756 from bp-kelley)
  - Add queryMol data member to MCSResult
 (github pull #2759 from ptosco)
  - Add functions to enable/disable the substructure matching monkey
patching in IPythonConsole.py
 (github issue #2786 from greglandrum)
  - Add a function to assign chiral tags from sss atom parity
 (github issue #2823 from ptosco)
  - Support MRV_IMPLICIT_H S groups when reading Mol blocks
 (github issue #2829 from greglandrum)
  - Unset executable flag
 (github pull #2833 from e-kwsm)
  - Remove O(N) behavior of getNumBonds
 (github pull #2847 from bp-kelley)
  - Feature proposal: add remove_stereochemistry=False flag for RemoveHs()
 (github issue #2848 from shayakhmetov)
  - Expose SubstructLibrary serialization stream
 (github pull #2853 from bp-kelley)
  - Fix typo
 (github pull #2862 from e-kwsm)
  - Rename RDK_OPTIMIZE_NATIVE to RDK_OPTIMIZE_POPCNT
 (github pull #2865 from ElianeBriand)
  - Update Draw.MolToImage() and Draw.MolToFile() to use the new drawing
code
 (github pull #2866 from greglandrum)
  - Improve PostgreSQL cartridge install documentation
 (github pull #2870 from yellowBirdy)
  - Fixes #2858
 (github pull #2871 from greglandrum)
  - Add a cartridge test to the azure devops config
 (github pull #2873 from greglandrum)
  - Add a new Cookbook v2 to the RDKit docs
 (github pull #2884 from vfscalfani)
  - Add MolVS tautomer canonicalization
 (github pull #2886 from greglandrum)
  - add a convenience function for RGD--Pandas integration
 (github pull #2887 from greglandrum)
  - run clang-tidy with readability-braces-around-statements
 (github pull #2899 from greglandrum)
  - Allow RDProps::clearProp to succeed even if the prop doesn't exist
 (github issue #2910 from greglandrum)
  - Add a scaffold network implementation
 (github pull #2911 from greglandrum)
  - cleanup of the SMILES/SMARTS parsing and writing code
 (github pull #2912 from greglandrum)
  - Add _ctab, _mol2, _pdb to allow direct mol construction from strings
 (github issue #2916 from greglandrum)
  - Parse and handle the stereoCare or STBOX flags in CTABs
 (github pull #2917 from greglandrum)
  - RDKit exceptions do not override the default `what()` method
 (github issue #2920 from ricrogz)
  - Allow custom post-match filters for substructure matching
 (github pull #2927 from greglandrum)
  - Proposed improvements to 2D Drawing Code
 (github issue #2931 from DavidACosgrove)
  - Include running the documentation tests as part of the CI runs
 (github pull #2932 from greglandrum)
  - Add support for phosphine and arsine chirality
 (github issue #2949 from wopozka)
  - A couple additions to the extended Hueckel integration
 (github pull #2955 from greglandrum)
  - Add BCUT 2D descriptors
 (github pull #2957 from bp-kelley)
  - Add multithreaded pattern/fp generator
 (github pull #2973 from bp-kelley)
  - Description for the data files.
 (github pull #2975 from zhentg)
  - Enable larger ring matches in SMARTS expressions
 (github pull #2981 from d-b-w)
  - ScaffoldNetwork rearrangements
 (github pull #2985 from greglandrum)
  - add add_hs() and remove_hs() to JS wrappers
 (github pull #2986 from greglandrum)
  - Add Atom Feature Vectors
 (github pull #2988 from thegodone)
  - Improve Conformational Sampling of Small and Large Ring Molecules
 (github pull #2731 from ptosco)
  - Add CoulombMat calculator
 (github pull #2993 from thegodone)
  - Update azure-pipelines.yml
 (github pull #2999 from hjuinj)
  - Fix atom highlighting in notebook PNGs
 (github pull #3000 from greglandrum)
  - adds a one-liner for getting a vector of random smiles for a molecule
 (github pull #3002 from greglandrum)
  - Allow enhanced stereo to be used in substructure search
 (github pull #3003 from d-b-w)
  - Add support for the rest of the v3000 atom properties
 (github pull #3007 from greglandrum)
  - Move jupyter extension logging to the python logger
 (github pull #3008 from bp-kelley)
  - Commit of 2D draw annotation.
 (github pull #3010 from DavidACosgrove)
  - Update Maeparser & Coordgen Dependencies
 (github pull #3011 from ricrogz)
  - Remove unnecessary files
 (github pull #3012 from e-kwsm)
  - allow retrieval of the atoms/bonds modified by the tautomerization
 (github pull #3013 from greglandrum)
  - Add 5 new recipes to Cookbook
 (github pull #3014 from vfscalfani)
  - Turns on cairo support (and testing) in the Azure DevOps CI builds
 (github pull #3022 from greglandrum)
  - Added support for Python FMCS functors
 (github pull #3023 from ptosco)
  - add random seed to docs to get reproducible conformations
 (github pull #3026 from greglandrum)
  - update docs for 2020.03
 (github pull #3028 from greglandrum)



## Deprecated code (to be removed in a future release):
- To improve API consistency of the exceptions in RDKit with the default
ones in
  the STL, the several `message()` methods and `Invariant::getMessage()` in
RDKit's
  exceptions are from now on deprecated in favor of `what()`. Both
`message()` and
  `Invariant::getMessage()` will be removed in the next release.
- The old MolHash code should be considered deprecated. This release
introduces
  a more flexible alternative. Specifically the following pieces will be
removed in the next release:
  - The python functionality
`rdkit.Chem.rdMolHash.GenerateMoleculeHashString()`
  - The C++ functionality directly present in the header file
`GraphMol/MolHash/MolHash.h`

Re: [Rdkit-devel] Fwd: [Boost-users] [Graph] Large incoming changes to Boost.Graph master.

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

Thanks for forwarding that Emanuel.

I just tried the dev version out (as John describes) with the RDKit and
everything looks good: the code builds and the tests all pass

-greg


On Thu, Jan 9, 2020 at 7:47 AM Emanuel Ehmki <ema...@gm...>
wrote:

> Dear all,
>
> is that something to consider?
>
> Kind regards,
> Emanuel
>
> ---------- Forwarded message ---------
> From: John Maddock via Boost-users <boo...@li...>
> Date: Wed, Jan 8, 2020, 18:57
> Subject: [Boost-users] [Graph] Large incoming changes to Boost.Graph
> master.
> To: <bo...@li...>, <boo...@li...>
> Cc: John Maddock <jz....@go...>
>
>
> Dear all,
>
> Boost.Graph has had no maintainer for some time, but the CMT has been
> busy fixing bugs none the less.  Unfortunately, other than some trivial
> fixes to docs and some directory refactoring, nothing much has been
> merged to master in a good while .
>
> On the plus side, develop is now in a better tested tested state than
> IMO it has ever been, however the change set is rather large so the
> potential to mess up somebodies code is certainly there:
> https://github.com/boostorg/graph/pull/196.
>
> So... this is both a heads up, and a plea: if you have any mission
> critical code using the Graph library, could you please test against
> current develop and report any problems?  If you don't want to mess
> about with git, download from
> https://github.com/boostorg/graph/archive/develop.zip and place
> zipfile-contents/libs/graph/include in your include path ahead of that
> for Boost-1.72.
>
> Many thanks, John.
>
> _______________________________________________
> Boost-users mailing list
> Boo...@li...
> https://lists.boost.org/mailman/listinfo.cgi/boost-users
> _______________________________________________
> Rdkit-devel mailing list
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>

[Rdkit-devel] Fwd: [Boost-users] [Graph] Large incoming changes to Boost.Graph master.

[Emanuel E. <ema...@gm...>]

Dear all,

is that something to consider?

Kind regards,
Emanuel

---------- Forwarded message ---------
From: John Maddock via Boost-users <boo...@li...>
Date: Wed, Jan 8, 2020, 18:57
Subject: [Boost-users] [Graph] Large incoming changes to Boost.Graph master.
To: <bo...@li...>, <boo...@li...>
Cc: John Maddock <jz....@go...>


Dear all,

Boost.Graph has had no maintainer for some time, but the CMT has been
busy fixing bugs none the less.  Unfortunately, other than some trivial
fixes to docs and some directory refactoring, nothing much has been
merged to master in a good while .

On the plus side, develop is now in a better tested tested state than
IMO it has ever been, however the change set is rather large so the
potential to mess up somebodies code is certainly there:
https://github.com/boostorg/graph/pull/196.

So... this is both a heads up, and a plea: if you have any mission
critical code using the Graph library, could you please test against
current develop and report any problems?  If you don't want to mess
about with git, download from
https://github.com/boostorg/graph/archive/develop.zip and place
zipfile-contents/libs/graph/include in your include path ahead of that
for Boost-1.72.

Many thanks, John.

_______________________________________________
Boost-users mailing list
Boo...@li...
https://lists.boost.org/mailman/listinfo.cgi/boost-users

Re: [Rdkit-devel] molecular representation underlying the postgresql cartridge for rdkit

[Peter S. <pet...@di...>]

On 2 Dec 2019, at 13:17, Greg Landrum <gre...@gm...<mailto:gre...@gm...>> wrote:

Hi Peter,

On Mon, Dec 2, 2019 at 10:11 AM Peter Schmidtke <pet...@di...<mailto:pet...@di...>> wrote:

I have a question regarding the underlying molecular representation used in the rdkit cartridge for postgresql.
I didn't dig yet too much into the underlying source code of the cartridge. Is it a normal rdkit like molecule used to store molecules?

Yes, the internal representation is currently the usual RDKit serialized molecule.
Ok that’s fine then.

What I want to make sure especially that it's not stored as smiles string!

Not currently. Why are you concerned about this?
Just I saw smiles printed in pgAdmin’s table representation … would like to avoid issues with stereo handling especially

Peter


-greg

Re: [Rdkit-devel] molecular representation underlying the postgresql cartridge for rdkit

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

Hi Peter,

On Mon, Dec 2, 2019 at 10:11 AM Peter Schmidtke <
pet...@di...> wrote:

>
> I have a question regarding the underlying molecular representation used
> in the rdkit cartridge for postgresql.
> I didn't dig yet too much into the underlying source code of the
> cartridge. Is it a normal rdkit like molecule used to store molecules?
>

Yes, the internal representation is currently the usual RDKit serialized
molecule.


> What I want to make sure especially that it's not stored as smiles string!
>

Not currently. Why are you concerned about this?


-greg