Re: [Rdkit-devel] problem building rdkit
Open-Source Cheminformatics and Machine Learning
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glandrum
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From: Greg L. <gre...@gm...> - 2018-03-19 14:04:59
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hmm, I'm stumped. I'm going to have to try to reproduce the problem on a linux box. Since I'm traveling this week (at the ACS in New Orleans), this may take a while. -greg On Mon, Mar 19, 2018 at 8:41 AM, TJ O'Donnell <tj...@ac...> wrote: > I grep'd with a slight mod to your suggestion and got these few lines. > There are many others with all lower case boost_thread and boost_serial > > tj@vmmint:~/RDKit/rdkit/build$ grep Boost_SERIAL CMakeCache.txt > Boost_SERIALIZATION_LIBRARY_DEBUG:FILEPATH=/usr/lib/x86_ > 64-linux-gnu/libboost_serialization.so > Boost_SERIALIZATION_LIBRARY_RELEASE:FILEPATH=/usr/lib/x86_ > 64-linux-gnu/libboost_serialization.so > //ADVANCED property for variable: Boost_SERIALIZATION_LIBRARY_DEBUG > Boost_SERIALIZATION_LIBRARY_DEBUG-ADVANCED:INTERNAL=1 > //ADVANCED property for variable: Boost_SERIALIZATION_LIBRARY_RELEASE > Boost_SERIALIZATION_LIBRARY_RELEASE-ADVANCED:INTERNAL=1 > > tj@vmmint:~/RDKit/rdkit/build$ grep Boost_THREAD CMakeCache.txt > Boost_THREAD_LIBRARY_DEBUG:FILEPATH=/usr/lib/x86_64- > linux-gnu/libboost_thread.so > Boost_THREAD_LIBRARY_RELEASE:FILEPATH=/usr/lib/x86_64- > linux-gnu/libboost_thread.so > //ADVANCED property for variable: Boost_THREAD_LIBRARY_DEBUG > Boost_THREAD_LIBRARY_DEBUG-ADVANCED:INTERNAL=1 > //ADVANCED property for variable: Boost_THREAD_LIBRARY_RELEASE > Boost_THREAD_LIBRARY_RELEASE-ADVANCED:INTERNAL=1 > > The case-insensitive search has lines like this and many more: > > tj@vmmint:~/RDKit/rdkit/build$ grep -i boost_SERIAL CMakeCache.txt > rdqueries_LIB_DEPENDS:STATIC=general;GraphMol;general; > RDGeometryLib;general;DataStructs;general;RDGeneral; > general;RDBoost;general;/usr/lib/x86_64-linux-gnu/libpython2.7.so > ;general;/usr/lib/x86_64-linux-gnu/libboost_python. > so;general;/usr/lib/x86_64-linux-gnu/libboost_thread.so; > general;/usr/lib/x86_64-linux-gnu/libboost_system.so; > general;/usr/lib/x86_64-linux-gnu/libpthread.so;general;/ > usr/lib/x86_64-linux-gnu/libboost_serialization.so; > rdtrajectory_LIB_DEPENDS:STATIC=general;Trajectory; > general;RDGeometryLib;general;RDGeneral;general;GraphMol; > general;/usr/lib/x86_64-linux-gnu/libpython2.7.so;general;/ > usr/lib/x86_64-linux-gnu/libboost_python.so;general;/ > usr/lib/x86_64-linux-gnu/libboost_thread.so;general;/ > usr/lib/x86_64-linux-gnu/libboost_system.so;general;/ > usr/lib/x86_64-linux-gnu/libpthread.so;general;/usr/ > lib/x86_64-linux-gnu/libboost_serialization.so; > > > > > On Mon, Mar 19, 2018 at 3:27 AM, Greg Landrum <gre...@gm...> > wrote: > >> Well, I don't see anything obvious there to explain why the serialization >> library is being treated differently from the others. >> >> Could you please look at (and send) the output of; >> grep boost_THREAD CMakeCache.txt >> grep boost_SERIAL CMakeCache.txt >> >> Best, >> -greg >> >> >> >> On Sun, Mar 18, 2018 at 10:31 PM, TJ O'Donnell <tj...@ac...> wrote: >> >>> FYI I cloned https://github.com/rdkit/rdkit.git >>> and get the same error >>> >>> TJ >>> >>> On Sun, Mar 18, 2018 at 7:31 PM, TJ O'Donnell <tj...@ac...> wrote: >>> >>>> Thanks for the quick reply, Greg. I just did a git pull and it merged >>>> in lots of files. >>>> I may try a clone to a "fresh" folder and see how that goes. >>>> Anyway, here's the output from VERBOSE=1 make FilterCatalog >>>> >>>> tj@vmmint:~/RDKit/rdkit/build$ VERBOSE=1 make FilterCatalog >>>> /usr/bin/cmake -H/home/tj/RDKit/rdkit -B/home/tj/RDKit/rdkit/build >>>> --check-build-system CMakeFiles/Makefile.cmake 0 >>>> make -f CMakeFiles/Makefile2 FilterCatalog >>>> make[1]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> /usr/bin/cmake -H/home/tj/RDKit/rdkit -B/home/tj/RDKit/rdkit/build >>>> --check-build-system CMakeFiles/Makefile.cmake 0 >>>> /usr/bin/cmake -E cmake_progress_start /home/tj/RDKit/rdkit/build/CMakeFiles >>>> 9 >>>> make -f CMakeFiles/Makefile2 Code/GraphMol/FilterCatalog/CM >>>> akeFiles/FilterCatalog.dir/all >>>> make[2]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make >>>> Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/RDGeneral >>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/RDGeneral >>>> /home/tj/RDKit/rdkit/build/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake >>>> --color= >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make >>>> Code/RDGeneral/CMakeFiles/RDGeneral.dir/build >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> make[3]: Nothing to be done for `Code/RDGeneral/CMakeFiles/RDG >>>> eneral.dir/build'. >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>>> 64 >>>> [ 11%] Built target RDGeneral >>>> make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make >>>> Code/DataStructs/CMakeFiles/DataStructs.dir/depend >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/DataStructs >>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/DataStructs >>>> /home/tj/RDKit/rdkit/build/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake >>>> --color= >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make >>>> Code/DataStructs/CMakeFiles/DataStructs.dir/build >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> make[3]: Nothing to be done for `Code/DataStructs/CMakeFiles/D >>>> ataStructs.dir/build'. >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>>> 7 >>>> [ 22%] Built target DataStructs >>>> make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make >>>> Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/Geometry >>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/Geometry >>>> /home/tj/RDKit/rdkit/build/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake >>>> --color= >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make >>>> Code/Geometry/CMakeFiles/RDGeometryLib.dir/build >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> make[3]: Nothing to be done for `Code/Geometry/CMakeFiles/RDGe >>>> ometryLib.dir/build'. >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>>> 66 >>>> [ 33%] Built target RDGeometryLib >>>> make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make >>>> Code/GraphMol/CMakeFiles/GraphMol.dir/depend >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol >>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol >>>> /home/tj/RDKit/rdkit/build/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake >>>> --color= >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make >>>> Code/GraphMol/CMakeFiles/GraphMol.dir/build >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> make[3]: Nothing to be done for `Code/GraphMol/CMakeFiles/Grap >>>> hMol.dir/build'. >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>>> 35 36 37 38 >>>> [ 77%] Built target GraphMol >>>> make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make >>>> Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/Subgraphs >>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/Subgraphs >>>> /home/tj/RDKit/rdkit/build/Code/GraphMol/Subgraphs/CMakeFile >>>> s/Subgraphs.dir/DependInfo.cmake --color= >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make >>>> Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> make[3]: Nothing to be done for `Code/GraphMol/Subgraphs/CMake >>>> Files/Subgraphs.dir/build'. >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMa >>>> keFiles >>>> [ 77%] Built target Subgraphs >>>> make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make >>>> Code/Catalogs/CMakeFiles/Catalogs.dir/depend >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/Catalogs >>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/Catalogs >>>> /home/tj/RDKit/rdkit/build/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake >>>> --color= >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make >>>> Code/Catalogs/CMakeFiles/Catalogs.dir/build >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> make[3]: Nothing to be done for `Code/Catalogs/CMakeFiles/Cata >>>> logs.dir/build'. >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMa >>>> keFiles >>>> [ 77%] Built target Catalogs >>>> make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make >>>> Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/SmilesParse >>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/SmilesParse >>>> /home/tj/RDKit/rdkit/build/Code/GraphMol/SmilesParse/CMakeFi >>>> les/SmilesParse.dir/DependInfo.cmake --color= >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make >>>> Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> make[3]: Nothing to be done for `Code/GraphMol/SmilesParse/CMa >>>> keFiles/SmilesParse.dir/build'. >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMakeFiles >>>> 71 >>>> [ 88%] Built target SmilesParse >>>> make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make >>>> Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/Substruct >>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/Substruct >>>> /home/tj/RDKit/rdkit/build/Code/GraphMol/Substruct/CMakeFile >>>> s/SubstructMatch.dir/DependInfo.cmake --color= >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make >>>> Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> make[3]: Nothing to be done for `Code/GraphMol/Substruct/CMake >>>> Files/SubstructMatch.dir/build'. >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> /usr/bin/cmake -E cmake_progress_report /home/tj/RDKit/rdkit/build/CMa >>>> keFiles >>>> [ 88%] Built target SubstructMatch >>>> make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make >>>> Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> cd /home/tj/RDKit/rdkit/build && /usr/bin/cmake -E cmake_depends "Unix >>>> Makefiles" /home/tj/RDKit/rdkit /home/tj/RDKit/rdkit/Code/GraphMol/FilterCatalog >>>> /home/tj/RDKit/rdkit/build /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog >>>> /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog/CMake >>>> Files/FilterCatalog.dir/DependInfo.cmake --color= >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make >>>> Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build >>>> make[3]: Entering directory `/home/tj/RDKit/rdkit/build' >>>> Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so >>>> cd /home/tj/RDKit/rdkit/build/Code/GraphMol/FilterCatalog && >>>> /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt >>>> --verbose=1 >>>> /usr/bin/c++ -fPIC -mpopcnt -Wno-deprecated -Wno-unused-function >>>> -fno-strict-aliasing -Wall -Wextra -fPIC -O3 -DNDEBUG -shared >>>> -Wl,-soname,libRDKitFilterCatalog.so.1 -o >>>> ../../../lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1 >>>> CMakeFiles/FilterCatalog.dir/Filters.cpp.o >>>> CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o >>>> CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o >>>> CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o >>>> CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o >>>> ../../../lib/libRDKitSubgraphs.so.1.2018.03.1.dev1 >>>> ../../../lib/libRDKitSubstructMatch.so.1.2018.03.1.dev1 >>>> ../../../lib/libRDKitSmilesParse.so.1.2018.03.1.dev1 >>>> ../../../lib/libRDKitGraphMol.so.1.2018.03.1.dev1 >>>> ../../../lib/libRDKitRDGeometryLib.so.1.2018.03.1.dev1 >>>> ../../../lib/libRDKitCatalogs.so.1.2018.03.1.dev1 >>>> ../../../lib/libRDKitRDGeneral.so.1.2018.03.1.dev1 >>>> -lBoost::serialization ../../../lib/libRDKitDataStructs.so.1.2018.03.1.dev1 >>>> ../../../lib/libRDKitRDGeneral.so.1.2018.03.1.dev1 -lboost_thread >>>> -lboost_system -lpthread -Wl,-rpath,/home/tj/RDKit/rdkit/build/lib: >>>> /usr/bin/ld: cannot find -lBoost::serialization >>>> collect2: error: ld returned 1 exit status >>>> make[3]: *** [lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1] Error 1 >>>> make[3]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make[2]: *** [Code/GraphMol/FilterCatalog/C >>>> MakeFiles/FilterCatalog.dir/all] Error 2 >>>> make[2]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make[1]: *** [Code/GraphMol/FilterCatalog/C >>>> MakeFiles/FilterCatalog.dir/rule] Error 2 >>>> make[1]: Leaving directory `/home/tj/RDKit/rdkit/build' >>>> make: *** [FilterCatalog] Error 2 >>>> >>>> On Sun, Mar 18, 2018 at 3:48 PM, Greg Landrum <gre...@gm...> >>>> wrote: >>>> >>>>> Hi TJ, >>>>> >>>>> Hrm, that's ugly. Just to confirm: Are you building the master branch >>>>> from github? >>>>> It looks like there's no fundamental problem with master; at least the >>>>> travis builds pass: https://travis-ci.org/rdkit/rdkit >>>>> >>>>> To help track this down, can you please send the results of doing: >>>>> VERBOSE=1 make FilterCatalog >>>>> >>>>> Best, >>>>> -greg >>>>> >>>>> >>>>> On Sun, Mar 18, 2018 at 11:27 PM, TJ O'Donnell <tj...@ac...> wrote: >>>>> >>>>>> I'm trying to build rdkit from the latest git source. >>>>>> Linux Mint 17 >>>>>> >>>>>> I get this error >>>>>> [ 57%] Building CXX object Code/GraphMol/FilterCatalog/CM >>>>>> akeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o >>>>>> Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so >>>>>> /usr/bin/ld: cannot find -lBoost::serialization >>>>>> collect2: error: ld returned 1 exit status >>>>>> make[2]: *** [lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1] Error 1 >>>>>> make[1]: *** [Code/GraphMol/FilterCatalog/C >>>>>> MakeFiles/FilterCatalog.dir/all] Error 2 >>>>>> make: *** [all] Error 2 >>>>>> >>>>>> but cmake seemed to find this lib OK >>>>>> cmake .. -DRDK_BUILD_INCHI_SUPPORT=ON >>>>>> -- The C compiler identification is GNU 4.8.4 >>>>>> -- The CXX compiler identification is GNU 4.8.4 >>>>>> .... >>>>>> -- Found Threads: TRUE >>>>>> -- Boost version: 1.54.0 >>>>>> -- Found the following Boost libraries: >>>>>> -- thread >>>>>> -- system >>>>>> -- Boost version: 1.54.0 >>>>>> -- Found the following Boost libraries: >>>>>> -- serialization >>>>>> == Using strict rotor definition >>>>>> == Updating Filters.cpp from pains file >>>>>> >>>>>> Can you help me figure out how to get past this? >>>>>> >>>>>> Thanks, >>>>>> TJ >>>>>> >>>>>> ------------------------------------------------------------ >>>>>> ------------------ >>>>>> Check out the vibrant tech community on one of the world's most >>>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>>>>> _______________________________________________ >>>>>> Rdkit-devel mailing list >>>>>> Rdk...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-devel >>>>>> >>>>>> >>>>> >>>> >>> >> > |