[Rdkit-discuss] Matching atom to substructure query atom
Hi all,
I want to find out whether an atom in a molecule matches to an atom in a
defined substructure.
Let's assume the following:
>>>m = Chem.MolFromSmiles('CS(=O)(=O)N')
>>>sub = Chem.MolFromSmarts('[C]S(=O)(=O)[ND1]')
>>>m.GetSubstructMatches(sub)
((0, 1, 2, 3, 4),)
How can I do the following:
>>>ox1 = m.GetAtomsWithIdx(2)
>>>ox2 = m.GetAtomsWithIdx(3)
>>>query_atom = sub.GetAtomsWithIdx(2)
>>> ox1 matches query_atom
True
>>> ox2 matches query_atom
True
Initially I thought I could use ox1.Matches(query_atom), but this seems to
match independently of the context of the query atom.
Thanks a lot for your help!
Andreas
--
*Andreas Tosstorff*
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*Computer Aided Drug Design | Roche Pharma Research and Early Development**F.
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Re: [Rdkit-discuss] Problems building RDKit + JavaWrappers
Have a look in 'Code/JavaWrappers/gmwrapper/' not 'build/Code/JavaWrappers/gmwrapper/' ? Tim On 22/04/2020 10:36, Thomas Eckert wrote: Hi folks, Trying to build RDKit + JavaWrappers from scratch but, in the end, the JAR files are missing. Working on a freshly installed Ubuntu 19.10 and followed the steps described at [1]. All dependencies installed via Ubuntu's apt, no manually installed libs. Cloned the RDKit sources to /home/thomas/git/rdkit and set env variables RDBASE=/home/thomas/git/rdkit LD_LIBRARY_PATH=/home/thomas/git/rdkit/lib:/lib/x86_64-linux-gnu/ Using this 'cmake' command cmake -DRDK_BUILD_PYTHON_WRAPPERS=OFF -DRDK_BUILD_SWIG_WRAPPERS=ON .. I get OK looking output except for CMake Warning (dev) at /usr/share/cmake-3.13/Modules/UseSWIG.cmake:564 (message): Policy CMP0078 is not set. Run "cmake --help-policy CMP0078" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): Code/JavaWrappers/gmwrapper/CMakeLists.txt:109 (SWIG_ADD_LIBRARY) This warning is for project developers. Use -Wno-dev to suppress it. but as the warning states, this seems to be fine for non-rdkit-dev users, so I just carry on. 'make' then runs happily with a few warnings on the first build but no errors are reported. It even states (...) [ 99%] Built target GraphMolWrap_swig_compilation [ 99%] Built target GraphMolWrap [100%] building jar [100%] Built target GraphMolWrapJar [100%] building test classes [100%] Built target BuildJavaWrapperTests which seems to mean the JavaWrappers were built. However this is then the case ~/git/rdkit/build$ ls -lha Code/JavaWrappers/gmwrapper/ total 16M drwxr-xr-x 3 thomas thomas 4,0K Apr 22 11:15 . drwxr-xr-x 4 thomas thomas 4,0K Apr 22 11:15 .. drwxr-xr-x 7 thomas thomas 4,0K Apr 22 11:15 CMakeFiles -rw-r--r-- 1 thomas thomas 2,6K Apr 22 10:47 cmake_install.cmake -rw-r--r-- 1 thomas thomas 13K Apr 22 10:47 CTestTestfile.cmake -rwxr-xr-x 1 thomas thomas 16M Apr 22 10:49 libGraphMolWrap.so -rw-r--r-- 1 thomas thomas 13K Apr 22 10:47 Makefile so no JAR files to be found even though the shared library mentioned in "Building the Java wrappers" at [1] is there. Thus I ran the tests /git/rdkit/build$ ctest Test project /home/thomas/git/rdkit/build (...) 73% tests passed, 39 tests failed out of 143 Total Test time (real) = 98.60 sec The following tests FAILED: 105 - JavaAromaticTests (Failed) 106 - JavaAtomPairsTests (Failed) 107 - JavaBasicMoleculeTests (Failed) 108 - JavaBasicMolecule2Tests (Failed) 109 - JavaChemAtomTests (Failed) 110 - JavaChemBondTests (Failed) 111 - JavaChemReactionTests (Failed) 112 - JavaChemSmartsTests (Failed) 113 - JavaChemTests (Failed) 114 - JavaChemv2Tests (Failed) 115 - JavaConformerTests (Failed) 116 - JavaDescriptorTests (Failed) 117 - JavaDistanceGeometryTests (Failed) 118 - JavaErrorHandlingTests (Failed) 119 - JavaFingerprintsTests (Failed) 120 - JavaForceFieldsTests (Failed) 121 - JavaHManipulationsTests (Failed) 122 - JavaLipinskiTests (Failed) 123 - JavaPicklingTests (Failed) 124 - JavaSmilesCreationTests (Failed) 125 - JavaSmilesDetailsTests (Failed) 126 - JavaSmilesTests (Failed) 127 - JavaSuppliersTests (Failed) 128 - JavaTrajectoryTests (Failed) 129 - JavaWrapperTests (Failed) 130 - JavaChemTransformsTests (Failed) 131 - JavaFMCSTests (Failed) 132 - JavaPDBTests (Failed) 133 - JavaSequenceTests (Failed) 134 - JavaAlignTests (Failed) 135 - JavaMolQueryTests (Failed) 136 - JavaFilterCatalogTests (Failed) 137 - JavaSubstructLibraryTests (Failed) 138 - JavaRGroupDecompositionTests (Failed) 139 - JavaScaffoldNetworkTests (Failed) 140 - JavaMolHashTest (Failed) 141 - JavaDiversityPickerTests (Failed) 142 - JavaBitOpsTests (Failed) 143 - MolStandardizeTest (Failed) Errors while running CTest At this point I cannot find anything in the documentation to proceed further. I'm not familiar with most of the stack used with/for RDKit either, so I don't know where to look. Any hints on where to look or what to check ? Regards, Thomas [1] https://www.rdkit.org/docs/Install.html#building-from-source ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Problems building RDKit + JavaWrappers
Hi folks, Trying to build RDKit + JavaWrappers from scratch but, in the end, the JAR files are missing. Working on a freshly installed Ubuntu 19.10 and followed the steps described at [1]. All dependencies installed via Ubuntu's apt, no manually installed libs. Cloned the RDKit sources to /home/thomas/git/rdkit and set env variables RDBASE=/home/thomas/git/rdkit LD_LIBRARY_PATH=/home/thomas/git/rdkit/lib:/lib/x86_64-linux-gnu/ Using this 'cmake' command cmake -DRDK_BUILD_PYTHON_WRAPPERS=OFF -DRDK_BUILD_SWIG_WRAPPERS=ON .. I get OK looking output except for CMake Warning (dev) at /usr/share/cmake-3.13/Modules/UseSWIG.cmake:564 (message): Policy CMP0078 is not set. Run "cmake --help-policy CMP0078" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): Code/JavaWrappers/gmwrapper/CMakeLists.txt:109 (SWIG_ADD_LIBRARY) This warning is for project developers. Use -Wno-dev to suppress it. but as the warning states, this seems to be fine for non-rdkit-dev users, so I just carry on. 'make' then runs happily with a few warnings on the first build but no errors are reported. It even states (...) [ 99%] Built target GraphMolWrap_swig_compilation [ 99%] Built target GraphMolWrap [100%] building jar [100%] Built target GraphMolWrapJar [100%] building test classes [100%] Built target BuildJavaWrapperTests which seems to mean the JavaWrappers were built. However this is then the case ~/git/rdkit/build$ ls -lha Code/JavaWrappers/gmwrapper/ total 16M drwxr-xr-x 3 thomas thomas 4,0K Apr 22 11:15 . drwxr-xr-x 4 thomas thomas 4,0K Apr 22 11:15 .. drwxr-xr-x 7 thomas thomas 4,0K Apr 22 11:15 CMakeFiles -rw-r--r-- 1 thomas thomas 2,6K Apr 22 10:47 cmake_install.cmake -rw-r--r-- 1 thomas thomas 13K Apr 22 10:47 CTestTestfile.cmake -rwxr-xr-x 1 thomas thomas 16M Apr 22 10:49 libGraphMolWrap.so -rw-r--r-- 1 thomas thomas 13K Apr 22 10:47 Makefile so no JAR files to be found even though the shared library mentioned in "Building the Java wrappers" at [1] is there. Thus I ran the tests /git/rdkit/build$ ctest Test project /home/thomas/git/rdkit/build (...) 73% tests passed, 39 tests failed out of 143 Total Test time (real) = 98.60 sec The following tests FAILED: 105 - JavaAromaticTests (Failed) 106 - JavaAtomPairsTests (Failed) 107 - JavaBasicMoleculeTests (Failed) 108 - JavaBasicMolecule2Tests (Failed) 109 - JavaChemAtomTests (Failed) 110 - JavaChemBondTests (Failed) 111 - JavaChemReactionTests (Failed) 112 - JavaChemSmartsTests (Failed) 113 - JavaChemTests (Failed) 114 - JavaChemv2Tests (Failed) 115 - JavaConformerTests (Failed) 116 - JavaDescriptorTests (Failed) 117 - JavaDistanceGeometryTests (Failed) 118 - JavaErrorHandlingTests (Failed) 119 - JavaFingerprintsTests (Failed) 120 - JavaForceFieldsTests (Failed) 121 - JavaHManipulationsTests (Failed) 122 - JavaLipinskiTests (Failed) 123 - JavaPicklingTests (Failed) 124 - JavaSmilesCreationTests (Failed) 125 - JavaSmilesDetailsTests (Failed) 126 - JavaSmilesTests (Failed) 127 - JavaSuppliersTests (Failed) 128 - JavaTrajectoryTests (Failed) 129 - JavaWrapperTests (Failed) 130 - JavaChemTransformsTests (Failed) 131 - JavaFMCSTests (Failed) 132 - JavaPDBTests (Failed) 133 - JavaSequenceTests (Failed) 134 - JavaAlignTests (Failed) 135 - JavaMolQueryTests (Failed) 136 - JavaFilterCatalogTests (Failed) 137 - JavaSubstructLibraryTests (Failed) 138 - JavaRGroupDecompositionTests (Failed) 139 - JavaScaffoldNetworkTests (Failed) 140 - JavaMolHashTest (Failed) 141 - JavaDiversityPickerTests (Failed) 142 - JavaBitOpsTests (Failed) 143 - MolStandardizeTest (Failed) Errors while running CTest At this point I cannot find anything in the documentation to proceed further. I'm not familiar with most of the stack used with/for RDKit either, so I don't know where to look. Any hints on where to look or what to check ? Regards, Thomas [1] https://www.rdkit.org/docs/Install.html#building-from-source ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
