Re: [Rdkit-discuss] Order of linking static libraries
I don't have this problem on mac/windows, but it came up on Linux. Rather than figure out which library or libraries to link twice I just use the idiom --start-group -llib1 -llib2 -llib3 --end-group Maybe that will help with your issue. Jason On Mon, Sep 14, 2020 at 10:46 AM topgunhaides wrote: > Hi guys, > > I am trying to get an executable that doesn't require an RDKit install to > run. > But found it is tricky to figure out the correct order of static libraries > for linking. > > Here is my dynamic linkage (successful): > > g++ -o test.exe test.cpp \ > -I$RDBASE/Code -L$RDBASE/lib \ > -lRDKitFileParsers \ > -lRDKitRDGeneral \ > -lRDKitDescriptors \ > -lRDKitDistGeomHelpers \ > -lRDKitForceField \ > -lRDKitForceFieldHelpers \ > -lRDKitMolAlign \ > -lRDKitShapeHelpers \ > -lRDKitGraphMol > > My RDKit-related header files in the code: > > #include > #include > #include > #include > #include > #include > #include > #include > #include > #include > > However, I still cannot figure out the correct static linkages. Here is > one example: > > g++ -o test.exe test.cpp \ > -I$RDBASE/Code -L$RDBASE/lib \ > -lRDKitForceFieldHelpers_static \ > -lRDKitForceField_static \ > -lRDKitRDGeneral_static \ > -lRDKitShapeHelpers_static \ > -lRDKitDistGeomHelpers_static \ > -lRDKitGraphMol_static \ > -lRDKitMolAlign_static \ > -lRDKitFileParsers_static \ > -lRDKitDescriptors_static > > which gave me a bunch of "undefined reference" errors. > > I guess that circular dependencies exist. I found some old discussions, > but the info is limited. > I mean shall we have documentation to explain those dependencies to help > establish static linkage? > Can anyone help me with this? Maybe with a couple of examples? I > appreciate it! > > Best, > Leon > ___ > 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] Order of linking static libraries
Hi guys, I am trying to get an executable that doesn't require an RDKit install to run. But found it is tricky to figure out the correct order of static libraries for linking. Here is my dynamic linkage (successful): g++ -o test.exe test.cpp \ -I$RDBASE/Code -L$RDBASE/lib \ -lRDKitFileParsers \ -lRDKitRDGeneral \ -lRDKitDescriptors \ -lRDKitDistGeomHelpers \ -lRDKitForceField \ -lRDKitForceFieldHelpers \ -lRDKitMolAlign \ -lRDKitShapeHelpers \ -lRDKitGraphMol My RDKit-related header files in the code: #include #include #include #include #include #include #include #include #include #include However, I still cannot figure out the correct static linkages. Here is one example: g++ -o test.exe test.cpp \ -I$RDBASE/Code -L$RDBASE/lib \ -lRDKitForceFieldHelpers_static \ -lRDKitForceField_static \ -lRDKitRDGeneral_static \ -lRDKitShapeHelpers_static \ -lRDKitDistGeomHelpers_static \ -lRDKitGraphMol_static \ -lRDKitMolAlign_static \ -lRDKitFileParsers_static \ -lRDKitDescriptors_static which gave me a bunch of "undefined reference" errors. I guess that circular dependencies exist. I found some old discussions, but the info is limited. I mean shall we have documentation to explain those dependencies to help establish static linkage? Can anyone help me with this? Maybe with a couple of examples? I appreciate it! Best, Leon ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] unique chemical representation
Hi, All the steps of ChEMBL's RDKit based standardiser are explained in the recently published manuscript: https://link.springer.com/article/10.1186/s13321-020-00456-1 Hope it helps! Regards, Eloy On Mon, 14 Sep 2020 at 04:32, Francois Berenger wrote: > On 12/09/2020 00:27, Mike Mazanetz wrote: > > Dear Forum, > > > > I'm curious as to how the community standardizes molecules to generate > > unique chemical representations. > > > > Please let me know what are people's referred means to treat: > > > > * Tautomers > > * Protomers > > * Resonance structures > > * Salts when the salt is larger than the ligand > > Here is how ChEMBL does it: > > https://github.com/chembl/ChEMBL_Structure_Pipeline > > Not sure they handle all the cases you listed, though. > > Regards, > F. > > > Particularly when converting between chemical representations SDF to > > smiles, SMARTS to smiles, and one flavour of smiles to another. > > > > And are there any caveats to consider, such as the correct assignment > > of heterocyclic nitrogens as aromatic ? > > > > I look forward to hearing your thoughts. > > > > Regards, > > > > mike > > ___ > > 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 mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Query about aromatic rings find in a molecule from a pdf file
Dear Members, I want to compute the number of aromatic rings present in a molecule from a pdf file format. Could you please help me to find the same using RDKit command. Best wishes, Goutam ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
