Thanks Greg, I remembered to include the library but then forgot to link it. You and Eddie deserve a prize for putting up with all of my questions, thanks again.
Best, Nick On 8 Mar 2012, at 13:07, Greg Landrum wrote: > Hi Nick, > > On Thu, Mar 8, 2012 at 1:10 PM, Nicholas Firth <[email protected]> > wrote: >> Hi All, >> Further to my post yesterday, I have most of my RDKit functionality back >> (hooray!). Now I'm going to ask the question I should of asked yesterday >> before I decided to 'fix' it myself. >> I'm trying to get Morgan fingerprints of molecules, the code that I'm using >> is >> … >> SparseIntVect<boost::uint32_t> *finger; >> ROMol *mol; >> while(!infile.eof()){ >> getline(infile, line); >> line = line.substr(0,line.size()-2); >> std::cout << line << "\n"; >> mol=SmilesToMol(line); >> finger = MorganFingerprints::getFingerprint(*mol, 2); >> } >> … >> >> This does not compile, I get the error >> >> 103528cthdt:MOOPGA nfirth$ g++ Fingerprint.cpp -I/usr/local/include/rdkit >> -L/usr/local/lib -lChemReactions -lFileParsers -lSmilesParse -lDepictor >> -lSubstructMatch -lGraphMol -lDataStructs -lRDGeometryLib -lRDGeneral >> Undefined symbols for architecture x86_64: >> "RDKit::MorganFingerprints::getFingerprint(RDKit::ROMol const&, unsigned >> int, std::vector<unsigned int, std::allocator<unsigned int> >*, >> std::vector<unsigned int, std::allocator<unsigned int> > const*, bool, bool, >> bool, std::map<unsigned int, std::vector<std::pair<unsigned int, unsigned >> int>, std::allocator<std::pair<unsigned int, unsigned int> > >, >> std::less<unsigned int>, std::allocator<std::pair<unsigned int const, >> std::vector<std::pair<unsigned int, unsigned int>, >> std::allocator<std::pair<unsigned int, unsigned int> > > > > >*)", >> referenced from: >> _main in ccezHfTZ.o >> ld: symbol(s) not found for architecture x86_64 >> collect2: ld returned 1 exit status > > Looks like that link command above is missing the fingerprinting library. > There should be a "-lFingerprints" in your link line. > > -greg The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. ------------------------------------------------------------------------------ Virtualization & Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/ _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
