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
So I investiagted and went to some of the test code in the RDKit source (the
fingerprint test) and that also didn't compile with similar errors. My
installation is the homebrew RDKit.
Thanks,
Nick
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