Hi Greg.
I've run into a few more problems with Fingerprinting, I'm trying to create a
database of these finger prints, I've tried a few different methods to write
the fingerprints
SparseIntVect<boost::uint32_t> *finger;
mol=SmilesToMol(line);
finger = MorganFingerprints::getFingerprint(*mol, 2);
cout << finger.toString() << endl;
Which returns
Fingerprint.cpp:49: error: request for member ‘toString’ in ‘finger’, which is
of non-class type ‘RDKit::SparseIntVect<unsigned int>*’
Then as a fix i tried intreated over the entries in the vector however firstly
I can't use the getLength function because of the same error above, and when I
put in an arbitrary depth and managed to get some output, however it seemed
only to output a huge amount of zero's
Thanks,
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]<mailto:[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
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