I thinks is a linking problem.
Do you link libSmilesParse.so?
from your line it seems that you link only -Llib/libGraphMol.so
-Llib/libDescriptors.so -Llib/libRDGeneral.so -Llib/libRDGeometryLib.so
Marco
> On 12 May 2015, at 12:53, Guillaume GODIN <[email protected]>
> wrote:
>
> Dear Marco,
>
> Thanks for the tips.
>
> I now look at expose the RDKit class directly in JS using emscripten.
>
> I have a issue there :
>
> //------****** code of the rdmol.cpp ********----
> #include <emscripten/bind.h>
>
> #include <GraphMol/ROMol.h>
>
> #include <GraphMol/SmilesParse/SmilesParse.h>
>
> #include <GraphMol/RDKitBase.h>
>
>
>
> using namespace emscripten;
>
> using namespace RDKit;
>
> typedef ROMol Mol;
>
>
>
> class Molecule {
>
>
> public:
>
>
> unsigned int getNA(ROMol *rdmol) {
>
> return rdmol->getNumAtoms();
>
> }
>
>
>
>
> ROMol* fromSmiles(char *smiles) {
>
> return SmilesToMol(smiles);
>
> }
>
>
>
>
> private:
>
> ROMol *rdmol;
>
> };
>
>
>
>
>
> // Binding code
>
> EMSCRIPTEN_BINDINGS(rdmol) {
>
> class_<Molecule>("Molecule")
>
> .constructor<>()
>
> .function("getNA",&Molecule::getNA, allow_raw_pointers())
>
> .function("fromSmiles", &Molecule::fromSmiles, allow_raw_pointers())
>
> ;
>
> }
>
> //------***** end code *******-----
>
>
> when I try to execute this command I add the following link issues. I cannot
> use the cmake / make procedure.
>
> /emscripten/emscripten/em++ --bind -o rdmol.js ../rdmol.cpp -Icode -Iinclude
> -Llib/libGraphMol.so -Llib/libDescriptors.so -Llib/libRDGeneral.so
> -Llib/libRDGeometryLib.so
>
>
>
> where -Icode and -Iinclude are the ln -fs to rdkit/code and boost/include
> folders
>
> and -Llib/ are ln -fs to rdkit/lib folder.
>
>
>
> my error is:
>
> sh-3.2# /emscripten/emscripten/em++ --bind -o rdmol.js ../rdmol.cpp -Icode
> -Iinclude -Llib/libGraphMol.so -Llib/libDescriptors.so -Llib/libRDGeneral.so
> -Llib/libRDGeometryLib.so
>
> warning: unresolved symbol: _ZNK5RDKit5ROMol11getNumAtomsEb
>
> warning: unresolved symbol:
> _ZN5RDKit11SmilesToMolENSt3__112basic_stringIcNS0_11char_traitsIcEENS0_9allocatorIcEEEEibPNS0_3mapIS6_S6_NS0_4lessIS6_EENS4_INS0_4pairIKS6_S6_EEEEEE
>
>
> warning: unresolved symbol: _ZTIN5RDKit5ROMolE
>
>
>
>
>
> Do you have any suggestions to solve that ?
>
>
>
> best regards
>
>
>
> Dr. Guillaume GODIN
>
> Project Manager
>
> Innovation
>
> CORPORATE R&D DIVISION
>
> DIRECT LINE +41 (0)22 780 3645
>
> MOBILE +41 (0)79 536 1039
>
> Firmenich SA
>
> RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
>
>
> De : Giuseppe Marco Randazzo [[email protected]]
> Envoyé : mardi, 12. mai 2015 10:36
> À : Guillaume GODIN
> Cc : [email protected]
> Objet : Re: [Rdkit-discuss] rdkit and emscripten
>
> Hello Guillaume,
>
> you have a vector of unsigned int "SparseIntVect<boost::uint32_t>” which is a
> vector of unsigned int.
>
> Looking at the C++ public member function you can find “getVal(int index)”
> which give to you the correspondent bit as integer value.
>
> So, you can iterate and convert to a string using stringstream.
>
> Second things… is better to use getHashedFingerprint to have a limited size
> of fingerprint (2048 bit).
>
> Here the fully woking example.
>
>
> /******* START C++ CODE ******/
> #include <GraphMol/FileParsers/MolSupplier.h>
> #include <RDGeneral/RDLog.h>
> #include <GraphMol/RDKitBase.h>
> #include <DataStructs/SparseIntVect.h>
> #include <GraphMol/Fingerprints/MorganFingerprints.h>
> #include <sstream>
>
> int main(int argc, char *argv[])
> {
> RDKit::SmilesMolSupplier supplier(argv[1], " \t", 0, 1, false, true);
> RDKit::ROMol* mol;
>
> while (!supplier.atEnd()){
> mol = new RDKit::ROMol;
> mol = supplier.next();
> if (mol){
> RDKit::SparseIntVect<boost::uint32_t> *finger =
> RDKit::MorganFingerprints::getHashedFingerprint((*mol), 2);
> std::stringstream out;
> for(uint i = 0; i < finger->size(); i++){
> out << finger->getVal(i);
> }
> std::cout << out.str() << std::endl;
> delete finger;
> }
> delete mol;
> mol = NULL;
> }
> }
>
> /******* END C++ CODE ******/
>
>
> /******** START CMakeListst.txt ********/
> project(examplerdkit)
> cmake_minimum_required(VERSION 3.0)
> include_directories(${RDKIT_INCLUDE_DIR} ${Boost_INCLUDE_DIR})
> add_executable(test1 main.cpp)
> target_link_libraries(test1 ${RDKIT_LIBRARIES})
> /******** END CMakeListst.txt ********/
>
> To compile:
>
> mkdir build
> cd build
>
> export RDLIB="/usr/local/lib/“;
> cmake .. -DRDKIT_INCLUDE_DIR=/usr/local/include/rdkit
> -DBoost_INCLUDE_DIR=/usr/local/include/boost/
> -DRDKIT_LIBRARIES="${RDLIB}/libRDGeometryLib.dylib;${RDLIB}/libDepictor.dylib;${RDLIB}/libSmilesParse.dylib;$RDLIB/libGraphMol.dylib;${RDLIB}/libRDGeneral.dylib;${RDLIB}/libFileParsers.dylib;${RDLIB}/libFingerprints.dylib”
>
> make
>
> to use
>
> echo "N1C=NC2=C1C(=O)N(C(=O)N2C)C caffeina” >> caffeina.smi
>
> ./test1 caffena.smi
>
> output:
>
> ./test1 caffeina.smi
> 00000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000200000000000000000000000000000000000000000000000000000000000000010000000000000000000001000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000110000000000000000000000000000000000000000000000000000000000020000000000000000000000000000000000000000000000000000000000000000000000000000000000000200000000000000000000000000000000000000000000000000000000000000100000000000000000000000000000000000000000000000000000000010000000000000000000000000000000000100000000000000000000000000010000000000000000000000000000000000000010000000000000000000000000000000000000000000000000000000000000200000000000000000000000000000000000000000000000000001000000000000000000000000000000000001000000000000000000000000000000002100000000000000000000000000000000000000000000000000000001000000000000000000000000000000200000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000040000000000000000000000000000000000000000000000000000000000000000000000010000100000000000000000000000000000000000000000000000000000000000000000000000010000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
>
>
>
> Best regards,
>
> Marco
>
>
>
>> On 11 May 2015, at 16:11, Guillaume GODIN <[email protected]
>> <mailto:[email protected]>> wrote:
>>
>> Dear Greg,
>>
>> Sorry, I forget that link point.
>>
>> So emscripten now see the fingerprint,
>>
>> how to convert it on a readable format like base64 or a string... ?
>>
>> Best regards,
>>
>> Guillaume
>>
>>
>>
>>
>>
>> Hi,
>>
>> Are you sure that you have included the Fingerprints library in the link
>> statement?
>>
>>
>> In the future please direct RDKit questions like this to the rdkit-discuss
>> mailing list. You can find subscription info here:
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>> <https://lists.sourceforge.net/lists/listinfo/rdkit-discuss>
>>
>> -greg
>>
>>
>> Dear Gregory Landrum,
>>
>> I started to build rdkit 2004_09 wrap to javascript using emscripten.
>>
>> I was able to expose all your descriptors in a string and see it in a
>> browser.
>>
>> But, I have trouble to expose the fingerprint, it's look like there is a
>> missing piece in the c++ implementation.
>>
>> When I try to compile this part of my code I have the following issue:
>>
>> SparseIntVect<boost::uint32_t> *finger;
>>
>> finger = MorganFingerprints::getFingerprint(*mol, 2);
>>
>> the compiler don't find the linking to your c++ code: warning: unresolved
>> symbol:
>> _ZN5RDKit18MorganFingerprints14getFingerprintERKNS_5ROMolEjPNSt3__16vectorIjNS4_9allocatorIjEEEEPKS8_bbbbPNS4_3mapIjNS5_INS4_4pairIjjEENS6_ISE_EEEENS4_4lessIjEENS6_INSD_IKjSG_EEEEEE
>>
>> Did you have any advise to determine where I can find this ?
>>
>> best regards,
>>
>> Dr. Guillaume GODIN
>>
>> Project Manager
>>
>> Innovation
>>
>> CORPORATE R&D DIVISION
>>
>> DIRECTLINE +41 (0)22 780 3645
>>
>> MOBILE +41 (0)79 536 1039
>>
>> Firmenich SA
>>
>> RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
>>
>>
>>
>> **********************************************************************
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>> This email and any files transmitted with it, including replies and
>> forwarded copies (which may contain alterations) subsequently transmitted
>> from Firmenich, are confidential and solely for the use of the intended
>> recipient. The contents do not represent the opinion of Firmenich except to
>> the extent that it relates to their official business.
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