Ciao Guillaume,
i want to contribute with pleasure :-)
Best regards
GMR
> On 14 May 2015, at 13:59, Guillaume GODIN <[email protected]>
> wrote:
>
> Dear Giuseppe,
>
> I make progress on this topic, if you want to participate?
>
> https://github.com/thegodone/RDKitjs <https://github.com/thegodone/RDKitjs>
>
> There are already some functions exposed like MMFF, addHs, fromSmiles,
> fromSmarts, ....
>
> 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 : Guillaume GODIN
> Envoyé : mardi, 12. mai 2015 18:01
> À : Giuseppe Marco Randazzo
> Cc : [email protected]
> Objet : RE:[Rdkit-discuss] rdkit and emscripten
>
> Dear Marco,
>
> I find a solution!
>
> I prepare a github to explain it
>
> 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 13:38
> À : Guillaume GODIN
> Cc : [email protected]
> Objet : Re: [Rdkit-discuss] rdkit and emscripten
>
> 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]
>> <mailto:[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]
>> <mailto:[email protected]>]
>> Envoyé : mardi, 12. mai 2015 10:36
>> À : Guillaume GODIN
>> Cc : [email protected]
>> <mailto:[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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