Dear Giuseppe,
I make progress on this topic, if you want to participate?
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 : rdkit-discuss@lists.sourceforge.net
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 [gmranda...@gmail.com]
Envoyé : mardi, 12. mai 2015 13:38
À : Guillaume GODIN
Cc : rdkit-discuss@lists.sourceforge.net
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
<guillaume.go...@firmenich.com<mailto:guillaume.go...@firmenich.com>> 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 [gmranda...@gmail.com<mailto:gmranda...@gmail.com>]
Envoyé : mardi, 12. mai 2015 10:36
À : Guillaume GODIN
Cc :
rdkit-discuss@lists.sourceforge.net<mailto:rdkit-discuss@lists.sourceforge.net>
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
<guillaume.go...@firmenich.com<mailto:guillaume.go...@firmenich.com>> 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
-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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