rdkit

RDKitjs

Port RDKit to js using emscripten with ASM & WASM

Emscripten installation & activation

Install emscripten (1.37.33 or higher). https://kripken.github.io/emscripten-site/docs/getting_started/downloads.html

RDKit emscripten binding

install RDKit 2015.3.1, 2016.3.5, 2016.9.4 (old version of Libraries). or install RDKit 2017.3.3, 2017.9.3 (New version of Libraries).

you need to add eigen3 include files for 3Ddescriptors (since RDkit 2017.3)

wget https://github.com/rdkit/rdkit/archive/Release_2017_09_3.tar.gz
wget https://github.com/rdkit/rdkit/archive/Release_2017_03_3.tar.gz
wget https://github.com/rdkit/rdkit/archive/Release_2016_09_4.tar.gz
wget https://github.com/rdkit/rdkit/archive/Release_2016_03_5.tar.gz
wget http://downloads.sourceforge.net/project/rdkit/rdkit/Q1_2015/RDKit_2015_03_1.tgz

Choose your version based on required RDkit functionnalities and compile RDKit first for emscripten:

tar -xf RDKit_20YY_0M_V.tgz
cd rdkit-Release_20YY_0M_V
mkdir build
cd build


cmake  .. \
-DCMAKE_TOOLCHAIN_FILE=/path/to/emsdk/emscripten/1.37.33/cmake/Modules/Platform/Emscripten.cmake \
-DRDK_BUILD_PYTHON_WRAPPERS=OFF \
-DRDK_BUILD_CPP_TESTS=OFF \
-DRDK_BUILD_SLN_SUPPORT=OFF \
-DBoost_INCLUDE_DIR=/path/to/boost/boost@1.60/1.60.0/include/ \
-DEIGEN3_INCLUDE_DIR=/path/to/eigen/3.3.4/include/eigen3/ \
-DTHREADS_PTHREAD_ARG=OFF

based on your number of CPU:

make -jX

Install RDKitjs

clone this repository

git clone https://github.com/thegodone/RDKitjs.git


cd /path/to/RDKitjs/
rm -rf build
mkdir build
cd build

for OSX

cmake .. \
-DCMAKE_TOOLCHAIN_FILE=/path/to/emscripten/1.37.33/cmake/Modules/Platform/Emscripten.cmake \
-DRDKIT_INCLUDE_DIR=/path/to/rdkitversion/rdkit-Release_2017_09_3/Code/ \
-DBoost_INCLUDE_DIR=/path/to/boost@1.60/1.60.0/include/  \
-DRDKIT_LIB_DIR=/path/to/rdkitversion/rdkit-Release_2017_09_3/build/lib/ \
-DRDKitNEWLIB=ON \
-DEMSCRIPTEN_BIN=/path/to/emscripten/1.37.33/

for Linux

cmake .. \
-DCMAKE_TOOLCHAIN_FILE=/path/to/emscripten/1.37.33/cmake/Modules/Platform/Emscripten.cmake \
-DRDKIT_INCLUDE_DIR=/path/to/rdkitversion/rdkit-Release_2015_03_1/Code \
-DBoost_INCLUDE_DIR=/path/to/boost/include \
-DRDKIT_LIB_DIR=/path/to/rdkitversion/rdkit-Release_2015_03_1/lib \
-DEMSCRIPTEN_BIN=/path/to/emscripten/1.37.33/

rm src/rdkit.js

make

cp src/rdkit.js ../build/src/rdkit.js

# create a web loading file
npm run build-test

# copy web loading file into the localhost folder
cp ../test/rdkit.js /path/to/localhostcode/rdkitjs/rdkit.js

Please take a look at those references:

=> Ubuntu 14.04:
http://baoilleach.blogspot.ch/2015/02/cheminformaticsjs-rdkit.html

http://gmrand.blogspot.ch/2015/03/howto-install-rdkit-and-emscripten-on.html

=> OSX: http://gmrand.blogspot.ch/2015/05/howto-install-rdkit-and-emscripten-on.html

P.S.: CAUTION due to a bug report we suggest to apply this patch to rdkit

ONLY for RDKIT version 2015.03.1 : Patching of RDKit files for emscripten binding

• adding class MMFFMolProperties in rdkit/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.h

  namespace RDKit {
    class ROMol;
    namespace MMFF {
+     class MMFFMolProperties;

• adding AtomTyper.h in rdkit/Code/GraphMol/ForceFieldHelpers/MMFF/MMFF.h

  #include <ForceField/ForceField.h>
+ #include "AtomTyper.h"
  #include "Builder.h"

Want to try it without compilation ? It's already possible

Thers is a first example in the visualizer project there:

https://www.cheminfo.org/Chemistry/Cheminformatics/RDKit_demo/index.html

You can draw a molecule in the botton module which will generate the 3D model using MMFF force field.

another example of javascript can be found there:
https://iwatobipen.wordpress.com/2015/05/21/rdkit-in-javascript/
thanks to iwatobipen!
source code: https://github.com/iwatobipen/rdkit_javascript

You can also use nodejs:
the current module is available for npm / nodejs:
https://www.npmjs.com/package/rdkit

Current stability status

This project is not stable but lot of basic RDKit functions are already ported look at the test/exemple.txt file for a example of function availables

to have a complete list of available function look at the EMSCRIPTEN_BINDINGS section in rdmol.h

there are two type of methods:

• create a molecule (class_function)
• apply functions on a created molecule (function)

Future requests / help / missing RDKit functions

If you want to contribute or need RDKit functions not already mapped please add a comment in the issues of this project.

Guillaume Godin