RDKitjs

Port RDKit to js using emscripten

First of all we need to install emscripten (1.32 or 1.34.6) and RDKit 2015.3.1. 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

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"

Install RDKitjs

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

cd RDKitjs

• mkdir build
• cd build

Commandline for OSX

cmake ..  \
-DCMAKE_TOOLCHAIN_FILE=/usr/local/Cellar/emscripten/1.32.0/libexec/cmake/Modules/Platform/Emscripten.cmake  \
-DRDKIT_INCLUDE_DIR=/Users/marco/Toolchain/rdkit-Release_2015_03_1/Code/  \
-DBoost_INCLUDE_DIR=/usr/local/Cellar/boost155/1.55.0_1/include/  \
-DRDKIT_LIB_DIR=/Users/marco/Toolchain/rdkit-Release_2015_03_1/lib/ \
-DEMSCRIPTEN_BIN=/usr/local/Cellar/emscripten/1.32.0/bin/

Commandline for Linux

cmake .. \
-DCMAKE_TOOLCHAIN_FILE=${HOME}/Toolchain/emsdk_portable/emscripten/master/cmake/Modules/Platform/Emscripten.cmake \
-DRDKIT_INCLUDE_DIR=${HOME}/Toolchain/rdkit-Release_2015_03_1/Code \
-DBoost_INCLUDE_DIR=${HOME}/Toolchain/boost.1.57.0/include \
-DRDKIT_LIB_DIR=${HOME}/Toolchain/rdkit-Release_2015_03_1/lib \
-DEMSCRIPTEN_BIN=${HOME}/Toolchain/emsdk_portable/emscripten/master

• finally $ make

Then you should obtain one new file => src/rdkit.js

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

Thers is a first example in the visualizer project there:

http://www.lactame.com/visualizer/head/index.html?viewURL=http://visualizer.epfl.ch/x/urhBCrzbZ0r75WWbEmRp/view.json&dataURL=http://visualizer.epfl.ch/x/urhBCrzbZ0r75WWbEmRp/data.json

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