cheminformatics.js: RDKit

Following on from the previous post, the second toolkit we'll look at is RDKit. Again, we want to convert RDKit to JavaScript and use it to depict SMILES in the browser.

And here's the result.

Here's how the sausage was made...

Compile RDKit with Emscripten

I used the latest RDKit release (2014-09-2). When configuring, the key insight is that by turning off every option, we don't need any boost libs. Yippee! I can see myself doing this more often in future...

~/Tools/cmake-3.1.2/bin/cmake .. -DCMAKE_TOOLCHAIN_FILE=/home/noel/Tools/emscripten/cmake/Modules/Platform/Emscripten.cmake -DRDK_BUILD_PYTHON_WRAPPERS=OFF -DRDK_BUILD_CPP_TESTS=OFF -DRDK_BUILD_SLN_SUPPORT=OFF -DBoost_INCLUDE_DIR=/home/noel/Tools/boostinstall/include
make -j2

Add RDKit to a webpage

Create a webdepict.cpp file with the SmilesToSVG functionality and compile it by linking against RDKit. The following CMakeLists.txt may be useful:

project(webdepict)
  cmake_minimum_required(VERSION 3.0)
  include_directories(${RDKIT_INCLUDE_DIR} ${Boost_INCLUDE_DIR})
  add_executable(webdepict webdepict.cpp)
  target_link_libraries(webdepict ${RDKIT_LIBRARIES})

...which can be configured with...

export RDLIB=/home/noel/Tools/rdkit-2014-09-2/lib
  ~/Tools/cmake-3.1.2/bin/cmake .. -DCMAKE_TOOLCHAIN_FILE=/home/noel/Tools/emscripten/cmake/Modules/Platform/Emscripten.cmake -DRDKIT_INCLUDE_DIR=/home/noel/Tools/rdkit-2014-09-2/Code -DBoost_INCLUDE_DIR=/home/noel/Tools/boostinstall/include -DRDKIT_LIBRARIES=${RDLIB}/libRDGeometryLib.so;${RDLIB}/libDepictor.so;${RDLIB}/libSmilesParse.so;$RDLIB/libGraphMol.so;${RDLIB}/libRDGeneral.so"

If tested with nodejs, it will write out the SVG for a molecule.

Finally, as with the previous toolkit, modify the CMake build command to create the HTML page which we then edit as desired. Note that this time we need to turn on exception catching:

/home/noel/Tools/emscripten/em++ -O3 @CMakeFiles/webdepict.dir/objects1.rsp -o webdepict.html @CMakeFiles/webdepict.dir/linklibs.rsp -s EXPORTED_FUNCTIONS="['_SmilesToSVG']" -s DISABLE_EXCEPTION_CATCHING=0