cheminformatics.js: Helium

The previous two posts covered some heavyweights; this time let's turn to a newer C++ toolkit called Helium, by Tim Vandermeersch. With this toolkit, as well as depiction, I also decided to showcase Tim's SMILES validator functionality (also to be found in Open Babel as the 'smy' SMILEY format).

And here's the result.

Coming up, how 'twas done.

Compile Boost with Emscripten

Unlike with RDKit where we managed to get around the use of Boost libraries, here we need to deal with Boost face-on as Helium links to five different Boost libraries.

Following this info on StackExchange, I ran bootstrap.sh 'normally' and then edited project-config.jam by replacing "using gcc" with:

using gcc : : "/home/noel/Tools/emscripten/em++" ;

Note that the spaces are significant (e.g. preceding the final semicolon). I also set the install directory as local:

option.set prefix : /home/noel/Tools/boostinstall ;
  option.set exec-prefix : /home/noel/Tools/boostinstall ;
  option.set libdir : /home/noel/Tools/boostinstall/lib ;
  option.set includedir : /home/noel/Tools/boostinstall/include ;

For building static libraries you need the following additional changes in tools/build/src/tools/gcc.jam. Change:

toolset.flags gcc.archive .AR $(condition) : $(archiver[1]) ;
     and
toolset.flags gcc.archive .RANLIB $(condition) : $(ranlib[1]) ;

to

toolset.flags gcc.archive .AR $(condition) : "/full/path/to/emscripten/emar" ;
     and
toolset.flags gcc.archive .RANLIB $(condition) : "/full/path/to/emscripten/emranlib" ;

Now use "./b2" to build the libraries (iostreams, chrono, timer, filesystem, system) as follows (the NO_BZIP2 was added because it was complaining about not being able to find the relevant header file):

./b2 link=static variant=release runtime-link=static threading=single --with-iostreams -sNO_BZIP2=1 --with-chrono --with-timer --with-filesystem --with-system  install

Compile Helium with Emscripten

CMake has some trouble finding the Boost libraries so you just have to set all of the variables manually:

cmake .. -DCMAKE_TOOLCHAIN_FILE=/home/noel/Tools/emscripten/cmake/Modules/Platform/Emscripten.cmake -DBOOST_ROOT=/home/noel/Tools/boostinstall -DBoost_INCLUDE_DIR=/home/noel/Tools/boostinstall/include -DBOOST_LIBRARYDIR=/home/noel/Tools/boostinstall/lib -DBoost_CHRONO_LIBRARY_RELEASE=/home/noel/Tools/boostinstall/lib/libboost_chrono.a -DBoost_SYSTEM_LIBRARY_RELEASE=/home/noel/Tools/boostinstall/lib/libboost_system.a -DBoost_TIMER_LIBRARY_RELEASE=/home/noel/Tools/boostinstall/lib/libboost_timer.a -DBoost_IOSTREAMS_LIBRARY_RELEASE=/home/noel/Tools/boostinstall/lib/libboost_iostreams.a -DBoost_FILESYSTEM_LIBRARY_RELEASE=/home/noel/Tools/boostinstall/lib/libboost_filesystem.a -DEIGEN3_INCLUDE_DIR=/usr/include/eigen3
make -j2

The default build has "-O2"; I changed this to "-O3" in the top-level CMakeLists.txt. It also (separately) had "-g" so I removed this.

To test, use nodejs to run helium.js.

Add Helium to a webpage

The easiest way to add an additional executable is to add another 'tool'. Place webdepict.cpp in the tools directory and edit tools/CMakeLists.txt to compile it. As before, looking at the output of "VERBOSE=1 make webdepict", we can modify it to generate the HTML page which is then tweaked as desired:

/home/noel/Tools/emscripten/em++   -O3  -pedantic -Wall -Wno-long-long -Wno-sign-compare     @CMakeFiles/webdepict.dir/objects1.rsp  -o webdepict.html  ../src/libhelium.so /home/noel/Tools/boostinstall/lib/libboost_chrono.a /home/noel/Tools/boostinstall/lib/libboost_timer.a /home/noel/Tools/boostinstall/lib/libboost_system.a /home/noel/Tools/boostinstall/lib/libboost_iostreams.a /home/noel/Tools/boostinstall/lib/libboost_filesystem.a -s EXPORTED_FUNCTIONS="['_ValidateSmiles', '_SmilesToSVG']" -s DISABLE_EXCEPTION_CATCHING=0  --closure 1