Compiling RDKit with MSVC 2012

Compiling RDKit is a bit like the recipe for Elephant Soup. It's straightforward, but first we have to compile Boost (as there are no binaries provided for MSVC 2012). Unfortunately, the boost build instructions are very poor. The HTML instructions are full of text, none of which will simply tell you how to get the job done.

Preparation
1. Just to be safe, as both Boost and RDKit compile against Python, I deleted all my Python install folders except C:\Python2.7.
2. Make sure that bison and flex are installed in Cygwin, and that they are on the PATH.

Compiling Boost 1.49
1. Choose the right version. Too new, and the API will have changed and RDKit will not compile; too old, and it won't compile with MSVC 2012. I'm using boost 1.49.
2. Unzip into C:\Boost\boost_1_49_0. Do not bother using a different folder as it will install into C:\Boost\lib in any case.
3. Compile bjam as follows:

cd C:\Boost\boost_1_49_0
bootstrap

4. Start the MSVC2012 command prompt (or else bjam won't find 'cl'). Now we're going to compile the bits of Boost that RDKit needs. Some of these are shared libraries and some are dynamically linked libraries.

bjam.exe --with-regex --with-python --with-date_time --with-thread link=shared toolset=msvc-11.0 release install -j4
bjam.exe --with-thread --with-date_time toolset=msvc-11.0 release stage -j4

5. Copy the files from C:\Boost\boost_1_49_0\stage\lib to C:\Boost\lib

Compiling RDKit Q3 2012
1. The setup is all done by one command:

C:\Tools\RDKit\newbuild>cmake -G "Visual Studio 11" ..\RDKit_2012_09_1
-- Check for working C compiler using: Visual Studio 11
-- Check for working C compiler using: Visual Studio 11 -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler using: Visual Studio 11
-- Check for working CXX compiler using: Visual Studio 11 -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Found PythonLibs: C:/Python27/libs/python27.lib (found version "2.7.3")
-- Found PythonInterp: C:/Python27/python.exe (found version "2.7.3")
-- Boost version: 1.49.0
-- Found the following Boost libraries:
--   python
-- Found BISON: C:/cygwin/bin/bison.exe
-- Found FLEX: C:/cygwin/bin/flex.exe
-- Looking for include file pthread.h
-- Looking for include file pthread.h - not found.
-- Found Threads: TRUE
-- Boost version: 1.49.0
-- Found the following Boost libraries:
--   regex
-- Configuring done
-- Generating done
-- Build files have been written to: C:/Tools/RDKit/newbuild

2. Type "start RDKit.sln", change to Release build, and build the ALL_BUILD target, followed by the INSTALL target.

Running the RDKit tests
1. Close Visual Studio, and at the command line type:

set RDBASE=C:\Tools\RDKit\RDKit_2012_09_1
set PYTHONPATH=%RDBASE%
set PATH=%RDBASE%\lib;C:\Boost\lib;%PATH%
start RDKit.sln

2. Now you can run the tests by 'building' the RUN_TESTS target

1>  100% tests passed, 0 tests failed out of 76
1>  
1>  Total Test time (real) =  82.36 sec

Notes: For a debug build, you need the debug build of Boost. Just replace release by debug in the bjam command-lines above (to speed things up, use 'stage' for both).