Try Python API with RDKit Native Code

Cheminformatics Tutorials - Herong's Tutorial Examples

∟RDKit: Open-Source Cheminformatics Software

∟Try Python API with RDKit Native Code

This section provides a tutorial example on how to connect the Python API to RDKit native code. Unfortunately, it is not working because of the missing boost_python library.

Now I am ready to try the RDKit Python API with the Python 2 engine. It should work with the build I did with "-DRDK_BUILD_PYTHON_WRAPPERS=OFF".

1. Import the "rdkit" package into Python 2. I see an "ImportError: No module named rdBase" error. I have no idea where "rdBase" module is located.

herong$ export PYTHONPATH=/home/herong/rdkit

herong$ python2

Python 2.7.16 (default, Nov 17 2019, 00:07:27)
[GCC 8.3.1 20190507 (Red Hat 8.3.1-4)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import rdkit import Chem
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/herong/rdkit/rdkit/__init__.py", line 2, in <module>
    from .rdBase import rdkitVersion as __version__
ImportError: No module named rdBase

2. Read RDKit Python documentation, I found this note: "Beginning with the 2019.03 release, the RDKit is no longer supporting Python 2. If you need to continue using Python 2, please stick with a release from the 2018.09 release cycle." So I have to rebuild RDKit with "-DRDK_BUILD_PYTHON_WRAPPERS=ON" to work with Python 3.

3. Unzip rdkit-master.zip into ~/rdkit and again build it again with no option, which takes the default setting of "-DRDK_BUILD_PYTHON_WRAPPERS=ON". I see errors on

herong$ unzip rdkit-master.zip

herong$ mv rdkit-master rdkit

herong$ cd rdkit

herong$ mkdir build

herong$ cd build

herong$ cmake ..
CMake Error: The following variables are used in this project, but
they are set to NOTFOUND. Please set them or make sure they are set
and tested correctly in the CMake files:
PYTHON_LIBRARY (ADVANCED)
linked by target "RDBoost" in directory /home/herong/rdkit/Code/RDBoost
linked by target "rdBase" in directory /home/herong/rdkit/Code/RDBoost/Wrap
...

4. Install "platform-python-devel" and run "cmake" again. I see the "No Boost libraries were found" error.

herong$ sudo dnf install platform-python-devel

...
Installed:
  platform-python-devel-3.6.8-15.1.el8.x86_64
  python-rpm-macros-3-37.el8.noarch
  python3-rpm-generators-5-4.el8.noarch

herong$ cmake ..
CMake Error at /usr/share/cmake/Modules/FindBoost.cmake:2044 (message):
  Unable to find the requested Boost libraries.
  Boost version: 1.66.0
  Boost include path: /usr/include
  Could not find the following Boost libraries:
          boost_python
  No Boost libraries were found. You may need to set BOOST_LIBRARYDIR to
  the directory containing Boost libraries or BOOST_ROOT to the location
  of Boost.
...

5. Search for boost_python library file. I see no boost_python library.

herong$ ls -l /usr/lib64/libboost_p*
     35 May 13  2019 /usr/lib64/libboost_prg_exec_monitor.so
                       -> libboost_prg_exec_monitor.so.1.66.0
  89688 May 13  2019 /usr/lib64/libboost_prg_exec_monitor.so.1.66.0
     34 May 13  2019 /usr/lib64/libboost_program_options.so
                       -> libboost_program_options.so.1.66.0
 701288 May 13  2019 /usr/lib64/libboost_program_options.so.1.66.0
...

herong$ dnf info boost
Installed Packages
Name         : boost
Version      : 1.66.0
Release      : 6.el8
Architecture : x86_64
Size         : 1.3 k
Source       : boost-1.66.0-6.el8.src.rpm
Repository   : @System
From repo    : AppStream
Summary      : The free peer-reviewed portable C++ source libraries
URL          : http://www.boost.org