30.1.2 General Installation Instructions

Python-OEChem is now provided in tar.gz format, which when un-tarred creates a directory tree just like all other OpenEye applications. If you already have an OpenEye tree, un-tar the Python distribution into the same directory. If not, un-tarring will create an entire directory structure starting with openeye.

All the Python related code will be found under openeye/python.

Next, you need to set an environment variable to allow Python to find the Python-OEChem extensions. Inside the openeye/python directory, there will be an examples directory and one or more directories named for the platform, compiler and Python version. Here is an example from a RedHat 9 installation. The distribution was un-tarred into /usr/local creating /usr/local/openeye as the top of the installation tree.

[user@crush local]$ ls openeye/python/
examples  redhat-9.0-g++3.2-i586-python2.3
[user@crush local]$

We need to set the PYTHONPATH environment variable, for Python to locate Python-OEChem. In your shell startup script (.bashrc for example) add the following 2 lines. (The syntax may vary if you use a shell other than bash

PYTHONPATH=/usr/local/openeye/redhat-9.0-g++3.2-i586-python2.3
export PYTHONPATH

Obviously, if you un-tarred in a different parent directory, you would use that actual location.

In order to lay the groundwork for end-user C++ OEChem modules, as well as Python wrappers around other OpenEye toolkits, that interoperate with Python-OEChem, as of version 1.3, Python-OEChem on most platforms now uses dynamic instead of static versions of the underlying OEChem C++ libraries. While this provides for great flexibility for future extension, it does create the added complexity of requiring the user to provide information to the run-time linker to find these shared libraries.

For most platforms, in order for shared libraries to work, we need to set an additional environment variable. For most platforms, this variable is LD_LIBRARY_PATH. Presuming the same directory tree as shown above, for Linux, Irix 6.5 and Tru64:

LD_LIBRARY_PATH=/usr/local/openeye/redhat-9.0-g++3.2-i586-python2.3:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH

For OS X, the variable is slightly different:

DYLD_LIBRARY_PATH=/usr/local/openeye/redhat-9.0-g++3.2-i586-python2.3:$DYLD_LIBRARY_PATH
export DYLD_LIBRARY_PATH

				OEChem - Python Theory Manual Version 1.3.1

				OEChem - Python Theory Manual Version 1.3.1