How can I run Py-OEChem from CYGWIN?
Py-OEChem is not available for use with the Python bundled with CYGWIN. However, by installing “Python for windows” from python.org and running that executable (normally /cygdrive/c/python23/python.exe) then Py-OEChem scripts may be run from CYGWIN. The one caveat is that absolute file pathnames must be specified in DOS format — with backslashes, etc. — though relative pathnames can be in CYGWIN/UNIX format.