B.2. AppArmor

AppArmor is a Linux Security Module implementation of name-based access controls. AppArmor confines individual programs to a set of listed files. The default configuration of AppArmor does not permit the use of Mychem. In fact, MySQL is not allowed to access the Open Babel library. To fix this problem, the following lines must be added to the /etc/apparmor.d/usr.sbin.mysqld file:

/usr/lib/openbabel/* m,
/usr/lib/openbabel/OPENBABEL_VERSION/* m,
/usr/share/openbabel/* r,
/usr/share/openbabel/OPENBABEL_VERSION/* r,


Replace OPENBABEL_VERSION by the version of OpenBabel on your system (2.3.0, 2.3.1, ...).