sci-chemistry/avogadro-1.2.0_p20170207 fails to build when the system has sci-chemistry/openbabel-2.3.2 installed. Upgrading to sci-chemistry/openbabel-2.4.1 prior to installing avogadro fixes the issue. So I`d like to suggest (pending, perhaps, confirmation by an expert) that the sci-chemistry/avogadro-1.2.0_p20170207 ebuild should require sci-chemistry/openbabel-2.4.1 or newer as a dependency.
It's unclear whether the build failed because sci-chemistry/openbabel was stale or because there was an actual version incompatibility, so please attach the entire (failing) sci-chemistry/avogadro build log to this bug report.
avogadro configure says: -- Checking for module 'openbabel-2.0>=2.3.0' -- Found OpenBabel 2.3 or later: openbabel -- Found OpenBabel2 executable: /usr/bin/babel Please re-open with the required information.