Support for the ARM 64 bit CPU architecture (aarch64) was introduced in autoconf 2.69. chemtool appears to use an earlier version of autoconf, preventing its being built. This can be fixed in of three ways (In order of preference): 1. Work with upstream to migrate the package to autoconf 2.69. 2. Rerun autoconf or autoreconf in %prep or %build prior to running configure. 3. Apply the patch at http://ausil.fedorapeople.org/aarch64/chemtool/chemtool-aarch64.patch which updates config.guess and config.sub to recognize aarch64.
Should be fixed now in my upstream package (1.6.14, autoreconf'd with 2.69). I also fixed a nasty double-free bug affecting all fig2dev-based output modes.
1.6.14-1.fc20 build completed in rawhide.