structure of single residues

This changes behaviors in MatchResidueByLocalAln and MatchResidueByGlobalAln (
or Superpose with match = local-aln or global-aln) which previously failed for
non-"protein" chains (i.e. anything w/o peptide bonds). Now, amino acid chains
without peptide bonds (e.g. CA-only) are acceptable and other chains (e.g.
ligands / water) are skipped correctly.

BOOST_MESSAGE has been obsolete since boost 1.34 (2007). So after 10 years, we
can finally get rid of it...

If nothing is specified, log level is 0.
Old: if last level was popped, level was set to 1.
New: level set to 0 in that case.