SCHWED-2440: use "peptide" flag to filter chains in mol.alg.Superpose.

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.