Fix g_chi -omega

Per IUPAC, we should calculate peptide omega angles from
Calpha-C-N-Calpha, and there are only n-1 such angles defined for a
polypeptide of n amino acid residues.

There are some other IUPAC violations in make_chi_ind(), but solving
those is deferred to 5.0, not least because there will be a
behavioural change when we conform to IUPAC.

The problem that led to the report had several causes. The hard-coding
of the string names for hydrogen bound to peptide nitrogen (which in
CHARMM27 is "HN") meant that an H atom was not found. has_dihedral()
then checked whether a Calpha was found, which was true. Then
make_chi_ind() computed the angle based on H without doing any further
check. So some garbage coordinate was looked up when computing the
angle.

A proper fix for this kind of stuff for 5.0 requires finding all the
places we try to guess what atoms are from their names and using
properly implemented selections.

Also removed orphaned header file.

Fixes #953, details and links there

Change-Id: I63257a1d6d8ed46d251b8bc0cb308dfbd2864a97