Omega angles and cis trans peptides
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The peptide bond is "almost" a double bond, and peptides can therefore
be either cis or in the trans conformation. This means that the angle
ω of the peptide has a few discrete values. Due to steric hindrance
trans peptides in nature are found significantly more often than
cis. But in real life (almost) there are always deviations from the
rules ;).

Questions:

- how many cis, how many trans peptides are there in PDB archive
  structures? Which more frequent? What is the ratio of their
  frequencies?

- is the frequency ratio of cis/trans peptides the same for all amino
  acids (a.r.)? If not, which ones have different cis/trans ratios?
  Which ones? Why?

- What are the acceptable values of the ω angle? What are the meanings
  distribution about these "typical" values? How likely deviation from
  these "typical" values? What statistical parameters best suited to
  answer these questions? As these parameters belongs to various a.r.,
  various a.r. to follow?

* (additional harder question): Knowing cis/trans peptides
  frequencies, estimate the energy difference (kJ/mol) of these
  conformations.

Program:

This research requires a program that reads PDB archive files and
determines and outputs the values of the angle ω and identifies
whether the residue is CIS, or TRANS.