refactor OMF

- Use bond/angle parameter of PeptideBuilder
  (https://github.com/clauswilke/PeptideBuilder/)
  RMSDs get lower as compared to the previously used parameters
  that were extracted from Charmm36 IC data.
- Introduce internal coordinates to reprent backbone positions.
  Problem with peptide chains is error propagation. An error
  introduced at one backbone dihedral propagates along the whole
  subsequent chain. We thus compress short fragments (tri-peptides)
  that are independent of each other.