Amino acid data

Various properties of the amino acid types can be specified in the form of a YAML file.

amino acid data:
  default atom data:
    (atom name): quantity [L]

  amino acids:
    (amino acid name):
      mass: quantity [M]
      alt atom radii:
        (atom name): quantity [L]
      side: list of atom names
      radius: quantity [L]
      polarization: one of [hydrophobic, polar]
      charge: quantity [(dim of e)]
      contact limits:
        back: integer
        side (all): integer
        side (hydrophobic): integer
        side (polar): integer

The fields alt atom radii, polarization and charge are optional. For more info, see the amino acids entry in the default.yml file.