Test cases for protein mutation protocol

[ijpulidos]

For testing the protein mutation protocol we want to have validation and integration tests covering the following cases:

• Capped AA tests:
  • ALA -> GLY and GLY -> ALA
  • Charged capped AA tests: LEU -> ASP and ASP -> LEU
• Convergence test: Adapt ALA dipeptide perses test case to feflow.
• Test insertion codes. For example ALA PDB with insertion codes.
• Check we can handle atom shifting mapping. For example when you pass a multisite mapping that it was multiple chains, how are the indices will be handled if there are for example water in-between the chains in the PDB or similar.
• Expected failed tests:
  • Test proline (PRO) mutations fail. We won't be supporting proline so far.
  • Test double (or more) charged mutations fail. For example. LYS -> GLU.
• More than one alchemical component fail