Changes to YAML syntax for multiple parameters and start from prmtop files

I’ve thought about how to change the syntax to accomodate both #360 and #384, and I’ve come to 2 conclusions.

• We can’t use normal lists to represent combinations, or we won’t be able to specify simple lists. I think we should change the syntax to become

molecules:
  mol_id:
    filepath: 'ligands.sdf'
    parameters: [leaprc.ff99SB, S2P.frcmod, S2P.off]
    select: !Combinatorial [0, 1, 5]

• We should separate system setup in its own block. The final part of the script would become

...

systems:
  system_from_files:
    complex_phase: 'my_complex.prmtop'
    solvent_phase: 'my_solvent.prmtop'
    ligand_dsl: 'resname MOL'
    solvent: PME-solvent
  system_automatic_setup:
    receptor: abl
    ligand: !Combinatorial [imatinib, bosutinib]
    solvent: PME-solvent
    pipeline: 'leap' # I'd add this once we have an OpenMM pipeline as well
    extra_tleap_commands:
    - loadAmberParams frcmod_S2P
    - anyOtherCommand

experiments:
  system: !Combinatorial [system_from_files, system_automatic_setup]
  protocol: absolute-binding

This also has the advantage that when we’ll split the setup pipline into its own tool, the YAML syntax will remain unchanged.

How does it look? Better solutions?

[jchodera]

I agree that the specification of the pipeline should go along that direction (although I would postpone some of those features after yank 1.0).

I am certainly onboard with that. The only thing to make sure of right now is that we have a concept of how it will be extensible without writing ourselves into a corner.

[jchodera]

This is fantastic! Sorry to have missed this. Please go ahead!