type info{
  string proteinId;
  int jobnum;
}

// Input types

type Fasta;
type SecSeq;
type PDB;

// OOPS Output types

type OOPSSecStr;
type OOPSLog;
type OOPSEnergy;
type OOPSpdt;
type OOPSrmsd;
type OOPSLibrary;

app (
    OOPSpdt pdt,
    OOPSEnergy e,
    OOPSLibrary lib,
    OOPSSecStr secstr,
    OOPSrmsd rmsd,
    OOPSLog log
)   runoops ( 
    Fasta fasta,
    SecSeq secseq,
    PDB pdb,
    int jobnum,
    string cfgParams[]
)
{
  runoops @fasta @secseq @pdb @pdt @rmsd jobnum cfgParams[*] stdout=@log;
}

/* Desired:

string config [] = [
  "TEMP UPDATE INTERVAL",  "10",
  "SMOOTH DEVIATION COEFFICIENT", "0.80001"
];

*/

// trying this:

string config [];

config[0] = "TEMP UPDATE INTERVAL";         config[1]="10";
config[2] = "SMOOTH DEVIATION COEFFICIENT"; config[3]="0.80001";

int iter[]=[1:1];

foreach j in iter {

  // map inputs

  Fasta fasta <"input/fasta/T1af7.fasta">;
  SecSeq secseq <"input/secseq/T1af7.secseq">;
  PDB native <"input/native/T1af7.pdb">;

  // map outputs

  OOPSpdt pdt <"output/out.pdt">;
  OOPSEnergy e <"output/out.Energy">;
  OOPSLibrary lib <"output/out.Library">;
  OOPSSecStr secstr <"output/out.SecStr">;
  OOPSrmsd rmsd <"output/out.rmsd">;
  OOPSLog log <"output/out.log">;

  ( pdt, e, lib, secstr, rmsd, log) = runoops( fasta, secseq, native, j, config );
}


/* TO DO:

info tparams[];
tparams[0].proteinId="T1af7";
tparams[0].jobnum = 0;


Args are passed to app by relative path, rel to workdir.

Then do mappings

how to compose unique outfile names?

Pass rel or abs infile names?


Experiment with:

- passing of strings for params with a single name (will it expand the
array?)

- passing of structs as args to an app: how will these be handled? How
will they be expanded with @filename?

- how *should* these cases be handled? Do they afford a compact notation for mapping?

- how to treat ooopsout{} as a struct, with some optional files?  Ditto oopsin?

*/

/* fossils

app (messagefile t) greeting(string s) {
  echo s stdout=@filename(t);
}

app (messagefile outfile) printinfo(info input,int jobnum) {
  echo input.wd input.prot input.round jobnum input.kill stdout=@outfile;
}

app (messagefile outfile) printout(info input,int jobnum) {
  printoops input.wd input.prot input.round jobnum input.kill stdout=@outfile;
}

*/