Order of program arguments

[filipsPL]

The order of arguments is not consistent across script(s), eg. in src/run.sh we have two orders of arguments:

First:

  echo "usage: $0 [receptor mol2: .mol2 file of receptor structure. Default: tests/input/receptor_ligand/receptor.mol2]
                  [ligand poses sd: .sd file containing all ligand posees. Default: tests/input/receptor_ligand/poses.sd]
                  [output file: where to save scores. Default: tests/score.txt]
                  [rmsd: 1, 1.5, 2, 2.5. Default: 2]
                  [eta: 2, 24, or 248 (2A, 2A and 4A, 2A 4A and 8A). Default: 248]
                  [stop frame: only score the first several poses. Default: -1 (using all frames)]"

(..., rmsd, eta, stop_frame)

And next:

    receptor=${1:-tests/input/1AM0/receptor.mol2}
    ligand=${2:-tests/input/1AM0/poses.sd}
    score=${3:-tests/output/1AM0.txt}
    stop_frame=${4:-"-1"}
    rmsd=${5:-2}
    eta=${6:-248}

(..., stop_frame, rmsd, eta)