[Swift-devel] script that returns bad parameter error

[Michael Wilde]

I need to take a close look later when I get a chance, but i'm a bit 
suspicious of the use of the file type variables receptor_file and 
ligand_file without the @ or @filename inside your app{} construct in 
run_fred().

Will check later if thats what gives this message.

you want to say:

         app {
              run_fred "-rec" @receptor_file "-dbase"
  @ligand_file "-prefix" ligand_prefix;>         }

See the users guide at http://www.ci.uchicago.edu/swift/guides/userguide.php
sec 2.3.1

and the tutorial example, Mike.

- MikeW


On 12/5/07 2:56 PM, Mike Kubal wrote:
> Any thoughts on what might cause? 
> 
> type file {}
> 
> (file score, file docked) run_fred (string
> ligand_prefix, file ligand_file, file receptor_file){
>         app {
>              run_fred "-rec" receptor_file "-dbase"
> ligand_file "-prefix" ligand_prefix;
>         }
> }
> 
> 
> string receptor_prefix = "1beh";
> 
> file receptor_file
> <single_file_mapper;file=@strcat(receptor_prefix,".oeb.gz")>;
> 
> file
> fls[]<filesys_mapper;pattern="Marsha_lig_*.mol2",location=".">;
> 
> foreach ligand_file in fls{
> 
>         string ligand_prefix =
> @strcut(@ligand_file,"\.\/(.*)\.mol2");
>         string score_file_name =
> @strcat(ligand_prefix,"_chemgauss3_scores.txt");
>         string docked_file_name =
> @strcat(ligand_prefix,"_chemgauss3_docked.mol2");
>         file score_file
> <single_file_mapper;file=@strcat(ligand_prefix,"_chemgauss3_scores.txt")>;
>         file docked_file
> <single_file_mapper;file=@strcat(ligand_prefix,"_chemgauss3_docked.mol2")>;
> 
>         (score_file,docked_file) =
> run_fred(ligand_prefix,ligand_file,receptor_file);
> 
> }
> 
> 
> Thanks,
> 
> Mike Kubal
> 
> 
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