[Swift-devel] script that returns bad parameter error

[Michael Wilde]

MikeK, did you see this message and adjust your code accordingly?

I suspect this is the problem.

- MikeW

On 12/5/07 5:47 PM, Michael Wilde wrote:
> 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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