What a small small world this is! Last month I needed to do something similar using ProFit. I didn't see the need to wrap the program with Perl though, since it's a command line application that supports scripting (you can pass your profit script using the -f flag).

So, to align an arbitrary number of structures, I created a text file that only said "fit", and then I looped using bash: 

for F in *.pdb; do profit -f script.txt complex.1.pdb $F \\ 
>> output.txt; done

[download]
Then I used grep to just keep the RMSD value of the run for each structure: 
cat output.txt | grep 'RMS' | awk '{print $2}' > rmsd.txt

[download]
Of course, for anything slightly more complicated than that, I see why you'll want to use Perl.

If you think it's worth it, consider writing a module under Bio::Tools::Run, so that you can later share your wrapper with everyone. You should look at the Bio::Tools::WrapperBase module and subclass from it; it'll give you a nice interface with all the error checking built in. I could help you do it if you want to!

In reply to Re: open3 buffering in linux vs. os x by bruno
in thread open3 buffering in linux vs. os x by Lexicon

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